Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results

Department of Pediatrics, Baylor Cancer Genetics Clinic, Baylor College of Medicine, Houston, Texas, USA.
Human Mutation (Impact Factor: 5.05). 11/2008; 29(11):1282-91. DOI: 10.1002/humu.20880
Source: PubMed

ABSTRACT Genetic testing of cancer susceptibility genes is now widely applied in clinical practice to predict risk of developing cancer. In general, sequence-based testing of germline DNA is used to determine whether an individual carries a change that is clearly likely to disrupt normal gene function. Genetic testing may detect changes that are clearly pathogenic, clearly neutral, or variants of unclear clinical significance. Such variants present a considerable challenge to the diagnostic laboratory and the receiving clinician in terms of interpretation and clear presentation of the implications of the result to the patient. There does not appear to be a consistent approach to interpreting and reporting the clinical significance of variants either among genes or among laboratories. The potential for confusion among clinicians and patients is considerable and misinterpretation may lead to inappropriate clinical consequences. In this article we review the current state of sequence-based genetic testing, describe other standardized reporting systems used in oncology, and propose a standardized classification system for application to sequence-based results for cancer predisposition genes. We suggest a system of five classes of variants based on the degree of likelihood of pathogenicity. Each class is associated with specific recommendations for clinical management of at-risk relatives that will depend on the syndrome. We propose that panels of experts on each cancer predisposition syndrome facilitate the classification scheme and designate appropriate surveillance and cancer management guidelines. The international adoption of a standardized reporting system should improve the clinical utility of sequence-based genetic tests to predict cancer risk.

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Available from: Sharon E Plon, Jul 28, 2015
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    • "Relevant to this topic, the International Society for Gastrointestinal Hereditary Tumours (InSIGHT) has recently described the procedure undertaken to validate integrated methods for classifying mismatch repair gene variants in order to use them in a clinical context for Lynch syndrome (Thompson et al., 2013). The authors underlined the need of an international support to standardize also the development of databases in which the final VUS classification should be provided (Plon et al., 2008; Thompson et al., 2013). "
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    ABSTRACT: CDKN2A codes for two oncosuppressors by alternative splicing of two first exons: p16INK4a and p14ARF. Germline mutations are found in about 40% of melanoma-prone families, and most of them are missense mutations mainly affecting p16INK4a. A growing number of p16INK4a Variants of Uncertain Significance (VUS) are being identified but, unless their pathogenic role can be demonstrated, they cannot be used for identification of carriers at risk. Predicting the effect of these VUS by either a “standard” in silico approach, or functional tests alone, is rather difficult. Here we report a protocol for the assessment of any p16INK4a VUS, which combines experimental and computational tools in an integrated approach. We analyzed p16INK4a VUS from melanoma patients as well as variants derived through permutation of conserved p16INK4a amino acids. Variants were expressed in a p16INK4a-null cell line (U2-OS) and tested for their ability to block proliferation. In parallel, these VUS underwent in silico prediction analysis and molecular dynamics simulations. Evaluation of in silico and functional data disclosed a high agreement for 15/16 missense mutations, suggesting that this approach could represent a pilot study for the definition of a protocol applicable to VUS in general, involved in other diseases, as well.This article is protected by copyright. All rights reserved
    Human Mutation 07/2014; 35(7). DOI:10.1002/humu.22550 · 5.05 Impact Factor
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    • "CMGS and VKGL (2007) and the American Board of Medical Genetics (Zhang and Wang 2012). Other examples for variant classification include the five class categorisation protocol developed for BRCA1/2 gene variants, where Class 1 variants are " not pathogenic or of no clinical significance " , Class 3 variants are " uncertain " and Class 5 variants are " definitely pathogenic " (Plon et al. 2008). Each class of variants has different consequences for clinical management. "
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    ABSTRACT: Massively parallel sequencing (MPS) has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in particular the annotation and clinical interpretation of genomic variants. Here, we describe annotation steps that can be automated and common strategies employed for variant prioritization. The definition of best practice standards for variant annotation and prioritization is still ongoing; at present, there is limited consensus regarding an optimal clinical sequencing pipeline. We provide considerations to help define these. For the first time, clinical genetics and genomics is not limited by our ability to sequence, but our ability to clinically interpret and use genomic information in health management. We argue that the development of standardised variant annotation and interpretation approaches and software tools implementing these warrants further support. As we gain a better understanding of the significance of genomic variation through research, patients will be able to benefit from the full scope that these technologies offer. This article is protected by copyright. All rights reserved.
    Human Mutation 04/2014; 35(4). DOI:10.1002/humu.22525 · 5.05 Impact Factor
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    • "(MLH1) NM_000179.2 (MSH6), and NM_000535.5 (PMS2), and classified using a five class system (1 = neutral, 2 = likely neutral, 3 = uncertain , 4 = likely pathogenic, and 5 = pathogenic) (Plon et al. 2008; Spurdle 2010 "
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    ABSTRACT: The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing.
    03/2014; 2(2):186-200. DOI:10.1002/mgg3.62
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