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Abstract
A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing has improved the sensitivity of structural variant discovery. Here, we conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover a landscape of 132,312 nonredundant structural variants, of which 45.2% are novel. The identified structural variants are of high-quality, with an estimated false discovery rate of 3.2%. The concatenated length of all the structural variants is approximately 13.2% of the human reference genome. We annotate 1,929 loss-of-function structural variants affecting the coding sequence of 1,681 genes. We discover rare deletions in HBA1/HBA2/HBB associated with anemia. Furthermore, we identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease.
Highlights
A complete characterization of genetic variation is a fundamental goal of human genome research
Our study reveals the landscape of structural variants (SVs) in the Chinese population and provides insights into their roles contributing to phenotypes, diseases, and population adaptation
long-read sequencing (LRS) technology such as Oxford Nanopore Technologies (ONT) with high sequence error is more likely to lead to mismapping against the reference genome and increase the false discovery of SVs25
Summary
A complete characterization of genetic variation is a fundamental goal of human genome research. We conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease. While substantial progress has been made in identifying SNVs and InDels based on short-read sequencing (SRS) technologies, the discovery and genotyping of SVs have been hampered due to the limited power of SRS to detect SVs that occur in repetitive regions with complex structures, which are common[7]. We identified SVs related to human immunity to differentiate northern and southern Chinese populations. Our study reveals the landscape of SVs in the Chinese population and provides insights into their roles contributing to phenotypes, diseases, and population adaptation
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