Search results for “annotation”

Streamlined Workflow for Identifying Candidate Functional Polymorphisms

Oct 4, 2012

Since Dr. Ken Kaufman gave his webcast on Identifying Candidate Functional Polymorphisms in SVS, we’ve been working with Dr. Kaufman to simplify and automate many of the steps in his workflow.  I touched on this in my last blog post, and I’m excited to report that with Ken’s help, we’ve…

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Announcing Technical Support Bulletins

Jul 20, 2012

Last month I was inspired to create a new way to keep our customers apprised of the latest information on Golden Helix software without cluttering inboxes and overwhelming our blog. I happened to receive a link to an article for one of Illumina’s bulletins and realized that was exactly what…

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My 23andMe Trio Exomes Arrived: Sneak Peek

Jul 18, 2012

There is nothing cooler than having something arrive that you have been excitedly waiting for: last week I got an email notification that my 23andMe exome results were ready. Actually, I got 3 emails that my exome results were ready. You see, I lucked out. It all began two years…

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What is Bioinformatic Filtering?

Jun 29, 2012

Recently I gave a presentation on bioinformatic filtering: the process of using quality scores, annotation databases, and functional prediction scores to intelligently and quickly reduce your variant search space. In this webcast, I mention that filtering is something we have been doing for a long time, and that there are…

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New Technical Support Bulletins (Forthcoming!), and a Known Bug with Filter Samples by Call Rate

Jun 27, 2012

As Product Quality Manager, I have been spending quite a bit of time lately thinking about the best way to communicate with our Golden Helix customers with regards to product quality and customer support issues. Most of our customers at this point have already seen several emails from me this…

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Why You Should Care About Segmental Duplications

Jun 6, 2012

My work in the GHI analytical services department gives me the opportunity to handle data from a variety of sources.  I have learned over time that every genotyping platform has its own personality.  Every time we get data from a new chip, I tend to learn something new about the…

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Guest Post: Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS

May 16, 2012

I’m a huge supporter of the Free and Open Source Software movement. I’ve written more about R than anything else on my blog, all the code I post on my blog is free and open-source, and a while back I invited you to steal my blog under a cc-by-sa license. Every now and then,…

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Analyzing PacBio Data with SNP & Variation Suite

Mar 21, 2012

As most in the Golden Helix community are aware, SNP & Variation Suite (SVS) can handle all sorts of data including files from Affymetrix, Illumina, Agilent, and Complete Genomics with its powerful data management capabilities. Announced in February, SVS is now part of the Pacific Biosciences Partner Program and has…

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Is NGS the Answer?

Nov 9, 2011

While there is a lot of excitement in the industry about Next-Generation Sequencing, questions remain as to whether it will be “the answer” to the ails of the genetic research industry. I recently had the opportunity to sit down with three of Golden Helix’s thought leaders and ask a few…

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Sequence Analysis Methods Not Just for Sequence Data

Oct 12, 2011

Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve in the past.  Whenever I make a breakthrough in one…

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Wondering what SVS can do for a PhD student? Just ask Sander.

Sep 14, 2011

Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s…

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Marker Map Manipulation Improvements in SVS 7.5

Aug 31, 2011

Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5.  Have you ever wanted to view annotation data next to marker map data?  Or expand the current marker map with spreadsheet data to create a custom map?  SVS 7.5 features two new functions…

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SVS 7.5 Now Available!

Jul 28, 2011

More powerful rare variant analysis and visualization techniques We are proud to unveil SNP & Variation Suite (SVS) 7.5! The fifth installment of SVS delivers the most powerful rare variant analysis tools with the latest advances in tertiary or “sense making” methods for DNA next-gen sequencing. This release also adds…

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Going Coast to Coast for the Latest NGS News

Jun 23, 2011

Last week I was able to attend two very interesting conferences about the latest developments in the analysis of sequence data.  I started the week in San Diego at the Illumina iDEA Conference and finished it in Philadelphia at Children’s Hospital of Philadelphia’s (CHOP) Third Annual Next-Generation Sequencing Symposium.  The…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 2

Dec 9, 2010

When you think about the cost of doing genetic research, it’s no secret that the complexity of bioinformatics has been making data analysis a larger and larger portion of the total cost of a given project or study. With next-gen sequencing data, this reality is rapidly setting in. In fact,…

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Recent Publications on Type 2 Diabetic Retinopathy, Grapevine Flavor, Pulminary Function, and Pharmacogenetics Testing

Nov 30, 2010

Let’s kick off this month’s recognition with Audrey Papp and Wolfgang Sadee at Ohio State University for their work on “Flavopiridol Pharmacogenetics: Clinical and Functional Evidence for the Role of SLCO1B1/OATP1B1 in Flavopiridol Disposition” just published in PLoS ONE. (All abstracts below.) Also in pharmacogenetics (albeit in mice) this month…

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Conference Report: International Genetic Epidemiology Society and Genetic Analysis Workshop

Oct 27, 2010

The week of October 10-16th was a busy time in our industry.  Hundreds of biostatisticians, genetic epidemiologists, and statistical geneticists gathered in Cambridge, MA for the annual conference of the International Genetic Epidemiology Society (IGES) on October 10-12, followed by the biennial Genetic Analysis Workshop (GAW) on October 13-16.  I…

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Best Practices for Incorporating Public Genotype Data in Your Study

Oct 12, 2010

The Golden Helix sales team recently came to me for recommendations regarding best practices for incorporating public controls in SNP GWAS.  It seems that there has been a surge of questions regarding this practice over the past few weeks from our customers.  Initially, I laughed at the irony of being…

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