Use Of Next-generation Sequencing Research Articles

Delivery of precision oncology in advanced lung cancer: Gaps, barriers, and potential solutions.

e13533 Background: Non-small cell lung cancer is the leading cause of cancer death. Significant survival gains have been achieved due to precision oncology, which involves testing for molecular markers that indicate sensitivity to targeted therapies. Precision oncology is essential to high-quality lung cancer care, but shortfalls in biomarker testing and targeted therapies limit improvements in lung cancer outcomes. We sought to characterize barriers and facilitators to precision oncology in academic and community practice settings. Methods: We conducted a mixed methods study on the delivery of precision medicine for patients with advanced lung cancer, including use of next generation sequencing (NGS), liquid biopsy, and targeted therapies, and the barriers and facilitators to effective delivery. Surveys and semi-structured interviews were conducted with a purposive sample of patient navigators, pathologists, and clinicians. Participants were recruited from community and academic settings in North Carolina (NC), using the NC Oncology Navigation Association and existing research networks. Results: Thirty-two participants completed the survey—9 navigators, 10 pathologists and 13 clinicians—with representation from community and academic sites. Five participants completed interviews—2 navigators, 2 pathologists and 1 clinician. Knowledge gaps about precision medicine were observed, with clinicians answering “not at all” or “a little bit” knowledgeable about NGS (23%), liquid biopsy (38%) and targeted therapies (23%). Navigators indicated feeling “somewhat” or “very” uncomfortable discussing these topics (55% for NGS, 44% for targeted therapies), and indicated having limited confidence in resolving barriers related to precision medicine. In interviews, potential solutions were highlighted, including use of financial aid from pharmaceutical companies, dedicated molecular pathology support, and partnership with social work and financial navigation to resolve barriers. Conclusions: Clinicians and navigators report gaps in knowledge and confidence in discussing precision oncology in advanced lung cancer. Qualitative data highlight several potential strategies for improving access, including addressing financial barriers. These findings suggest a need for education and financial assistance to support delivery of precision oncology in advanced lung cancer.[Table: see text]

Comparison of next-generation sequencing and flow cytometry in detecting minimal residual disease in adult acute lymphoid leukemia: Evaluating clinical outcomes in a single-center study.

7033 Background: Detection of measurable residual disease (MRD) is an important biomarker to direct treatment for adult patients with acute lymphoblastic leukemia (ALL). Currently, multiparameter flow cytometry (MFC) is standard of care and can detect residual leukemia cells in 1 out of 100,000 cells (1 × 10−5). Routine use of next-generation sequencing (NGS) assays with higher levels of sensitivity may improve disease-free survival and overall survival in adult ALL patients. The clonoSEQ MRD assay (Adaptive Biotechnologies Corporation, USA) can detect MRD at a sensitivity of 1 × 10−6 . In this study, we compare the detection of MRD by clonoSEQ assay and MFC in adult ALL patients at a single institution. Methods: We performed a retrospective study evaluating 92 adult patients with B- or T-ALL admitted to Norris Comprehensive Cancer Center between 2014 and 2022. Patients were excluded if they did not achieve complete remission (N=9) or if they presented with prior relapse (N=27). Median time to first complete remission (CR1) was 2.38 months. Among our cohort (N=56 patients), all patients underwent pre-treatment bone marrow sampling which was used for Clonoseq assay. 52 patients had contemporaneous MFC which was used for comparative analysis. MRD on MFC was defined as residual leukemia cells at a sensitivity of 1 × 10−5. MRD on Clonoseq assay was evaluated at 1 × 10−6; residual cells under this limit were considered MRD−. Results: Demographics are summarized in the table. Median time to follow-up from MRD assessment was 18.0 months. 10 patients relapsed (17.9%), 3 patients died (5.4%), and 20 patients (35.7%) underwent allogeneic transplant during first remission. Among 52 patients analyzed by both MFC and NGS at CR, 26 (50%) were concordantly MRD− by NGS and NGF, 13 (25%) were discordantly MRD− by NGF but MRD+ by NGS, and 13 (25%) concordantly MRD+ by NGS and NGF. Residual cell levels between NGS and NGF were strongly correlated (R-Squared = 0.6744, p<0.001), however, MRD status was significantly different between NGS and NGF (p<0.001 using Fisher’s Exact Test). This difference was likely driven by disparities in the limits of detection between both methods. Conclusions: Assessment of MRD using the clonoSEQ assay over a standard MFC-based approach adds crucial prognostic information among adult ALL patients who achieved CR. [Table: see text]

RET testing and treatment patterns among patients with aNSCLC in US clinical practice.

