Bone Therapeutics, a cell therapy company addressing unmet medical needs in orthopedics and other diseases, and Rigenerand SRL, a biotech company that both develops and manufactures medicinal products for cell therapy applications, primarily for regenerative medicine and oncology, have signed an agreement for a process development partnership. Allogeneic mesenchymal stem cell (MSC) therapies are currently being developed at a fast pace and are evaluated in numerous clinical studies covering diverse therapeutic areas such as bone and cartilage conditions, liver, cardiovascular and autoimmune diseases in which MSCs could have a significant positive effect. Advances in process development to scale up these therapies could have major impacts for both their approval and commercial viability. This will be essential to bring these therapies to market to benefit patients as quickly as possible, said Miguel Forte, chief executive officer, Bone Therapeutics. While Bone Therapeutics is driving on its existing clinical development programs, we have signed a first formal agreement with Rigenerand as a fellow MSC-based organization. This will result in both companies sharing extensive expertise in the process development and manufacturing of MSCs and cell and gene therapy medicinal products. Bone Therapeutics also selected Rigenerand to partner with for their additional experience with wider process development of advanced therapy medicinal products (ATMPs), including the conditioning and editing of MSCs. The scope of collaborations between Bone Therapeutics and Rigenerand aims to focus on different aspects of product and process development for Bone Therapeutics expanding therapeutic portfolio. Rigenerand will contribute to improving the processes involved in the development and manufacture of Bone Therapeutics MSC based allogeneic differentiated cell therapy products as they advance towards patients. The first collaboration between the two organizations will initially focus on augmented professional bone-forming cellscells that are differentiated and programmed for a specific task. There is also potential for Bone Therapeutics to broaden its therapeutic targets and explore new mechanisms of action with potential gene modifications for its therapeutic portfolio. In addition to Rigenerands MSC expertise, Bone Therapeutics also selected Rigenerand as a partner for Rigenerands GMP manufacturing facility. This facility, situated in Modena, Italy, has been designed to host a number of types of development processes for ATMPs. These include somatic, tissue engineered and gene therapy processes. These multiple areas of Rigenerand capabilities enable critical development of new processes and implementation of the gene modification of existing processes. In addition, Rigenerand has built considerable experience in cGMP manufacturing of MSC-based medicinal products, including those that are genetically modified. Process development and manufacturing is a key part of the development for ATMPs internationally. Navigating these therapies through the clinical development phase and into the market requires a carefully considered process development pathway, said Massimo Dominici, scientific founder, Rigenerand, professor of medical oncology, and former president of the International Society for Cell & Gene Therapy (ISCT). This pathway needs to be flexible, as both the market and materials of these therapies continues to evolve alongside an improved clinical efficacy. Giorgio Mari, chief executive officer, Rigenerand, said, Rigenerand will offer considerable input from its experience of MSC-based therapies to enable Bone Therapeutics to keep and further accelerate the pace in development of the product processes of its MSC based allogeneic differentiated cell therapy as they advance towards patients. We will continue to use our MSC expertise in the development of Rigenerands own products, as well as in process development and manufacturing cell and gene therapies for partner organizations across the globe.
Category Archives: Somatic Stem Cells
Bone Therapeutics and Rigenerand sign partnership for cell therapy process development – GlobeNewswire
January 14, 2021 01:00 ET | Source: Bone Therapeutics SA
Gosselies, Belgium and Modena, Italy, 14January 2021, 7am CET BONE THERAPEUTICS (Euronext Brussels and Paris: BOTHE), the cell therapy company addressing unmet medical needs in orthopedics and other diseases, and Rigenerand SRL, the biotech company that both develops and manufactures medicinal products for cell therapy applications, primarily for regenerative medicine and oncology, today announce the signing of a first agreement for a process development partnership.
Allogeneic mesenchymal stem cell (MSC) therapies are currently being developed at an incredible pace and are evaluated in numerous clinical studies covering diverse therapeutic areas such as bone and cartilage conditions, liver, cardiovascular and autoimmune diseases in which MSCs could have a significant positive effect. Advances in process development to scale up these therapies could have major impacts for both their approval and commercial viability. This will be essential to bring these therapies to market to benefit patients as quickly as possible, said Miguel Forte, CEO, Bone Therapeutics. Hence, whilst Bone Therapeutics is driving on its existing clinical development programs, we have signed a first formal agreement with Rigenerand as a fellow MSC-based organization. This will result in both companies sharing extensive expertise in the process development and manufacturing of MSCs and cell and gene therapy medicinal products. Bone Therapeutics also selected Rigenerand to partner with for their additional experience with wider process development of advanced therapy medicinal products (ATMPs), including the conditioning and editing of MSCs. Rigenerand was founded by Massimo Dominici, a world opinion leader in the cell therapy with an unparalleled MSC expertise and knowledge.
The scope of collaborations between Bone Therapeutics and Rigenerand aims to focus on different aspects of product and process development for Bone Therapeutics expanding therapeutic portfolio. Rigenerand will contribute to improving the processes involved in the development and manufacture of Bone Therapeutics MSC based allogeneic differentiated cell therapy products as they advance towards patients. The first collaboration between the two organizations will initially focus on augmented professional bone-forming cells cells that are differentiated and programmed for a specific task. There is also potential for Bone Therapeutics to broaden its therapeutic targets and explore new mechanisms of action with potential gene modifications for its therapeutic portfolio.
In addition to Rigenerands MSC expertise, Bone Therapeutics also selected Rigenerand as a partner for Rigenerands GMP manufacturing facility. This facility, situated in Modena, Italy, has been designed to host a number of types of development processes for ATMPs. These include somatic, tissue engineered and gene therapy processes. These multiple areas of Rigenerand capabilities enable critical development of new processes and implementation of the gene modification of existing processes. In addition, Rigenerand has built considerable experience in cGMP manufacturing of MSC-based medicinal products, including those that are genetically modified.
Process development and manufacturing is a key part of the development for ATMPs internationally. Navigating these therapies through the clinical development phase and into the market requires a carefully considered process development pathway, said Massimo Dominici, scientific founder, Rigenerand, professor of medical oncology, and former President of the International Society for Cell & Gene Therapy (ISCT). This pathway needs to be flexible, as both the market and materials of these therapies continues to evolve alongside an improved clinical efficacy.
Rigenerand will offer considerable input from its experience of MSC-based therapies to enable Bone Therapeutics to keep and further accelerate the pace in development of the product processes of its MSC based allogeneic differentiated cell therapy as they advance towards patients, said Giorgio Mari, CEO, Rigenerand. We will continue to use our MSC expertise in the development of Rigenerands own products, as well as in process development and manufacturing cell and gene therapies for partner organizations across the globe.
About Bone Therapeutics
Bone Therapeutics is a leading biotech company focused on the development of innovative products to address high unmet needs in orthopedics and other diseases. The Company has a, diversified portfolio of cell and biologic therapies at different stages ranging from pre-clinical programs in immunomodulation to mid-to-late stage clinical development for orthopedic conditions, targeting markets with large unmet medical needs and limited innovation.
Bone Therapeutics is developing an off-the-shelf next-generation improved viscosupplement, JTA-004, which is currently in Phase III development for the treatment of pain in knee osteoarthritis. Consisting of a unique combination of plasma proteins, hyaluronic acid - a natural component of knee synovial fluid, and a fast-acting analgesic, JTA-004 intends to provide added lubrication and protection to the cartilage of the arthritic joint and to alleviate osteoarthritic pain and inflammation. Positive Phase IIb efficacy results in patients with knee osteoarthritis showed a statistically significant improvement in pain relief compared to a leading viscosupplement.
Bone Therapeutics core technology is based on its cutting-edge allogeneic cell therapy platform with differentiated bone marrow sourced Mesenchymal Stromal Cells (MSCs) which can be stored at the point of use in the hospital. Currently in pre-clinical development, BT-20, the most recent product candidate from this technology, targets inflammatory conditions, while the leading investigational medicinal product, ALLOB, represents a unique, proprietary approach to bone regeneration, which turns undifferentiated stromal cells from healthy donors into bone-forming cells. These cells are produced via the Bone Therapeutics scalable manufacturing process. Following the CTA approval by regulatory authorities in Europe, the Company has initiated patient recruitment for the Phase IIb clinical trial with ALLOB in patients with difficult tibial fractures, using its optimized production process. ALLOB continues to be evaluated for other orthopedic indications including spinal fusion, osteotomy, maxillofacial and dental.
Bone Therapeutics cell therapy products are manufactured to the highest GMP (Good Manufacturing Practices) standards and are protected by a broad IP (Intellectual Property) portfolio covering ten patent families as well as knowhow. The Company is based in the BioPark in Gosselies, Belgium. Further information is available at http://www.bonetherapeutics.com.
Rigenerand SRL is a biotech company that both develops and manufactures medicinal products for cell therapy applications, primarily for regenerative medicine and oncology and 3D bioreactors as alternative to animal testing for pre-clinical investigations.
Rigenerand operates through three divisions:
Rigenerand is developing RR001, a proprietary ATMP gene therapy medicinal product for the treatment of pancreatic ductal adenocarcinoma (PDAC). RR001 has been granted an Orphan Drug Designation (ODD) by US-FDA and from the European Medicine Agency. The Clinical trial is expected to start in Q2 2021.
Rigenerand is headquartered in Medolla, Modena, Italy, with more than 1,200 square metres of offices, R&D and quality control laboratories and a cell factory of 450 square metres of sterile cleanroom (EuGMP Grade-B) with BSL2/BSL3 suites for cell and gene therapies manufacturing. It combines leaders and academics from biopharma and medical device manufacturing sectors.
For further information, please contact:
Bone Therapeutics SA Miguel Forte, MD, PhD, Chief Executive Officer Jean-Luc Vandebroek, Chief Financial Officer Tel: +32 (0)71 12 10 00 firstname.lastname@example.org
For Belgian Media and Investor Enquiries: Bepublic Catherine Haquenne Tel: +32 (0)497 75 63 56 email@example.com
For French Media and Investor Enquiries: NewCap Investor Relations & Financial Communications Pierre Laurent, Louis-Victor Delouvrier and Arthur Rouill Tel: +33 (0)1 44 71 94 94 firstname.lastname@example.org
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Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing – Science Advances
The process of single-nucleotide variant (SNV) accumulation is an important universal element of cancer initiation and progression. While the genetic landscape of the most common malignancies has been broadly described (13), accurate identification of driver mutations in specimens with low cancer DNA purity continues to be of great importance yet presents substantial challenges. Hybrid-capturebased next-generation sequencing (NGS) is one of the most common techniques being used for circulating tumor DNA profiling (4, 5), detection of therapy-resistant clones (6, 7) and preleukemia (8, 9), and monitoring disease burden during therapy (10). Nevertheless, in all of these settings, the relevant genomic alterations typically exist at low relative abundance.
