Category Archives: Bioinformatic support

Between Two Bases: Coordinate Representations for Describing Variants

Have you ever scratched your head when looking up a variant and it seems like the number you have for its position is one off from what it looks like in the file or database? You may be running into the dreaded world of 1-based versus 0-based coordinate representation! If it’s any consolation, I can promise that all the bioinformaticians… Read more »

Accurate Annotations: Updates to the NHLBI Exome Sequencing Project Variant Catalog

Since its early release in early 2012, the population frequencies from the GO Exome Sequencing Project (ESP) – from the National Heart, Lung and Blood Institute (NHLBI) have been a staple of the genomic community. With the recent release of ExAC exome variant frequencies, the ESP has been surpassed as the largest cohort of publicly available variant frequencies (by nearly… Read more »

Genetic Testing for Cancer

      Andreas Scherer    January 20, 2015    No Comments on Genetic Testing for Cancer

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 help us to understand mutations associated with cancer development and… Read more »

Analyzing Whole Exome, Large-n Cohorts in SVS

It’s come to my attention in recent weeks, through various customer interactions, that many are not aware of the fantastic functionalities that exist in SNP and Variation Suite (SVS) for large-n DNASeq workflows; this includes large cohort analyses with case/control variables. The data you’ll see below is the publically available 1kG Phase 1 v3 Exome sequences from 1,092 individuals with… Read more »

6 Population Catalogs Compared with the ExAC 61,486 Exomes

To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement. Basically, there were two types of talks at ASHG. Those that proceeded the official ExAC release talk and referred to it, and those that followed the talk and referred to it. Why is this… Read more »