9091 Background: Biomarker testing, including for rearrangement during transfection (RET), is recommended and important in selecting efficacious targeted therapy for patients with advanced non-small cell lung cancer (aNSCLC). This retrospective cohort study characterized RET testing and treatment patterns among aNSCLC patients in clinical practice. Methods: We used the nationwide Flatiron Health electronic health record-derived de-identified database to select patients diagnosed with aNSCLC (stage ≥IIIB) from 2017-2022. We measured rates of RET testing (test result ≤90 days after advanced diagnosis). We used logistic regression to identify baseline characteristics predictive of timely testing. Finally, we described treatment patterns for patients with RET+ aNSCLC before and after the US approval of RET inhibitors. Results: Among 26,329 aNSCLC patients, rates of RET testing ≤90 days after advanced diagnosis increased from 25% (2017 Q1) to 73% (2022 Q1). Patients were less likely to receive RET testing within 90 days if they were Black (multivariate odds ratio [OR] 0.8) or Hispanic (OR 0.8) compared to White, or had Medicare (OR 0.9; all p<0.001) compared to commercial insurance. Patients were more likely to receive RET testing within 90 days if they were in the highest socioeconomic quintile (OR 1.4), had de novo disease (OR 2.1), or no history of smoking (OR 1.3; all p<0.001). Between 2017 and 2022, there were increases in the use of next-generation sequencing (66% to 89%) and blood samples for biomarker testing (25% to 49%) and a decrease in mean days from diagnosis to test result (33 to 28) for the first RET test among those who had testing within 90 days. Among all patients with aNSCLC tested within 90 days (n=12,275), 73 were RET+ and received 1L treatment ≤90 days after advanced diagnosis. The most common 1L treatments before (n=35) and after (n=38) RET inhibitor approval were chemotherapy (40%) and RET inhibitor (42%), respectively (Table). Conclusions: RET testing has increased over time, but certain patient subgroups are less likely to receive timely RET testing and therefore may not be optimally treated. Among patients with RET+ aNSCLC identified after RET inhibitor approval, only 42% were treated with a RET inhibitor in the 1L setting. These results suggest both disparities in access to RET testing and unmet medical need among patients with RET+ aNSCLC. [Table: see text]

Characteristics and predictive modeling of HER2 mutation in patients with non-small cell lung cancer.

e13559 Background: Recent advances in targeted therapies have increased the survival and quality of life for non-small cell lung cancer (NSCLC) patients. Understanding clinical characteristics and predicting HER2 status may facilitate efficient use of next-generation sequencing (NGS) testing and promote precision medicine/targeted therapies. Methods: NSCLC patients ≤65 years old, diagnosed between 01/2011 and 06/2021 who have NGS test results were identified in from two National Cancer Institute designated cancer centers in the Northeastern region of the United States. Demographics, behavioral, and clinical characteristics were extracted from electronic health record (EHR) data and EHR-linked cancer registry. Prevalence prediction modelling of HER2/ERBB2 mutation was performed using machine learning (ML) methods including logistic regression (LR), random forest (RF), naïve Bayes (NB), extreme gradient boosting (XGBoost) and multi-layer perceptron (MLP). 10- fold cross validation and k-nearest neighbor method were used to impute missing values. Under-sampling, oversampling and feature selection methods were tried. Results: Among 761 NSCLC patients with NGS reports available, 353 (46%) were ≤65 years old. Among 353 (mean age 57, 58% female, 88% non-Hispanic, 69% white, 57% had metastasis, 58% prescribed chemotherapy) 25 (7%) had a HER2 mutation. Based on univariate significance tests with LR on the complete data: cerebrovascular disease, BMI between 27.5-29.9, KRAS, EGFR and MET were significant with odds ratios (ORs) ranging from 0.2-3.9. In our prediction models, BMI, cerebrovascular disease, weight loss, hepatic metastases, diabetes, congestive heart failure, and KRAS, EGFR, MET and RET alteration status were significant predictors in multivariate analyses, suggesting the potential usefulness of these features in predicting HER2 mutation among patients with NSCLC. Area under the ROC curve (AUC) varied across different models from 70.9% (RF), 70% (XGB and MLP), 69.5% (LR) to 68.2% (Naïve Bayes). The best performing model with RF yielding an AUC ~71% can provide relative high specificity and acceptable sensitivity depending on the cut off. Conclusions: Our prediction models yielded AUC around 70% with the best performing model’s AUC being 71% in a subgroup aged ≤65. After further validation, our prediction model may be used to identify patients appropriate for repeat NGS testing who did not have HER2 testing in first molecular profiling. Future work is needed to predict status in repeat testing with previously test negative patients who relapse or have progression of disease. Random forest (RF) Model performance across different cutoff for the predicted probability. [Table: see text]

Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach.

The neurotrophic tropomyosin receptor kinase (NTRK) family gene rearrangements have been recently incorporated as predictive biomarkers in a "tumor-agnostic" manner. However, the identification of these patients is extremely challenging because the overall frequency of NTRK fusions is below 1%. Academic groups and professional organizations have released recommendations on the algorithms to detect NTRK fusions. The European Society for Medical Oncology proposal encourages the use of next-generation sequencing (NGS) if available, or alternatively immunohistochemistry (IHC) could be used for screening with NGS confirmation of all positive IHC results. Other academic groups have included histologic and genomic information in the testing algorithm. To apply some of these triaging strategies for a more efficient identification of NTRK fusions within a single institution, so pathologists can gain practical insight on how to start looking for NTRK fusions. A multiparametric strategy combining histologic (secretory carcinomas of the breast and salivary gland; papillary thyroid carcinomas; infantile fibrosarcoma) and genomic (driver-negative non-small cell lung carcinomas, microsatellite instability-high colorectal adenocarcinomas, and wild-type gastrointestinal stromal tumors) triaging was put forward. Samples from 323 tumors were stained with the VENTANA pan-TRK EPR17341 Assay as a screening method. All positive IHC cases were simultaneously studied by 2 NGS tests, Oncomine Comprehensive Assay v3 and FoundationOne CDx. With this approach, the detection rate of NTRK fusions was 20 times higher (5.57%) by only screening 323 patients than the largest cohort in the literature (0.30%) comprising several hundred thousand patients. Based on our findings, we propose a multiparametric strategy (ie, "supervised tumor-agnostic approach") when pathologists start searching for NTRK fusions.

Targeted therapy and immunotherapy for T cell acute lymphoblastic leukemia/lymphoma.

T cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is an aggressive malignancy of progenitor T cells. Despite significant improvements in survival of T-ALL/LBL over the past decades, treatment of relapsed and refractory T-ALL (R/R T-ALL/LBL) remains extremely challenging. The prognosis of R/R T-ALL/LBL patients who are intolerant to intensive chemotherapy remains poor. Therefore, innovative approaches are needed to further improve the survival of R/R T-ALL/LBL patients. With the widespread use of next-generation sequencing in T-ALL/LBL, a range of new therapeutic targets such as NOTCH1 inhibitors, JAK-STAT inhibitors, and tyrosine kinase inhibitors have been identified. These findings led to pre-clinical studies and clinical trials of molecular targeted therapy in T-ALL/LBL. Furthermore, immunotherapies such as CD7 CAR T cell therapy and CD5 CAR T cell therapy have shown profound response rate in R/R T-ALL/LBL. Here, we review the progress of targeted therapies and immunotherapies for T-ALL/LBL, and look at the future directions and challenges for the further use of these therapies in T-ALL/LBL.

Novel Tools for Diagnosis and Monitoring of AML.

In recent years, major advances in the understanding of acute myeloid leukemia (AML) pathogenesis, together with technological progress, have led us into a new era in the diagnosis and follow-up of patients with AML. A combination of immunophenotyping, cytogenetic and molecular studies are required for AML diagnosis, including the use of next-generation sequencing (NGS) gene panels to screen all genetic alterations with diagnostic, prognostic and/or therapeutic value. Regarding AML monitoring, multiparametric flow cytometry and quantitative PCR/RT-PCR are currently the most implemented methodologies for measurable residual disease (MRD) evaluation. Given the limitations of these techniques, there is an urgent need to incorporate new tools for MRD monitoring, such as NGS and digital PCR. This review aims to provide an overview of the different technologies used for AML diagnosis and MRD monitoring and to highlight the limitations and challenges of current versus emerging tools.