Several different methods have been developed in recent years to address the barrier of identifying the minute fraction of DNA molecules harboring an alteration against the high background of NGS-associated errors. Among the various methods, state-of-the-art techniques for error suppression typically can be categorized into two groups: (i) those that incorporate unique molecular identifiers (UMIs) to suppress library amplification errors by the assembly of consensus sequences (1113) and (ii) those that use probabilistic models to estimate background sequencing noise. The latter group can be further segregated into those that generate models that estimate error rates by the analysis of data from a single sample (i.e., single sample/tumor-only mode) (1416), data from a single control sample (1618), or data from multiple control samples (e.g., cohort of healthy controls) (1921). In the case of paired patients tumor and matched normal sample, Bayesian statistics models are commonly used to identify tumor-specific somatic variants that are distinguishable from the background and the germline variants detected within the matched normal sample (22, 23). Some techniques rely on a ploidy assumption to calculate genotype probabilities (24), while others have adapted statistical models to analyze allele frequencies directly (16), thus allowing the identification of rare subclones in existing, complex cancer genomes. Since a single control sample cannot fully account for the stochastic nature of NGS errors, other algorithms have been developed to generate site-specific error estimations using a larger cohort of controls (1921). This approach could be problematic as proper control samples are not always available. When control samples are completely lacking, stringent preprocessing steps can be applied to prioritize high-confidence mutations, for instance, thresholds on base quality scores, supporting read counts, and variant allele frequencies.
Despite advances enabled by the diverse approaches mentioned above, each is associated with inherent disadvantages that can lead to increased assay complexity, elevated sequencing costs, and/or suboptimal exchange between sensitivity and specificity (fig. S1, table S1, and Supplementary Note). To overcome these limitations, we characterized the contextual patterns of high-frequency errors observed during targeted hybrid-capture NGS in >1000 samples, divided across multiple technically diverse and clinically relevant human cohorts. On the basis of these patterns, we developed Espresso, a novel UMI-independent method that optimizes the suppression of artifacts from deep NGS for accurate SNV mutation calling.
To demonstrate the challenges associated with lowvariant allele fraction (VAF) mutation calling from hybrid-capturetargeted NGS, we interrogated multiple benchmarking datasets that differ by their library preparation techniques, captured genomic loci, number of samples, and sequencing depths (Fig. 1A, table S2, and Materials and Methods). Briefly, these datasets include the following: (i) CB: a human cord blood dataset; (ii) CL: a cell line dilution series using genomic DNA from the acute myeloid leukemia (AML) cell line MOLM13 and the colon cancer cell line SW48; (iii and iv) pre-AML1 and pre-AML2: peripheral blood DNA from two separate cohorts, each composed of pre-AML cases (that is, blood was drawn before clinical diagnosis of AML) and age- and sex-matched controls (9); and (v) AML-MRD: a cohort composed of peripheral blood DNA samples obtained from patients with AML during the course of treatment.
(A) Raw, SSCS, and duplex average sequencing depths across all the samples included in this study. Different colors represent different datasets, and these are consistent across all of the figure panels. (B) Sample-wide error abundance in the diverse NGS cohorts. The fraction of genomic positions being observed with at least one nonreference allele supporting read in each sample is indicated. Error burden is significantly different among the investigated datasets (Mann-Whitney test: P < 1.2 1053 for the indicated comparisons). (C) Inverse correlation between the abundance of genomic positions with nonreference allele and their corresponding allele frequencies is demonstrated (Spearmans rank order correlation: r = 0.95; *P < 2.2 1016). Each dot represents a single sample. (D) Panel-wide error abundance in the diverse NGS cohorts as determined by the inclusion of positions with a minimum of one nonreference supporting read in at least one sample. NA, not applicable.
Three different target panels were used to sequence these cohorts, resulting in 83,000 to 1.2 million interrogated bases (table S2). Investigating these genomic loci revealed that the percentage of positions with nonreference alleles per sample varied widely among the different datasets and, in some cases, among samples within a particular dataset (Fig. 1B). Samples with a lower percentage of positions with nonreference alleles displayed higher average error rates (Fig. 1C). Furthermore, almost all genomic positions sequenced harbored a nonreference allele in at least one sample in each dataset (Fig. 1D). Overall, these observations reveal the magnitude of the challenge presented by potential false-positive variants produced by hybrid-capture NGS. Since such a large number of technical artifacts may mask clinically relevant variants, we conducted an unbiased exploration of multiple strategies aiming to specifically suppress NGS errors while maintaining high sensitivity in identifying real mutations.
To evaluate the contextual dependencies of errors in the datasets described above, we investigated how error rates differ with respect to the substitution type, and its 5 and 3 one-base flanking genomic sequence. We found that error rates are highly heterogeneous across the 192 distinct trinucleotide sequence contexts (Fig. 2A, top, and fig. S2) and are highly variable between samples within the same experimental cohort (Fig. 2A, bottom). High error rates were frequently observed at C>A and C>T substitutions (Fig. 2, A and B, and fig. S2). C>T error rates were particularly high when they occurred at a CpG context (Fig. 2, A and C, and fig. S2). Initiated by spontaneous deamination of 5-methylcytosine, real mutations in this context accumulate during aging (25), are frequent in germline cells (Supplementary Note), and are also highly prevalent in cancer genomes (26), emphasizing the importance of evaluating error rates in relation to their associated genomic contexts.
(A) Nonreference average error rates at the 192 distinct trinucleotide contexts are shown using the AML-MRD dataset. Vertical lines in each box represent individual samples. Samples order is kept among distinct contexts. Arrows represent a group of samples with high error rates across multiple contexts. The bottom panels exemplified variation among contextual error rates (*Wilcoxon signed-rank test: P < 1.8 1017) and samples (Mann-Whitney test, samples with the highest and lowest error rates. C[G>T]C: P < 7.7 1041, T[A>C]C: P < 3.6 106). (B). C>T and C>A substitutions are more frequent (Wilcoxon signed-rank test, P < 1.4 10252 for all the comparisons with the other substitution types). (C) High error rates at CpG sites (Wilcoxon signed-rank test, P < 1.1 1064 for all comparisons). (D) Error rates vary between error contexts and their reciprocals (Wilcoxon rank sum test, P < 0.05; #significance was not reached). (E) Average sequencing depths. Arrows represent a group of samples with low sequencing depths across multiple contexts. (F) Reduced sequencing depth at contexts that include reference cytosine and an increasing number of guanine (Pearson correlation: r = 0.35; P = 2.3 10264) and at contexts that include reference guanine with an increasing number of cytosine (r = 0.29; P = 8.6 10179). (G) Low sequencing depth at contexts with C>G or G>C base substitutions (Wilcoxon signed-rank test: P = 1.7 10217). (H) Inverse correlation between depth and error rates (black dashed line, log-log scaled Pearson correlation: r = 0.27; P = 9.7 10308). Correlation strengths differ among different error contexts (colored dashed lines). (I) The number of nonreference supporting reads at the 192 distinct trinucleotide contexts is shown. The samples order is identical across (A), (E), and (I).
While contextual error patterns were generally similar between their complementary counterparts, they did not always mirror each other perfectly within any particular sample (fig. S3A). Small yet statistically significant asymmetric error rates were consistently observed among the majority of error contexts in each of the cohorts (Fig. 2D and fig. S3B). For instance, we measured asymmetric error rates involving G>T/C>A, in line with prior observations (27). Error rate asymmetries were markedly directional and consistently elevated in specific contexts as compared with their matched reciprocals in all of the investigated datasets. As an example, each of the 16 trinucleotide contexts containing A>T substitutions demonstrated elevated error rates as compared with their corresponding reciprocal contexts containing T>A substitutions. Together, these results indicate that 192, rather than 96, contextual error types would need to be considered to accurately model error rates.
Next, we investigated how sequencing depth may influence error frequencies. As with error rates, sequencing depth differed between distinct contextual error types (Fig. 2E). We noticed a marked inverse correlation between sequencing depth and guanine or cytosine content within specific trinucleotide contexts, a possible reflection of the systemic under-coverage in GC-rich regions reported in NGS (Fig. 2F) (28, 29). Sequencing depth was also lower within trinucleotide contexts that included C>G and G>C substitutions as compared with those that included nucleotide substitutions that reduce GC content (Fig. 2G). These data illustrate how sequencing depth can be influenced by both the trinucleotide context and the nonreference allele.
Overall, a modest, statistically significant inverse correlation was observed between sequencing depth and error rates (Fig. 2H). Correlation strengths were not equal among distinct contextual error types. Further supporting this trend, individual samples with lower average sequencing depth displayed high error rates in multiple contextual error types (see arrows in Fig. 2, A and E). In contrast to the error rates, the absolute number of nonreference supporting reads at the distinct contextual error types showed reduced inter-sample differences in those samples; however, the differences between distinct contextual errors were preserved (Fig. 2I). Collectively, the results obtained here suggest that integration of intra-sample contextual error modeling of nonreference supporting reads at each of the 192 contexts may be a promising strategy for accurate suppression of errors produced by hybrid-capture NGS.
As described above, errors varied across samples yet were highly stereotypical according to sequence context and sequencing depth. We reasoned that intra-sample contextual error patterns could be leveraged for in silico error suppression. Such an approach could have several inherent advantages over existing error suppression methods that rely on UMIs, apply thresholds based on intra-samplewide error rates, or use control samples to train error rate models. Therefore, we devised a computational approach, called Espresso, to model within a sample of interest the nonreference allele counts at each of the 192 distinct contextual error types. Espresso incorporates three distinct features that make it robust to different sequencing datasets (Supplementary Note): (i) pragmatic pre-filters that prepare the dataset for error modeling (fig. S4), (ii) automatic selection of the most appropriate probabilistic distribution for error modeling at a particular contextual error type (fig. S5), and (iii) utilization of nonreference supporting reads as opposed to VAF for error modeling (fig. S6). Unlike applying fixed and arbitrary cutoffs (e.g., minimum VAF, coverage, and number of supporting reads), nonreference alleles would not be indiscriminately eliminated by such an approach; rather, mutations would only be called if they reached statistical significance when compared to their corresponding error distributions (Fig. 3, A to E, and Materials and Methods).
