Golden Helix Newsletter

The State of NGS Variant Calling: DON'T PANIC!!
The State of NGS Variant Calling: DON'T PANIC!!
by Gabe Rudy, Vice President of Product Development

I'm a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of thousands or even millions of candidates. When these signals sit right in the genomic "sweet spot" of mappable regions with high coverage, you don't need fancy heuristics or statistics to tell you what the genotype is of the individual you're looking at. In fact, it gives us the confidence to think that at the end of the day, we should be able to make accurate variant calls, and once done, throw away all these huge files of reads and their alignments, and qualities and alternate alignments and yadda yadda yadda (yes I'm talking BAM files). But we can't. Continue reading »

Population Structure + Genetic Background + Environment = Mixed Model
by Bryce Christensen, Director of Services/Statistical Geneticist
The State of NGS Variant Calling: DON'T PANIC!!

A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics. Population structure is frequently cited as a major source of confounding in GWAS, but the authors suggest that the problems often blamed on population structure actually result from the environment and the genetic background of the study population. Continue reading »

Follow Along on an Analyst's Journey to Filter Whole Genome Data to Four Candidate Variants in SVS
by Greta Peterson, Product Quality Manager/Senior Statistician

Follow Along on an Analyst's Journey to Filter Whole Genome Data to Four Candidate Variants in SVS

Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented a webcast. In it, Khanh-Nhat highlighted tools available in SVS that might be under used or were recently updated. These tools were used in his last three filtering steps to bring down the number of variants from 1,900 to only 9. However, there were three filtering steps used before he got to these last three steps that were not covered as part of the webcast. Continue reading »
   Latest Webcast
Knowing Your NGS Upstream: Alignment and Variants


   Featured SVS Script
Select Rows from String of Values
Download » | Script repository »

Mendelspod Interview: Looking at the Big Picture of Bioinformatics
At the end of March, Dr. Christophe Lambert conducted an interview with Mendelspod discussing a range of topics including solving tough problems for a small market, the end user for bioinformatics, and Illumina competing with their customers.
Listen to the podcast » (37 mins)

Where will we see you next?
TCGC Annual Clinical Genome Conference
San Francisco, CA  |  Jun 25-28

Providence, RI  |  Aug 19-20

Chicago, IL  |  Sep 15-17

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Recent Customer Success Highlights

PLoS Genetics
Complex Patterns of Genomic Admixtrue within Southern Africa
Petersen, D et al.
J. Craig Venter
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A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe
Khrunin, A et al.
Russian Academy of Sciences
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PLoS Genetics
Fine Mapping for Weaver Syndrome in Brown Swiss Cattle and the Identification of 41 Concordant Mutations across NRCAM, PNPLA8 and CTTNBP2
McClure, M et al.
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About Golden Helix
Founded in 1998, Golden Helix is known for helping genetic research groups working with large-scale DNA-sequencing or microarray data overcome the frustration and challenges of bioinformatic roadblocks: delayed projects, lack of quality findings, and low productivity. By empowering researchers with highly effective software tools, world-class support, and an array of complementary analytic services, we refute the notion that analysis has to be difficult or time consuming. Golden Helix's flagship software product, SNP & Variation Suite (SVS), is an integrated collection of powerful data management, quality assurance, visualization, and tertiary analysis tools for genetic data. SVS is delivered in a user-friendly, scalable platform and is supported by a team of highly trained bioinformaticians, statistical geneticists, and computer scientists that together make advanced statistical and bioinformatic methods accessible to scientists of all levels.


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