Interpretation Of Gene Variants Research Articles

Chinese expert consensus statement on the classification and interpretation of variants in genes associated with common inherited cardiovascular diseases

Chinese expert consensus statement on the classification and interpretation of variants in genes associated with common inherited cardiovascular diseases

Metabolomics in paraganglioma: applications and perspectives from genetics to therapy.

Metabolites represent the highest layer of biological information. Their diverse chemical nature enables networks of chemical reactions that are critical for maintaining life by providing energy and building blocks. Quantification by targeted and untargeted analytical methods using either mass spectrometry or nuclear magnetic resonance spectroscopy has been applied to pheochromocytoma/paraganglioma (PPGL) with the long-term goal to improve diagnosis and therapy. PPGLs have unique features that provide useful biomarkers and clues for targeted treatments. First, high production rates of catecholamines and metanephrines allow for specific and sensitive detection of the disease in plasma or urine. Secondly, PPGLs are associated with heritable pathogenic variants (PVs) in around 40% of cases, many of which occur in genes encoding enzymes, such as succinate dehydrogenase (SDH) and fumarate hydratase (FH). These genetic aberrations lead to the overproduction of oncometabolites succinate or fumarate, respectively, and are detectable in tumors and blood. Such metabolic dysregulation can be exploited diagnostically, with the aim to ensure appropriate interpretation of gene variants, especially those with unknown significance, and facilitate early tumor detection through regular patient follow-up. Furthermore, SDHx and FH PV alter cellular pathways, including DNA hypermethylation, hypoxia signaling, redox homeostasis, DNA repair, calcium signaling, kinase cascades, and central carbon metabolism. Pharmacological interventions targeted toward such features have the potential to uncover treatments against metastatic PPGL, around 50% of which are associated with germline PV in SDHx. With the availability of omics technologies for all layers of biological information, personalized diagnostics and treatment is in close reach.

Long-Term Follow-Up of Three Family Members with a Novel NNT Pathogenic Variant Causing Primary Adrenal Insufficiency.

Nicotinamide nucleotide transhydrogenase (NNT) deficiency causes primary adrenal insufficiency (PAI) and possibly some extra-adrenal manifestations. A limited number of these patients were previously described. We present the clinical and genetic characteristics of three family members with a biallelic novel pathogenic variant in the NNT gene. The patients were followed until the ages of 21.6, 20.2, and 4.2 years. PAI was diagnosed in the eldest two brothers after an Addisonian crisis and the third was diagnosed at the age of 4.5 months in the asymptomatic stage due to the genetic screening of family members. Whole exome sequencing with a targeted interpretation of variants in genes related to PAI was performed in all the patients. The urinary steroid metabolome was determined by gas chromatography–mass spectrometry in the asymptomatic patient. The three patients, who were homozygous for c.1575dup in the NNT gene, developed isolated glucocorticoid deficiency. The urinary steroid metabolome showed normal excretion of cortisol metabolites. The adolescent patients had slow pubertal progression with low–normal testicular volume, while testicular endocrine function was normal. Bone mineral density was in the range for osteopenia in both grown-up siblings. Echocardiography revealed no structural or functional heart abnormalities. This article is among the first with a comprehensive and chronologically-detailed description of patients with NNT deficiency.

Determination of Pathogenicity of Breast Cancer 1 Gene Variants using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines.