The Clinical Laboratory Is an Integral Component to Health Care Delivery : An Expanded Representation of the Total Testing Process.

Developing an expanded representation of the total testing process that includes contemporary elements of laboratory practice can be useful to understanding and optimizing testing workflows across clinical laboratory and patient care settings. Published literature and meeting reports were used by the coauthors to inform the development of the expanded representation of the total testing process and relevant examples describing its uses. A visual representation of the total testing process was developed and contextualized to patient care scenarios using a number of examples covering the detection of blood culture contamination, use of next-generation sequencing, and pharmacogenetic testing. The expanded representation of the total testing process can serve as a model and framework to document and improve the use of clinical testing within the broader context of health care delivery. This representation recognizes increased engagement among clinical laboratory professionals with patients and other health care providers as essential to making informed decisions. The increasing use of data is highlighted as important to ensuring quality, appropriate test utilization, and sustaining an efficient workflow across clinical laboratory and patient care settings. Maintaining a properly resourced and competent workforce is also featured as an essential component to the testing process.

World Marrow Donor Association guidelines for the reporting of novel HLA alleles.

The guidelines for the implementation and reporting of HLA nomenclature for the World Marrow Donor Association have served as a reliable standard for communication of HLA data in the hematopoietic cell transplantation process. Wider use of next-generation sequencing made a special provision of the guidelines increasingly pertinent: how to communicate novel HLA alleles. Novel alleles need to be recognized by the WHO Nomenclature Committee for Factors of the HLA system to obtain official allele designations. Until then they have to be handled according to the specific rules. Leaving the actual rules basically unchanged we give some advice on how to communicate novel alleles to best facilitate the search process for cases where novel alleles are identified on donor or patient side.

Kidney Disease Associated With Mono-allelic COL4A3 and COL4A4 Variants: A Case Series of 17 Families.

Mono-allelic variants in COL4A3 and COL4A4 (COL4A3/COL4A4) havebeen identified in a spectrum of glomerular basement membrane nephropathies, including thin basement membrane nephropathy and autosomal dominant Alport syndrome. With the increasing useof next generation sequencing, mono-allelic COL4A3/COL4A4 variants are detected morefrequently, but phenotypic heterogeneity impedes counseling. We aimed to investigate the phenotypic spectrum, kidney biopsy results, and segregation patterns of patients with mono-allelic COL4A3/COL4A4 variants identified by whole exome sequencing. Case series. We evaluated clinical andpathologic characteristics of 17 Dutch index patients with mono-allelic variants in COL4A3/COL4A4 detected by diagnostic whole exome sequencing and 25 affected family members with variants confirmed by Sanger sequencing. Eight different mono-allelic COL4A3/COL4A4 variants were identified across members of 11 families, comprising 7 glycine substituted missense variants and 1 frameshift variant. All index patients had microscopic hematuria at clinical presentation (median age 43 years) and 14 had (micro)albuminuria/proteinuria. All family members showed co-segregation of the variant with at least hematuria. At end of follow-up of all 42 individuals (median age 54 years), 16/42 patients had kidney function impairment, of whom 6 had kidney failure.Reports of kidney biopsies of 14 patients described thin basement membrane nephropathy, focal segmental glomerulosclerosis, minimal change lesions, and Alport syndrome. Electron microscopy images of 7 patients showed a significantly thinner glomerular basement membrane compared with images of patients with idiopathic focal segmental glomerulosclerosis and other hereditary glomerular diseases. No genotype-phenotype correlations could be established. Retrospective design, ascertainment bias toward severe kidney phenotypes, and familial hematuria. This study confirms the wide phenotypic spectrum associated with mono-allelic COL4A3/COL4A4 variants, extending from isolated microscopic hematuria to kidney failure with high intra- and interfamilial variability.

Precision Oncology: Evolving Clinical Trials across Tumor Types.

