Protocol to analyze population structure and migration history based on human genome variation data
Summary: We describe a protocol to integrate genome variation data from different datasets and explore the population structure and migration history of human populations. This protocol provides semi-automated scripts to perform and visualize the effect of variant filtering strategy on eliminating b...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722008085 |
| _version_ | 1828090975846662144 |
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| author | Zicheng Zhao Yinan Wang Zhe Zhang Shuai Cheng Li |
| author_facet | Zicheng Zhao Yinan Wang Zhe Zhang Shuai Cheng Li |
| author_sort | Zicheng Zhao |
| collection | DOAJ |
| description | Summary: We describe a protocol to integrate genome variation data from different datasets and explore the population structure and migration history of human populations. This protocol provides semi-automated scripts to perform and visualize the effect of variant filtering strategy on eliminating batch effects, principal component analysis, ancestry component analysis, historical population effective size inference, and migration and isolation analysis based on independent biallelic SNPs, genotype likelihoods, and haplotypes. The protocol can be adapted to variation data from other sources.For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T06:04:49Z |
| format | Article |
| id | doaj.art-faf451a040ad4d0fbe9aeadd91b09cf5 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T06:04:49Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-faf451a040ad4d0fbe9aeadd91b09cf52022-12-22T04:41:32ZengElsevierSTAR Protocols2666-16672023-03-0141101928Protocol to analyze population structure and migration history based on human genome variation dataZicheng Zhao0Yinan Wang1Zhe Zhang2Shuai Cheng Li3Department of Computer Science, City University of Hong Kong, Kowloon 999077, Hong Kong; Shenzhen Byoryn Technology Co., Ltd., Shenzhen 518000, ChinaPeking University Shenzhen Hospital, 1120 Lianhua Road, Shenzhen 518036, China; School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, ChinaDepartment of Cardiology, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), No. 79 Kanning Road, Zhuhai 519000, ChinaDepartment of Computer Science, City University of Hong Kong, Kowloon 999077, Hong Kong; Corresponding authorSummary: We describe a protocol to integrate genome variation data from different datasets and explore the population structure and migration history of human populations. This protocol provides semi-automated scripts to perform and visualize the effect of variant filtering strategy on eliminating batch effects, principal component analysis, ancestry component analysis, historical population effective size inference, and migration and isolation analysis based on independent biallelic SNPs, genotype likelihoods, and haplotypes. The protocol can be adapted to variation data from other sources.For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722008085BioinformaticsGenomicsComputer sciencesEvolutionary biology |
| spellingShingle | Zicheng Zhao Yinan Wang Zhe Zhang Shuai Cheng Li Protocol to analyze population structure and migration history based on human genome variation data STAR Protocols Bioinformatics Genomics Computer sciences Evolutionary biology |
| title | Protocol to analyze population structure and migration history based on human genome variation data |
| title_full | Protocol to analyze population structure and migration history based on human genome variation data |
| title_fullStr | Protocol to analyze population structure and migration history based on human genome variation data |
| title_full_unstemmed | Protocol to analyze population structure and migration history based on human genome variation data |
| title_short | Protocol to analyze population structure and migration history based on human genome variation data |
| title_sort | protocol to analyze population structure and migration history based on human genome variation data |
| topic | Bioinformatics Genomics Computer sciences Evolutionary biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722008085 |
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