A report from the World Congress of Psychiatric Genetics
Earlier this month, while much of the genetics community was scrambling to edit and print their posters for ASHG, I had the opportunity to attend WCPG, the World Congress of Psychiatric Genetics, in Boston. This was my second trip to WCPG and it is becoming one of my favorite events to attend. WCPG stands out to me as one of the largest conferences where the majority of content is reports of applied gene-finding activities. It seemed like almost every speaker told about the results of a GWAS or sequencing experiment. It is energizing to hear so many success stories about analysis projects that turned out well and informative to hear the cautionary tales about challenges encountered by others. It’s impossible to recount everything that I heard and learned, but I’ll try to share a few highlights and quotable quotes, mostly from the final day of the conference.
“Intriguing findings are for romance novels”
This juicy quote came from Patrick Sullivan during the plenary panel discussion on the future of psychiatric genetics. Continue reading
Hey everyone! It’s time once again for the illustrious ASHG – this year in Boston, MA. We are very excited to get to see all of our colleagues and friends and hear about what you’ve been up to.
This year we will have six in-booth (#618) demonstrations by Gabe Rudy, VP of Product Development, showcasing SVS 8.0:
- Identifying Candidate Functional Polymorphisms Using Trio Family Whole Exome DNA Data
(Wed at 11 am & Thurs at 1 pm)
- Making NGS Data Analysis Clinically Practical: Repeatable and Time-Effective Workflows
(Wed at 1 pm & Fri at 1 pm)
- Leveraging Collapsing Methods to Find Complex Disease Associations in Large-Scale NGS Data
(Thurs at 11 am)
- Exploring and Visualizing Somatic Mutations in Cancer Using GenomeBrowse
(Fri at 11 am)
You can also pick up one of our ever popular t-shirts after any of the above events. But beware: we always run out so get yours before they’re gone!
We are also for the second year sponsoring EA’s “Leave Your Fingerprint on the Cure” to benefit the Floating Hospital for Children. Stop by booth #944 to leave your fingerprint.
See you next week!
Last week, we presented a webcast on Workflow Automation in SVS. If you were unable to attend, a recording of it is on our website: http://www.goldenhelix.com/Events/recordings/making-ngs-data-analysis-clinically-practical/index.html
In this post I’ll respond to some of the questions we were unable to answer within the allotted time.
Will you provide a link for the software used in the webcast?
I used Golden Helix’s SNP & Variation Suite for the analysis portion of the webcast. You can request a free trial of the software here: http://www.goldenhelix.com/SNP_Variation/forms/svsevaluation.html.
I used GenomeBrowse for the visualization portion of the webcast. This tool is completely free and can be downloaded here: http://www.goldenhelix.com/GenomeBrowse/index.html#download.
Kellie Carey discussing her treatment with her doctor. Image by Jesse Neider for The Wall Street Journal
Just a few weeks ago, the case of Kellie Carey made it to the front page of the Wall Street Journal. Initially, her prognosis in 2010 was very dire. Three months. Lung Cancer.
As I write this article, Ms. Carey is still alive because they were able to prescribe a drug based on the results of sequencing her tumor. It turned out that Ms. Carey has one of at least 15 lung cancer variations, which were classified in the last decade using next-generation sequencing of tumors. Based on this knowledge, some major cancer centers are beginning to rethink their approach to treating the disease, and drug companies have begun the laborious process of creating drugs to specifically target one specific type of cancer.
According to the WSJ: “Doctors now talk about a ‘precision medicine’ approach in which those pinpoint drugs can treat tumors far more effectively than catchall chemotherapy.”
Ms. Carey is just one example. Here at Golden Helix, we are seeing this shift in our daily work as the latest research is now used more and more to diagnose diseases and find the best possible treatment for a particular patient. Clinicians and researchers are working hand in hand in a way that wasn’t previously possible. This trend is particularly evident in major cancer centers as well as children’s hospitals. While research may lead the way to clinical diagnosis, it is also the case that clinical data is reviewed by researchers to deepen our understanding of the cause and effect leading to a disease or trait. Continue reading
Presenter: Autumn Laughbaum, Biostatistician with introduction by Dr. Andreas Scherer, President & CEO
Date: September 10, 2013
Duration: 60 Minutes
Exploring next-generation sequence data requires an iterative process whereby a researcher can find a “needle in the haystack” that contributes to a particular disease or other phenotype. Once that needle has been found, a workflow can be established for analyzing other samples or to create a repeatable, time-effective process for clinical usage.
Yet, repeating a workflow that involves several different quality control, filtering, and analysis steps is burdensome and error-prone.
To solve this problem, we introduce custom workflow automation in SVS, which allows you to collapse dozens of steps into a few run-specific options. This click-and-go process saves an exponential amount of time while eliminating the inevitable user error that happens with tedious repetition and ensures that the exact same protocol is followed with each run, a critical requirement for use in the clinic.
Utilizing Identical Twins Discordant for Schizophrenia to Uncover de novo Mutations
We are living in exciting times – the reality of high-resolution microarrays and individual genome sequencing now offers renewed hope in the search for the causes of complex diseases. When this technology is combined with genetic relationships, individual sequences add unrivaled proficiency.
Our lab is located in London, Ontario, Canada at the University of Western Ontario, and our interest is in elucidating aspects of the underlying genetic mechanisms contributing to complex disease. The project I am working on focuses on the use of identical twins discordant for schizophrenia and their families to uncover de novo mutations that may contribute to one twin having the disease and the other not. Given the nearly equivalent genetic structure of identical twins, any difference between identical twins discordant for a disease will have a likelihood of being involved in disease pathology. Continue reading
Genotype imputation is a common and useful practice that allows GWAS researchers to analyze untyped SNPs without the cost of genotyping millions of additional SNPs. In the Services Department at Golden Helix, we often perform imputation on client data, and we have our own software preferences for a variety of reasons. However, other imputation software packages have their own advantages as well. This motivated us to perform some tests to assess certain performance features, such as accuracy and computation time, of a few common imputation software programs.
For this comparison, we tested three imputation softwares: BEAGLE, IMPUTE2, and Minimac. Imputation was performed both with and without pre-phasing the sample data with BEAGLE and IMPUTE2. Minimac is an implementation of the MaCH method that utilizes pre-phasing. We did not run MaCH without pre-phasing due to computational constraints. Pre-phasing is a technique that can significantly improve computation time with a slight accuracy trade-off by phasing the sample data prior to running imputation (as opposed to phasing the sample data during imputation). Continue reading
Presenter: Dr. Bryce Christensen, Statistical Geneticist
Date: July 24, 2013
Duration: 60 Minutes
Golden Helix GenomeBrowse™, a free visualization tool for all types of sequence data, was introduced in 2012 to broad acclaim. Researchers using GenomeBrowse discovered a product far beyond the status quo with seamless navigation of sequence alignments and other genomic data using a fluid, fast, and intuitive interface that just “made sense.” Recent updates to GenomeBrowse, including support for VCF files and BED files and the ability to export tables of data extracted from viewable annotation tracks, further improved the product and created new synergy with Golden Helix SNP & Variation Suite (SVS).
This webcast will demonstrate the ability of GenomeBrowse to stream sequence alignment data from the Amazon Cloud, seamlessly transitioning between whole genome views and base-pair resolution in the context of both public and custom annotation tracks. We will show how GenomeBrowse can be used in conjunction with SVS to highlight false variant calls, confirm the inheritance pattern of putative functional variants, and aid in the interpretation of a variant’s impact. Examples of RNA-seq expression analysis, somatic variation in cancer, and family-based DNA-seq analysis will be included.
Humans are said to have a 0.1% rate of diversity, seemingly small, but actually quite significant when considering the future of personalized medicine. Gaining a deeper understanding of this genetic variance can help determine susceptibility to disease as well as medicinal response and outcomes.
One-third of human genetic diversity can be found in a likely contender for the birthplace of mankind: Southern Africa. Africa as a whole boasts over 2,000 distinct languages and cultures. The magnitude of ethnic diversity was a signal for Dr. Vanessa Hayes, Dr. Desiree Petersen, and their team at the J. Craig Venter Institute. For that reason, it has been their mission to make sure that African genomes are examined and represented sufficiently in databases worldwide. Continue reading
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 The Clinical Genome Conference – a newly-created conference by Cambridge Healthtech Institute. It was less than 100 people – very close-knit. And everyone was sort of feeling their way around. This year, it will be much much larger due to the popularity of the topic.
Jessica: What’s the subject matter like?
Gabe: When creating the content for 2013, the organizers realized they were trying to pack too much into a short amount of time with the different parts of translating NGS to the clinic. So they created two sections. The first is on advancements in science, bioinformatics, and interpretation. The second section on Thursday and Friday is about the business of running NGS labs and translating and providing NGS services in a clinical context. It will be exciting to see both sides get their own weight because there’s obviously no NGS market for the clinic if people are unable to figure out how to sustainably provide it. Continue reading