Search Results for: annotation

Our top 5 most visited blog posts

         March 24, 2015

Over the last year our blog has seen a boom in visits and of course, I became curious. What brings people to “Our 2 SNPs…”? So, I decided to take a look at the blog posts that our community find the most intriguing. Here are my findings: Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory… Read more »

Question and Answers: Cancer Gene Panels Webcast

         March 17, 2015

Last week we conducted a webcast on “Cancer Gene Panels”; you can find the recording here. 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 the way to… Read more »

Analyzing a Unique Family Structure in VarSeq 1.1.1

         March 12, 2015

I am constantly on the lookout for fun or interesting datasets to analyze in SVS or VarSeq and recently came across a study looking into inherited cardiac conduction disease in an extended family (Lai et al. 2013). The researchers sequenced the exomes from five family members including three affected siblings and their unaffected mother and an unaffected child of one… Read more »

What TriCon 2015 Foreshadows for Clinical Genomics

         February 25, 2015

I spent a very eventful week at the Molecular TriCon in downtown San Francisco, and have been pondering the very clear trends that emerged by attending the clinical and NGS focused talks. Cancer gene panels make sense economically and as “massively parallel” tests to inform therapy, but they are bound to get more complex. Liquid biopsies of circulating tumor DNA… Read more »

Q&A Surrounding Population-Based DNA Variant Analysis

         February 17, 2015

Last month, Dr. Bryce Christensen presented Population-Based DNA Variant Analysis via webcast. The webcast reviewed the fundamentals of population-based variant analysis and demonstrated some of the tools available in SVS for analysis of both common and rare variants such as the SKAT-O method, as well as other functions for annotation, visualization, quality control and statistical analysis of DNA sequence variants. Here… Read more »

Tri-Con 2015 – just 5 days away!

         February 10, 2015

In just 5 days, the 22nd International Molecular Medicine Tri-Conference (Tri-Con) will kick off in San Francisco. This year, Tri-Con will offer over 3,000 attendees 6 symposia, over 20 short courses, and 17 conference programs focused on drug discovery, genomics, diagnostics, and information technology surrounding, molecular medicine. Both Dr. Andreas Scherer, CEO of Golden Helix and Gabe Rudy, our Vice President of… Read more »

SVS, Population Genetics, and 1000 Genomes Phase 3

         January 27, 2015

One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes project for some examples.

In Pursuit of Longevity: Analyzing the Supercentenarian Whole Genomes with VarSeq

         January 13, 2015

If you haven’t been closely watching the twittersphere or other headline sources of the genetics community, you may have missed the recent chatter about the whole genome sequencing of 17 supercentenarians (people who live beyond 110 years). While genetics only explains 20-30% of the longevity of those with average life-spans, it turns out there is a number of good reasons… Read more »

VarSeq: A bioinformatics Swiss Army knife

         December 5, 2014

If you’ve seen the recent webinars given by Gabe Rudy and Bryce Christensen, you’ve no doubt been impressed by the capabilities of VarSeq when it comes to annotation and filtering. However, we sometimes forget that the power that enables all this complex analysis can also be used in more mundane tasks like VCF subsetting. And although these day-to-day tasks don’t… Read more »

6 Population Catalogs Compared with the ExAC 61,486 Exomes

         November 13, 2014

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 »

Don’t miss the VarSeq user experience webcast tomorrow!

         November 4, 2014

We are shortly approaching the public launch (November 5th!) of our first clinical product, VarSeq. We could not have predicted how well the market would accept VarSeq – but we couldn’t be happier! For those of you who have not yet seen our newest product in action, I invite you to register for tomorrow’s webcast: The Golden Helix VarSeq User Experience.

New Plugin for Ion Torrent Server

         October 21, 2014

Golden Helix is proud to announce the release of the Golden Helix GenomeBrowse Plugin for Ion Torrent server. The new plug-in enables adding selected BAM files from Torrent Server reports directly into GenomeBrowse. The BAM files remain on the torrent server and are streamed from the server on demand using your credentials. This feature allows GenomeBrowse users to visualize genomic… Read more »

ASHG Happenings

         October 8, 2014

It’s that time of year again. The mornings are chilly, the leaves are falling, and ASHG is right around the corner. This year will mark my very first ASHG and I am really looking forward to meeting some of the Golden Helix community! The team has been hard at work preparing for a great conference and I wanted to give you… Read more »

VarSeq: Making Variant Discovery and Gene Panels Easy

         September 29, 2014

Last week, our CEO Andreas Scherer announced our entrance into the clinical testing market with VarSeq. This week, I will be giving a webcast on Wednesday introducing this new tool and demonstrating its capabilities. (Register for the webcast) VarSeq’s focused purpose is making NGS gene testing and variant discovery efficient, scalable and accessible to users with a broad range of backgrounds and specialties. In this blog post, we will examine the use cases that VarSeq supports in more detail,… Read more »

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

         August 28, 2014

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying it was only 65 years from lift off at Kitty Hawk to the landing of a man on the moon…. Read more »

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

         August 14, 2014

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in fact, there is more complexity here than you ever really wanted to know about. Andrew Jesaitis covered some of this… Read more »

SVS 8.2 – New Capabilities and Features

         August 7, 2014

Earlier this year we completed the marriage of SVS and GenomeBrowse. When we released Version 8 of SVS we completed a major engineering task. A lot of things under the hood of both products had been changed to create a seamless experience for our users. The new and improved SVS platform is based on a technology stack that allows us… Read more »

Have you ever had a bad experience with a VCF file?

         August 5, 2014

“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of… Read more »

New MM-KBAC Method Explained

         July 29, 2014

Last month, June 2014, we announced a new method that Golden Helix developed–the soon to be available MM-KBAC. MM-KBAC, or Mixed Model Kernel Based Adaptive Clustering combines the KBAC method developed by Lui and Leal (2010) with a random effects matrix to adjust for relationships between samples. The KBAC algorithm takes a binary dependent variable and transformations are used to convert… Read more »

The added value of GenomeBrowse

         July 17, 2014

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data. GenomeBrowse allows a user to sift through vast amounts of genomic data, and make it easy to focus on a single part… Read more »