Flowchart illustrating the error modeling technique that is implemented by Espresso. (A) Following the summarization of the sequencing data to include the dominant alleles at each investigated genomic position, their corresponding read counts, and the average mapping read qualities in each sample of interest, a set of filters is being applied, aiming to deplete potential somatic SNVs and common polymorphism from being included in the error models. (B) On the basis of the distribution of the nonreference supporting reads in the enriched error list, Espresso selects between either the exponential or the Weibull probabilistic approaches. (C) The nonreference supporting read (SR) counts in each sample are being grouped based on the genomic sequence context to generate 192 context-specific distribution models. (D) The models are being reapplied to the entire samples data for outlier identification. True positives are being determined if they reach statistical significance when compared to their corresponding error distribution. (E) The cumulative distribution function graph displays the empirical data (black dots) and the theoretical data (blue line) generated by the 192 models in all the samples included in the CB dataset (top, exponential models) and the AML-MRD dataset (bottom, Weibull models). (F) Panel-wide error rates defined as the number of nonreference alleles supporting reads following error suppression, divided by all the reads from the same category (i.e., raw, SSCS, and duplex reads) across the entire 1,264,830-bp panel and (G) percentage of error-free positions in the 10 cord blood samples are illustrated. For error suppression, a cutoff P value 0.05 (Bonferroni-adjusted) was used. SSCS and duplex cutoffs are 1 nonreference supporting read unless indicated otherwise. * indicates Wilcoxon signed-rank test: P < 0.002.
To evaluate the performance of Espresso, we first applied it to the CB dataset. We reasoned that CB would have a minimal burden of somatic mutations, allowing for a more precise estimation of true error rates. We also tested in parallel other common error suppression techniques for unbiased comparative performance assessment (Materials and Methods). The techniques selected for comparison were representative of the spectrum of previously published tools. Specifically, we used two UMI-based methods, namely, single-strand consensus sequences (SSCSs) and duplex sequences (12), and two statistical methods for error correction that model background error distributions differently. Among the two statistical methods used, one relies on a training cohort to estimate error rates at the allele level (termed AL here) (20), and the other estimates error rates at the sample level (termed SL here) (14) without consideration for distinct sequence contexts.
Panel-wide error rates were highly similar among the 10 CB samples but varied significantly among the different error suppression methods (Fig. 3F). As compared with the various statistical approaches (i.e., SL, AL, and Espresso), the UMI-based methods demonstrated inferior error suppression capabilities. A minimum of nine nonreference supporting SSCS reads or three nonreference supporting duplex reads were required to achieve panel-wide error rates comparable to that of SL and Espresso in the CB dataset. We observed similar relative performance among the methods to maximize the number of error-free positions across the entire target panel (Fig. 3G). Considering the highest panel-wide error rate obtained by Espresso (2.74 106) and the lowest of the panel-wide error rate observed without error suppression (0.025) across the CB samples, Espresso achieved an error rate reduction of more than 9000-fold.
To evaluate the sensitivity and specificity exchange delivered by Espresso, we analyzed the sequencing data from the CL dataset, which consisted of a dilution series using two cancer cell lines, MOLM13 and SW48. For sensitivity measurements, we assessed the ability of the different methods to detect 119 MOLM13-specific germline variants at the different dilutions (table S3). To evaluate specificity, we assessed the miscalling of 186 AML-related somatic hotspot mutations that are covered by the target panel but are absent from both cell lines (table S3). Espresso outperformed all the other methods in distinguishing between true and false variants (Fig. 4A). In contrast, duplex sequencing achieved the smallest area under the receiver operator curve (AUC), highlighting the low diagnostic accuracy of this method and, consequently, its limited clinical utility in detecting variants across large hybrid-capture panels.
(A) Espresso demonstrates improved sensitivity versus specificity and (B) preferable precision-recall trade-offs as compared with the various indicated methods. The ability of each method to differentiate between 119 positive alleles and 186 negative control variants in a set of serially diluted cell line DNA samples was tested. (C and D) No substantial benefit of using UMIs to augment Espressos performance could be determined. Sensitivities and specificities were measured at all the possible combinations of the unique P values outputted by Espresso and the unique numbers of SSCS or duplex nonreference supporting reads that were observed in the dataset. The maximum sensitivities at each calculated value of specificity are illustrated. (E to H) Sensitivity versus specificity trade-offs derived by the reduced and extended contextual error modeling approaches are illustrated in comparison with Espresso. Ninety-five percent confidence intervals (shaded colors) and average values were derived by three random subsets of the data for each one of the indicated in silico decreased panel sizes. (I) Heatmap illustrating the percentage of contextual models that can be generated by Espresso when data are being restricted by either panel size reduction or sequencing depth reduction, or both. Data removal was controlled for both the reference and nonreference supporting reads, thus keeping the variant allele frequencies of the nonreference alleles similar to those in the original samples. The red line illustrates such combinations, of which 90% or more of the distinct contextual models could have been generated in every sample in the CL dataset. With datasets that fall below this line, the 12-model contextual error modeling approach can be used in addition to Espresso.
The use of hybrid-capture NGS panels allows for the detection of mutations at thousands of genomic positions. However, their use also creates unique challenges for true variant identification across so many bases. In addition to high sensitivity and specificity, positive predictive value (PPV) must be prioritized to maximize utility. We assessed PPV in conjunction with sensitivity (i.e., precision-recall analysis). We focused on variants with expected VAF 0.2%, since accurate variant detection below this threshold is clinically important yet has proven to be a great challenge for existing hybrid-capture NGS platforms (5, 30). Espresso provided a sensitivity of 19.9%, thus achieving the highest number of true-positive, low-VAF alleles at 100% PPV among the tested methods (Fig. 4B). This corresponds to a 6.8-fold improvement as compared to AL, which was the next best-performing method to detect low-VAF alleles without scarifying PPV. Notably, SL performed far worse in this analysis than the other methods due to a high number of false-positive calls across various sensitivity thresholds. This result highlights the limited power of noncontextual, sample-level error modeling in detecting mutations with very low read support despite its ability to achieve an extremely high level of error suppression (Fig. 3, F and G). Further supporting this, we compared the false-positive and true-positive calls obtained by Espresso with that of Mutect2 (16) at tumor-only mode. Once more, Espresso demonstrated superior results (table S4).
Previously, the suppression of errors through statistical error modeling was shown to be enhanced by combination with UMI-based approaches (20). However, integrating UMI information with Espresso did not confer significant performance improvements (Fig. 4, C and D), suggesting that accurate detection of low-frequency variants can be achieved with Espresso alone. Collectively, the comparative analysis using the CL dataset indicates that the bioinformatic strategy applied here outperformed other methods in the reliable distinction of low-frequency errors from real SNVs.
To characterize pragmatic constraints of our method, we compared Espresso with alternative sequence context-based error models. Specifically, we included (i) a simplified 12-model design that accounts only for the 12 possible distinct substitution types without consideration of flanking bases and (ii) an expanded 3072-model design that accounts for the substitution type and for two additional 3 and 5 flanking bases. We evaluated the impact of panel size (i.e., number of interrogated bases) and sequencing depth on the performance of Espresso and the alternative sequence context-based models using the CL dataset.
This comparative analysis exposed critical factors affecting the performance of the alternative models. On the one hand, the performance of the 3072-model approach suffered with reduced panel size (Fig. 4, E to H, and fig. S7A). This is an expected observation that is attributed to the reduction in the number of nonreference alleles being used to populate a relatively high number of models, thus resulting in either model generation failure or an inadequate estimation of the background error noise. In contrast, performance of the 12-model approach was less dependent on panel size since the relatively small number of models was easily populated with nonreference alleles (Fig. 4, E to H, and fig. S7B); however, Espresso consistently outperformed the 12-model approach, presumably because the 12 models were insufficient to account for errors arising within distinct sequence contexts. Moreover, the 12-model approach performed poorly on the largest panel size, possibly as a result of model overfitting from high-VAF errors that escape the initial filtering steps (Materials and Methods). The performance of Espresso was relatively consistent across a broad range of panel sizes from ~1 Mb down to ~50 kb (Fig. 4, E to H, and fig. S7C).
Next, we serially downsampled the CL dataset to simulate various practical scenarios of panel sizes (1 Mb to 32.5 kb) and sequencing depths (4500 to 1000). At each simulated panel-depth combination, we determined the percentage of trinucleotide contexts that could be modeled directly by Espresso (Fig. 4I). Notably, low represented nonreference alleles that cannot be modeled directly by Espresso would still be analyzed automatically by alternative techniques that are included in the software package (see Data and materials availability). Overall, these results illustrate the performance dependencies of Espresso and related sequence contextbased models to assist with their implementation in a wide range of sequencing settings.
Having demonstrated Espressos high analytical performance in the CB and CL datasets, we next sought to evaluate its clinical utility. The presence of persistent AML clones that carry genetic abnormalities during or after treatment has been shown to carry crucial prognostic information (31). Therefore, we assembled a cohort of 42 patients with AML (AML-MRD; table S5) whose mutations were previously determined at diagnosis (table S3). Forty of the 42 patients had serial samples analyzed by ultra-deep hybrid-capture NGS at two time points during therapy; for the other two patients, single follow-up samples were available.
Since minimal/measurable residual disease (MRD) monitoring may guide clinical decisions (3234), in addition to true positives, both false positives and false negatives could have tremendous implications for patient care. We therefore evaluated F1 scores, which represent the harmonic mean of PPV and sensitivity. For comparative performance evaluation, mutations reported at diagnosis were considered as true positives if they were detected in the follow-up samples of the same patient or as false positives if they were detected in other patients. We first applied a cutoff of 0.05 (Bonferroni-adjusted) for the probabilistic methods SL, AL, and Espresso and a heuristic threshold of 1 nonreference supporting reads for the UMI-based methods SSCS and duplex. Tested on the subset of samples obtained at either the first time point (T1, closer to diagnosis) or the second time point (T2, further into treatment), Espresso delivered the highest F1 scores (0.71 at T1 and 0.74 at T2) followed by AL and duplex (Fig. 5A). We next applied the optimized SSCS and duplex cutoffs used in the CB analysis (i.e., 9 and 3 nonreference supporting reads, respectively). Although F1 scores improved with these parameters, they still fell short due to an increased number of false positives for SSCS 9 and an increased number of false negatives for duplex 3 in both the T1 and the T2 data subsets as compared with Espresso (Fig. 5B).
