Biology subjects

Evans, E. A.

Publications and source records attributed to Evans, E. A..

5 recordsLinked to original sources

bioRxiv2017

Development and validation of an expanded carrier screen that optimizes sensitivity via full-exon sequencing and panel-wide copy-number-variant identification

PurposeBy identifying pathogenic variants across hundreds of genes, expanded carrier screening (ECS) enables prospective parents to assess risk of transmitting an autosomal recessive or X-linked condition. Detection of at-risk couples depends on the number of conditions tested, the diseases respective prevalences, and the screens sensitivity for identifying disease-causing variants. Here we present an analytical validation of a 235-gene sequencing-based ECS with full coverage across coding regions, targeted assessment of pathogenic noncoding variants, panel-wide copy-number-variant (CNV) calling, and customized assays for technically challenging genes.\n\nMethodsNext-generation sequencing, a customized bioinformatics pipeline, and expert manual call review were used to identify single-nucleotide variants, short insertions and deletions, and CNVs for all genes except FMR1 and those whose low disease incidence or high technical complexity precludes novel variant identification or interpretation. Variant calls were compared to reference and orthogonal data.\n\nResultsValidation of our ECS data demonstrated >99% analytical sensitivity and >99% specificity. A preliminary assessment of 15,177 patient samples reveals the substantial impact on fetal disease-risk detection attributable to novel CNV calling (13.9% of risk) and technically challenging conditions (15.5% of risk), such as congenital adrenal hyperplasia.\n\nConclusionValidated, high-fidelity identification of different variant types--especially in diseases with complicated molecular genetics--maximizes at-risk couple detection.

genetics↗

bioRxiv2016

Noninvasive Prenatal Screening at Low Fetal Fraction: Comparing Whole- Genome Sequencing and Single-Nucleotide Polymorphism Methods

ObjectivePerformance of noninvasive prenatal screening (NIPS) methodologies when applied to low fetal fraction samples is not well established. The single-nucleotide polymorphism (SNP) method fails samples below a predetermined fetal fraction threshold, whereas some laboratories employing the whole-genome sequencing (WGS) method report aneuploidy calls for all samples. Here, the performance of the two methods was compared to determine which approach actually detects more fetal aneuploidies.\n\nMethodsComputational models were parameterized with up-to-date published data and used to compare the performance of the two methods at calling common fetal trisomies (T21, T18, T13) at low fetal fractions. Furthermore, clinical experience data were reviewed to determine aneuploidy detection rates based on compliance with recent invasive screening recommendations.\n\nResultsThe SNP methods performance is dependent on the origin of the trisomy, and is lowest for the most common trisomies (maternal M1 nondisjunction). Consequently, the SNP method cannot maintain acceptable performance at fetal fractions below ~3%. In contrast, the WGS method maintains high specificity independent of fetal fraction and has >80% sensitivity for trisomies in low fetal fraction samples.\n\nConclusionThe WGS method will detect more aneuploidies below the fetal fraction threshold at which many labs issue a no-call result, avoiding unnecessary invasive procedures.

genomics↗

bioRxiv2016

Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment

The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screens high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers.

genetics↗

bioRxiv2016

Smith-Lemli-Opitz syndrome carrier frequency and estimates of in utero mortality rates

Objective: To tabulate individual allele frequencies and total carrier frequency for Smith-Lemli-Opitz syndrome (SLOS) and compare expected versus observed birth incidences.\n\nDesign: Retrospective analysis of patients from the general population who have undergone carrier screening for SLOS.\n\nSetting: Individuals were offered and elected carrier screening in their respective physicians offices.\n\nPatients: 262,399 individuals with no indication of family or personal history of Smith-Lemli-Opitz syndrome, primarily US-based, screened for Smith-Lemli-Opitz syndrome mutations as part of an expanded carrier screening panel.\n\nIntervention(s): Data on mutations in the DHCR7 gene causing SLOS were analyzed to estimate carrier frequencies in multiple ethnic groups. SLOS birth incidences obtained from existing literature are then compared to our data to estimate the effect of SLOS on fetal survival.\n\nMain Outcome Measure(s): Individual and cumulative allele frequencies stratified by self-reported patient ethnicity.\n\nResults: SLOS carrier frequency is highest in individuals of Ashkenazi Jewish ancestry (1 in 43) and Northern Europeans (1 in 54). Comparing predicted birth incidence to that observed in published literature suggests that approximately 42% to 88% of affected conceptuses experience fetal demise.\n\nConclusion: SLOS is relatively frequent in certain populations and, due to its impact on fetal survival, merits preconception screening.

genetics↗

bioRxiv2016

Systematic Design and Comparison of Expanded Carrier Screening Panels

Purpose: The recent growth in pan-ethnic expanded carrier screening (ECS) has raised questions about how such panels might be designed and evaluated systematically. Design principles for ECS panels might improve clinical detection of at-risk couples and facilitate objective discussions of panel choice.\n\nMethods: Guided by medical-society statements, we propose a method for the design of ECS panels that aims to maximize the aggregate and per-disease sensitivity and specificity across a range of Mendelian disorders considered serious by a systematic classification scheme. We evaluated this method retrospectively using results from 474,644 de-identified carrier screens. We then constructed several idealized panels to highlight strengths and limitations of different ECS methodologies.\n\nResults: Based on modeled fetal risks for \"severe\" and \"profound\" diseases, a commercially available ECS panel (Counsyl) is expected to detect 183 affected conceptuses per 100,000 US births. A screens sensitivity is greatly impacted by two factors: (1) the methodology used (e.g., full-exon sequencing finds up to 46 more affected fetuses per 100,000 than targeted genotyping with an optimal 50 variant panel), and (2) the detection rate of the screen for diseases with high prevalence and complex molecular genetics (e.g., fragile X syndrome, spinal muscular atrophy, 21-hydroxylase deficiency, and alpha-thalassemia account for 54 affected fetuses per 100,000).\n\nConclusion: The described approaches allow principled, quantitative evaluation of which diseases and methodologies are appropriate for pan-ethnic expanded carrier screening.

genetics↗