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新加坡三个亚洲族群的大规模全基因组测序结果

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发表于 2018-8-13 11:05 | 显示全部楼层 |阅读模式
Large-scale whole-genome sequencing of three diverse Asian populations in Singapore


Degang Wu et al.

bioRxiv preprint first posted online Aug. 11, 2018
https://www.biorxiv.org/content/early/2018/08/11/390070

Abstract:  Asian populations are currently underrepresented in human genetics research. Here we present whole-genome sequencing data of 4,810 Singaporeans from three diverse ethnic groups: 2,780 Chinese, 903 Malays, and 1,127 Indians. Despite a medium depth of 13.7×, we achieved essentially perfect (>99.8%) sensitivity and accuracy for detecting common variants and good sensitivity (>89%) for detecting extremely rare variants with <0.1% allele frequency. We found 89.2 million single-nucleotide polymorphisms (SNPs) and 9.1 million small insertions and deletions (INDELs), more than half of which have not been cataloged in dbSNP. In particular, we found 126 common deleterious mutations (MAF>0.01) that were absent in the existing public databases, highlighting the importance of local population reference for genetic diagnosis. We describe fine-scale genetic structure of Singapore populations and their relationship to worldwide populations from the 1000 Genomes Project. In addition to revealing noticeable amounts of admixture among three Singapore populations and a Malay-related novel ancestry component that has not been captured by the 1000 Genomes Project, our analysis also identified some fine-scale features of genetic structure consistent with two waves of prehistoric migration from south China to Southeast Asia. Finally, we demonstrate that our data can substantially improve genotype imputation not only for Singapore populations, but also for populations across Asia and Oceania. These results highlight the genetic diversity in Singapore and the potential impacts of our data as a resource to empower human genetics discovery in a broad geographic region.

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 楼主| 发表于 2018-8-13 11:06 | 显示全部楼层
本帖最后由 cpan0256 于 2018-8-13 11:08 编辑

Figure 2. Population structure of SG10K and 1KG3 samples.
(A) PCA of the SG10K and 1KG3 data. Proportion of variance explained by each PC is indicated in the axis label.

f2a.jpg
 楼主| 发表于 2018-8-13 11:10 | 显示全部楼层
(B) ADMIXTURE analysis of the SG10K and 1KG3 data (K=10). Each colored bar represents one individual and the length of each colored segment represents admixture proportion of an ancestral component. 100 unrelated individuals from each Singapore population were included in the analyses of (A) and (B).  (C) ADMIXTURE analysis of 4,446 unrelated individuals from SG10K (K=3 and K=7).  (D) ADMIXTURE analysis of 4,446 unrelated SG10K individuals together with South Asians and East Asians from 1KG3 (K=9).

f2bcd.jpg
 楼主| 发表于 2018-8-13 11:11 | 显示全部楼层
(E) Geographic distribution of the nine ancestry components in (D). Each pie chart represents the ancestry proportions averaged across individuals from the same population. Heterozygosity for each population was shown in the parentheses. Populations in 1KG3: ACB, African Caribbean; ASW, African American; ESN, Esan; GWD, Gambian; LWK, Luhya; MSL, Mende; YRI, Yoruba; CLM, Colombian; MXL, Mexican; PEL, Peruvian; PUR, Puerto Rican; CEU, Northern and Western European; FIN, Finnish; GBR, British; IBS, Iberian; TSI, Toscani; BEB, Bengali; GIH, Gujarati; ITU, Telugu; PJL, Punjabi; STU, Sri Lankan Tamil; CDX, Chinese Dai; CHB, Han Chinese in Beijing; CHS, Southern Han Chinese; JPT, Japanese; KHV, Kinh.

f2e.jpg
发表于 2018-8-13 13:25 | 显示全部楼层
本帖最后由 MNOPS 于 2018-8-13 13:27 编辑

没什么新东西,基本都是陈词滥调。北汉接近京族也不是不能理解的,毕竟越南北部曾经被中国统治了一千多年,且在越南的一份数据中也发现了7%的Q,很可能是秦汉时期南下带过来的。

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发表于 2018-8-13 13:31 | 显示全部楼层
另外某人一直不敢贴出来的鬼门洞和东亚其他人群的常染图片也被老永挖出来了,谎言总是有被攻破的那一天

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发表于 2018-8-13 14:28 | 显示全部楼层
没什么新东西,基本都是陈词滥调。北汉接近京族也不是不能理解的,毕竟越南北部曾经被中国统治了一千多年,且在越南的一份数据中也发现了7%的Q,很可能是秦汉时期南下带过来的。

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发表于 2018-8-13 14:29 | 显示全部楼层
另外某人一直不敢贴出来的鬼门洞和东亚其他人群的常染图片也被老永挖出来了,谎言总是有被攻破的那一天

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发表于 2018-8-13 17:01 | 显示全部楼层
本文发现了更多的SNP与INDELs,good~
不过ADM图做的太差,似乎是色弱+表达障碍症的结果,呵呵

非常有价值的是,文中提供的全球Fst数值图,可以比较清楚地看到东亚各族群之间的遗传距离,如下:


Fst-东亚-马来-墨西哥-2018新加坡.jpg

可以看到,与前不久本坛转发的中日韩东亚族群遗传距离的论文比较一致,中日韩傣京依然是聚合为东亚的大簇(本文没有提供北亚与东北亚的数据)。

值得注意的是,日本数据(估计应该是指本岛而不包括琉球)相对最接近北汉,但是北汉除了最接近南汉,其他族系最接近的却是京族而不是日本,这个倒是有点意思~~
发表于 2018-8-13 17:09 | 显示全部楼层
论文附件提供的新加坡闽粤琼省籍汉族的基因成分与距离蛮有意思的,拿上来给大家做一个看图说话的脑力游戏,呵呵

K7新加坡-闽粤琼-2018.jpg

Fst-闽粤琼-2018新加坡.jpg
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