In a couple of short weeks, Gabe is headed off to TCGC in San Francisco where he will be giving part of a short course. He was super excited about it last year and is even more so this year. I sat down with him yesterday to find out why. Jessica: What’s TCGC? Gabe: Last year I got to attend… Read more »
Thanks to everyone for the great webcast yesterday. We had over 850 people register for the event and actually broke the record! Take that Bryce and Gabe! If you would like to see the recording, view it at: Mixed Models: How to Effectively Account for Inbreeding and Population Structure in GWAS. While preparing for this webcast, we chose to focus… Read more »
Last month, Bryce Christensen wrote a little about mixed models and their application in GWAS. He promised that this analysis would be available in SNP & Variation Suite (SVS) “soon,” but didn’t elaborate. We are now excited to announce that three mixed model methods are available in SVS: GBLUP, EMMAX, and MLMM! To help demonstrate their utility and when to… Read more »
Presenter: Greta Linse Peterson, Senior Statistician Date: Wednesday, June 5th, 2013 Time: 12:00 pm EDT, 60 minutes Abstract Population structure and inbreeding can confound results from a standard genome-wide association test. Accounting for the random effect of relatedness can lead to lower false discovery rates and identify the causative markers without over-correcting and dampening the true signal. This presentation will… Read more »
Thirteen years ago, Dr. Robert Kleta had never heard of a genome-wide association study (GWAS), let alone considered doing one. Now, Dr. Kleta and his colleagues at the University College of London regularly publish articles in The New England Journal of Medicine and other journals on the genetics of rare diseases and their associated phenotypes. States Kleta, “For rare diseases,… Read more »
Time goes by fast. With the completion of the Human Genome Project in 2003, scientists worldwide were trying to understand the cause and effect of variations in the genome as they relate to functionalities, traits and disease. Along the way, we at Golden Helix helped researchers analyze data, discover variations and draw conclusions. It turns out that the real bottleneck… Read more »
When researchers realized they needed a way to report genetic variants in scientific literature using a consistent format, the Human Genome Variation Society (HGVS) mutation nomenclature was developed and quickly became the standard method for describing sequence variations. Increasingly, HGVS nomenclature is being used to describe variants in genetic variant databases as well. There are some practical issues that researchers… Read more »
Presenter: Dr. Bryce Christensen, Statistical Geneticist and Director of Services Date: Wednesday, May 15th, 2013 Time: 12:00 pm EDT Abstract Next-Generation Sequencing analysis workflows typically lead to a list of candidate variants that may or may not be associated with the phenotype of interest. Any given analysis may result in tens, hundreds, or even thousands of genetic variants which must… Read more »
Recently, Dr. Christophe Lambert joined the esteemed Theral Timpson over at Mendelspod to talk a bit about the big picture of bioinformatics. This 37 minute podcast references a recent blog post by Christophe on Illumina competing with its customers, the notion that if the end user isn’t buying that no one is selling, and learning from our GWAS mistakes. One… Read more »
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… Read more »
A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics by authors Bjarni J. Vilhjalmsson and Magnus Nordborg. Population structure is frequently cited as a major source of confounding in GWAS, but the authors of the article suggest that the problems often blamed on population structure actually result from the environment… Read more »
Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented the webcast: Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics. (That link has the recording if you are interested in viewing.) 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… Read more »
In 2011, I was looking for my next move and happened to attend a lecture given by Gabe Rudy at Montana State University. I was immediately struck by his passion and intelligence about the field of bioinformatics. He ended his talk by mentioning that Golden Helix was hiring, and I decided to apply. During my interviews, I discovered that these… Read more »
Presenter: Khanh-Nhat Tran-Viet, MHA, Manager/Research Analyst II at Duke University Date: March 7, 2013 Time: 12:00 pm EST, 60 Minutes Abstract Technological advances in next generation sequencing provide clinicians and researchers with more effective methods to identify pathogenic gene mutations for heritable diseases. To date, the National Eye Institute Bank lists over 450 genes associated with eye-related disorders. Analytical processing… Read more »
My investigation into my wife’s rare autoimmune disease I recently got invited to speak at the plenary session of AGBT about my experience in receiving and interpreting my Direct to Consumer (DTC) exomes. I’ve touched on this before in my post discussing my own exome and a caution for clinical labs setting up a GATK pipeline based on buggy variants… Read more »
In a recent GenomeWeb article by Tony Fong, “Sequenom’s CEO ‘Puzzled’ by Illumina’s Buy of Verinata, Lays out 2013 Goals at JP Morgan,” Harry Hixson, Sequenom’s CEO, expresses puzzlement over why its major supplier, Illumina, is acquiring a Sequenom competitor in Non-Invasive Prenatal Testing (NIPT), and thus apparently competing with one of its major customers. In a JP Morgan interview… Read more »
Twenty-four new variants discovered, each conferring more than a 2-fold risk of developing ASD Date: January 29, 2013, Noon EST, 90 minutes Presenters: Dr. Hakon Hakonarson, Director of the Center for Applied Genomics, Children’s Hospital of Philadelphia Dr. Mark F. Leppert, Professor of Human Genetics at the University of Utah and Chief Science Advisor at Lineagen Dr. Michael Paul, President… Read more »
We are excited to let you know about new scripts to aid in filtering rows/columns and identifying unique values in a column, as well as two updated scripts. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed via an RSS reader, receive email updates, or see the… Read more »
As a senior studying statistics at Montana State University, I was fortunate to be granted the opportunity to intern with the development team at a local software company. I was even more fortunate when this internship turned into full-time employment after I graduated. Working on a team with extremely talented individuals, I realized the significant impact our company makes through… Read more »
Happy new year! We hope all of our readers, clients, and users had a great holiday season filled with friends and family! While Golden Helix did take a break from blogging in December, we’ve still been pretty busy bringing you new and exciting things. We’re pleased to announce the addition of genome maps and annotation tracks for two new plant… Read more »
