Clinical exome performance for reporting secondary genetic findings.

BACKGROUND : Reporting clinically actionable incidental genetic findings in the course of clinical exome testing is recommended by the American College of Medical Genet- ics and Genomics (ACMG). However, the performance of clinical exome methods for reporting small subsets of genes has not been previously reported. METHODS : In this study, 57 exome data sets performed as clinical (n ! 12) or research (n ! 45) tests were retrospec- tively analyzed. Exome sequencing data was examined for adequacy in the detection of potentially pathogenic variant locations in the 56 genes described in the ACMG incidental findings recommendation. All exons of the 56 genes were examined for adequacy of sequencing coverage. In addition, nucleotide positions annotated in HGMD (Human Gene Mutation Database) were examined. RESULTS : The 56 ACMG genes have 18336 nucleotide variants annotated in HGMD. None of the 57 exome data sets possessed a HGMD variant. The clinical exome test had inadequate coverage for " 50% of HGMD vari- ant locations in 7 genes. Six exons from 6 different genes had consistent failure across all 3 test methods; these exons had high GC content (76%–84%). CONCLUSIONS : The use of clinical exome sequencing for the interpretation and reporting of subsets of genes requires recognition of the substantial possibility of inadequate depth and breadth of sequencing coverage at clinically relevant locations. Inadequate depth of coverage may contribute to false-negative clinical ex- ome results

Reanalysis and reclassification of rare genetic variants associated with inherited arrhythmogenic syndromes

Background: Accurate interpretation of rare genetic variants is a challenge for clinical translation. Updates in recommendations for rare variant classification require the reanalysis and reclassification. We aim to perform an exhaustive re-analysis of rare variants associated with inherited arrhythmogenic syndromes, which were classified ten years ago, to determine whether their classification aligns with current standards and research findings. Methods: In 2010, the rare variants identified through genetic analysis were classified following recommendations available at that time. Nowadays, the same variants have been reclassified following current American College of Medical Genetics and Genomics recommendations. Findings: Our cohort included 104 cases diagnosed with inherited arrhythmogenic syndromes and 17 post-mortem cases in which inherited arrhythmogenic syndromes was cause of death. 71.87% of variants change their classification. While 65.62% of variants were classified as likely pathogenic in 2010, after reanalysis, only 17.96% remain as likely pathogenic. In 2010, 18.75% of variants were classified as uncertain role but nowadays 60.15% of variants are classified of unknown significance. Interpretation: Reclassification occurred in more than 70% of rare variants associated with inherited arrhythmogenic syndromes. Our results support the periodical reclassification and personalized clinical translation of rare variants to improve diagnosis and adjust treatment

Criteria for reporting incidental findings in clinical exome sequencing : a focus group study on professional practices and perspectives in Belgian genetic centres

Background: Incidental and secondary findings (IFs and SFs) are subject to ongoing discussion as potential consequences of clinical exome sequencing (ES). International policy documents vary on the reporting of these findings. Discussion points include the practice of unintentionally identified IFs versus deliberately pursued SFs, patient opt-out possibilities and the spectrum of reportable findings. The heterogeneity of advice permits a non-standardised disclosure but research is lacking on actual reporting practices. Therefore, this study assessed national reporting practices for IFs and SFs in clinical ES and the underlying professional perspectives. Methods: A qualitative focus group study has been undertaken, including professionals from Belgian centres for medical genetics (CMGs). Data were analysed thematically. Results: All Belgian CMGs participated in this study. Data analysis resulted in six main themes, including one regarding the reporting criteria used for IFs. All CMGs currently use ES-based panel testing. They have limited experience with IFs in clinical ES and are cautious about the pursuit of SFs. Two main reporting criteria for IFs were referred to by all CMGs: the clinical significance of the IF (including pathogenicity and medical actionability) and patient-related factors (including the patient's preference to know and patient characteristics). The consensus over the importance of these criteria contrasted with their challenging interpretation and application. Points of concern included IFs' pathogenicity in non-symptomatic persons, IFs concerning variants of uncertain significance, the requirement and definition of medical actionability and patient opt-out possibilities. Finally, reporting decisions were guided by the interaction between the clinical significance of the IF and patient characteristics. This interaction questions the possible disclosure of findings with context-dependent and personal utility, such as IFs concerning a carrier status. To evaluate the IF's final relevance, a professional and case-by-case deliberation was considered essential. Conclusions: The challenging application of reporting criteria for IFs results in diversified practices and policy perspectives within Belgian CMGs. This echoes international concerns and may have consequences for effective policy recommendations