Advances in molecular technologies and targeted therapeutics have accelerated the implementation of precision oncology, resulting in improved clinical outcomes in selected patients. The use of next-generation sequencing and assessments of immune and other biomarkers helps optimize patient treatment selection. In this review, selected precision oncology trials including the IMPACT, SHIVA, IMPACT2, NCI-MPACT, TAPUR, DRUP, and NCI-MATCH studies are summarized, and their challenges and opportunities are discussed. Brief summaries of the new ComboMATCH, MyeloMATCH, and iMATCH studies, which follow the example of NCI-MATCH, are also included. Despite the progress made, precision oncology is inaccessible to many patients with cancer. Some patients' tumors may not respond to these treatments, owing to the complexity of carcinogenesis, the use of ineffective therapies, or unknown mechanisms of tumor resistance to treatment. The implementation of artificial intelligence, machine learning, and bioinformatic analyses of complex multi-omic data may improve the accuracy of tumor characterization, and if used strategically with caution, may accelerate the implementation of precision medicine. Clinical trials in precision oncology continue to evolve, improving outcomes and expediting the identification of curative strategies for patients with cancer. Despite the existing challenges, significant progress has been made in the past twenty years, demonstrating the benefit of precision oncology in many patients with advanced cancer.

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea

BackgroundSequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.ResultsA total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83–97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71–94.54% and 99.48–96.91% for bacteria and archaea, respectively.ConclusionsGiven the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature.BaWjngsRiAeBWt8MJdkB1wVideo

Social Diversification Driven by Mobile Genetic Elements.

Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.

HAP1, a new revolutionary cell model for gene editing using CRISPR-Cas9.

The use of next-generation sequencing (NGS) technologies has been instrumental in the characterization of the mutational landscape of complex human diseases like cancer. But despite the enormous rise in the identification of disease candidate genetic variants, their functionality is yet to be fully elucidated in order to have a clear implication in patient care. Haploid human cell models have become the tool of choice for functional gene studies, since they only contain one copy of the genome and can therefore show the unmasked phenotype of genetic variants. Over the past few years, the human near-haploid cell line HAP1 has widely been consolidated as one of the favorite cell line models for functional genetic studies. Its rapid turnover coupled with the fact that only one allele needs to be modified in order to express the subsequent desired phenotype has made this human cell line a valuable tool for gene editing by CRISPR-Cas9 technologies. This review examines the recent uses of the HAP1 cell line model in functional genetic studies and high-throughput genetic screens using the CRISPR-Cas9 system. It covers its use in an attempt to develop new and relevant disease models to further elucidate gene function, and create new ways to understand the genetic basis of human diseases. We will cover the advantages and potential of the use of CRISPR-Cas9 technology on HAP1 to easily and efficiently study the functional interpretation of gene function and human single-nucleotide genetic variants of unknown significance identified through NGS technologies, and its implications for changes in clinical practice and patient care.

Congenital Athymia: Unmet Needs and Practical Guidance.

Inborn errors of thymic stromal cell development and function which are associated with congenital athymia result in life-threatening immunodeficiency with susceptibility to infections and autoimmunity. Athymic patients can be treated by thymus transplantation using cultured donor thymus tissue. Outcomes in patients treated at Duke University Medical Center and Great Ormond Street Hospital (GOSH) over the past three decades have shown that sufficient T-cell immunity can be recovered to clear and prevent infections, but post-treatment autoimmune manifestations are relatively common. Whilst thymus transplantation offers the chance of long-term survival, significant challenges remain to optimise the outcomes for the patients. In this review, we will discuss unmet needs and offer practical guidance based on the experience of the European Thymus Transplantation programme at GOSH. Newborn screening (NBS) for severe combined immunodeficiency (SCID) and routine use of next-generation sequencing (NGS) platforms have improved early recognition of congenital athymia and increasing numbers of patients are being referred for thymus transplantation. Nevertheless, there remain delays in diagnosis, in particular when the cause is genetically undefined, and treatment accessibility needs to be improved. The majority of athymic patients have syndromic features with acute and chronic complex health issues, requiring life-long multidisciplinary and multicentre collaboration to optimise their medical and social care. Comprehensive follow up after thymus transplantation including monitoring of immunological results, management of co-morbidities and patient and family quality-of-life experience, is vital to understanding long-term outcomes for this rare cohort of patients. Alongside translational research into improving strategies for thymus replacement therapy, patient-focused clinical research will facilitate the design of strategies to improve the overall care for athymic patients.

