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Whole Genome Sequencing

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Full Genomes has some news:

The new year is starting off with a brand-new test offering from Full Genomes: whole-genome sequencing.

As a whole-genome sequencing (WGS) product, this represents the most comphrehensive genetic analysis available today and greatly expands the scope of our product line. We have recently completed a pilot study and the results are impressive, leading us to now officially launch this as a standard product; this will supplement our existing Y Elite and Y Prime tests, which target the Y chromosome and are only applicable to males. By using Illumina’s groundbreaking HiSeq X next-generation sequencing platform, we are able to provide high-quality WGS results at a best-in-market sub-$2000 price for individual customers.

Details of results delivery are still being developed and refined, but we are currently set up to provide the following:

  • BAM file (roughly 50 GB)
  • variant summary reports from SnpEff and VEP
  • autosomal and chrX variant identification (as two VCF files):
    1. novel variants (annotated with SnpEff and VEP)
    2. results for a set of over 100 million known SNPs from dbSNP build 142
  • mtDNA sequence (as FASTA file)
  • Y-DNA analysis (for males)

In terms of the technical details of the underlying raw data, the sequencing produces:

  • 2 x 150 bp paired-end reads
  • approximately 30x average depth of coverage

Although Full Genomes is not providing any interpretation of autosomal and X chromosome results, the raw data are provided in a format compatible with a number of tools that provide the opportunity for in-depth analysis. Examples of currently-available online analysis tools include:

As with other Full Genomes products, this is intended for ancestry/research-use only, and should not be relied upon for medical or diagnostic purposes.

Interested customers can order the WGS product through the Full Genomes website here.

Happy SNP’ing!

The FGC Team

Readers are invited to put notes from other firms offering retail whole genome sequencing. I put quotations in the title since there will always be gaps in the genome because of limitations in the current technology. It’s important to emphasize that this is “30 x” coverage. So decent quality.

 
• Category: Science • Tags: Whole Genome Sequencing 
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Perhaps. The New York Times has a piece out reviewing the vogue for sequencing the genomes of children who have mysterious diseases. The numbers are what matters here I think:

A few years ago, this sort of test was so difficult and expensive that it was generally only available to participants in research projects like those sponsored by the National Institutes of Health. But the price has plunged in just a few years from tens of thousands of dollars to around $7,000 to $9,000 for a family. Baylor College of Medicine and a handful of companies are now offering it. Insurers usually pay.

Demand has soared — at Baylor, for example, scientists analyzed 5 to 10 DNA sequences a month when the program started in November 2011. Now they are doing more than 130 analyses a month. At the National Institutes of Health, which handles about 300 cases a year as part of its research program, demand is so great that the program is expected to ultimately take on 800 to 900 a year.

Experts caution that gene sequencing is no panacea. It finds a genetic aberration in only about 25 to 30 percent of cases. About 3 percent of patients end up with better management of their disorder. About 1 percent get a treatment and a major benefit.

It seems this is a floor in terms of the results outcome for these children, as some of them may receive better or more effective treatments in the future, because the specific nature of their disease is already known. Since most medical treatments today are marginal in effect these outcomes don’t surprise or depress me, and the price point is sure to come down. In the near future I imagine that everyone will have a whole genome sequence, and relevant information about your specific genetic profile in relation to the sea of biomedical literature constantly coming out may be sent to you in a drip, drip, fashion by a phone or web app.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Personal Genomics, Whole Genome Sequencing 
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The firm GenomeQuest has a blog, and on that blog they have a post, Implications of exponential growth of global whole genome sequencing capacity. In that post there are some bullet points with numbers. Here they are:

* 2001-2009: A Human Genome

* 2010: 1,000 Genomes – Learning the Ropes

* 2011: 50,000 Genomes – Clinical Flirtation

* 2012: 250,000 Genomes – Clinical Early Adoption

* 2013: 1 Million Genomes – Consumer Awareness

* 2014: 5 Million Genomes – Consumer Reality

* 2015-2020: 25 Million Genomes And Beyond – A Brave New World

Let’s transform these projections into charts.


genomeseq1

genomseq2

Of course GenomeQuest sells analytics tools for the tsunami of genomic data which they see cresting. Though if only 25,000,000 people have whole genome sequenced by the year 2020, I’m not sure if we’ll feel that it’s a “tsunami” of data at that point. I’m sure there would be plenty of stories about the “sequencing gap” between different communities, by class and race and what not. But what do you think about GenomeQuest’s projections?

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Genomics, Sequencing, Whole Genome Sequencing 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"