(A) Espresso provides a preferred balance between precision (PPV) and recall (sensitivity), as determined by the inspection of 78 SNVs reported across 35 of 42 patients at the time of AML diagnosis. Mutations were called in the patients sample at 21 different iterations. In each iteration, 6 random patients of the 42 were excluded. Median F1 scores and 1 SD are shown for the various methods tested at two time points during the course of treatment (T1 and T2, Wilcoxon signed-rank test: P 6.4 105 for all the comparisons with Espresso). (B) The variation in the mutations being called by Espresso ( 0.05, Bonferroni-adjusted), SSCS (9 nonreference supporting reads), and duplex (3 nonreference supporting reads) is illustrated. Red color indicates called mutations, while blue color indicates that mutations were not detected. FP, false positives; FN, false negatives. (C) Sensitivity versus specificity as determined by the different tested methods. (D) Enrichment of clones, carriers of TP53, and DNMT3A mutations is observed in patients with AML following therapy. The y axis represents the number of mutations detected, classified by the affected genes.
Despite the technical differences between the CL and AML-MRD datasets, Espresso once again produced the most preferred balance between sensitivity and specificity (Fig. 5C). We compared Espresso with additional algorithms and saw consistent outcomes. Espresso outperformed Mutect2 (16) in both the tumor-only mode and the panel of normals mode when samples obtained from 14 healthy adults were used (table S4). Espresso also outperformed deepSNV (18), a statistical algorithm that was developed specifically for the accurate detection of SNVs from deep targeted sequencing experiments. The comparison with deepSNV extrapolates beyond the probabilistic approaches being used and illustrates the benefits of other features implemented in our bioinformatic pipeline for the reduction of false-positive calls (fig. S8).
Having established Espresso as the preferred methodology to maximize the accuracy of SNV detection from peripheral blood, we next sought to implement it for the characterization of clonal dynamics in patients with AML. Since the competitive balance among different hematopoietic clones is likely to change during multiple rounds of chemotherapy, we hypothesized that Espresso would enable the identification of resistant clones that were not reported at diagnosis. We therefore extended our analysis to include an additional 147 highly recurrent AML SNVs that are covered by the AML-MRD hybrid-capture panel (table S3). Across all the samples, Espresso identified 92 mutations ( 0.05, Bonferroni-adjusted) with the lowest being reported at VAF = 0.0135% (table S6 and fig. S9). These correspond to 59 distinct mutations, out of which 47 (~80%) were present in at least two samples of the same patient (that is, reported at diagnosis and detected in at least one additional time point by Espresso or detected in the two follow-up samples by Espresso). Such a high percentage of validated mutations is an indicator of Espressos reliable mutation calling. Among these, Espresso has enabled the detection of 22 new putative driver SNVs not reported at diagnosis in 15 patients, including in 3 of the 7 patients (~43%) with no SNVs in the diagnostic report (table S6). Further supporting the validity of the mutations called by Espresso, most of these newly identified mutations were in genes that commonly contribute to positive clonal selection following cytotoxic chemotherapy (3537), including TP53 and DNMT3A (Fig. 5D).
Together, our results demonstrate substantial advantages of Espresso over other methods for SNV detection from peripheral blood of patients with AML during the course of therapy. Encouraged by a recent consensus document release from the European LeukemiaNet MRD Working Party (38), many studies are now underway to evaluate the prognostic and predictive significance of clonal dynamics in AML and the proposed role of MRD detection as a surrogate endpoint for clinical trials (39). Implementation of Espresso in these contexts has the potential for significant clinical utility.
Age-related clonal hematopoiesis (ARCH) is a common phenomenon evident by the presence of somatic mutations in hematopoietic stem cells of otherwise healthy individuals that cause a clonal expansion of the stem cells and their progeny (40). Recently, our group reported several hundred ARCH-associated mutations spread across 27 genes with various contributions to the risk of AML transformation (9). Our study provided a proof of concept for risk prediction of AML. Nevertheless, large population screens using broad sequencing panels remain socioeconomically unattractive because of high costs, the relatively low incidence of AML, and the relatively high incidence of ARCH in the general population.
To address these challenges, we reasoned that interrogating a small number of highly recurrent AML mutations would be a more tractable approach than broad hybrid-capture sequencing. This approach could theoretically result in improved segregation between pre-AML and controls while reducing sequencing costs. The success of this approach relies on the accurate identification of preleukemic mutations in asymptomatic individuals.
We first compiled datasets that would allow comparisons among the distinct methods used in our previous analyses. For this reason, we focused initially on the pre-AML1 dataset, which contains UMIs in the sequencing reads, and the CB dataset, which could be used as a training set for error rate estimation at the AL. Putative driver SNVs (that is, mutations in coding sequences other than synonymous SNVs and mutations at splice sites) identified by each method at the recurrently mutated genomic loci were used to derive random forest classifiers that were trained and tested on their corresponding methods mutation calls (table S7). For the probabilistic methods, 0.05 (Bonferroni-adjusted) was used, and for the UMI-dependent methods, we applied either a threshold of one supporting consensus read or SSCS 9 and duplex 3. The Espresso-derived classifier exhibited the highest level of performance for discriminating pre-AML from controls (AUC: 0.74) and reported the highest sensitivity (46.8%) at 100% specificity (Fig. 6A). A reduction in specificity down to 96.3 or 93.7% was needed to achieve the same sensitivity with the SL-derived and SSCS-derived classifiers, respectively. The SSCS-derived model also underperformed the Espresso-derived classifier when the SSCS 1 cutoff was applied (AUC: 0.66, Fig. 6A, dashed line). The duplex 3 derived classifier had the poorest performance (AUC: 0.42), owing to poor duplex consensus efficiency (fig. S1B), low duplex coverage (Fig. 1A), and subsequent dropout of mutations not meeting the required cutoff. On the contrary, with a threshold of one supporting duplex read, a large number of putatively false-positive SNVs were called, resulting in poor classification accuracy (AUC: 0.65, Fig. 6A, dashed line). The AL-derived classifier also performed poorly due to a high number of false-positive SNVs (AUC: 0.62).
Classification performance evaluation of pre-AML and control, mutated samples. (A) Each classifier was trained and tested on the mutations that were obtained from the classifiers corresponding method. (B) Comparison between the Espresso and the SL-derived classifiers. In this iteration, each classifier was trained using its corresponding methods mutation calls and was tested in its accuracy to classify pre-AML cases and controls, including mutated samples identified by the other method as well. (C) Comparative performance validation between the Espresso and the SL-derived classifiers to differentiate between pre-AML and control samples obtained from an additional validation dataset (8). Information regarding the study participants age, specific mutations, and their VAFs was obtained directly from the main text. (D) Performance estimation using the validation dataset and simulated controls. (E) Precision-recall trade-offs are calculated at the individual level (that is, serial samples are accounted for single individuals and individuals without any mutations are also included in the performance measurements). The red dot indicates AMLs incidence rate. This is equivalent to a situation where no screen is being conducted at all [PPV = incidence rate = 0.006% (44), SN = 100%]. The green dot indicates the model performance using an additional published dataset consisting of 11,262 individuals when the model was set to achieve 100% specificity in the training set. Horizontal color bars represent PPV ranges determined for screening mammography for breast cancer (54) and fecal immunochemical test for advanced adenomas and colorectal cancer (CRC) (55). Comparison with the genetic risk model performance shows the extent to which sensitivity must be compromised to achieve PPV comparable with these widely applied early detection tests.
There is a low cumulative risk of ARCH progression to hematologic neoplasms (41). For this reason, the implementation of a population-based pre-AML genomic screening test would need to achieve exceedingly high specificity and low false-positive rate. We therefore prioritized the Espresso- and SL-derived classifiers for subsequent performance evaluation. Additional mutations that were found by Espresso and SL in the pre-AML2 dataset were included in the analysis (table S7). Each classifier was trained on the mutations found by its corresponding method in both the datasets (pre-AML1 and pre-AML2) and tested on the data that include all the mutations detected by either of the two methods. The Espresso-derived classifier once more provided a better overall sensitivity-specificity balance and a greater sensitivity at 100% specificity (Fig. 6B). Similar trends were observed when both the classifiers were applied to an external validation set consisting of mutations called in 188 pre-AMLs and 181 controls (8), with the Espresso-derived classifier again displaying higher discriminatory accuracy (Fig. 6C). Together, the superior classifier performance using mutations called by Espresso illustrates that accurate mutation calling is imperative when designing genetic risk prediction models.
To estimate how well the winning classifier would perform as a population-wide screening test, we spiked the validation set into >4 million in silico simulated controls (prevalence ~0.005%; Materials and Methods). Despite the small genomic footprint (table S8), the Espresso-derived classifier resulted in accurate identification of the mutated pre-AML samples (AUC: 0.84; Fig. 6D). As an example, when the model was tuned to minimize false-positive calls based on the pre-AML1/pre-AML2 merged training dataset, a sensitivity of 29.3% and a specificity of 99.8% were obtained. Precision-recall analysis revealed the extent to which the Espresso-derived classifier may enrich for individuals at high risk of developing AML as compared with current practice (no screening, i.e., AML incidence rate) (Fig. 6E). Sensitivity was 4.8% at 100% PPV; this small subset detected with no false positives was enriched for highly penetrant SRSF2/IDH2 double-positive individuals with the highest risk for AML development (table S9). Last, we estimated the model performance in an additional published cohort of 11,262 individuals (42). In this cohort, when the model was tuned to minimize false positives within the training dataset, a sensitivity of 14.3% and a PPV of 4.8% were obtained (Fig. 6E and table S9).