Implementation of Precision Oncology in Clinical Practice: Results of a National Survey for Health Care Professionals.

Two main aspects lead the implementation of precision oncology into clinical practice: the adoption of extended genome sequencing technologies and the institution of the Molecular Tumor Boards (MTBs). CIPOMO (Italian Association of Heads of Oncology Department) promoted a national survey across top health care professionals to gain an understanding of the current state of precision oncology in Italy. Nineteen questions were sent via the SurveyMonkey platform to 169 heads of oncology departments. Their answers were collected in February 2022. Overall, 129 directors participated; 113 sets of answers were analyzed. Nineteen regions out of 21 participated as a representative sample of the Italian health care system. The use of next-generation sequencing (NGS) is unevenly distributed; informed consent and clinical reports are managed differently, as the integration of medical, biologic, and informatics domains in a patient-centered workflow is inconsistent. A heterogeneous MTB environment emerged. A total of 33.6% of the responding professionals did not have access to MTBs while 76% of those who have did not refer cases. NGS technologies and MTBs are not homogeneously implemented in Italy. This fact potentially jeopardizes equal access chances to innovative therapies for patients. This survey was carried out as part of an organizational research project, pursuing a bottom-up approach to identify the needs and possible solutions to optimize the process. These results could be a starting point for clinicians, scientific societies, and health care institutions to outline the best practices and offer shared recommendations for precision oncology implementation in current clinical practice.

Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses.

Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants. Overall, we confirmed an excess of rare variants compared with ethnicity-matched controls and identified 2 known genes (GATA6, NOTCH1) and 4 candidate genes supported by the literature (ANKRD11, DOCK6, NPHP4, and STRA6). Ultrarare variant analysis was performed in combination with 3 other published studies (n=1451) and identified 3 genes (FLT4, NOTCH1, TBX1) to be significant, whereas a subgroup analysis involving 391 Chinese subjects identified only GATA6 as significant. Conclusions We suggest that these significant genes in our rare and ultrarare burden analyses warrant prioritization for clinical testing implied for rare inherited and de novo variants. Additionally, associations on ClinVar for these genes were predominantly variants of uncertain significance. Therefore, a more stringent assessment of gene-disease associations in a larger and ethnically diverse cohort is required to be prudent for future curation of conotruncal cardiac defect genes.

Distribution and Detectability of EGFR Exon 20 Insertion Variants in NSCLC

IntroductionEGFR exon 20 insertion (ex20ins) mutations represent 5% to 10% of EGFR mutations in NSCLC. Identifying patients with EGFR ex20ins is challenging owing to the limited coverage of polymerase chain reaction (PCR) assays and the relatively recent use of next-generation sequencing (NGS). This study analyzes the spectrum of EGFR ex20ins variants in a large patient population from a global clinical trial and several real-world cohorts and the ability of PCR kits to identify these alterations. MethodsWe conducted this retrospective analysis in patients with NSCLC who underwent NGS or other sequencing testing and had a known EGFR ex20ins mutation. Patients were gathered from a clinical trial (NCT02716116), a chart review study in Germany, and the LC-SCRUM-Japan, GENIE, and U.S. COTA databases. Proportions of patients with ex20ins variants that could have been detected by six commercially available and widely used PCR kits were calculated in each data set. ResultsOverall, 636 patients with NSCLC harboring EGFR ex20ins mutations were included in this analysis and 104 unique EGFR ex20ins variants were identified across the data sources. The proportion of patients whose ex20ins could have been detected by any PCR test alone ranged from 11.8% to 58.9% across the data sources. ConclusionsOur findings suggest that the PCR tests evaluated would have missed more than 40% of patients with NSCLC harboring EGFR ex20ins mutations. NGS-based genetic testing is preferable than standard PCR assays and can substantially improve the identification of the diverse profile of EGFR ex20ins variants in NSCLC.

