scholarly journals Incidental findings from cancer next generation sequencing panels

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Nika Maani ◽  
Karen Panabaker ◽  
Jeanna M. McCuaig ◽  
Kathleen Buckley ◽  
Kara Semotiuk ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Incidental Findings ◽  
Complete Blood Count ◽  
Hematologic Malignancy ◽  
Retrospective Chart Review ◽  
Hematologic Malignancies ◽  
Next Generation ◽  
Inclusion Criteria ◽  
Pathogenic Variants ◽  
Generation Sequencing

AbstractNext-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings.

scholarly journals 2443 Attitudes and preferences for return of results from next-generation sequencing

2018 ◽  
Vol 2 (S1) ◽  
pp. 79-79
Author(s):  
Matthew Neu ◽  
Jaimie Richards ◽  
Sara J. Knight
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Incidental Findings ◽  
Return Of Results ◽  
Medical Setting ◽  
Specific Gene ◽  
Next Generation ◽  
Inclusion Criteria ◽  
Secondary Findings ◽  
Generation Sequencing

OBJECTIVES/SPECIFIC AIMS: Objectives: Decreasing costs and increasing evidence for clinical utility have contributed to whole genome sequencing (WGS) becoming a clinical reality. While previous studies have surveyed the attitudes of patients and community members towards specific gene tests, an emerging literature has begun to describe the preferences of diverse recipients for WGS results. In this study, we sought to identify and synthesize the quantitative evidence on preferences for results from WGS using a systematic review of the literature. METHODS/STUDY POPULATION: We conducted a search of articles on PubMed including subject index terms WGS, whole exome sequencing, genome sequencing, secondary findings, incidental findings, attitudes, preferences, choices, utilities, stated-preferences, discrete choice experiment, and willingness-to-pay. We conducted 11 formal searches to refine the strategy and conducted a final search in December 2017. Duplicates were eliminated and a title and abstract review was conducted to select articles meeting inclusion criteria. RESULTS/ANTICIPATED RESULTS: Our search strategy identified 79 publications meeting initial search criteria with 30 manuscripts meeting inclusion criteria. Of these, most studies were conducted with patient-participants enrolled in existing sequencing studies, while few engaged members of the general public. Of the studies conducted on patients, most were on the medical setting of cancer and related syndromes. The earliest publication date of a manuscript meeting our inclusion criteria was in 2012, yet the majority were published in 2015 or later. DISCUSSION/SIGNIFICANCE OF IMPACT: Between 2012 and 2015, we saw an increasing focus in the medical literature on understanding public and patient preferences for return of results from WGS and WES. Both public and patient populations participating in surveys expressed preferences for receiving results from next-generation sequencing, even if the results are secondary or incidental findings unrelated to the primary indication for sequencing. A primary factor related to patient interest in incidental or secondary findings is the extent to which these results can inform medical intervention. Few studies surveyed representative population-based samples, and this may be an area for future investigation.

scholarly journals Proficiency Testing of Standardized Samples Shows High Interlaboratory Agreement for Clinical Next-Generation Sequencing–Based Hematologic Malignancy Assays With Survey Material–Specific Differences in Variant Frequencies

2020 ◽  
Vol 144 (8) ◽  
pp. 959-966 ◽  
Author(s):  
Alissa Keegan ◽  
Julia A. Bridge ◽  
Neal I. Lindeman ◽  
Thomas A. Long ◽  
Jason D. Merker ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Proficiency Testing ◽  
Hematologic Malignancy ◽  
False Negative ◽  
False Negative Rate ◽  
Hematologic Malignancies ◽  
Variant Allele ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Generation Sequencing

Context.— As laboratories increasingly turn from single-analyte testing in hematologic malignancies to next-generation sequencing–based panel testing, there is a corresponding need for proficiency testing to ensure adequate performance of these next-generation sequencing assays for optimal patient care. Objective.— To report the performance of laboratories on proficiency testing from the first 4 College of American Pathologists Next-Generation Sequencing Hematologic Malignancy surveys. Design.— College of American Pathologists proficiency testing results for 36 different engineered variants and/or allele fractions as well as a sample with no pathogenic variants were analyzed for accuracy and associated assay performance characteristics. Results.— The overall sensitivity observed for all variants was 93.5% (2190 of 2341) with 99.8% specificity (22 800 of 22 840). The false-negative rate was 6.5% (151 of 2341), and the largest single cause of these errors was difficulty in identifying variants in the sequence of CEBPA that is rich in cytosines and guanines. False-positive results (0.18%; 40 of 22 840) were most likely the result of preanalytic or postanalytic errors. Interestingly, the variant allele fractions were almost uniformly lower than the engineered fraction (as measured by digital polymerase chain reaction). Extensive troubleshooting identified a multifactorial cause for the low variant allele fractions, a result of an interaction between the linearized nature of the plasmid and the Illumina TruSeq chemistry. Conclusions.— Laboratories demonstrated an overall accuracy of 99.2% (24 990 of 25 181) with 99.8% specificity and 93.5% sensitivity when examining 36 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 10% or greater. The data also highlight an issue with artificial linearized plasmids as survey material for next-generation sequencing.

