Golden Helix Newsletter

Variant Annotation
Introducing Phenotype Gene Ranking in VarSeq
by Dr. Andreas Scherer,
President & CEO

Personal genome sequencing is rapidly changing the landscape of clinical genetics. With this development also comes a new set of challenges. For example, every sequenced exome presents the clinical geneticist with thousands of variants. The job at hand is to find out which one might be responsible for the person's illness.

In order to reduce the search space, clinicians use various methods to filter out noise. Case-cohort analysis or sequencing additional family members can also improve diagnostic accuracy by eliminating variants that are present in non-carriers that are also present in the cases. There have been a vast amount of algorithms and filters developed for those scenarios.
Continue reading »

Supercentenarian Variant Annotation: Complex to Primitive
by Gabe Rudy, VP of Product & Engineering

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for annotation and filtering.

Well, we just published the track last week, and I'm excited to share some of the details involved in its making. Continue reading »

2nd Annual Abstract Challenge Winners
by Dr. Andreas Scherer, President & CEO

This year's abstract challenge was another great success. We received over 30 submissions and topics ranged from GWAS to RNA Seq to exome sequencing, and the list goes on. With so many excellent submissions this year, we chose 4 winners, with a tie for 3rd place.

Our first place winner is Dr. Sergey Kornilov, a Postdoctoral Associate in the Child Study Center at Yale University's School of Medicine. Kornilov is part of the EGLab which performs research and clinical services focused on behavioral and molecular genetics. His submission focused on the genetic basis of developmental language disorder in a geographically isolated Russian-speaking population. Kornilov will present his work to the Golden Helix community in October and will receive a new Dell laptop as well as a free license of both SVS and VarSeq.Continue reading »

What TriCon 2015 Foreshadows for Clinical Genomics
by Gabe Rudy,
VP of Product & Engineering

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 (ctDNA) have the potential to impact how we conduct clinical trials, build early detection regiments and monitor for recurrence of cancer.
  • Clinical Exomes have excellent diagnosis yields, but whole genome sequencing provides a better exome and is close to price competitive.
Continue reading »

Variant Annotation
Analyzing a Unique Family Structure in VarSeq 1.1.1
by Ashley Hintz, Field Application Scientist

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 of the siblings. I'm going to take you through how I was able to analyze, annotate and filter this unique family structure in VarSeq.Continue reading »
   Latest Webcast
Cancer Gene Panels
Cancer is a leading cause of death in developed countries. In this webcast Dr. Andreas Scherer will explain how personalized medicine can transform our approach to fighting this disease. He will also discuss current roadblocks and diagnostic challenges, and the pivotal role of Next Gen Sequencing to overcome these challenges.

The webcast will inform about best practices to design and implement a cancer testing pipeline: from sample preparation, to sequencing, to secondary and tertiary analysis of sequencing data. The goal is to rapidly identify clinically actionable data that allows an oncologist to quickly determine the best available treatment options.
View recording »

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About Golden Helix
Golden Helix has been delivering industry leading bioinformatics solutions for the advancement of life science research and translational medicine for over 16 years. Our innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from microarrays and next-generation sequencing. With our solutions, hundreds of the world's top pharmaceutical, biotech, and academic research organizations are able to harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine. Golden Helix products and services have been cited in over 850 peer-reviewed publications.