Validation of the Molecular International Prognostic Scoring System in patients with myelodysplastic syndromes

Letter to Blood| April 6, 2023 Validation of the Molecular International Prognostic Scoring System in patients with myelodysplastic syndromes Clinical Trials & Observations Tariq Kewan, Tariq Kewan Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OHDepartment of Hematology and Oncology, Yale University, New Haven, CT https://orcid.org/0000-0003-4651-5125 Search for other works by this author on: This Site PubMed Google Scholar Waled Bahaj, Waled Bahaj Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH Search for other works by this author on: This Site PubMed Google Scholar Arda Durmaz, Arda Durmaz Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OHSystems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH https://orcid.org/0000-0001-8394-600X Search for other works by this author on: This Site PubMed Google Scholar Mai Aly, Mai Aly Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OHFaculty of Medicine, Assiut University, Assiut, Egypt https://orcid.org/0000-0002-3926-6856 Search for other works by this author on: This Site PubMed Google Scholar Olisaemeka D. Ogbue, Olisaemeka D. Ogbue Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH Search for other works by this author on: This Site PubMed Google Scholar Hetty E. Carraway, Hetty E. Carraway Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH https://orcid.org/0000-0001-5241-3614 Search for other works by this author on: This Site PubMed Google Scholar Mikkael A. Sekeres, Mikkael A. Sekeres Department of Hematology and Oncology, University of Miami, Miami, FL Search for other works by this author on: This Site PubMed Google Scholar Valeria Visconte, Valeria Visconte Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH Search for other works by this author on: This Site PubMed Google Scholar Carmelo Gurnari, Carmelo Gurnari Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OHDepartment of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy https://orcid.org/0000-0001-6829-5544 Search for other works by this author on: This Site PubMed Google Scholar Jaroslaw P. Maciejewski Jaroslaw P. Maciejewski Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH Search for other works by this author on: This Site PubMed Google Scholar Blood (2023) 141 (14): 1768–1772. https://doi.org/10.1182/blood.2022018896 Article history Submitted: October 28, 2022 Accepted: January 17, 2023 Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Request Permissions Cite Icon Cite Search Site Citation Tariq Kewan, Waled Bahaj, Arda Durmaz, Mai Aly, Olisaemeka D. Ogbue, Hetty E. Carraway, Mikkael A. Sekeres, Valeria Visconte, Carmelo Gurnari, Jaroslaw P. Maciejewski; Validation of the Molecular International Prognostic Scoring System in patients with myelodysplastic syndromes. Blood 2023; 141 (14): 1768–1772. doi: https://doi.org/10.1182/blood.2022018896 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBlood Search Subjects: Clinical Trials and Observations, Myeloid Neoplasia TO THE EDITOR: Myelodysplastic syndrome (MDS) represents a heterogeneous group of disorders encompassing a wide range of pathologically distinct subtypes associated with different outcomes. Until recently, clinical and cytogenetic features have dominated the pathological classification and the prognostication of MDS.1-3 The wide use of next-generation sequencing and subsequent molecular studies have examined the impact of different genetic alterations on the pathogenetic derivation, diagnostic assignment, and disease prognosis.4-9 The latest contribution to the task of adopting molecular features into the clinical prognostic scheme is represented by the Molecular International Prognostic Scoring System (IPSS-M), a product of the International Working Group for Prognosis in MDS (IWG-PM).10 Here, we took advantage of a large cohort of patients with MDS (n = 1281, supplemental Methods, available on the Blood website) to validate the novel IPSS-M and to compare the score with the...

Historical evaluation of the in vivo adventitious virus test and its potential for replacement with next generation sequencing (NGS).

The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) collected historical data from 20 biopharmaceutical industry members on their experience with the in vivo adventitious virus test, the in vitro virus test, and the use of next generation sequencing (NGS) for viral safety. Over the past 20 years, only three positive in vivo adventitious virus test results were reported, and all were also detected in another concurrent assay. In more than three cases, data collected as a part of this study also found that the in vivo adventitious virus test had given a negative result for a sample that was later found to contain virus. Additionally, the in vivo adventitious virus test had experienced at least 21 false positives and had to be repeated an additional 21 times all while using more than 84,000 animals. These data support the consideration and need for alternative broad spectrum viral detection tests that are faster, more sensitive, more accurate, more specific, and more humane. NGS is one technology that may meet this need. Eighty one percent of survey respondents are either already actively using or exploring the use of NGS for viral safety. The risks and challenges of replacing in vivo adventitious virus testing with NGS are discussed. It is proposed to update the overall virus safety program for new biopharmaceutical products by replacing in vivo adventitious virus testing approaches with modern methodologies, such as NGS, that maintain or even improve the final safety of the product.