scholarly journals Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis

2021 ◽  
Vol 9 (11) ◽  
pp. 2309
Author(s):  
Wang-Da Liu ◽  
Ting-Yu Yen ◽  
Po-Yo Liu ◽  
Un-In Wu ◽  
Prerana Bhan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hematologic Malignancies ◽  
Blood Cultures ◽  
Diagnostic Methods ◽  
Next Generation ◽  
Viral Loads ◽  
A Prospective Study ◽  
Positive Results ◽  
Serology Testing ◽  
Generation Sequencing

Background: Sepsis remains a common but fatal complication among patients with immune suppression. We aimed to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in patients with hematologic malignancies. Methods: We performed a prospective study from June 2019 to December 2019. Adult patients with hematologic malignancies and a clinical diagnosis of sepsis were enrolled. Conventional diagnostic methods included blood cultures, serum galactomannan for Aspergillus, cryptococcal antigen and cytomegalovirus (CMV) viral loads. Blood samples for mNGS were collected within 24 h after hypotension developed. Results: Of 24 patients enrolled, mNGS and conventional diagnostic methods (blood cultures, serology testing and virus RT-PCR) reached comparable positive results in 9 cases. Of ten patients, mNGS was able to identify additional pathogens compared with conventional methods; most of the pathogens were virus. Conclusion: Our results show that mNGS may serve as adjunctive diagnostic tool for the identification of pathogens of hematologic patients with clinically sepsis.

scholarly journals Male Infertility Diagnosis: Improvement of Genetic Analysis Performance by the Introduction of Pre-Diagnostic Genes in a Next-Generation Sequencing Custom-Made Panel

2021 ◽  
Vol 11 ◽  
Author(s):  
Vincenza Precone ◽  
Rossella Cannarella ◽  
Stefano Paolacci ◽  
Gian Maria Busetto ◽  
Tommaso Beccari ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Male Infertility ◽  
Next Generation ◽  
Male Population ◽  
Pathogenic Variants ◽  
Custom Made ◽  
Number Of Genes ◽  
General Male Population ◽  
Generation Sequencing ◽  
Spermatogenic Failure

BackgroundInfertility affects about 7% of the general male population. The underlying cause of male infertility is undefined in about 50% of cases (idiopathic infertility). The number of genes involved in human spermatogenesis is over two thousand. Therefore, it is essential to analyze a large number of genes that may be involved in male infertility. This study aimed to test idiopathic male infertile patients negative for a validated panel of “diagnostic” genes, for a wide panel of genes that we have defined as “pre-diagnostic.”MethodsWe developed a next-generation sequencing (NGS) gene panel including 65 pre-diagnostic genes that were used in 12 patients who were negative to a diagnostic genetic test for male infertility disorders, including primary spermatogenic failure and central hypogonadism, consisting of 110 genes.ResultsAfter NGS sequencing, variants in pre-diagnostic genes were identified in 10/12 patients who were negative to a diagnostic test for primary spermatogenic failure (n = 9) or central hypogonadism (n = 1) due to mutations of single genes. Two pathogenic variants of DNAH5 and CFTR genes and three uncertain significance variants of DNAI1, DNAH11, and CCDC40 genes were found. Moreover, three variants with high impact were found in AMELY, CATSPER 2, and ADCY10 genes.ConclusionThis study suggests that searching for pre-diagnostic genes may be of relevance to find the cause of infertility in patients with apparently idiopathic primary spermatogenic failure due to mutations of single genes and central hypogonadism.

scholarly journals Identification of Genetic Hereditary Predisposition to Hematologic Malignancies By Clinical Next-Generation Sequencing

