Once upon a time, when I was working for one of my prior employers (you can guess which one it was as the company name started with an ‘I’), the offer was made to have 23andMe to do whole-genome genotyping of myself and my immediate family. It being 2007 or so, the cost was not unreasonable in terms of the ’employee discount’ (23andMe used the company’s equipment and microarrays to do the genotyping) and after thinking about it for a few minutes, I decided to decline the offer.
This past week I attended the Cambridge Healthtech Institute’s “Applying Next Generation Sequencing” meeting in Providence R.I. Attendance was down which is an indicator of the maturity of NGS technology, constrained travel budgets, or an oversupply of NGS conferences, and probably a combination of all three.
Way back in 1997 a company launched one of the first commercial expression microarrays. The company was Affymetrix, the technology was micro-lithography, and the excitement around this new technology was palpable in the days before even the Human Genome Project had been completed.
Every mother-to-be who has what is considered an ‘at-risk’ pregnancy is informed of the risks to the fetus of a genetic abnormality. ‘At-risk’ can involve a long list of medical conditions (diabetes or cancer for example) or poor health choices (illegal drug use or smoking). Yet a common cause of an at-risk pregnancy is age, having a child before the age of 17 or older than 35. In the US, no less than 750,000 are considered at-risk.
Immunology is a fascinating subject. Immense in its complexity, debilitating when the immune system malfunctions, our ability to fend off bacterial and viral infection, cancers of different types, and other foreign invaders is a remarkable biological capability.
The NIH estimates 24M Americans are affected with an autoimmune disorder, but that number rises to 50M when the definition is expanded from a list of 24 disorders to over 100 by the American Autoimmune Related Disease organization. It is the second highest form of chronic illness, arthritis being the most familiar to many.
A few weeks ago this paper appeared in Nature Biotechnology, “Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly”. It was the first publication of a startup company in San Diego called BioNano Genomics.
NanoString is a startup company that has commercialized a product called the nCounter™ system. It is able to take an RNA sample and look at the expression level of up to 800 genes per sample, and recent news indicates that it is in current preparation for an IPO.
Today I learned that Charles Lindbergh flew non-stop from New York City to Paris in 1927 as a result of a $25,000 prize put up by a hotel owner, Raymond Orteig, way back in 1919. Worth some $325K in 2012 dollars, the prize was renewed in 1924 when the technology was advanced enough so that winning it became feasible.
There is a lot of interest in what is the Next Big Thing in next-generation sequencing. The case can be made that the clinical application of NGS (either targeted sequencing or WES or WGS for cancer genomics) will be that growth driver, but I suspect it will be the next generation of next-generation sequencing.
This week a remarkable paper was published in Nature, called “Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells”. What makes it remarkable is the ability of this method to obtain rare variant phase information by changing the library preparation method. Until now to obtain completely phased individual genomes required a fair amount of laboratory manipulation.
Although the whole genome versus whole exome discussion was held previously, details around the methods of selecting out the whole exome have been not discussed (also called ‘targeted selection’), and the wide array of methods, costs, and effort required can be a rather complicated affair.
In previous posts I covered the basics of next-generation sequencing – library preparation, template preparation, and the sequencing methodology itself, whether by pyrophosphate detection, single base extension with reversible terminators, or probe addition by ligation. And single molecule sequencing’s attractiveness as a technology has been covered here, but here I’ll detail how the startup Pacific Biosciences does it’s magic. (For some additional commentary on the company and its prospects check here.)