Bina Bloggers

Variant Standardization Utilizing Variant Normalization

Posted by Emre Colak on Apr 21, 2016 10:00:00 AM

The Bina AAiM software is designed to provide deeper insight into variants identified by next-generation sequencing. After uploading a vcf file to the software, variants are annotated against a number of databases that provide information such as predicted pathogenicity, disease association, population frequency, and more. While at small scale, the operation is usually a simple lookup in a text file or a database, performing this annotation for large datasets and at scale is a challenge. Further, due to the variability in the way variants are represented across data sources and VCF files, finding all matching variants requires careful standardization of how variants are represented. Variant normalization and lift-over to a consistent reference genome are two standardization steps that the Bina AAiM software applies in order to find the maximum number of matching variants, which we will explore in this blog post and the next.

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Topics: Bina Tools & Workflows, Bina Technologies, AAiM, structural variation, big data, standardization, ESP, deletion, ClinVar, normalization, VCF, dbSNP, whole genome

Assessing and Improving Accuracy of Next-Generation Sequencing Informatics. Watch Video!

Posted by Jenny Hsu on Apr 19, 2016 10:00:00 AM

Advancements in next-generation sequencing (NGS) technologies have produced massive number of short read sequences, making secondary analysis a challenging big data problem. In this seminar presented at Molecular Tri-Con 2016, Bina’s Senior Director of Bioinformatics, Hugo Lam, shared current approaches at Bina in assessing and improving the accuracy of NGS algorithms. Specifically, he touched on how Bina's research expanded the benchmarking toolset through the availability of a better gold set and a variant simulation and validation framework.

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Topics: Bina Technologies, Events & Conferences, Videos, VarSim, MetaSV, SomaticSeq, Data Challenges, huref, Molecular Med, Mutation Detection, NGS, Tri-Con, Presentation

AACR Poster Presentation: Gene-Specific Modeling for Somatic Mutations

Posted by Jenny Hsu on Apr 14, 2016 10:00:00 AM

The much anticipated AACR annual meeting aims to bring together basic, translational and clinical researchers in the field of cancer. To take place April 16-20 in New Orleans, Roche Diagnostics welcomes you to discover an array of cutting-edge technologies and to share your innovations in cancer research with us at booth #922.

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Topics: Somatic Mutation Detection, Bina Technologies, Events & Conferences, Cancer, Bioinformatics, Roche, AACR, genomics, Abstract, Poster, Presentation

Join Our Luncheon Seminar at Stanford Center for Genomics and Personalized Medicine

Posted by Jenny Hsu on Apr 12, 2016 10:00:00 AM

Bina is proud to be sponsoring a free luncheon presentation next week with the Stanford Center for Genomics and Personalized Medicine (SCGPM), where we will present our latest scientific advancements in next-generation sequencing analysis. Register and come hungry! 

TIME AND PLACE:

Tuesday, April 19, 2016 from 12:00 PM to 1:00 PM. James H. Clark Center Room S360

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Topics: Bina Technologies, Events & Conferences, personalized medicine, structural variation, genomics, MetaSV, NGS, SCGPM, Eventbrite, Stanford University

Beyond the N-of-Two: Strength in Numbers

Posted by Anoop Grewal on Apr 7, 2016 10:00:00 AM

In the previous series of posts, I’ve highlighted the clinical value gained from the first molecular diagnosis of a disease (part 1) and the increasing value as more cases come to light (part 2, part 3). But parents of rare disease sufferers have also found great emotional value in discovering their child, a rare disease sufferer, is not alone.

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Topics: structural variation, genomics, NGLY1, Exomes, phenotypes, PACS1, Sequencing, Rare Disease

Striving For Fewer Diagnostic Odysseys

Posted by Anoop Grewal on Apr 5, 2016 10:00:00 AM

The recurring theme for many rare disease sufferers and their families in the past has been one of a diagnostic odyssey. It’s difficult to imagine the parents’ anguish upon discovering their baby’s potentially severe condition, and then add to that the continual testing, a multitude of referrals from one specialist to the next, mounting medical bills, and a string of changing diagnoses each with their requisite treatment. One can only have deep empathy and admiration for what the family and the affected child endure, and the sacrifices they make.

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Topics: structural variation, genomics, Exomes, phenotypes, diagnostic odyssey, Sequencing, Rare Disease

With N-of-Two, Future Diagnoses Come Easier

Posted by Anoop Grewal on Mar 31, 2016 10:00:00 AM

In the previous post, I shared the riveting case of Bertrand Might, as the first known sufferer from a disease due to mutations in the NGLY1 gene, and how his father’s blog helped a researcher at Baylor, Matthew Bainbridge, realize that NGLY1 mutations were giving rise to his patient’s condition as well [1,2].

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Topics: structural variation, genomics, NGLY1, Mutation Detection, Exomes, phenotypes, Gene Identification, Rare Disease, OMIM

Bina Named Finalist for Bio-IT Best Practices Award

Posted by Jenny Hsu on Mar 29, 2016 10:00:00 AM

With Bio-IT World Conference & Expo approaching, one of the traditions that attendees and sponsors look forward to is the award ceremony that recognizes outstanding technology innovators and research collaborations. Last year Bina beat out numerous contenders and was crowned winner of the Best of Show Award for the Genetic Analysis category. This year we have our eye on the prize for the Best Practices Award, and are honored to be amongst the 17 finalists that were recently selected. Winners will be announced during the Bio-IT plenary session on April 6 at 9:30 am.

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Topics: Events & Conferences, BioIT, Bina, hg38, Exomes, Awards, Best Practices, AstraZeneca, NGS, TCGA, Finalist

Upon an N-of-Two in Exome Studies

Posted by Anoop Grewal on Mar 24, 2016 10:00:00 AM

First you have to get to N-of-one

Matt-and-Bertrand-Might-Sep-2013-small.png
Image Source

In the New Yorker article, “One of a Kind: What do you do if your child has a condition that is new to science?”[1], Seth Mnookin chronicles the life of the Mights family whose first son, Bertrand, was born in 2007 with a condition that evaded diagnosis until he was tested with clinical exome sequencing in 2012. Bertrand suffered from a disorder that left him with limited mobility, seizures and an inability to speak, among many other symptoms. The article describes the family’s odyssey - diagnostic odyssey and beyond - as a sufferer of a rare disease. At initial diagnosis, Bertrand appeared to be the first known individual whose disease was due to a mutation in the NGLY1 gene that codes for a de-glycosylation enzyme, resulting in barely detectable levels of the protein.

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Topics: NGLY1, Mutation Detection, Exomes, Sequencing, Rare Disease

Bio-IT World Conference & Expo, April 5-7

Posted by Jenny Hsu on Mar 22, 2016 10:00:00 AM

Looks like the annual Bio-IT World Conference & Expo may arrive just before the snow melts! To take place at the Seaport World Trade Center in Boston from April 5-7, the event is packed with 13 parallel tracks and 16 workshops with topics on trends in big data, IT informatics, cloud computing, security and privacy for biomedical research.

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Topics: Events & Conferences, Cancer, Bioinformatics, BioIT, big data, Bina, Luncheon, NGS

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