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3854-3854 ◽  
Author(s):  
Amy E Knight Johnson ◽  
Lucia Guidugli ◽  
Kelly Arndt ◽  
Gorka Alkorta-Aranburu ◽  
Viswateja Nelakuditi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Family Members ◽  
Hematologic Malignancies ◽  
Dyskeratosis Congenita ◽  
Molecular Diagnostic ◽  
Next Generation ◽  
Hereditary Predisposition ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Introduction: Myelodysplastic syndrome (MDS) and acute leukemia (AL) are a clinically diverse and genetically heterogeneous group of hematologic malignancies. Familial forms of MDS/AL have been increasingly recognized in recent years, and can occur as a primary event or secondary to genetic syndromes, such as inherited bone marrow failure syndromes (IBMFS). It is critical to confirm a genetic diagnosis in patients with hereditary predisposition to hematologic malignancies in order to provide prognostic information and cancer risk assessment, and to aid in identification of at-risk or affected family members. In addition, a molecular diagnosis can help tailor medical management including informing the selection of family members for allogeneic stem cell transplantation donors. Until recently, clinical testing options for this diverse group of hematologic malignancy predisposition genes were limited to the evaluation of single genes by Sanger sequencing, which is a time consuming and expensive process. To improve the diagnosis of hereditary predisposition to hematologic malignancies, our CLIA-licensed laboratory has recently developed Next-Generation Sequencing (NGS) panel-based testing for these genes. Methods: Thirty six patients with personal and/or family history of aplastic anemia, MDS or AL were referred for clinical diagnostic testing. DNA from the referred patients was obtained from cultured skin fibroblasts or peripheral blood and was utilized for preparing libraries with the SureSelectXT Enrichment System. Libraries were sequenced on an Illumina MiSeq instrument and the NGS data was analyzed with a custom bioinformatic pipeline, targeting a panel of 76 genes associated with IBMFS and/or familial MDS/AL. Results: Pathogenic and highly likely pathogenic variants were identified in 7 out of 36 patients analyzed, providing a positive molecular diagnostic rate of 20%. Overall, 6 out of the 7 pathogenic changes identified were novel. In 2 unrelated patients with MDS, heterozygous pathogenic sequence changes were identified in the GATA2 gene. Heterozygous pathogenic changes in the following autosomal dominant genes were each identified in a single patient: RPS26 (Diamond-Blackfan anemia 10), RUNX1 (familial platelet disorder with propensity to myeloid malignancy), TERT (dyskeratosis congenita 4) and TINF2 (dyskeratosis congenita 3). In addition, one novel heterozygous sequence change (c.826+5_826+9del, p.?) in the Fanconi anemia associated gene FANCA was identified. . The RNA analysis demonstrated this variant causes skipping of exon 9 and results in a premature stop codon in exon 10. Further review of the NGS data provided evidence of an additional large heterozygous multi-exon deletion in FANCA in the same patient. This large deletion was confirmed using array-CGH (comparative genomic hybridization). Conclusions: This study demonstrates the effectiveness of using NGS technology to identify patients with a hereditary predisposition to hematologic malignancies. As many of the genes associated with hereditary predisposition to hematologic malignancies have similar or overlapping clinical presentations, analysis of a diverse panel of genes is an efficient and cost-effective approach to molecular diagnostics for these disorders. Unlike Sanger sequencing, NGS technology also has the potential to identify large exonic deletions and duplications. In addition, RNA splicing assay has proven to be helpful in clarifying the pathogenicity of variants suspected to affect splicing. This approach will also allow for identification of a molecular defect in patients who may have atypical presentation of disease. Disclosures No relevant conflicts of interest to declare.

scholarly journals Next‐generation sequencing for the diagnosis of MYH9 ‐RD: Predicting pathogenic variants

2019 ◽  
Vol 41 (1) ◽  
pp. 277-290 ◽  
Author(s):  
Loredana Bury ◽  
Karyn Megy ◽  
Jonathan C. Stephens ◽  
Luigi Grassi ◽  
Daniel Greene ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Pathogenic Variants ◽  
Generation Sequencing

scholarly journals Next Generation Sequencing Identifies Five Novel Mutations in Lebanese Patients with Bardet–Biedl and Usher Syndromes

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1047 ◽  
Author(s):  
Lama Jaffal ◽  
Wissam H Joumaa ◽  
Alexandre Assi ◽  
Charles Helou ◽  
George Cherfan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Usher Syndrome ◽  
Bioinformatic Analysis ◽  
Next Generation ◽  
Novel Mutations ◽  
Pathogenic Variants ◽  
Whole Exome ◽  
Targeted Ngs ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Aim: To identify disease-causing mutations in four Lebanese families: three families with Bardet–Biedl and one family with Usher syndrome (BBS and USH respectively), using next generation sequencing (NGS). Methods: We applied targeted NGS in two families and whole exome sequencing (WES) in two other families. Pathogenicity of candidate mutations was evaluated according to frequency, conservation, in silico prediction tools, segregation with disease, and compatibility with inheritance pattern. The presence of pathogenic variants was confirmed via Sanger sequencing followed by segregation analysis. Results: Most likely disease-causing mutations were identified in all included patients. In BBS patients, we found (M1): c.2258A > T, p. (Glu753Val) in BBS9, (M2): c.68T > C; p. (Leu23Pro) in ARL6, (M3): c.265_266delTT; p. (Leu89Valfs*11) and (M4): c.880T > G; p. (Tyr294Asp) in BBS12. A previously known variant (M5): c.551A > G; p. (Asp184Ser) was also detected in BBS5. In the USH patient, we found (M6): c.188A > C, p. (Tyr63Ser) in CLRN1. M2, M3, M4, and M6 were novel. All of the candidate mutations were shown to be likely disease-causing through our bioinformatic analysis. They also segregated with the corresponding phenotype in available family members. Conclusion: This study expanded the mutational spectrum and showed the genetic diversity of BBS and USH. It also spotlighted the efficiency of NGS techniques in revealing mutations underlying clinically and genetically heterogeneous disorders.

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