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AJHG: 100个马来西亚人的全基因组

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发表于 2016-5-3 09:26 | 显示全部楼层 |阅读模式
本帖最后由 Ryan 于 2016-5-3 15:55 编辑

Am J Hum Genet. 2013 Jan 10;92(1):52-66. doi: 10.1016/j.ajhg.2012.12.005. Epub  2013 Jan 3.


Deep whole-genome sequencing of 100 southeast Asian Malays.
Wong LP1, Ong RT, Poh WT, Liu X, Chen P, Li R, Lam KK, Pillai NE, Sim KS, Xu H, Sim NL, Teo SM, Foo JN, Tan LW, Lim Y, Koo SH, Gan LS, Cheng CY, Wee S, Yap EP, Ng PC, Lim WY, Soong R, Wenk MR, Aung T, Wong TY, Khor CC, Little P, Chia KS, Teo YY.


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AbstractWhole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.

http://www.cell.com/ajhg/abstract/S0002-9297%2812%2900639-8
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542459/
 楼主| 发表于 2016-5-3 10:05 | 显示全部楼层
Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.

Teo YY, Sim X, Ong RT, Tan AK, Chen J, Tantoso E, Small KS, Ku CS, Lee EJ, Seielstad M, Chia KS.

Genome Res. 2009 Nov;19(11):2154-62. doi: 10.1101/gr.095000.109. Epub 2009 Aug 21.
 楼主| 发表于 2016-5-3 10:06 | 显示全部楼层
PLoS Genet. 2014 May 15;10(5):e1004377. doi: 10.1371/journal.pgen.1004377. eCollection 2014.

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.
Wong LP, Lai JK, Saw WY, Ong RT, Cheng AY, Pillai NE, Liu X, Xu W, Chen P, Foo JN, Tan LW, Koo SH, Soong R, Wenk MR, Lim WY, Khor CC, Little P, Chia KS, Teo YY.



http://www.ncbi.nlm.nih.gov/pubmed/24832686
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