Protocol for genetic analysis of population-scale ultra-low-depth sequencing data
Summary: Non-invasive prenatal testing (NIPT) not only enables the detection of chromosomal anomalies in fetuses but also generates vast amounts of ultra-low-depth sequencing data, which can be leveraged for population genomic studies. Here, we present a protocol designed for massive ultra-low-depth...
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| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724007445 |
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| author | Jingyu Zeng Linxuan Li Ying Lin Xianmei Lan Xinyi Zhang Yingying Wang Mingzhi Liao Xin Jin Huanhuan Zhu |
| author_facet | Jingyu Zeng Linxuan Li Ying Lin Xianmei Lan Xinyi Zhang Yingying Wang Mingzhi Liao Xin Jin Huanhuan Zhu |
| author_sort | Jingyu Zeng |
| collection | DOAJ |
| description | Summary: Non-invasive prenatal testing (NIPT) not only enables the detection of chromosomal anomalies in fetuses but also generates vast amounts of ultra-low-depth sequencing data, which can be leveraged for population genomic studies. Here, we present a protocol designed for massive ultra-low-depth sequencing datasets. We detail the steps for data processing, quality control, and genotype imputation, followed by genome-wide association study (GWAS) and post-GWAS analyses. This protocol applies to a wide range of ultra-low-depth sequencing studies, extending beyond data from NIPT.For complete details on the use and execution of this profile, please refer to Xiao et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-0413132357e34a329acda24498ef56e3 |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-0413132357e34a329acda24498ef56e32025-01-18T05:05:14ZengElsevierSTAR Protocols2666-16672025-03-0161103579Protocol for genetic analysis of population-scale ultra-low-depth sequencing dataJingyu Zeng0Linxuan Li1Ying Lin2Xianmei Lan3Xinyi Zhang4Yingying Wang5Mingzhi Liao6Xin Jin7Huanhuan Zhu8College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; BGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; Corresponding authorBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, ChinaCollege of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, ChinaBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China; Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China; Corresponding authorBGI Research, Shenzhen 518083, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen 518083, China; Corresponding authorSummary: Non-invasive prenatal testing (NIPT) not only enables the detection of chromosomal anomalies in fetuses but also generates vast amounts of ultra-low-depth sequencing data, which can be leveraged for population genomic studies. Here, we present a protocol designed for massive ultra-low-depth sequencing datasets. We detail the steps for data processing, quality control, and genotype imputation, followed by genome-wide association study (GWAS) and post-GWAS analyses. This protocol applies to a wide range of ultra-low-depth sequencing studies, extending beyond data from NIPT.For complete details on the use and execution of this profile, please refer to Xiao et al.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/S2666166724007445BioinformaticsSequence analysisGeneticsGenomics |
| spellingShingle | Jingyu Zeng Linxuan Li Ying Lin Xianmei Lan Xinyi Zhang Yingying Wang Mingzhi Liao Xin Jin Huanhuan Zhu Protocol for genetic analysis of population-scale ultra-low-depth sequencing data STAR Protocols Bioinformatics Sequence analysis Genetics Genomics |
| title | Protocol for genetic analysis of population-scale ultra-low-depth sequencing data |
| title_full | Protocol for genetic analysis of population-scale ultra-low-depth sequencing data |
| title_fullStr | Protocol for genetic analysis of population-scale ultra-low-depth sequencing data |
| title_full_unstemmed | Protocol for genetic analysis of population-scale ultra-low-depth sequencing data |
| title_short | Protocol for genetic analysis of population-scale ultra-low-depth sequencing data |
| title_sort | protocol for genetic analysis of population scale ultra low depth sequencing data |
| topic | Bioinformatics Sequence analysis Genetics Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724007445 |
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