Ethical values supporting the disclosure of incidental and secondary findings in clinical genomic testing : a qualitative study

Background: Incidental findings (IFs) and secondary findings (SFs), being results that are unrelated to the diagnostic question, are the subject of an important debate in the practice of clinical genomic medicine. Arguments for reporting these results or not doing so typically relate to the principles of autonomy, nonmaleficence and beneficence. However, these principles frequently conflict and are insufficient by themselves to come to a conclusion. This study investigates empirically how ethical principles are considered when actually reporting IFs or SFs and how value conflicts are weighed. Methods: A qualitative focus group study has been undertaken, including a multidisciplinary group of professionals from Belgian centres for medical genetics. The data were analysed thematically. Results: All eight Belgian centres participated in this study. Ethical values were frequently referred to for disclosure policies on IFs and SFs. Participants invoked respect for patient autonomy to support the disclosure of IFs and optout options for IFs and SFs, non-maleficence for the professional delineation of reportable IFs and opt-out options for IFs and SFs and (the particular scope of) beneficence for the mandatory reporting of actionable IFs, the delineation of reportable IFs and a current decline of actively pursued SFs. Professional assumptions about patients’ genetic literacy were an important factor in the weighing of values. Conclusions: In line with the traditional bioethical discourse, the mandatory reporting of actionable IFs might be interpreted as a “technological, soft paternalism”. Restricting patients’ choices might be acceptable, but then its motives should be valid and its beneficent outcomes highly plausible. Hence, the presuppositions of technological, soft paternalism - patients’ inability to make informed decisions, normative rationality, the efficacy of beneficent outcomes and the delineated spectrum of beneficence - should be approached critically. Moreover, distributive justice should be considered an important value in the delineation of the current scope of the ethical debate on IFs and SFs. This study of guiding values may stimulate the debate on the ethical grounds for a solid policy on IFs and SFs internationally

Optimizing genetics online resources for diverse readers.

PurposeClear and accurate genetic information should be available to health-care consumers at an individualized level of comprehension. The objective of this study is to evaluate the complexity of common online resources and to simplify text content using automated text processing tools.MethodsWe extracted all text from Genetics Home Reference and MedlinePlus in bulk and analyzed content using natural language processing. We applied custom tools to improve the readability and compared readability before and after text optimization.ResultsCommonly used educational materials were more complex than the recommended reading level for the general public. Genetic health information entries from Genetics Home Reference (n = 1279) were written at a median 13.0 grade level. MedlinePlus entries, which are not exclusively genetic (n = 1030), had a median grade level of 7.7. When we optimized text for the 59 actionable conditions by prioritizing medical details using a standard structure, the average reading grade level improved.ConclusionFactors that increase complexity are long sentences and difficult words. Future strategies to reduce complexity include prioritizing relevant details and using more illustrations. Simplifying and providing standardized online health resources would benefit diverse consumers and promote inclusivity

Assimilation of SAR and optical data into an agro-meteorological model for monitoring yield of corn

This study aims to assess the contribution of SAR and optical satellite images to estimate corn biophysical parameters and crop yield at field scale. Satellite data are assimilated into a simple agro-meteorological model named SAFY-WB (Simple Algorithm For Yield estimates combined with a Water Balance model), in order to simulate leaf area index, dry mass and yield. The method has been assessed thanks to data collected over two study areas (both located in the South-West of France), during two experimental campaigns: MCM'10 and MCM'15 (Multispectral Crop Monitoring), respectively performed in 2010 and 2015. SAR backscattering coefficients were acquired in the C-band, and extracted from two satellites: Radarsat-2 (full-polarization states) and Sentinel-1 (VV and VH polarizations) in 2010 and 2015 respectively. Vegetation indices (NDVI, MTVI2) have been extracted from optical images at high spatial resolution (i.e. Landsat, Spot and Formosat satellite missions). First results demonstrate that optical and SAR (σ°HV) data can be used for monitoring leaf area index and dry mass of the corn during the growing period, until flowering. From the end of the growing period and during the senescence, the SAR signals saturate and are weakly sensitive to the decrease of the crop water content, contrary to optical reflectance that strongly decrease with the color change of leaves and stems. Consequently, the best approach consists in assimilating SAR or optical data until flowering and mainly assimilating optical data from flowering to harvest, for best performances in the monitoring of yield, leaf area index and dry mass of corn