In this study, we described the rationale, technical performance characteristics, and potential clinical utility for Espresso, a novel method to improve hybrid-capture sequencingbased SNV detection. Unlike many other NGS error suppression methods, including the representative published UMI-based and probabilistic modelbased approaches tested here, Espresso does not rely on UMIs or a training set of controls for error rate estimations; therefore, Espresso improves practicality by reducing library preparation complexity, assay costs, and analysis time. We observed additional notable advantages of Espresso over alternative methods, and these were consistent across diverse datasets. Specifically, Espresso produced superior error suppression and an improved trade-off between sensitivity and specificity for detection of low-VAF alleles.
These advantages of Espresso were the result of several key features. First, Espresso applies a set of pre-filters to prepare the data for error modeling. Second, Espresso automatically selects between two statistical models to estimate the number of alternative supporting reads rather than the VAFs; thus, in addition to selecting the more appropriate error distribution model, it better accounts for error rate bias resulting from variation in sequencing depth within hybrid-capture NGS datasets. Third, Espresso markedly reduces false-positive calls by considering only the dominant nonreference allele at each interrogated genomic position. Fourth, Espresso leverages a large number of errors that share the same trinucleotide sequence context within the investigated sample; thus, it reduces the potential for misrepresentation of real error rates by relatively small control cohorts.
To explore its potential use in clinical settings, we tested the performance of Espresso to detect SNVs in serial peripheral blood samples from 42 patients with AML who achieved clinical remission. Consistent with the performance in the other investigated datasets, Espresso outperformed all the other tested methods in this setting. Using Espresso, we found resistant subclones enriched for TP53 and DNMT3A mutations that were genetically distinct from the AML clones present at diagnosis. In the future, more extensive cohort studies are needed to determine whether the selection and enrichment of such clones following induction therapy may affect patient outcomes in a nonautonomous fashion, similar to the observations in solid malignancies (43). Furthermore, combining accurate detection of persistent mutations together with other independent prognostic markers will be necessary to build clinically relevant models for accurate determination of the risk of relapse.
Our results emphasize the importance of accurate mutation detection for the derivation of classification models in the setting of early detection of AML. Using Espresso, we derived a risk prediction model that is focused on a minimal yet highly informative set of genomic loci that are recurrently mutated in patients with AML. With only 1594 genomic bases being interrogated, our results imply that up to 29.3% of de novo AML cases can be predicted years in advance with a specificity of 99.8%. Although sensitivity may greatly suffer with elevated PPV, considering the incidence rates of AML in the general population (~6:100,000) (44), our approach would still provide meaningful patient enrichment. Modest sensitivity may be acceptable when screening the general population as long as specificity and PPV remain high. Further prospective validation studies are required to assess the feasibility, utility, and cost-effectiveness of this targeted approach. Our findings should also be extended to incorporate additional predictive biomarkers. As AML is a blood-borne disease, we envision that epigenetic and metabolomic perturbations within leukocytes may further improve prediction accuracy, thus making AML predictions more clinically useful. Our results indicate that certain biomarker-enriched populations may be at an exceedingly high risk of developing AML. In time, novel therapeutic developments and targeted therapies against blood cells with high-risk mutations may provide the minimal side effects necessary to deliver a favorable risk-benefit ratio that justifies the initiation of early intervention clinical studies.
In summary, we have described, benchmarked, and validated a new practical NGS error suppression technique. We have demonstrated the superiority of Espresso in detecting somatic SNVs as compared with existing state-of-the-art approaches and defined its limitations with respect to sequencing depths and hybrid-capture panel sizes. We used Espresso to derive new biological insights, augmenting our understanding of the genetic mutations that define high-risk malignant transformation and therapy resistance clones in patients with AML. We envision that Espresso will prove useful in guiding clinical decisions and scientific research alike.
CB dataset: This dataset is composed of 10 human umbilical cord blood genomic DNA samples obtained from Trillium Hospital (Mississauga, Ontario, Canada) with informed consent in accordance with guidelines approved by the University Health Network Research Ethics Board. Cord blood was processed 24 to 48 hours after delivery. Mononuclear cells were enriched using Ficoll-Paque followed by red blood lysis by ammonium chloride and CD34+ selection before DNA extraction. CL dataset: MOLM13 cell line DNA was mixed with SW48 cell line DNA at relative concentrations of 100, 5, 1, 0.2, 0.04, and 0% and was sequenced in duplicate. Pre-AML1 and pre-AML2 datasets: Detailed information regarding these cohorts is described elsewhere (9). Briefly, the pre-AML1 dataset contains peripheral blood genomic DNA samples obtained from a total of 509 individuals upon enrollment into the European Prospective Investigation into Cancer and Nutrition (EPIC) study (45) between 1993 and 1998. Together, 414 control individuals who did not develop any hematological disorders during the extended follow-up period and 95 individuals who developed AML were included in this study. The pre-AML2 dataset contains peripheral blood genomic DNA samples obtained from individuals enrolled in the EPIC-Norfolk longitudinal cohort study between 1994 and 2010. Samples were available from 37 patients with AML and 262 age- and sex-matched controls without a history of cancer or any hematological conditions. Samples taken at multiple time points were available for a fraction of the participants in this cohort. Notably, samples from eight pre-AML patients in the pre-AML2 cohort were separately sequenced in the pre-AML1 dataset (by independent investigators using a different methodology). To avoid statistical misrepresentation of AML predictions, we removed those samples from the pre-AML2 dataset before the derivation of the described genetic risk models. AML-MRD dataset: This dataset is composed of peripheral blood genomic DNA from 42 patients with AML treated at the Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. All 42 patients achieved morphologic leukemia-free state (MLFS) on chemotherapy. Complete count recovery occurred when absolute neutrophil count recovered to 1 109/liter and platelet count recovered to 100 109/liter up to 7 days following the bone marrow assessment that confirmed MLFS status. All patients were deidentified with patient IDs. Their demographic and clinical features were captured (table S5). All the samples in this study, including healthy individuals and patients with cancer, were collected with informed consent for research use and were approved by Institutional Review Boards in accordance with the Declaration of Helsinki. Protocols were approved by the following ethics committees: (i) International Agency for Research on Cancer Ethics Committee approval #14-31, (ii) East of EnglandCambridgeshire and Hertfordshire Research Ethics Committee reference number 98CN01, and (iii) University Health Network Research Ethics Board # 01-0573.24.
Library construction and sequencing were done as previously described (9). Briefly, for each sample in the CB, CL, and pre-AML1 datasets, 100 ng of genomic DNA was sheared to 250base pair (bp) fragments before library construction (KAPA HyperPrep Kit KK8504, Kapa Biosystems) with a Covaris E220 instrument using the recommended settings. After end repair and A-tailing, ligation of UMI-containing adaptors was performed with 100-fold molar excess. Agencourt AMPure XP beads (Beckman Coulter) were used for library cleanup following eight cycles of fragment amplification with 0.5 M Illumina universal and indexing primers. Targeted hybrid-capture was carried out on pools of three indexed libraries. Five microliters of Cot-I DNA (1 mg ml1; Invitrogen) and 1 nmol each of xGen Universal Blocking Oligo, TS-p5, and xGen Universal Blocking Oligo, TS-p7 (8 nucleotides) were added to each pool of adaptor-ligated DNA. The mixture was dried using a SpeedVac and then was resuspended in 1.1 l of water, 3.4 l of NimbleGen hybridization component A, and 8.5 l of NimbleGen 2 hybridization buffer. The mixture was heat-denatured at 95C for 10 min following the addition of 4 l of xGen Lockdown Probes (3 pmol; xGen AML Cancer Panel v.1.0). Hybridization was conducted at 47C for 72 hours. Washing and recovery of the captured DNA were initiated with 100 l of clean streptavidin beads that were added to each capture. Following separation of the libraries and the supernatant using a magnet, 200 l of 1 Stringent Wash Buffer was added, and the reaction was incubated for 5 min at 65C. The supernatant containing unbound DNA was removed before repeating the high stringency wash for the second time. The bound DNA was then washed one time with 200 l of each of the following: 1 Wash Buffer, 1 Wash Buffer II, and 1 Wash Buffer III. The washed DNA on beads was resuspended in 40 l of nuclease-free water, and this volume was divided into two polymerase chain reaction (PCR) tubes that were subjected to 10 cycles of post-capture amplification (Kapa Biosystems, recommended conditions). Libraries were spiked with 2% PhiX before sequencing. The procedure used for the pre-AML2 dataset is described elsewhere (referred to as the validation cohort) (9). For each sample in the AML-MRD dataset, peripheral blood samples were collected during remission in PAXgene Blood DNA Tubes (PreAnalytiX, Hombrechtikon, Switzerland). DNA was extracted according to the manufacturers instructions. Illumina-compatible libraries were constructed from 100 ng of sheared genomic DNA using the Covaris M220 sonicator (Covaris, Woburn, MA, USA) and the KAPA HyperPrep Kit (#KK8504, Kapa Biosystems, Wilmington, MA, USA). Following end repair and A-tailing, adapter ligation was performed for 16 hours at 4C using 100-fold molar excess of adapters. Agencourt AMPure XP beads (Beckman Coulter) were used for library cleanup, and ligated fragments were amplified by PCR for 6 cycles using 0.5 M universal and indexed primers. Following hybrid-capture at 47C for 72 hours, the captured DNA fragments were enriched with 12 cycles of PCR. Paired-end 2 125-bp sequencing was performed on an Illumina HiSeq 2500 instrument with eight libraries multiplexed into each lane.
Paired-end sequencing data from the Illumina platform were converted to FASTQ format. When included, the unique molecular barcode information at each read of the pair was trimmed and was added to the read header. The Burrows-Wheeler aligner (BWA-mem) (46) was used for the alignment of the processed FASTQ files to the reference hg19 genome. To eliminate the chance of ambiguous short indel alignment on neighboring SNV miscalls, we removed reads with indels. We further cleaned the data from short and hard clipped reads and any nonunique read alignments. We found that, together, these preprocessing steps can improve SNV detection (fig. S8). Consensus read assembly into read families was done in a similar way to previous reports (47, 48). Specifically, reads that share the same molecular barcode sequence, the genomic position of where each read of the pair maps to the reference, and the CIGAR string were grouped. Families that consisted of at least two reads were used to generate SSCS, and a consensus base was called when there was full agreement. When a consensus base was called, it was assigned with the maximum base quality score observed in its corresponding precollapsed reads. Similarly, when two SSCSs with corresponding UMIs on the reciprocal strand were observed, duplex reads were generated. After converting the raw-, SSCS-, and duplex-containing sam files into coordinate-sorted bam files, we used samtools (49) version 1.2 and Varscan2 (14) version 2.2.8 to summarize the data. The following parameters were used: (i) mpileup parameters: -s -x -BQ0 -q1 -d100000 and (ii) pileup2cns parameters: --min-coverage 10 --min-reads2 1 --min-avg-qual 30 --min-var-freq 0.0001 --p-value 1 --strand-filter 0. These are rather permissive parameters allowing the output of all the dominant alleles in each one of the investigated genomic positions. To allow unbiased performance comparisons, we used this format as an input for all the probabilistic methods (SL, AL, and Espresso) and the UMI-based methods (SSCS and duplex).
