By Kevin Davies
March 13, 2008 | Just weeks after Illumina announced it had cracked the $100,000 threshold for sequencing a human genome, Applied Biosystems has sequenced a complete human genome sample using its new SOLiD next-generation sequencing platform, reportedly for less than $60,000.
Applied Biosystems says the $60,000 price tag refers to the cost of the reagents for the SOLiD platform's sample prep and ligation chemistry. It does not include staff, overhead, or instrument depreciation costs.
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| Kevin McKernan |
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"We believe this project validates the promise of next-generation sequencing technologies, which is to lower the cost and increase the speed and accuracy of analyzing human genomic information," said
Kevin McKernan, Applied Biosystems' senior director of scientific operations, who directed the work. "With each technological milestone, we are moving closer to realizing the promise of personalized medicine."
The DNA belongs to an anonymous Nigerian donor of the International HapMap Project. The data were deposited with the National Center for Biotechnology Information (NCBI) earlier this week. A spokeswoman said that plans are in progress to submit an article to a peer-review journal.
McKernan's group produced a total of 36 gigabases of sequence data -- the equivalent of 12-fold coverage -- in seven runs of the SOLiD system, reaching a maximum sequence output of an impressive nine gigabases in a single instrument run (see The Drive for the $1000 Genome, Bio-IT World, May 2007.)
The team used a paired-end library strategy using various DNA insert sizes. This helps produce the final assembly, given that each individual fragment sequenced is relatively short -- under 50 bases in length. Applied Biosystems also says that the inherent accuracy of SOLiD's two-base color encoding system resulted in almost 99.95 percent accuracy in distinguishing millions of naturally occurring polymorphisms, from artifacts and sequencing errors.
The sequence files are publicly available via the NCBI website. The trace files are available from the NCBI via FTP: ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000272
Alternatively, they can be tracked using the project name: SOLiD Human HapMap Sample NA18507 Whole Genome Sequence under accession number SRA000272. Subsets of data are available to software developers for research into new bioinformatics tools.
The sequence files are subdivided according to the SOLiD instrument in Beverly, Mass., that initially produced the sequence. McKernan's group names each of its instruments after a famous female scientist. The instruments contributing to this project were named Amelia, Barb, Clara, Florence, Joan and Liz.
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