ObjectivesMolecular diagnostic laboratories screen for mutations in disease-causing genes in order to confirm a clinical diagnosis. The classification of DNA variants as ‘pathogenic’ or ‘likely pathogenic’ mutations creates a workflow bottleneck, which becomes increasingly challenging as greater number of genes are screened. The classification challenge is also acute if there are conflicting reports regarding pathogenicity and differing classification criteria between laboratories. This study aimed to compare two procedures for the classification of variants in the breast cancer (BRCA)1 gene.MethodsThis bioinformatic study was conducted at LabPLUS, Auckland, New Zealand, from February to June 2017. DNA was extracted from peripheral blood samples of 30 patients and gene library construction was carried out using a commercially available targeted panel for the BRCA1 and BRCA2 genes. The genes were subsequently sequenced and the sequence data analysed. The guidelines published by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) provides a comprehensive framework for the interpretation of variants in genes that are associated with Mendelian disorders. The use of these guidelines were compared to the variant classifications that were achieved by reference to those reported in the BRCA Exchange database.ResultsThe results showed concordance between the two classification protocols for a panel of 30 BRCA1 gene variants, although the transparency in following the ACMG/AMP guidelines provides a diagnostic laboratory with a generalisable approach that allows laboratory-directed revisions to be undertaken in light of new information.ConclusionThe ACMG/AMP-based guidelines were applied to a cohort of patients with BRCA1 gene variants. The use of these guidelines provides a system which creates consistency in variant interpretation and supports subsequent clinical management.

Molecular Autopsy for Sudden Cardiac Death: Current State and Considerations

The study of the genetic basis of sudden cardiac death has been impacted by advances in sequencing technology, gene variant interpretation, and additional evaluation into the ideal clinical approach to assessing cause of death and the medical and psychological risks of surviving family members. This short review aims to summarize recent publications as well as provide context for future directions for the care of families faced with sudden cardiac death. The molecular autopsy is a critical method in determining cause of death, particularly in autopsy-negative sudden cardiac death. Although the cost and availability of exome sequencing have improved in the past few years, its utility in the postmortem evaluation has not significantly improved yield. This is primarily due to the increase in genetic variants detected through this sequencing modality and the difficulty in interpreting these results. Medical examiners are essential in the proper identification and referral of surviving relatives to multidisciplinary clinics that include an expert cardiologist, cardiac genetic counselor, and clinical psychologist that can provide appropriate education, clinical evaluation, and psychological support. Future studies need to build on the improvement in variant interpretation and appropriate education and support of medical examiners. This will ensure family members are referred to appropriate providers such that they can receive medical and psychological care that will improve overall health outcomes and reduce the incidence of subsequent sudden cardiac death in the family.

Panel-Based Exome Sequencing for Neuromuscular Disorders as a Diagnostic Service.

Neuromuscular disorders (NMDs) are clinically and genetically heterogeneous. Accurate molecular genetic diagnosis can improve clinical management, provides appropriate genetic counseling and testing of relatives, and allows potential therapeutic trials. To establish the clinical utility of panel-based whole exome sequencing (WES) in NMDs in a population with children and adults with various neuromuscular symptoms. Clinical exome sequencing, followed by diagnostic interpretation of variants in genes associated with NMDs, was performed in a cohort of 396 patients suspected of having a genetic cause with a variable age of onset, neuromuscular phenotype, and inheritance pattern. Many had previously undergone targeted gene testing without results. Disease-causing variants were identified in 75/396 patients (19%), with variants in the three COL6-genes (COL6A1, COL6A2 and COL6A3) as the most common cause of the identified muscle disorder, followed by variants in the RYR1 gene. Together, these four genes account for almost 25% of cases in whom a definite genetic cause was identified. Furthermore, likely pathogenic variants and/or variants of uncertain significance were identified in 95 of the patients (24%), in whom functional and/or segregation analysis should be used to confirm or reject the pathogenicity. In 18% of the cases with a disease-causing variant of which we received additional clinical information, we identified a genetic cause in genes of which the associated phenotypes did not match that of the patients. Hence, the advantage of panel-based WES is its unbiased approach. Whole exome sequencing, followed by filtering for NMD genes, offers an unbiased approach for the genetic diagnostics of NMD patients. This approach could be used as a first-tier test in neuromuscular disorders with a high suspicion of a genetic cause. With uncertain results, functional testing and segregation analysis are needed to complete the evidence.

High-throughput sequencing for diagnosing platelet disorders: lessons learned from exploring the causes of bleeding disorders.