Outcomes of Genetic Testing in a Genitourinary Genetics Clinic

Several known hereditary cancer syndromes confer an increased risk for genitourinary (GU)related malignancies. Various guidelines indicate when to refer patients to genetic counseling for GU-related hereditary cancer syndromes but there is limited research on the clinical picture of these patients, including their cancerous and non-cancerous features, the genetic testing strategy for this population, and the probability of having a positive germline mutation if testing is performed. The purpose of this study is to determine the most common indications for ordering genetic testing in a GU Genetics Clinic and evaluate whether there is a relationship between the indication for genetic testing and genetic testing outcome. An institutional review board-approved retrospective chart review was performed for 220 patients seen in the GU Genetics Clinic at M.D. Anderson Cancer Center. Patients were stratified into groups based on their indication for genetic testing and an exact binomial test was used to compare the proportion of patients with a positive genetic test from various groups. The majority of patients (92%) were seen for genetic evaluation related to either renal cell carcinoma (RCC) or prostate cancer. Among patients seen for RCC-related evaluation (N=107), meeting published clinical criteria for a hereditary RCC syndrome significantly predicted positive genetic testing (

MANAGING VARIANT DISCREPANCY IN HEREDITARY CANCER: CLINICAL PRACTICE, BARRIERS, AND DESIRED RESOURCES

Variants are changes in the DNA whose phenotypic effects may or may not be definitively understood. Because variant interpretation is a complex process, sources sometimes disagree on the classification of a variant, which is called a variant discrepancy. This study aimed to determine the practice of genetic counselors regarding variant discrepancies and to identify the barriers to counseling a variant discrepancy in hereditary cancer genetic testing. This investigation was unique because it was the first to address variant discrepancies from a clinical point of view. An electronic survey was sent to genetic counselors in the NSGC Cancer Special Interest Group. The vast majority of counselors (93%) had seen a variant discrepancy in practice. The most commonly selected barriers to counseling a variant discrepancy were lack of data sharing (90%) and lack of a central database (76%). Most counselors responded that the ideal database would be owned by a non-profit (59%) and obtain information directly from laboratories (91%). When asked how they approached counseling sessions involving variant discrepancies, the free responses emphasized that counselors consider family history and psychosocial concerns, showing that genetic counselors tailored the session to each individual. Variant discrepancies are an ongoing concern for clinical cancer genetic counselors, as demonstrated by the fact that counselors desired further resources to aid in addressing variant discrepancies, including a centralized database (89%), guidelines from a major organization (88%), continuing education about the issue (74%) and functional studies (58%)

Development and Validation of Clinical Whole-Exome and Whole-Genome Sequencing for Detection of Germline Variants in Inherited Disease

Context.-With the decrease in the cost of sequencing, the clinical testing paradigm has shifted from single gene to gene panel and now whole-exome and whole-genome sequencing. Clinical laboratories are rapidly implementing next-generation sequencing-based whole-exome and whole-genome sequencing. Because a large number of targets are covered by whole-exome and whole-genome sequencing, it is critical that a laboratory perform appropriate validation studies, develop a quality assurance and quality control program, and participate in proficiency testing. Objective.-To provide recommendations for wholeexome and whole-genome sequencing assay design, validation, and implementation for the detection of germline variants associated in inherited disorders. Data Sources.-An example of trio sequencing, filtration and annotation of variants, and phenotypic consideration to arrive at clinical diagnosis is discussed. Conclusions.-It is critical that clinical laboratories planning to implement whole-exome and whole-genome sequencing design and validate the assay to specifications and ensure adequate performance prior to implementation. Test design specifications, including variant filtering and annotation, phenotypic consideration, guidance on consenting options, and reporting of incidental findings, are provided. These are important steps a laboratory must take to validate and implement whole-exome and whole-genome sequencing in a clinical setting for germline variants in inherited disorders