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After Publishing Korean Genome, Researchers Work on De Novo Assembly, Cancer Genome Sequencing


This article was originally published on June 4.

Scientists at Gachon University of Medicine and Science in Korea who last month published the first genome sequence of a Korean individual are working on a de novo assembly of the data. In addition, they have started to sequence the genomes of members of families as well as human gastric cancers, In Sequence has learned.

For their study, which was published in Genome Research last month (see In Sequence 6/2/2009), the researchers sequenced the genome of Seong-Jin Kim, the director of the Lee Gil Ya Cancer and Diabetes Institute at Gachon and the project leader, to almost 30-fold coverage, using paired-end reads generated on the Illumina Genome Analyzer.

Sung-Min Ahn, an assistant professor at the Lee Gil Ya Cancer and Diabetes Institute and the first author of the study, told In Sequence last week that the project took about eight months, including a "period of trial and error," and that the team completed generating the sequence data in February. Besides the Illumina Genome Analyzer used in this study, the institute has two Applied Biosystems SOLiD 3 instruments installed, he said.

Project costs totaled approximately $250,000, not including labor and instrument amortization, according to Ahn.

That cost is on the same order as other recent human-genome sequencing projects: for example, last fall, researchers at Washington University School of Medicine reported that the total cost of sequencing a cancer genome at approximately 30-fold coverage, and its normal control at about half that coverage, using unpaired Illumina reads, was $700,000, including labor, informatics, data storage, and instrument amortization. At the time, the WashU scientists predicted that their second cancer genome, sequenced with paired-end technology, would cost on the order of $200,000 in total (see In Sequence 10/14/2008).

Ahn told In Sequence that he and his colleagues started out in early 2008 to sequence the genome of the founder of the Gachon Gil Foundation, a woman, but that after releasing pilot data at the centennial conference of the Korean Medical Association, she "faced enormous objection from her friends and staff" over concerns that her genome information may reveal "potential health problems." As a result, the scientists switched over to sequencing Kim's genome.

In their paper, the researchers stated that his genome "will be further analyzed by the combination of conventional de novo genome assembly and targeted gap filling."
According to Ahn, they have identified a strategy for the de novo assembly but cannot release more information about the project at present.

In addition, he said, they have started to sequence an undisclosed number of human genomes as part of a family study and a gastric cancer genome sequencing project.

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