A set of novel SNP loci for differentiating continental populations and three Chinese populations
In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Ch...
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PeerJ Inc.
2019-03-01
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| author | Xiao-Ye Jin Yuan-Yuan Wei Qiong Lan Wei Cui Chong Chen Yu-Xin Guo Ya-Ting Fang Bo-Feng Zhu |
| author_facet | Xiao-Ye Jin Yuan-Yuan Wei Qiong Lan Wei Cui Chong Chen Yu-Xin Guo Ya-Ting Fang Bo-Feng Zhu |
| author_sort | Xiao-Ye Jin |
| collection | DOAJ |
| description | In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research. |
| first_indexed | 2024-03-09T07:03:05Z |
| format | Article |
| id | doaj.art-4ca34587096248478ac16aeb72d415ec |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:03:05Z |
| publishDate | 2019-03-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-4ca34587096248478ac16aeb72d415ec2023-12-03T09:46:20ZengPeerJ Inc.PeerJ2167-83592019-03-017e650810.7717/peerj.6508A set of novel SNP loci for differentiating continental populations and three Chinese populationsXiao-Ye Jin0Yuan-Yuan Wei1Qiong Lan2Wei Cui3Chong Chen4Yu-Xin Guo5Ya-Ting Fang6Bo-Feng Zhu7Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, ChinaKey laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, ChinaDepartment of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, ChinaKey laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, ChinaKey laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, ChinaKey laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, ChinaDepartment of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, ChinaKey laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, ChinaIn recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.https://peerj.com/articles/6508.pdfAncestry informative markersBiogeographical originsSNPChinese populationsContinental populations |
| spellingShingle | Xiao-Ye Jin Yuan-Yuan Wei Qiong Lan Wei Cui Chong Chen Yu-Xin Guo Ya-Ting Fang Bo-Feng Zhu A set of novel SNP loci for differentiating continental populations and three Chinese populations PeerJ Ancestry informative markers Biogeographical origins SNP Chinese populations Continental populations |
| title | A set of novel SNP loci for differentiating continental populations and three Chinese populations |
| title_full | A set of novel SNP loci for differentiating continental populations and three Chinese populations |
| title_fullStr | A set of novel SNP loci for differentiating continental populations and three Chinese populations |
| title_full_unstemmed | A set of novel SNP loci for differentiating continental populations and three Chinese populations |
| title_short | A set of novel SNP loci for differentiating continental populations and three Chinese populations |
| title_sort | set of novel snp loci for differentiating continental populations and three chinese populations |
| topic | Ancestry informative markers Biogeographical origins SNP Chinese populations Continental populations |
| url | https://peerj.com/articles/6508.pdf |
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