The New VSClinical ACMG Guidelines Tutorial

Nov 21, 2019

Our tutorials are a popular resource for prospective users. We have added a tutorial to help introduce customers to the ease and utility of the ACMG Guidelines incorporated in VSClinical. The ACMG Guidelines are a collection of 33 criteria that are used to determine a variant’s level of pathogenicity. VSClinical…

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All New VSClinical AMP Workflow Tutorial

Nov 5, 2019

We have recently added a tutorial to help introduce customers to the ease and utility of the AMP Guidelines incorporated in VarSeq’s VSClinical package. The AMP Guidelines allow users to sort through available clinical evidence in a streamlined fashion to arrive at final classification and interpretation and then transfer that…

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Copy Number Variants Using AMP Guidelines

Oct 10, 2019

The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the…

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Oncogenicity Scoring in VSClinical

Oct 1, 2019

Before examining the clinical evidence associated with a specific mutation, a clinician must establish that the variant is likely to be a driver mutation which generates functional changes that enhance tumor cell proliferation. Our recent blog series “Following the AMP Guidelines with VSClinical” briefly mentioned how the oncogenicity scoring system…

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Following the AMP Guidelines with VSClinical: Part II

Sep 5, 2019

VSClinical  users can interpret and report genomic mutations in cancer following the AMP guidelines which we’re demonstrating in this “Following the AMP Guidelines with VSClinical” blog series. Part I introduced the hands-on analysis steps involved in creating a high-quality clinical report for targeted Next-Generation Sequencing (NGS) assays. We reviewed sample and variant quality, including the depth of coverage over the target…

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Following the AMP Guidelines with VSClinical: Part I

Aug 23, 2019

In the world of genomics shaping precision medicine in oncology, the limiting factor is the time-to-sign-out of a fully interpreted molecular profile report. There are many components of the entire testing process that add to the turn-around time of each test. Many of these steps, such as sample prep, sequencing, and automated secondary analysis,…

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Variant Interpretation with VSClinical: Non-Small Cell Lung Cancer

Aug 20, 2019

With the increasing knowledge of mutations involved in cancer, it is imperative to have a tertiary analysis pipeline that provides users with the most up to date information on somatic mutations. VSClinical’s Cancer Add-On does just that and more; with this feature, users can investigate and report on SNVs, indels,…

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Variant Interpretation with VSClinical: Huntington’s Disease (HD)

Aug 12, 2019

Huntington’s Disease (HD) Background Huntington’s Disease (HD) is an autosomal dominant neurodegenerative disease that is caused by a mutation in the huntingtin (HTT) gene resulting in 36 or more CAG trinucleotide repeats in exon 1. Individuals affected by HD experience motor disorders including involuntary movements and poor coordination, cognitive impairments…

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Variant Interpretation with VSClinical: Congenital Myasthenic Syndromes (CMS)

Jul 26, 2019

Congenital Myasthenic Syndromes (CMS) History: Congenital Myasthenic Syndromes (CMS) are a group of rare hereditary conditions that can cause seizures, severe muscle weakness, respiratory problems, and potentially disabling weaknesses shortly after birth or early childhood (1). CMS is the result of abnormalities in acetylcholine proteins residing in the motor endplate…

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Variant Interpretation with VSClinical: Evaluation of Hypertrophic Cardiomyopathy

Jul 9, 2019

Hypertrophic Cardiomyopathy History It was December 9th, 1989, when one of Loyola Marymount’s strongest inside players, Hank Gathers, collapsed during the middle of a collegiate level basketball game against UC Santa Barbara. Measuring in at 6’7” and weighing 210 pounds, Gathers was diagnosed with exercise-induced ventricular tachycardia, or in layman’s…

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Clinical Variant Analysis for Cancer: Part V

Jul 2, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Detecting cancer at an early stage can make it much more treatable. Developing tests and making them clinically actionable is crucial to beat this disease. This eBook covers the state-of-the-art gene panel tests for cancer. Of course,…

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Limited-Time Offer for VSClinical’s Cancer Add-On

Jun 27, 2019

We are upgrading all VSClinical +Cancer Add-On purchases to a 15-months license! The individualized nature of tumors requires genomic testing for providing the best outcomes for patients. Next-Gen Sequencing enables the detection of small mutations, copy number changes, and common fusions affordably and with high precision. However, the interpretation of…

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Clinical Variant Analysis for Cancer: Part IV

Jun 25, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Somatic variants can manifest in different ways: There is a difference between the interpretation of germline and somatic variants. The former is exclusively focused on establishing the level of pathogenicity vis a vis a particular disease. In…

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Clinical Variant Analysis for Cancer: Part III

Jun 18, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants As described in my eBook “Genetic Testing for Cancer,” any bioinformatic pipeline for cancer ultimately calls variants based on the aligned reads that the sequencer generated. Variant calling is the process of reviewing a sequence alignment, typically…

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Clinical Variant Analysis for Cancer: Part II

Jun 13, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Analogous to the ACMG guidelines for germline mutations, the Association for Molecular Pathologists (AMP) has issued guidelines to assess and report on somatic variants. The key paper in this area was published by Li et. al (2017)…

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Clinical Variant Analysis for Cancer: Part I

Jun 11, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Precision Medicine uses genetic information from individual patients. This may include the following areas: Specifically, in the cancer space, data derived from Next-Gen Sequencing (NGS) is used to diagnose and prognose diseases, select a targeted therapy and…

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Variant Interpretation with VSClinical: Evaluation of an X-linked Recessive Mutation

May 21, 2019

Overview VSClinical enables users to evaluate variants according to the ACMG guidelines in a high-throughput fashion and obtain consistent results and accurate variant interpretations. This feature is tightly integrated into our VarSeq platform as well, and when paired together, users can evaluate NGS data and obtain clinical reports all in…

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Variant Interpretation with VSClinical: Clinical Example for Congenital Indifference to Pain

May 16, 2019

VSClinical provides a rapid-fire way to investigate any variant’s impact by following the ACMG Guidelines process for classification. We will be demonstrating this by looking at interesting examples of rare disorders and showcasing some evaluation steps users may deploy in their analysis. Our first example in this blog series is…

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Clinical Variant Analysis: Part V

Mar 5, 2019

Examples of Clinical Variant Interpretation with VSClinical In this chapter, I’d like to go through a few examples for variants that have been classified with the help of VSClinical. This will give you a better understanding of how data sources are actually being represented in the software and how those…

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Clinical Variant Analysis: Part IV

Feb 28, 2019

Rules for Combining Various Classification Criteria Now that we have a solid understanding of how the various criteria are meant to be applied, it’s time to look at how the evidence collectively leads to the clinical categorization of a variant. Let’s go through the rule framework for combining the various…

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