With Espresso, we deployed a novel approach to model errors based on their association with either one of the 192 contextual contexts (Fig. 3, A to E). These correspond to 12 base substitution types, four alternative 5 bases, and four alternative 3 bases. To mitigate the impact of outliers and real mutations on overfitting, a set of filters is applied to exclude specific variants from the contextual error models (Supplementary Note and fig. S4). These include the removal of alleles (i) that are observed as germline variants in the general population (50, 51) with minor allele frequency 0.1%, (ii) with VAF/error rates 5%, (iii) that have MapQual<59 and MapQual!=0 [for additional information, please refer to the manual of Varscan2 (14)], (iv) that describe recurrent cancer mutations, and (v) that disproportionally persist across multiple samples in the dataset (see the Flagged alleles section; Materials and Methods). Notably, to prevent performance comparison bias, we used these filters together with all the probabilistic methods (SL, AL, and Espresso) and the UMI-based methods (SSCS and duplex) tested.
To determine the more appropriate distribution type for error modeling, Espresso first investigates the overall distribution of nonreference supporting reads in a context-independent manner, in the samples filtered, error-enriched list. On the basis of the observed peak occurrence, either exponential or Weibull distribution models are selected to generate all the contextual models. If the peak corresponds to a single nonreference supporting read, exponential distribution will be used to represent the data; otherwise, if this value is larger than 1, Weibull distribution will be used. Either the pexp or pweibull R functions are then being used together with the modeled parameters from the fitdistrplus package (either rate or shape and scale) to determine how high any nonreference allele of interest is being represented above its corresponding contextual background. A Bonferroni-corrected P value 0.05 was used to determine whether any nonreference allele received significantly more supported reads.
For comparative performance analysis, error rate models at the AL were constructed as previously described (20). Briefly, if the total number of nonzero allele frequencies seen in the training set used for error modeling was 5, we used Gaussian distribution; otherwise, we fit a Weibull distribution to the allele frequencies observed in the training set. Specifically, the pnorm or pweibull R functions were used together with the modeled parameters (either mean and SD or shape and scale) to estimate the likelihood that any allele frequency value of interest is above the corresponding modeled distribution derived for the same interrogated position in the corresponding training set. The yielded P values were adjusted by incorporating the fraction of nonzero allele frequencies into the final models [for additional information, please refer to iDES (20)]. Training datasets were constructed as follows: (i) The pre-AML1 dataset was used for the CB analysis (Fig. 3) and the CL analysis (Fig. 4). (ii) A training set composed of peripheral blood genomic DNA samples from 14 healthy individuals was sequenced and used in the analysis of the AML-MRD data (Fig. 5). (iii) The CB dataset was used as a training set for the derivation of the AL-based model for AML risk prediction (Fig. 6). To evaluate allele mutated status at the SL, we used Varscan2 (14) that computes statistical significance in single samples by Fishers exact test.
While parameters such as specific genomic context, the presence of a repetitive region, and low base or read mapping quality may explain the basis of some errors, these do not always capture artifacts that may persist across multiple samples. We therefore derived a statistical approach to flag recurrently specious alleles. To flag potentially low-frequency artifactual alleles that escaped conventional filtering, we iterated between the 99 and 99.9% nonreference allele frequency quantiles in the entire investigated cohort in increments of 0.1% (user-defined parameters). The 10 derived VAF values were used consecutively to apply Fishers exact tests, determining whether errors with VAF above the quantile-derived cutoff distribute proportionately among all the observed nonreference alleles in the dataset or being clustered in a low number of alleles across many samples in an unbalanced fashion. Then, if included, we removed recurrent Catalogue of Somatic Mutations in Cancer (COSMIC) (52) mutations (that is, SNVs with classification other than synonymous with at least three case reports of hematopoietic and lymphoid tissues; COSMIC version 80) to derive a final list of dataset-specific flagged alleles to be excluded from contextual error modeling.
To derive with a list of mutations that are highly associated with leukemic transformation for AML risk prediction model derivation, we interrogated the COSMIC database (52) and ranked variants according to their evidence for functional relevance in AML. All the SNVs with classification other than synonymous with at least 10 case reports of hematopoietic and lymphoid tissues were considered hotspot variants. For the future implementation of our findings, we reasoned that any hybrid-capture probe design and short sequencing reads would efficiently encompass at least several genomic bases surrounding these hotspots. Therefore, we extended the variant calls to capture mutations with a putative deleterious effect that are within fiveamino acid distance surrounding each hotspot variant. Genomic loci that were found to be mutated in the training cohort (pre-AML1 and pre-AML2) were used for the final model derivation (table S8). Notably, we discarded genomic loci with mutations in KIT, KRAS, and PHF6 as these were found solely in the training sets controls. Such enrichment surely does not correlate with real-life evidence and can bias classification. We then used a random forest algorithm via the R package randomForest. Mutations were grouped by genes, and their VAFs were used to train the model together with the age of the individuals at sampling and the number of the mutations that they carry. If more than one mutation was detected in the same gene, the highest VAF was used. The number of features used for each one of the 5000 generated trees was two.
To simulate a large population screen, we used the mutations detected by Espresso in the controls from the pre-AML1 and pre-AML2 (termed merged dataset here). We first calculated the frequency of controls that carry at least one mutation at the following age groups: 20 to 49, 50 to 64, 65 to 74, and >75 years old. For these age groups, we obtained the incidence rates of AML through the Surveillance, Epidemiology, and End Results Program (53). By assuming similar age distribution for the validation cohort (8) and the individuals interrogated in the merged dataset and knowing the number of pre-AML cases interrogated in the validation cohort (n = 188), we were able to estimate the number of simulated controls needed to mimic real incidence rates for each age group. Overall, 4,033,904 controls were simulated.
The frequency of ARCH and the number of mutations that each individual carries within each control age group from the merged dataset helped us to estimate how many of the simulated individuals are expected to carry mutations in the relevant genomic loci (table S8). Overall, 5.05, 7.69, 10.70, and 19.09% of the individuals within the age range of 20 to 49, for 50 to 64, for 65 to 74, and 75 years, respectively, were simulated to have ARCH. A total of 285,629 individuals (~7%) were simulated to carry one mutation, 934 with two mutations (~0.02%), and 156 with three mutations (~0.004%). We next assigned the specific mutations to the simulated individuals based on their association with each age group. For example, for the 149,423 simulated mutated controls with a simulated age of 50 to 64, we populated a list of 149,423 specific mutations that were detected in control individuals in the same age group or in younger age groups in the merged dataset. We also allowed 10% of the mutations detected in the merged dataset in one age group older to be randomly included. Last, we aimed to assign VAF to the simulated mutations. We observed that the VAF of the detected mutations in the merged dataset did not significantly correlate with age [R(Pearson) = 0.20; P = 0.07] and that a lognormal distribution accurately captures the VAF distribution among all the detected mutations. We therefore used the rlnorm R function to simulate VAFs. This resulted with a median VAF of 1.45% and a mean VAF of 2.45% for the simulated controls; 37.46% of the simulated VAFs received a value of VAF 2%. As intended, these values are highly comparable with those of the mutations found in the merge datasets controls (table S7).
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Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing - Science Advances
A study presented during the 2020 ASH Annual Meeting has suggested that certain driver mutations for myeloproliferative neoplasms (MPNs) can be traced back to when they were acquired as early as in utero.
If you can not only detect clones early but then calculate their rates of growth with a repeat sample you can then plot the growth trajectory of these clones and estimate the latency to a potential clinical manifestation, thus offering opportunities for early preventive strategies, said Jyoti Nangalia, MBBChir, senior study author, and cancer research UK clinician scientist at Sanger Institute, in a virtual presentation of the data.
The study comprised a cohort of 10 patients with essential thrombocythemia (ET), polycythemia vera (PV), and myelofibrosis (MF), with a median age of 48.5 (range, 20-76).
Each patients peripheral blood and bone marrow samples were grown into single cellderived hematopoietic colonies. Each colony underwent whole-genome sequencing. A total of 952 whole-genome sequences were produced, each reflecting that of the single cell from which the colony was derived.
Right from the start of life, as our cells are dividing, mutations are being acquired, and theyre being passed down from generation to generation such that at any one time, the mutations within individual cells represent natural bar codes that can be used to trace back the ancestry of those cells right to the start of life, and so we did this in MPNs, said Nangalia.
Phylogenetic trees were drawn based on the somatic mutations that had been identified. Driver mutations were subsequently assigned to the tree and evaluated for appearance patterns across each colony, reflecting the relative development of the driver mutations in each patient.
Because the total number of somatic mutations in an individual colony was shown to correlate with age, investigators converted the relative development of mutations to absolute development to more accurately understand clonal evolution.
Our blood stem cells require mutations throughout life, roughly 18 mutations across the genome per year. Therefore, by applying patient-specific mutation rates and clone-specific mutation rates, we were able to put a start time and an end time to each individual branch across the phylogenetic trees in our cohort, said Nangalia.
In the first patient who had been diagnosed with ET at the age of 21, the JAK2 mutation was acquired early, timing between 6.2 weeks post-conception and 1.3 years of age. In the phylogenetic tree, the branching downstream of JAK2 demonstrated how the single stem cell that acquired JAK2 expanded into a clone of stem cells in rapid succession.
