This year’s abstract challenge was another great success. We received over 30 submissions and topics ranged from GWAS to RNA Seq to exome sequencing, and the list goes on. With so many excellent submissions this year, we chose 4 winners, with a tie for 3rd place.
Dr. Sergey Kornilov
Our first place winner is Dr. Sergey Kornilov, a Postdoctoral Associate in the Child Study Center at Yale University’s School of Medicine. Kornilov is part of the EGLab which performs research and clinical services focused on behavioral and molecular genetics. His submission focused on the genetic basis of developmental language disorder in a geographically isolated Russian-speaking population. Kornilov will present his work to the Golden Helix community in October and will receive a new Dell laptop as well as a free license of both SVS and VarSeq.
I spent a very eventful week at the Molecular TriCon in downtown San Francisco, and have been pondering the very clear trends that emerged by attending the clinical and NGS focused talks.
Cancer gene panels make sense economically and as “massively parallel” tests to inform therapy, but they are bound to get more complex.
Liquid biopsies of circulating tumor DNA (ctDNA) have the potential to impact how we conduct clinical trials, build early detection regiments and monitor for recurrence of cancer.
Clinical Exomes have excellent diagnosis yields, but whole genome sequencing provides a better exome and is close to price competitive.
The only constant is change: we all expect the FDA to say more about Laboratory Developed Tests (LDTs) and sequencing platform innovation to change the landscape for test developers.
TriCon 2015 was well worth the visit to San Francisco. The combination of extensive programming in conjunction with a large exhibition makes it a must-attend event for scientist and professionals in our industry and the conference seems to grow year over year.
This year, we paid a lot of attention to the Clinical Sequencing portion of the event. In this track we learned about the clinical utility of NGS analysis in areas such as Oncology, Non-invasive Prenatal Testing and Infectious Diseases.
A number of presenters covered the clinical relevance of leveraging circulating DNA not only for the initial diagnosis, but also the ongoing monitoring of patients going through cancer therapy. This was a great validation of our view of the market as we announced a strategic partnership with Fluxion Bio in this space on the first day of TriCon.
A few of our customers have published recently and I would like to take the time to both recognize them for their achievement and pass on their articles. Enjoy!
If you have recently published and we happened to miss your publication, please do let us know at firstname.lastname@example.org.
Last month, Dr. Bryce Christensen presented Population-Based DNA Variant Analysis via webcast. The webcast reviewed the fundamentals of population-based variant analysis and demonstrated some of the tools available in SVS for analysis of both common and rare variants such as the SKAT-O method, as well as other functions for annotation, visualization, quality control and statistical analysis of DNA sequence variants.
Here are questions generated by the attendees. Feel free to reach us at email@example.com if you have more questions.
Question: How does CMC combine rare and common variants and prioritize variants for follow up? Do you use same p-value for both?
Today, Golden Helix and Fluxion Biosciences announced a collaboration in a value-added reseller relationship. The relationship will bring the VarSeq software application to Fluxion’s global client base providing them with a method to study tumor DNA in the circulation. Fluxion is proud to offer the capability as it helps move them toward their goal of offering a complete sample-to-answer workflow for NGS profiling of cancer from a blood sample.
Fluxion is a leader in the molecular profiling of tumor cells using a routine blood draw, having commercialized the IsoFlux System for routine sequencing of circulating tumor cells (CTCs) using targeted cancer panels. This partnership will leverage the VarSeq software in order to provide IsoFlux customers with clinical analytic capabilities.
Golden Helix sees the analysis of blood samples for cancer diagnosis as a key area to advancing precision medicine and we are excited to support Fluxion Biosciences and their clients.
The full press release can be read on our website here.
Our Genomic Prediction webcast in December discussed using Bayes-C pi and Genomic Best Linear Unbiased Predictors (GBLUP) to predict phenotypic traits from genotypes in order to identify the plants or animals with the best breeding potential for desirable traits.
The webcast generated a lot of good questions as our webcasts generally do. I decided to begin to share these Q&A sessions with the community. If the questions below spark new questions or need clarification, feel free to get in touch with us at firstname.lastname@example.org.
Question: Does the program (SNP & Variation Suite (SVS)) allow fitting fixed effects in GBLUP?
Answer: The answer to that is, absolutely yes. There is an option to add additional covariates into the model, and any numeric or binary variable or categorical variable, can be accounted for in that manner.
Question: Is it possible to use several phenotypes in the analysis and get prediction based on a combination of those, potentially with specific weighting?
Answer: This is a bit more of a challenge. The best available option to take would be to incorporate those additional phenotypes as covariates.
In just 5 days, the 22nd International Molecular Medicine Tri-Conference (Tri-Con) will kick off in San Francisco. This year, Tri-Con will offer over 3,000 attendees 6 symposia, over 20 short courses, and 17 conference programs focused on drug discovery, genomics, diagnostics, and information technology surrounding, molecular medicine.
Both Dr. Andreas Scherer, CEO of Golden Helix and Gabe Rudy, our Vice President of Product & Engineering will be in attendance as well as giving a couple of talks and short course.
Dr. Scherer will present Bioinformatics of Cancer Gene Panels: Challenges to Creating Effective Testing Workflows on Wednesday, February 18th at 4:10 pm. The talk will address the transition of NGS to the clinic and the bioinformatic tools and best practices needed for providing clinically actionable results from gene panel tests.
Gabe Rudy will give the dinner course on Sunday, February 15th from 5:30-8:30 pm; Knowing Your NGS Analysis Upstream: Alignments and Variants. The course will take a hands on approach to covering the alignment and variant calling algorithms in use today and the implications of their performance on variant discovery and interpretation. In the course you can expect to learn: Continue reading
Today, we at Golden Helix announced our collaboration with PreventionGenetics as they prepare to implement the VarSeq software into their exome sequencing pipeline.
The VarSeq software will allow PreventionGenetics to offer an exome test by dramatically speeding up the analysis process. VarSeq will narrow down sequence data into gene(s) of interest based on inheritance patterns, facilitating the identification of clinically relevant variants based on DNA sequence. PreventionGenetics plans to release exome sequencing for clinical diagnostics by mid-2015.
We are extremely pleased that VarSeq will help PreventionGenetics realize their goal of offering exome testing and we look forward to serving the evolving needs in the clinical market. The full press release can be read on our website here or on GenomeWeb here.
Genotype imputation is a statistical technique for estimating sample genotypes at loci that were not directly assayed by sequencing or microarray experiments. There are several reasons why you might want to use imputation in a research study. For example:
- Improve call rates in GWAS by imputing sporadic missing genotypes
- Harmonize the data content from different GWAS genotyping platforms so that they can be analyzed together in meta-analysis or mega-analysis
- Increase density of genotype calls for fine mapping or to identify candidate causal variants at a susceptibility locus.
These are all important applications for imputation technology, and can make significant contributions to a successful study. There is also a fourth application often cited for imputation: