Bryce Christensen

Admixture and Blaine Bettinger

BlainBettinger

Allow me to introduce you to Blaine Bettinger.  Blaine is a patent attorney who holds a PhD in Biochemistry with a concentration in genetics.  He is also a family history enthusiast who writes the Genetic Genealogist blog, where he gives commentary on applications of genomic science for advancing personal and family history research.  I first learned about Blaine last May when he announced that he was committing his genomic data to the public domain and challenged any interested parties to analyze it and tell him what they learned.  As a scientist, he was aware of the limitations of the technology, but was curious to know if anybody might find something surprising.  As an intellectual property lawyer, he expressed interest in the question of whether it was even possible to truly commit one’s genomic data to the public domain.  (Anybody who attended ICHG/ASHG in Montreal may have heard some of the debate about whether genomic research data belongs to the researcher, the study subject, the funding agency, or some other entity.)  I immediately downloaded the data with grand visions of what I might do with it, but set it aside due to other obligations and forgot about it until rediscovering it just a few weeks ago.

I contacted Blaine to ask him about his experience since posting his data.  He replied that he has yet to receive any real response to his challenge–a result which we both found very interesting in itself.  Why hasn’t he received a response?  Perhaps the reason is that the field of personal genomics is still in embryonic stages, and there just isn’t very much that we can do with SNP genotype data from a single genome.  Indeed, Blaine has already published analysis results very similar to everything that I considered doing with his data.  He posted information about his autosomal admixture from multiple tests, suggesting that he is between 84% and 98% European depending on the method used.  He posted his mitochondrial haplogroup (Native American maternal lineage) and Y haplogroup (continental European paternal lineage).  He posted Promethease reports that give insight into his susceptibility to a variety of traits based on published research.  For example, he may have reduced risk of rheumatoid arthritis, but increased risk of type-2 diabetes.  To me, family history research and determining disease risk seem like the most probable reasons for a person to pursue direct-to-consumer (DTC) genotyping services, and Blaine has covered those topics fairly well.  I was fascinated by the information he posted and decided to take a little bit of time to understand his results and see what else could be learned from his genotypes. Continue reading

Posted in General statistical genetics principles, Personal Genomics | Leave a comment
Christophe Lambert

Never Let the Important Become Urgent: A reflection on the genetics supply chain and our need to increase value to the end patient

Never let the important become urgent

The turning of the calendar from 2011 to 2012 has been a good time for me to reflect on the lessons of the year and make resolutions for the new one. It is also the opportunity to step back and look at some of the larger systemic trends in our field and think about whether we are doing as much as we can with genetics to accelerate the delivery of healthcare solutions to the patient. I’d like to tie together several threads in this article. The first is to pay homage to a man who has done more for me than any other in understanding the nature of reality, Eli Goldratt. Drawing from his lessons on systems and supply chains, I’ll then make some observations about our field’s own genetics supply chain and the consequences of not producing enough value for the end patient. Further, as 2011 marks the 40th year of the war on cancer, Goldratt’s death by the same can lead us to pause and reflect on our own vulnerability to disease and spur us to not just redouble our efforts, but to ask ourselves what we might do systemically to accelerate the translation of innovations in genetics to the clinic. Continue reading

Posted in Big picture | Leave a comment
Jessica Vionas

Can SVS Help Plant Genetics Researchers too? You betcha!

Dr. Raman Babu

Dr. Raman Babu is a Maize Molecular Breeder at the International Maize and Wheat Improvement Center (CIMMYT). Like his counterparts conducting human genetic research, Babu used to rely entirely on free, open-source tools to complete his work. Frustrated with continual crashes and technology that was developed in the pre-SNP era, Babu switched to SNP & Variation Suite (SVS) almost a year ago. Here’s a bit about his experience.

Jessica: Can you tell us a little about your research?

Babu: My job at CIMMYT is primarily focused on molecular marker technology to develop varieties of maize with improved traits that farmers can grow in their field. In maize we are particularly interested in drought tolerance, nitrogen use efficiency, nutritional traits such as pro-vitamin B and protein quality in terms of amino acid balance, and resistance to the most prevalent diseases in Africa, Asia, and Latin America. Continue reading

Posted in Customer success | Leave a comment
Greta Linse Peterson

New Plant/Animal Genomes and Annotation Tracks Now Available

Plant & Animal Genomes

Recently we have expanded our annotation track offerings with new human variant frequency catalogs such as the 1000 Genomes Phase 1 Data. Of course, we also curate data for plant and animal genomes – some of which are currently available in our software and some of which will be available in our next release. In this blog post, I will fill you in on these new plant and non-human genomes and what to look for in the near future for annotation tracks. Also, I encourage you to contact us if you are working with SNP & Variation Suite (SVS) and a genome not currently available in our software, in order to let us know what genome and annotation tracks are important to you and your research. Continue reading

Posted in News, events, & announcements, Plant & Animal, Support | 1 Comment
Jessica Vionas

Leaky Sprinklers and “The Future of NGS Market Study 2011”

Jessica and Ben's house in Bozeman, MT

Have you ever chosen to do something yourself instead of paying money for the alternative, when, in the long run, the alternative is not really that expensive? We all have, as we all have limited budgets. One particular example comes to mind in my own life.

My boyfriend, Ben, and I bought a house in April. Unfortunately, it wasn’t properly winterized last winter and the sprinkler system leaked. Ben and I decided we could fix it, and so Ben smeared sealant on the parts of the pipe that were dripping. He let it dry for two days before turning the water to the lawn back on. Continue reading

Posted in Big picture | Leave a comment
Jessica Vionas

Is NGS the Answer?

Is NGS the Answer?

While there is a lot of excitement in the industry about Next-Generation Sequencing, questions remain as to whether it will be “the answer” to the ails of the genetic research industry. I recently had the opportunity to sit down with three of Golden Helix’s thought leaders and ask a few questions about NGS – Gabe Rudy, Vice President of Product Development; Dr. Bryce Christensen, Statistical Geneticist and Director of Services; and Dr. Christophe Lambert, Chairman & CEO. Here’s what they had to say:

Jessica: Is the missing heritability going to be found in Next-Generation Sequencing (NGS) data?

Gabe: Maybe, maybe not. There has been the challenge in finding strong causal signals in single loci of common variants for awhile. So we are now looking for compound effects of multiple loci and aggregating to the level of genes. Or even taking a systems biology approach and looking for strong signals at functional units larger than genes and test some compound genetic signal. Another theory is that complex diseases may not be explained by common variants, but may actually be an aggregation of smaller or more private mutations that present similarly in the clinic.

Bryce: The consensus seems to be that causal variants for complex diseases can only be discovered with huge case/control studies, which is also the belief in GWAS. So we shouldn’t panic if early sequencing efforts don’t immediately answer the outstanding questions for all of the complex diseases we are studying. We need to be patient and let the science evolve. Continue reading

Posted in Big picture | Leave a comment
Greta Linse Peterson

Creating Annotation Tracks from 1000 Genomes Phase 1 Data

People

If you have ever worked with NGS variant data, you may have come to realize that the first task at hand is the seemingly simple categorization of your variants into two bins: known and novel.

Of course, if you’ve ever worked with NGS variant data, you may have also come to the realization that this step is more complex than it seems. It requires the important choice of how you define a variant as “known” or “common” and what the implications of that choice are for your analysis. You are not short on choices of sources for known variants from the venerable dbSNP archive to the clean-slate 1000 Genomes project. It was even mentioned at ASHG/ICHG this year that Complete Genomics intends to add a “globally diverse” panel of reference genomes to their current repository of 69 public genomes. Continue reading

Posted in How to's and advanced workflows | Leave a comment
Bryce Christensen

Sequence Analysis Methods Not Just for Sequence Data

Sometimes genetic anaylsis reaches a "dead end"

Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve in the past.  Whenever I make a breakthrough in one project, I find I want to abandon the current project and go apply the new approach to an old project to see if I can make progress where there was previously a dead end.  I think this is a common trait among analysts and even among scientists in general.  We are naturally curious and don’t like to leave any question unanswered.

It is therefore not surprising that whenever Golden Helix introduces new features in the SNP & Variation Suite (SVS) software package we immediately get questions from researchers who want to know how the features might apply to their specific situation, even if it may seem unrelated on the surface.  In recent months we have received numerous questions about how our new sequence analysis tools might apply to data from standard GWAS arrays.  This is a very interesting question, and there are numerous potential applications for sequence tools in GWAS data. Continue reading

Posted in Assessment of new methods, How to's and advanced workflows | Leave a comment
Jessica Vionas

Has it already been a year? The 61st Annual ASHG (and 12th ICHG)!

ashg2011-sticker

I can’t believe it’s that time again! Next week we are heading off to Montreal, Canada for the week of October 11-15 for the 2011 American Society of Human Genetics annual meeting, this year in conjunction with the 12th International Congress of Human Genetics. We are excited as ever to hear what everyone has been up to, how your studies are going, and the latest advancements in the field! Continue reading

Posted in News, events, & announcements | Leave a comment
Christophe Lambert

Influencing the Global Dialog on Healthcare

On September 16-17th, I attended the Asia-Pacific Economic Cooperative (APEC) Health Systems Innovation Policy Dialog in San Francisco. It was a stimulating opportunity to look at global healthcare concerns from the perspective of developing and developed economies. There was much opportunity to  dialog and frame the issues around transforming healthcare systems to meet pressing problems such as aging populations, the burden of non-communicable disease, regulatory harmonization, and the problem of rising healthcare costs with diminishing returns and more.

In the sphere of government and international relations, ideas and influence are the currency. APEC as a body operates mainly as a forum of ideas and provides a vehicle for harmonization of purpose across member economies. It has been described to me as being more on the leading edge of ideas than, say the World Trade Organization, particularly because member economies can openly talk over ideas without end products of treaties and binding resolutions in mind. The mindset shifts that occur at these meetings eventually percolate into public policy initiatives in individual nations and organizations such as the UN and the WTO. Continue reading

Posted in Big picture | Leave a comment