Similarly, in the second patient diagnosed with PV at the age of 31, the JAK2 mutation was acquired early, timing between 4.2 weeks post-conception and 8.6 years of age. Clonal expansion also demonstrated a DNMT3A mutation, which is the most common mutation in age-related clonal hematopoiesis, said Nangalia. However, in this patient, the mutation was also acquired early, timing between 4.6 weeks post-conception and 7.8 years of age, growing slowly before reaching a detectable clonal fraction.
In some patients, the JAK2 and DNMT3A mutations were acquired very early, including in utero. In one patient diagnosed with PV at age 33, the JAK2 mutation was acquired between 9.1 weeks post-conception and 4.1 months after birth, and the DNMT3A mutation was acquired between 19.4 weeks and 22.2 weeks post-conception. Another patient with PV showed that the DNMT3A mutation was acquired as early as between 1.2 weeks and 7.9 weeks post-conception.
In the patient with PV diagnosed at age 33, evidence of clonal evolution in the MPN clone was shown over 3 decades, cascading from a JAK2 mutation 4.1 months post-birth to homozygous JAK2 at 17.8 years to 1q amplification at 33 years.
In other patients, JAK2 was acquired as the second driver mutation in an already expanded DNMT3A-mutated clone.
Notably, a patient diagnosed with ET at age 54 had acquired DNMT3A R882H by 2 years of age, which is one of the most common mutations found in acute myeloid leukemia, said Nangalia. However, in another patient who had been diagnosed with ET at 76 years of age, there was a driverless clonal expansion.
We know that clonal hematopoiesis can often lack driver mutations and is thought to be the case in up to 50% of patients with clonal hematopoiesis. Here, we showed that that also has a single-cell origin. What is driving clonal expansion in this individual in that particular clone, we do not know, said Nangalia.
Across the cohort, recurrent or similar genetic aberrations were found in individual patients. A patient diagnosed with PV at age 53, who acquired a JAK2 exon 12 mutation in childhood, developed 3 independent DNMT3A mutations and 4 independent homozygous acquisitions stemming from their JAK2 exon 12 mutation.
Other patients demonstrated evidence of independent acquisitions of 1q amplifications, leading to myelofibrotic transformation. Another patient demonstrated evidence of multiple independent acquisitions of JAK2 V617F, suggesting that factors other than driver mutations, such as the patients germline or microenvironment within the bone marrow, also influence clonal evolution.
In the second portion of the study, investigators revisited the patients for whom phylogenetic trees had been drawn and re-sequenced the mutations that had been identified in the phylogenetic trees in the whole blood.
Combining the mutant clonal fractions in blood with the pattern of branching in the trees, investigators calculated the rate at which the clones had been growing over each patients lifespan.
Clone rates varied significantly. For example, in a patient with 3 mutant clones that had been acquired in uteroDNMT3A, JAK2, and JAK2/TET2the rates of annual growth were 9% (95% CI, 5%-25%), 67% (95% CI, 6%-246%), and 233% (95% CI, 143%-360%), respectively, the latter of which translates to a doubling-in-size time of every 7 months.
Regarding clones that had the same genetic makeup, such as clones consisting solely of the JAK2 V617F driver mutation, the annual growth rate varied among individual patients, ranging from 18% (95% CI, 13%-23%) to 68% (95% CI, 41%-95%).
This again suggests that there are factors other than JAK2 that determine the consequences of acquiring it in individual patients, said Nangalia.
Additional results revealed that the rate of growth was associated with the time of diagnosis. In patients with slow growth rates of less than 50%, over 50 years had gone by prior to diagnosis, whereas in patients with growth rates over 100%, it took less than 10 years before a diagnosis was made.
In retroactively calculating what the clonal fractions would have been leading up to diagnosis, the slow growing JAK2 clones could have been detected with sensitive assays 40 years prior to diagnosis and up to 10 years before diagnosis for faster growing clones.
Providing additional perspective during a press briefing, Robert Brodsky, MD, moderator, and director of the Division of Hematology at Johns Hopkin Medicine stated, These results suggest that there may be untapped opportunities to detect these conditions much earlier and potentially intervene and prevent disease development.
Williams N, Lee J, Moore L, et al. Driver mutation acquisition in utero and childhood followed by lifelong clonal evolution underlie myeloproliferative neoplasms. Presented at: 2020 ASH Annual Meeting & Exposition; December 5-8, 2020; virtual. Abstract LBA-1.
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MPN Driver Mutations Can Be Acquired as Early as in Utero, Study Shows - Targeted Oncology
Accumulated genetic variations: What they are and why they matter to a complete health picture – MedCity News
Genes are by no means a crystal ball, but they can be used to forecast susceptibility to a variety of conditions, from cancers and heart disease to chronic inflammatory conditions. As such, they can help healthcare professionals and patients make better care decisions.
Generally speaking, whenpeople today think about genetic predispositions, theythink about their parents and family trees.However, those inherited genetic variationsbequeathed by ourparents and grandparents are only a portion ofacomplete genetic picture and often not the most revealing one.Thegenetic variationsmost commonly linked to disease are actually?not?the ones from your parents; rather, they areacquiredas one ages.
Mom and Dad Cant Take All the Heat forAll Health Challenges Unlike inheritedgenetic predispositions,accumulatedgenetic changes(otherwise known as somatic)are the result ofenvironmental influences, such as smoking, chemicals or ultra-violet radiation. They can also stem from common errorscells make as they duplicate themselves over time.The expansion of these detrimental variations cause damage to DNA within blood cells,aphenomenon known as clonal hematopoiesis (CH), whichincreases susceptibility to many diseases, including many types of cancer.
Germline variations in genes still indicate potential vulnerabilities, with one in five healthy adults estimated to carry an inherited marker. However, these genetic abnormalities represent a static metric. Once individuals are tested for inherited variations, they will never need to do so again. Whats more, many of the predispositions that surfaced through this testing can be addressed through lifestyle and medical interventions. It boils down to being aware of them.
Somatic changes, on the other hand, can happen at any stage of life. While many of these changes have no clinical ramifications, some of them can exacerbate predispositions inherited from our parents because the disease is often the result of multiple genetic variations banding together, inherited or acquired.
The chances of an acquired variation accumulating and accelerating within the body increase significantly as we age, generally after the age of 40 and growing each decade. This could drastically change a patients health profile, casting inherited vulnerabilities into a new light without any warning or symptoms.
Understanding Accumulated VariationsA growing body of research links somatic changes to an increased likelihood of blood cancers and cardiovascular disease, both heart disease and stroke. The same research reveals that these accumulated genetic variations contribute to infection and severe inflammatory reactions, some of which are associated with severe cases of Covid-19.
A study conducted byJAMA Cardiologyexplores theconnectionbetween accumulated genetic change anda pro-inflammatory immune response that resembles the exaggerated cytokine release syndrome (CRS)experienced by patients with severeCovid-19.Notably,the researchfoundthat patients who experienced the most extreme inflammatory response carried variationsTET2 and DMNT3A, both of which accumulate in genes over time.
Another research report published inCancersanalyzingpatients hospitalized with severe Covid-19disease found a much higher frequency of clonal hematopoiesis (CH) of indeterminate potential (sometimes called clonal hematopoiesis of indeterminate potential or CHIP) ),an age-associated condition in cells,in all age groups.
Additionally,accumulatedDNA damage to the JAK2 gene has been found in alargeproportion of cancer-free patients with venous thrombosis, a known complicationof Covid-19.While preliminary,the findingsdemonstratecompellingcorrelations betweensomaticgenetic change andCovid-19 severity that could be used to identify patients prone to complications early, intervene soonerand inform treatment strategies.
It is believed thatproviders can applythese correlations to other areas of care toassess an individuals susceptibilityto a wide range of diseases, and ultimately improve and extend quality of life.
Improving Care Decisions with Somatic insights Augmenting currenthealth assessmentsand care strategies with accumulated geneticdatacan open new pathways for disease detection, response and prevention.The scientificand medicalcommunitieshaveonly scratched the surface ofwhat we can learn from these insights. Even so,understanding somatic damage showsgreatpromise for helping individualsstay ahead of their health concerns and respond in a more informed way.
Photo: Andy, Getty Images
The South and Central America cell therapy instruments market is expected to reach US$ 462.05 million in 2027 from US$ 1,074.99 million in 2019 -…
NEW YORK, Nov. 24, 2020 /PRNewswire/ -- The South and Central America cell therapy instruments market is expected to reach US$ 462.05 million in 2027 from US$ 1,074.99 million in 2019. The market is estimated to grow with a CAGR of 11.4% during the forecast period.
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The surge in the number of cell therapy transplantation procedures, growing research and development activities, and rising investments in building production facilities for cell and gene therapy products drive the growth of the South and Central America cell therapy instruments market. However, the low success rate of cell therapies and the high cost of cell-based research is expected to restrain the market growth during the forecast period.
Cell therapy typically involves the administration of somatic cell preparations by injecting or grafting it into the patient's body for the treatment of diseases or traumatic damages.The procedure is used to cure diabetes, neurological disorders, related injuries, several cancer types, bones and joints, and genetic disorders.
Continuous research and development activities have led to unique cell therapeutic instruments for the improvement of immune system and efficient treatment of genetic disorders. Various market players provide several consumables such as reagent kits and enzymes as well as devices, equipment, and software to perform various cell therapy processes.
The cell therapy products are derived from animals or human cells and thus need to be protected from contamination.The instruments used in cell therapies help provide protection against contamination and allow scaling up of transplantation.
Companies such as Hitachi Chemical Advanced Therapeutics Solutions; Corning Incorporated; Thermo Fisher Scientific Inc.; MiltenyiBiotec; LLC; Invetech; and Cytiva (General Electric Company) have introduced various equipment and consumables for the cell therapy procedures.
Various US-based companies have their manufacturing units in the South and Central America countries; the lockdown imposed in response to the COVID-19 pandemic in multiple countries has affected the supply of instruments in this region. Therefore, many organizations are collaborating with other companies to overcome the adverse effects of the pandemic by using cell therapies for the treatment of COVID 19.
On the basis of product, the South and Central America cell therapy instruments market is further segmented into consumables, software, equipment, and systems.The consumables segment held the largest share of the market in 2019 and is expected to register the highest CAGR during the forecast period.
On the basis of cell type, the cell therapy instruments market is segmented into animal cells and human cells. The human cells segment held a larger share of the market in 2019 and is estimated to register a higher CAGR during the forecast period.
The South and Central America cell therapy instruments market, based on process, is segmented into cell processing; cell preservation, distribution, and handling; and process monitoring and quality control.The cell processing segment held the larger share of the market in 2019 and is estimated to register the highest CAGR during the forecast period.
Based on enduser, the South and Central America cell therapy instruments market is segmented into life science research companies, research institutes, and other end users. The life science research companies segment grasped the largest share of the market in 2019 and is anticipated to register the highest CAGR during the forecast period.
A few of the major primary and secondary sources referred to while preparing this report on the South and Central America cell therapy instruments market include National Center for Biotechnology Information (NCBI);World Health Organization (WHO); Brazilian Health Regulatory Agency(ANVISA); and Global Institute of Stem Cell Therapy and Research (GIOSTAR).
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For the first time, researchers at the Center for Cell-Based Therapy (CTC) in Ribeiro Preto, Brazil, have identified a non-hereditary mutation in blood cells from a patient with GATA2 deficiency.
GATA2 deficiency is a rare autosomal disease caused by inherited mutations in the gene that encodes GATA-binding protein 2 (GATA2), which regulates the expression of genes that play a role in developmental processes and cell renewal.
An article on the study is publishedin the journalBlood.
The non-hereditary mutation may have acted as a natural gene therapy which prevented the disease from damaging the process of blood cell renewal. This meant that the patient did not develop such typical clinical manifestations as bone marrow failure, hearing loss, and lymphedema.
The researchers say that the findings pave the way for the use of gene therapy and changes to the process of checking family medical history and medical records for families with the hereditary disorder.
Luiz Fernando Bazzo Catto, first author of the article, said: When a germline [inherited] mutation in GATA2 is detected, the patients family has to be investigated because there may be silent cases.
The discovery was made when two sons were receiving medical treatment at the blood centre of the hospital run by FMRP-USP, both of which, in post-mortem DNA sequencing, showed germline mutations and GATA2 deficiency diagnosis. The researchers used next generation sequencing to estimate the proportion of normal blood cells in the fathers bone marrow, preventing clinical manifestations of GATA2 deficiency, and of cells similar to his childrens showing that 93% of his leukocytes had the mutation that protects from the clinical manifestations of GATA2 deficiency.
Following the sequencing of the fathers T-lymphocytes, the researchers found that the mutation occurred early in their lives and in the development of hematopoietic stem cells, which have the potential to form blood.
They also measured the activity of the blood cells, to see if they could maintain the activity of inducing normal cell production for a long time, by measuring the telomeres of his peripheral blood leukocytes. Telomeres are repetitive sequences of non-coding DNA at the tip of chromosomes that protect them from damage. Each time cells divide, their telomeres become shorter. They eventually become so short that division is no longer possible, and the cells die or become senescent.
The telomeres analysed by the researchers were long, indicating that the cells can remain active for a long time.
The researchers hypothesised that the existence of the somatic mutation in the fathers blood cells, and its restoration of the blood cell renewal process, may have contributed to the non-manifestation of extra-haematological symptoms of GATA2 deficiency such as deafness, lymphedema, and thrombosis.
Professor Rodrigo Calado, a corresponding author of the article, said: A sort of natural gene therapy occurred in this patient. Its as if he embodied an experiment and a medium-term prospect of analogous gene therapy treatment in patients with GATA2 deficiency.
The findings help us understand better how stem cells can recover by repairing an initial genetic defect.
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Non-hereditary mutation acts as natural gene therapy for GATA2 deficiency - Health Europa
Cell Therapy Market Attractiveness, Competitive Landscape and Key Players MEDIPOST, Kolon TissueGene, NuVasive, Fibrocell Science – The Think…
The Insight Partners adds Cell Therapy Market Forecast to 2027 COVID-19 Impact and Global Analysis to its store providing analysis of the current and future market competition in the market. Insightful review of the key industry drivers, opportunities, barriers and challenges. Each trend is independently researched to provide qualitative analysis of its implications.
The study provides details such as the market share, Market Insights, Strategic Insights, Segmentation and key players in the Cell Therapy Market.
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Cell therapy (CT) is the process of transplanting human cells to replace or repair damaged tissue or cells. Various methods can be used to carry out cell therapy. For instance, hematopoietic stem cell transplantation, also known as bone marrow transplant, is the most widely used cell therapy. It is used to treat a variety of blood cancers and blood-related conditions.
Some of the Major Market Players Are:
Kolon TissueGene, Inc. MEDIPOST JCR Pharmaceuticals Co. Ltd. Stemedica Cell Technologies, Inc. Osiris Therapeutics, Inc. NuVasive, Inc. Fibrocell Science, Inc. Vericel Corporation Cells for Cells Celgene Corporation
Note The Covid-19 (coronavirus) pandemic is impacting society and the overall economy across the world. The impact of this pandemic is growing day by day as well as affecting the supply chain. The COVID-19 crisis is creating uncertainty in the stock market, massive slowing of supply chain, falling business confidence, and increasing panic among the customer segments. The overall effect of the pandemic is impacting the production process of several industries. This report on Cell Therapy Market provides the analysis on impact on Covid-19 on various business segments and country markets. The reports also showcase market trends and forecast to 2027, factoring the impact of Covid -19 Situation.
The global cell therapy market is segmented on the basis of therapy type, product, technology, application, end user. Based on the therapy type the market is classified as autologous, and allogeneic. Based on product the market is segmented as equipment, consumables, software and services. Based on technology the market is segmented as somatic cell technology, cell immortalization technology, viral vector technology, genome editing technology, cell plasticity technology, and three-dimensional technology. Based on application the market is classified as oncology, cardiology, orthopedic, wound management and others. And based on end user the market is divided into hospitals, regenerative medicine centers, and research institutes.
The objective of the researchers is to find out the sales, value, and status of the In Cell Therapy industry at the international levels. While the status covers the years of 2020 2027, the forecast is for the period 2020 2027 that will enable market players to not only plan but also execute strategies based on the market needs.
The study wanted to focus on key manufacturers, competitive landscape, and SWOT analysis for the In Cell Therapy Market. Apart from looking into the geographical regions, the report concentrated on key trends and segments that are either driving or preventing the growth of the industry. Researchers have also focused on individual growth trends besides their contribution to the overall market.
An outline of the regional analysis:
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The cell and gene therapy CDMO will build additional facilities at its German and Japanese locations.
The contract development and manufacturing organization (CDMO) specializing in cell and gene therapies announced two separate investments of $40.7 million (34.2 million) into its Ottobrunn, Germany, site, and $23.8 million for its Yokohama, Japan, site.
Both regions now come under the umbrella of Minaris Regenerative Medicine, a subsidiary of Showa Denko Materials, after a rebrand in September to unify the name of its three businesses located in North America (previously, Hitachi Chemical Advanced Therapeutics Solutions (HCATS)), Europe (apceth Biopharma), and Japan (Hitachi Chemical).
The Japanese company acquired apceth last year for $86 million and will now add a 6,650-square-meter facility to the German site. The space will include additional clean rooms, quality control laboratories, warehousing, cryo-storage and office space.
Once operational in 2023, the facility will more than triple the current clean room capacity.
A spokesperson for Minaris explained that the facility will feature a modular design, which allows the company to combine two smaller units into one large ball room and to shift from a grade B to grade C to grade B environment according to our clients needs.
The European site became one of the first CDMOs to manufacture a commercial gene therapy, after agreeing a deal with bluebird bio to manufacture its Zynteglo (autologous CD34+ cells encoding A-T87Q-globin gene) product last year.
While the companys Japanese site will also receive an additional facility, which will cover 4,000-square-meters and is scheduled to start operations in October 2022.
The space will be used specifically for the commercial manufacture of regenerative medicine, particularly cancer immunotherapies and somatic stem cells, doubling the sites existing capacity.
Minaris global presence for a cell and gene specialist is unusual for an industry often concentrated in the US. However, the spokesperson for Minaris outlined that a global position confers an advantage to our clients that are seeking a global manufacturer to produce their product in different regions for example, clients with autologous cell products that need a manufacturing site close to the patients.
Additionally, We have regulatory expertise in Europe, Japan and the US and can leverage the expertise of one region to another, the spokesperson added.
Cell Therapy Manufacturing Market: Applications and Regional Insights During the Forecasted Period 2020-2030 – PRnews Leader
Prophecy Market Insights added a recent Cell Therapy Manufacturing market report with Revenue, Key Developments, Top Countries Data, SWOT Analysis, COVID-19 impact, Growth and Outlook To 2029 to its research database. The report includes analysis of different factors that drives the market growth. It includes drivers, restrains, opportunities, and trends for the market. Further, the report provides the scope of different segments and applications which can promote the market over the forecast period. The in-depth information is based on historic milestones and current trends.
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The report offers detailed information of the growth and other aspects of the Cell Therapy Manufacturing market in different regions, including North America, Europe, Asia pacific, and Middle East & Africa. Key regions covered in the report are the U.S., Canada, Germany, France, U.K., Italy, Russia, China, Japan, South Korea, Taiwan, Southeast Asia, Mexico, and Brazil, etc.
Australia, New Zealand, Rest of Asia-Pacific
Further, the report also provides the economic, environmental, social, technological, and political status of each region. This section also analyses region-wise revenue and volume for the forecasted period 2019-2029.
Cell Therapy Manufacturing Market by Top Manufacturers:
harmicell, Merck Group, Dickinson and Company, Thermo Fisher, Lonza Group, Miltenyi Biotec GmBH, Takara Bio Group, STEMCELL Technologies, Cellular Dynamics International, Becton, Osiris Therapeutics, Bio-Rad Laboratories, Inc., Anterogen, MEDIPOST, Holostem Terapie Avanazate, Pluristem Therapeutics, Brammer Bio, CELLforCURE, Gene Therapy Catapult EUFETS, MaSTherCell, PharmaCell, Cognate BioServices and WuXi AppTec.
Competitive landscape section of the Cell Therapy Manufacturing report includes top ten manufacturers along with heat map analysis. The comprehensive report provides a significant microscopic look offering product portfolio, key highlights, financial overview, and business strategies.
Key Takeaways of the market report:
Key Topics Covered:
Important Questions Answered in Cell Therapy Manufacturing Market Report:
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Provides recent collaborations, mergers, acquisitions, and partnerships along with regulatory framework across vast regions impacting the market trajectory
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