Search results for “Cancer”

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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New eBook Release: Clinical Variant Analysis for Cancer

Jun 6, 2019

Applying AMP Guidelines to Analyze Somatic Variants Today, I am thrilled to share with you the launch of a brand new eBook titled “Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants”. We would happy to send you a complimentary copy which can be requested on…

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Genetic Testing for Cancer – New Version Release

Jun 5, 2019

Yesterday, I released a new version of my eBook, “Genetic Testing for Cancer – Third Edition”. We would be happy to send you one! To download a complimentary copy, please submit a request on our site here. In 1914, the German cytologist Theodor Boveri coined the phrase “Cancer is a…

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Processing Hereditary Cancer Panels in VarSeq: Webcast Q&A

Aug 16, 2018

Our “Processing Hereditary Cancer Panels in VarSeq” webcast was a great lesson for viewers to learn more about the functionality of our software. If you didn’t have a chance to join us for the live event, you can watch the recording on our site here. Q: What is the best…

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Annotation Education Series: Cancer Annotations

Oct 5, 2017

CIViC The Clinical Interpretations of Variants in Cancer, better known as CIViC, is an open access open source, community-driven web resource available to all VarSeq users. Nature Genetics published an article that states, “CIViC accepts public knowledge contributions but requires that experts review these submissions”. Fundamentally, the focus behind CIViC…

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Cancer Gene Panels Tutorial

Jun 13, 2017

VarSeq enables breakthrough discoveries in cancer diagnostics by supporting gene panel testing and whole exome and genome analysis. We wanted to share our Cancer Gene Panel tutorial which covers a basic gene panel workflow with an emphasis on adding, modifying and manipulating filter chains. This tutorial will start with creating a…

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Annotating Cancer Mutations with CIViC

Nov 15, 2016

While clinical assessments of germline mutations have been collected in ClinVar under the stewardship of the NCBI and the collaborate effort of many testing labs, the same type of resource has been missing for mutations that could informal clinical care in Cancer. Or at least, that is what I thought until…

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ICGC: The Next Generation Cancer Mutation Database Now Available

Apr 21, 2016

ICGC’s database is now available For quite a while, COSMIC has been synonymous with the catalog of “known somatic mutations”. It is the ClinVar of cancer mutations and invests heavily in “expert curation” (having human experts read papers and pull out references to published somatic mutations). But it turns out…

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Cancer eBook – 2nd Edition

Mar 10, 2016

In 1914, the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome”. At this time, his ideas were as equally revolutionary as they were highly contested. Fast forward. More than a hundred years later, Next-Generation Sequencing effectively permits a highly sensitive analysis of cancer cells.…

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Cancer Workflows in VarSeq

Feb 19, 2016

Wednesday, March 2nd 12:00 pm EST Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will…

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Question and Answers: Cancer Gene Panels Webcast

Mar 17, 2015

Last week we conducted a webcast on “Cancer Gene Panels”. We had some excellent questions which we answered during the webcast and a few more that we didn’t get to in the allotted time. Please find answers to those questions here: 1. Are Cancer Gene Panels just another stepping stone on…

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Genetic Testing for Cancer

Jan 20, 2015

In 1914 the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome”. At this time his ideas were equally revolutionary as they were highly contested. Fast forward. More than hundred years later, Next-Generation Sequencing effectively permits a highly sensitive analysis of cancer cells. It can…

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Dr. Folefac Aminkeng Saves Time and Increases Productivity with SVS to Study the Pharmacogenomics of Adverse Drug Reactions in Cancer Therapy

Oct 17, 2012

Dr. Folefac Aminkeng is a Postdoctoral Fellow at The Centre for Molecular Medicine and Therapeutics (CMMT) at the University of British Columbia in Vancouver, BC, Canada. He utilizes GWAS studies to identify single-nucleotide polymorphisms (SNPs) that might be associated with serious adverse drug reactions (ADRs) in cancer therapeutics. The field…

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Recent Publications on Asthma, Schizophrenia, Peripheral Neuropathy, Rheumatoid Arthritis, Alzheimer Disease, and Esophageal Cancer

Feb 17, 2011

As you may have guessed from the title of this post, we’ve had a lot of customers publishing in the first six weeks of 2011. We are always excited to hear about about our customers’ findings and how they were able to use SNP & Variation Suite to accelerate their…

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Recent Publications on Bladder Cancer, Schizophrenia, Childhood IgA Nephropathy, and Ancestry Markers

Nov 5, 2010

Recognition this month begins with Eric Londin at Coriell Institute for Medical Research for his publication in PLoS ONE: “CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins.” (Abstract below). Also recently published in PLoS ONE is Chiara Magri with Brescia University School of Medicine on her…

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Your Variant Knowledge Base

Apr 9, 2026

Getting the Most from Assessment Catalogs in VSWarehouse One of the most frequent questions from our customers is some version of: “How do we keep our team from re-evaluating the same variant every time it shows up in a new sample?” The answer, in nearly every case, is assessment catalogs and more…

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National Genome Projects are Foundational to Precision Medicine at Scale

Mar 26, 2026

Precision medicine has reached an inflection point. The science is proven, clinical relevance is clear, and the cost of genomic technologies continues to decline. What now determines impact is scale. National genome projects represent one of the most powerful mechanisms for translating genomic science into measurable population health outcomes. By…

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