Golden Helix Newsletter

 

NGS Tools and Formats for Secondary Analysis: A Primer
by Gabe Rudy, Vice President of Product Development NGS Tools and Formats

After the publication of my three-part series: A Hitchhiker's Guide to Next Generation Sequencing, we have had quite a few requests for more details on the file formats and programs involved in getting data ready for tertiary analysis. Sequencing service providers most likely will have a set of tools orchestrated into a secondary analysis pipeline to process the sequence data from the machine to the point of being deliverable for tertiary analysis. But there are good reasons to understand this pipeline yourself in more detail. For one, you may want to know what to expect or ask from a service provider, internal core lab, or collaborating bioinformatician. Or you may simply want to learn about the types of files produced by various pipelines and what that means for your tertiary analysis. Continue reading on "Our 2 SNPs" »

I Want a GPU for Computational Analysis! Which One Should I Get?
by Mike Thiesen, Computer Engineer

A GPU can produce an enormous boost in performance for many scientific computing applications. Since we announced the availability of SNP & Variation Suite's incorporation of GPUs to dramatically speed up copy number segmentation, we've received numerous inquiries on recommendations for what GPU to purchase. Unfortunately the technical terminology and choices can be a bit confusing. In this article I cut through the jargon and give helpful advice on what to consider when choosing a GPU for computational analysis. Continue reading on "Our 2 SNPs" »

 
   New Add-On Scripts
Access all scripts »


   SNP-ITS
Cancer Center Licenses SVS to Continue Performing Innovative Research
The University of Texas MD Anderson Cancer Center has licensed SNP & Variation Suite (SVS) for the sixth consecutive year as an integral part of their tool set for conducting research on the genetic factors linked to cancer.
Read more »

 


Recent Customer Success Highlights

New England Journal of Medicine
Risk HLA-DQA1 and PLA2R1 Alleles in Idiopathic Membranous Nephropathy
Stanescu, H et al.
University College London, UK
Read the article »

PLoS Genetics
Risk Alleles for Systemic Lupus Erythematosus in a Large Case-Control Collection and Associations with Clinical Subphenotypes
Taylor, K et al.
University of California San Francisco, California
Read the article »

PLoS ONE
The Ghrelin Signalling System Is Involved in the Consumption of Sweets
Landgren, S et al.
University of Gothenburg, Sweden
Read the article »

Psychiatric Genetics
Genome-wide association study of personality traits in bipolar patients
Alliey-Rodriguez, N et al.
University of Chicago, Illinois
Read the abstract »

 

Fertility and Sterility
Replication of association of a novel insulin receptor gene polymorphism with polycystic ovary syndrome
Goodarzi, M et al.
Cedars-Sinai Medical Center, Los Angeles, California
Read the abstract »

 

Birth Defects Research: Part A: Clinical and Molecular Teratology
Racial differences in gene-specific DNA methylation levels are present at birth
Adkins, R et al.
University of Tennessee Health Science Center, Memphis, Tennessee
Read the abstract »

BMC Medical Genetics
Comprehensive genetic assessment of a functional TLR9 promoter polymorphism: no replicable association with asthma or asthma-related phenotypes
Lange, N et al.
Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
Read the article »

American Journal of Medical Genetics Part A
Genetic dosage compensation in a family with velo-cardio-facial/DiGeorge/22q11.2 deletion syndrome
Alkalay, A et al.
Albert Einstein College of Medicine, Bronx, New York
Read the abstract »

International Archives of Allergy and Immunology
Possible Association of SLC22A2 Polymorphisms with Aspirin-Intolerant Asthma
Park, T et al.
Sogang University, Seoul, Korea
Read the abstract »

Journal of Dairy Science
Variants in the pregnancy-associated plasma protein-A2 gene on Bos taurus autosome 16 are associated with daughter calving ease and productive life in Holstein cattle
Wickramasinghe, S et al.
University of California, Davis, California

Pharmacogenetics and Genomics
Role of nucleoside transporters SLC28A2/3 and SLC29A1/2 genetics in ribavirin therapy: protection against anemia in patients with chronic hepatitis C
Doehring, A et al.
Johann Wolfgang Goethe-University Hospital, Frankfurt, Germany
Read the abstract »

Urologic Oncology: Seminars and Original Investigations
Apoptosis gene polymorphisms and risk of prostate cancer: A hospital-based study of German patients treated with brachytherapy
Meyer, A et al.
Hannover Medical School, Hannover, Germany

Psychiatric Genetics
Association between polymorphisms of TAL1 gene and schizophrenia in a Korean population
Bae, J et al.
Kyung Hee University, Seoul, Korea
Read the abstract »

PLoS ONE
Interactions of the Apolipoprotein A5 Gene Polymorphisms and Alcohol Consumption on Serum Lipid Levels
Yin, R et al.
Guangxi Medical University, Guangxi, China
Read the article »

European Journal of Neurology
Genetic variation in complement component C3 shows association with ischaemic stroke
Olsson, S et al.
University of Gothenburg, Sweden
Read the article »

Journal of Korean Neurosurgical Society
Association of Toll-Like Receptor 5 Gene Polymorphism with Susceptibility to Ossification of the Posterior Longitudinal Ligament of the Spine in Korean Population
Sung, W et al.
Kyung Hee University, Seoul, Korea
Read the article »

Biological Psychiatry
The Complement Control-Related Genes CSMD1 and CSMD2 Associate to Schizophrenia
Havik, B et al.
University of Bergen, Norway

Annals of the Rheumatic Diseases
Potential association of muscarinic receptor 3 gene variants with primary Sjogren's syndrome
Appel, S et al.
University of Bergen, Norway
Read the article »

BMC Medical Genetics
Parental ages and levels of DNA methylation in the newborn are correlated
Adkins, R et al.
University of Tennessee
Read the article »

Urologic Oncology: Seminars and Original Investigations
GSTT1, GSTM1, and CYP1B1 gene polymorphisms and susceptibility to sporadic renal cell cancer
Salinas-Sanchez, A et al.
Hospital and University Complex of Albacete, Spain

Urologic Oncology: Seminars and Original Investigations
Differential major histocompatibility complex class I chain-related A allele associations with skin and joint manifestations of psoriatic disease
Pollock, R et al.
University of Toronto, Ontario, Canada
Read the article »

Journal of Neurology
No evidence for an association between genetic variation at the SERPINI1 locus and ischemic stroke
Tjarnland-Wolf, A et al.
University of Gothenburg, Sweden
Read the article »


 
About Golden Helix
We are inspired by significance. Not only statistical, but technological, scientific, and personal significance. It's embodied in everything we and our customers do. And we believe the only way to achieve significance is by transcending the status quo. Every day we strive for extraordinary analytic and technological advancements that empower scientists around the world to pursue that which is truly significant: from uncovering the genetic causes of disease and transforming drug discovery to developing genetic diagnostics and advancing the quest for personalized medicine. To learn more about how we are accelerating the quest for significance visit www.goldenhelix.com.

 


Copyright 2000-2011 Golden Helix, Inc. All Rights Reserved.
Golden Helix, Inc. | 203 Enterprise, Blvd. | Bozeman, MT | 59718