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whole-genome sequencing

Wednesday 28 March 2007

Whole genome sequencing provides the most comprehensive collection of an individual’s genetic variation.

With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodologies for whole genome sequencing.

There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. In the de novo assembly approach, sequence reads are compared to each other, and then overlapped to build longer contiguous sequences.

The reference-based assembly approach involves mapping each read to a reference genome sequence.

Sequencing

Video : Comparison of primary and metastatic acral melanoma by whole genome sequencing.

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See also

- genetic variation

- sequencing technologies
- human genome
- DNA sequencing

Links

- Next Generation Sequencing Technologies (Next-Gen)

References

- Whole genome sequencing. Ng PC, Kirkness EF. Methods Mol Biol. 2010;628:215-26. PMID: 20238084

- Targeted investigation of the Neandertal genome by array-based sequence capture. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S. Science. 2010 May 7;328(5979):723-5. PMID: 20448179

- Clinical assessment incorporating a personal genome. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB. Lancet. 2010 May 1;375(9725):1525-35. PMID: 20435227

- Challenges in the clinical application of whole-genome sequencing. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, Ashley EA, Greely HT. Lancet. 2010 Apr 29. PMID: 20434765

- Sequencing technologies - the next generation. Metzker ML. Nat Rev Genet. 2010 Jan;11(1):31-46. PMID: 19997069

- Whole-genome sequencing identifies Mendelian mutations. Swami M. Nat Rev Genet. 2010 May;11(5):313. PMID: 20414984

- Genetics of neurodegenerative diseases: insights from high-throughput resequencing. Tsuji S. Hum Mol Genet. 2010 Apr 22. PMID: 20413655 [Free]