Andreas Scherer

Question and Answers: Cancer Gene Panels Webcast

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 whole exome/genome analysis?

Cancer gene panels answer a very targeted question. Is this tumor mutated in a gene that has a known association to cancer AND do we have a treatment option for this particular mutation? If so, the clinician can continue the work of finalizing the diagnosis and putting a treatment plan together. If not, then we are dealing with a case that requires a more research oriented focus. Along the same lines, the usage of a panel approach minimizes the issue of incidental findings.
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Ashley Hintz

Analyzing a Unique Family Structure in VarSeq 1.1.1

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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.

The original dataset was downloaded from the European Nucleotide Archive:  ENA Project PRJNA222575. The FASTQ files were aligned using BWA (Burrows-Wheeler Aligner) to generate BAM/BAI files, reads being 76bp paired-end. The five family members’ BAM files were given to GATK Unified Genotyper and variants were called across samples to recognize reference calls between samples that may be important for family variant analysis.
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Posted in Clinical genetics, How to's and advanced workflows | Tagged , , | 1 Comment
Cheryl Rogers

Recent Customer Publications

Several of our customers have published recently, using the SVS software and I wanted to share their work. Congrats to all!

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Andreas Scherer

Final thoughts on AGBT 2015

It was a great trip down to Florida this year. AGBT 2015 was an exciting event with lots of great presentations. For us in this tightly-knit community it is an excellent networking opportunity to catch up with existing clients and partners, but also to make new connections.

Now, it is impossible to reflect on all the great talks. We were wowed by excellent research and the most recent findings. AGBT 2015 had four days full of premium research content. I am sure we all had our favorites. Here is a short list of talks that I found very entertaining:
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Andreas Scherer

Introducing Phenotype Gene Ranking in VarSeq

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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.
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Andreas Scherer

2nd Annual Abstract Challenge Winners

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.

Dr. Sergey Kornilov

Dr. Sergey Kornilov

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.

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Gabe Rudy

What TriCon 2015 Foreshadows for Clinical Genomics

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.

  • The only constant is change: we all expect the FDA to say more about Laboratory Developed Tests (LDTs) and sequencing platform innovation to change the landscape for test developers.

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Andreas Scherer

TriCon 2015

TriCon 2015 was well worth the visit to San Francisco. The combination of extensive programming in conjunction with a large exhibition makes it a must-attend event for scientist and professionals in our industry and the conference seems to grow year over year. 

This year, we paid a lot of attention to the Clinical Sequencing portion of the event. In this track we learned about the clinical utility of NGS analysis in areas such as Oncology, Non-invasive Prenatal Testing and Infectious Diseases.

A number of presenters covered the clinical relevance of leveraging circulating DNA not only for the initial diagnosis, but also the ongoing monitoring of patients going through cancer therapy. This was a great validation of our view of the market as we announced a strategic partnership with Fluxion Bio in this space on the first day of TriCon.
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Cheryl Rogers

Recent Customer Success

A few of our customers have published recently and I would like to take the time to both recognize them for their achievement and pass on their articles. Enjoy!

If you have recently published and we happened to miss your publication, please do let us know at info@goldenhelix.com.

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Cheryl Rogers

Q&A Surrounding Population-Based DNA Variant Analysis

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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 are questions generated by the attendees. Feel free to reach us at info@goldenhelix.com if you have more questions.

Question: How does CMC combine rare and common variants and prioritize variants for follow up? Do you use same p-value for both?
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