Inherited platelet disorders (IPDs) are a heterogeneous group of disorders caused by multiple genetic defects. Obtaining a molecular diagnosis for IPD patients using a phenotype- and laboratory-based approach is complex, expensive, time-consuming, and not always successful. High-throughput sequencing (HTS) methods offer a genotype-based approach to facilitate molecular diagnostics. Such approaches are expected to decrease time to diagnosis, increase the diagnostic rate, and they have provided novel insights into the genotype-phenotype correlation of IPDs. Some of these approaches have also focused on the discovery of novel genes and unexpected molecular pathways which modulate megakaryocyte and platelet biology were discovered. A growing number of genetic defects underlying IPDs have been identified and we will here provide an overview of the diverse molecular players. Screening of these genes will deliver a genetic diagnosis for about 40%-50% of the IPDs patients and we will compare different HTS applications that have been developed. A brief focus on gene variant interpretation and classification in a diagnostic setting will be given. Although it is true that successes in diagnostics and gene discovery have been reached, a large fraction of patients still remains without a conclusive diagnosis. In these patients, the sum of non-diagnostic variants in known genes or in potential novel genes might only be proven informative in future studies with larger patient cohorts and by data sharing among the diverse genome medicine initiatives. Finally, we still do not understand the role of the non-coding genome space for IPDs.

Abstract 4260: Standardized decision support in next-generation sequencing (NGS) reports of somatic cancer variants

Abstract Introduction: Of hundreds to thousands of somatic mutations that exist in each cancer genome, a large number are unique and non-recurrent variants. Many such variants occur in tumor genes that have well-established biological and clinical relevance and are putative targets of molecular therapy, however, most variants are still of unknown significance. Prioritizing and reporting genetic variants identified via NGS technologies remains a major challenge. Methods: Based on a systematic framework for cancer variant annotation/prioritization, we propose a structured molecular pathology report using standardized terminology in order to best inform oncology clinical practice. In parallel with the variant interpretation pipeline, we developed a comprehensive knowledge database (Kdb) that integrates tumor types, genes, variants, response/resistance patterns to approved and experimental agents and PubMed identifiers. Results: As physicians rely heavily on limited subsets of data and frequently apply rules based on strength of evidence in the decision-making process, NGS results are presented in a very discrete manner, avoiding detailed descriptions of each genomic aberration. Reportable variants are grouped in three categories: (i) actionable, which support treatment recommendation, enrollment in clinical trials and/or have prognostic or diagnostic implications; (ii) biologically relevant but not clearly actionable, including novel variants lacking functional preclinical validation in known cancer genes; and (iii) variants of unknown significance. Predictive associations are reported according to tumor type and classified in a hierarchical way based on the strength of evidence: (i) late trials; (ii) early trials; (iii) case reports; and (iv) preclinical data being explored in clinical trials. In our internal Kdb, tumor types with the largest number of emerging predictive associations are acute leukemias, non-small cell lung cancer, brain tumors, melanoma, colorectal, ovarian and breast cancers, comprising more than 100 unique gene - drug interactions. Further interpretation of gene variants requires a team with strong background in cancer biology, careful evaluation of the published literature and ability to match a patient's tumor genotype to clinical trials in the context of multiple aberrations. Conclusions: With large amounts of data being generated as high throughput sequencing assays enter the clinical realm, there is a growing need to better communicate relevant findings in a timely manner while remaining cognizant of the potential consequences of misuse or overinterpretation of genomic information. The scientific knowledge on actionable events should be presented the report, so that physicians can make evidence-based decisions and patients may benefit from treatment with matched targeted agents. We hope that our experience in this process will help other institutions implement similar programs. Citation Format: Rodrigo Dienstmann, Fei Dong, Darrell Borger, Dora Dias Santagata, Leif W. Ellisen, Long P. Le, A. John Iafrate. Standardized decision support in next-generation sequencing (NGS) reports of somatic cancer variants. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4260. doi:10.1158/1538-7445.AM2014-4260