Search results for “annotation”

Updated PhoRank with OMIM Phenotype Terms and Improved Rankings

Apr 12, 2017

In our latest VarSeq release, we updated our PhoRank algorithm with the ability to specify OMIM phenotype terms not present in HPO, as well as a general update to the algorithm to improve the results. In this post, we review the fundamentals of how PhoRank determines the ranking of genes…

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Springtime for SVS: Updates to PhoRank, Platform Support and Genotype Imputation

Apr 11, 2017

Recently, we added a natively supported Genotype Phasing and Imputation capability in SNP & Variation Suite 8.7.0. Since then we have had fantastic feedback and adoption as folks take advantage of the BEAGLE 4.0 and 4.1 algorithms from within their existing SNP GWAS and agrigenomic workflows. One piece of feedback…

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We’re heading to Phoenix for ACMG 2017

Mar 16, 2017

ACMG 2017 is just around the corner! We are halfway through March already and it’s just about time to head off to sunny and warm Phoenix, Arizona. While the temps have been mostly mild for the last few weeks in Montana, I bet those of you in the northeast are…

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Coming Soon! The genome Aggregation Database (gnomAD)

Mar 15, 2017

Ever since the MacArther Lab announced the new gnomAD browser at last year’s ASHG conference, we have had many requests from our customers to make this new variant frequency source available within both VarSeq and SVS. This new dataset includes variants obtained from 123,136 exome sequences and 15,496 whole-genome sequences.…

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Paying Attention to the Quality Fields in ExAC: A Case Study

Mar 7, 2017

In the past couple of weeks, the topic of the Filter and Quality fields in the popular ExAC population catalog has come up a number of times. It turns out that unlike the 1000 Genomes project, which decided to very heavily filter their variant list to only contain variants they…

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Adding RSIDs to your SVS marker mapped spreadsheet

Feb 14, 2017

In the new Genotype Imputation tool that is coming soon to SVS, allele encoding is an important part of matching data between the target and the reference panels. If the same platform provider is being used, then A/B encoding can be used. However, it’s better to use the Reference/Alternate allele…

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PhoRank in SVS: Gene Ranking for Your Research Genotypes

Feb 9, 2017

Since we released our Phenotype Gene Ranking algorithm in VarSeq, it has become a staple of the way people conduct their analysis. It allows for a combination of filtering with ranking to prioritize follow-up interpretations of analysis results. Our PhoRank algorithm will be available in our upcoming SVS release to…

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Clinical Reporting Made Easy

Feb 2, 2017

Join our upcoming webcast – Clinical Reporting Made Easy Wednesday, February 15th 12:00 pm EST Clinical labs need to be able to process samples down to a short list of variants and publish a professional report. VSReports helps scientists and clinicians alike create timely, actionable reports that can improve clinical…

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Massive Variant Boost to ClinVar & PubMed Citation Fields

Jan 24, 2017

It may have been easy to miss in the drum-beat of monthly annotation updates we do here at Golden Helix, but there are a couple of things that are very special about the January update to the ClinVar database: We added new fields including HGVS names of variants and citations…

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Utilizing VSReports in Your Clinical Workflow

Jan 12, 2017

Clinical labs need to be able to process samples down to a short list of variants and publish a professional report. VSReports helps scientists and clinicians alike create timely, actionable reports that can improve clinical decision making and streamline patient care by seamlessly incorporating the results of tertiary analysis into…

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Using Assessment Catalogs in your VarSeq workflow

Dec 15, 2016

Variant interpretation is an integral part of any workflow that results in some decisions being made about the validity and suspected functional impact of a variant in a given sample and their presenting phenotypes. The VarSeq Assessment Catalog functionality is designed to assist the VarSeq user in streamlining this process.…

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ExAC CNVs: The First Large Scale Public Exome CNV Variant Set

Dec 8, 2016

ExAC CNVs were released publicly with a recent publication, providing the full set of rare CNVs called on ~60K human exomes. While there are many public CNV databases out there, this is the first one that was derived from exome data, and thus includes both extremely rare and very small CNV…

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Exporting Data From VarSeq to Excel

Nov 17, 2016

True to its nature, VarSeq offers multiple data export options. You can export result tables from VarSeq to Text, VCF, a VarSeq annotation file and most importantly an XLSX (Excel) File. VarSeq’s Excel export options provide a lot of flexibility in the information that is exported and preserve the formatting of…

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Annotating Cancer Mutations with CIViC

Nov 15, 2016

While clinical assessments of germline mutations have been collected in ClinVar under the stewardship of the NCBI and the collaborate effort of many testing labs, the same type of resource has been missing for mutations that could informal clinical care in Cancer. Or at least, that is what I thought until…

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How To Annotate and Filter Variants in SVS

Oct 20, 2016

The new Annotate and Filter algorithm is now available with the release of SVS 8.6.0, see the release notes for full details on all new and updated features. To access this new functionality, you simply need to update your SVS installation to the new version. The update can be done…

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Big Data Webcast Q&A

Sep 22, 2016

Gabe Rudy’s webcast yesterday, Big Data at Golden Helix: Scaling to Meet the Demand of Clinical and Research Genomics, was a huge success with well over 300 registered. In today’s blog post, I wanted to recap the Q&A session with Gabe. If you missed the webcast, check it out! Question:  What is…

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Let There Be Genomes: Big Data Genomics Webcast Teaser

Sep 15, 2016

Big data is here, but fear not, you don’t need a Hadoop cluster to analyze your genomes or your cohorts of tens of thousands of samples! It turns out, for the kind of algorithms employed in variant annotation and filtering, running optimized local programs is often faster anyway. As we…

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FAQ: Creating Repeatable Clinical Workflows

Aug 18, 2016

Question: Now that I’ve added annotation sources for my sample, filtered down to a list of interesting variants, flagged those variants and generated a clinical report, can I save or copy the annotation sources and filters for use on another sample? Short Answer: Yes! Long Answer: VarSeq was created with…

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Our 5 Most Watched Webcasts

Jul 21, 2016

Every month hundreds of clinicians and researchers access the variety of free resources on the Golden Helix website. Our resource library hosts eBooks, webcasts and tutorials to keep the community apprised of new methods, informed on best practices and to help our customers get the most out of their software purchase.…

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Finding Rare Mutations at the Center for Rare Jewish Genetic Disorders

Jul 14, 2016

Since 1999, Bonei Olam has been providing large-scale funding for fertility treatment and research. The non-profit’s mission is to provide whatever means or resources necessary to help childless couples achieve the dream of parenthood. Today, it is recognized in the worldwide medical arena for its leadership role at the forefront…

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