CRISPR-based targeted haplotype-resolved assembly of a megabase region

Taotao Li, Duo Du, Dandan Zhang, Yicheng Lin, Jiakang Ma, Mengyu Zhou, Weida Meng, Zelin Jin, Ziqiang Chen, Haozhe Yuan, Jue Wang, Shulong Dong, Shaoyang Sun, Wenjing Ye, Bosen Li, Houbao Liu, Zhao Zhang, Yuchen Jiao, Zhi Xie, Wenqing Qiu () and Yun Liu ()
Additional contact information
Taotao Li: Fudan University
Duo Du: Fudan University
Dandan Zhang: Fudan University
Yicheng Lin: Fudan University
Jiakang Ma: Fudan University
Mengyu Zhou: Fudan University
Weida Meng: Fudan University
Zelin Jin: Fudan University
Ziqiang Chen: Fudan University
Haozhe Yuan: Fudan University
Jue Wang: Fudan University
Shulong Dong: Fudan University
Shaoyang Sun: Fudan University
Wenjing Ye: Fudan University
Bosen Li: Fudan University
Houbao Liu: Fudan University
Zhao Zhang: Fudan University
Yuchen Jiao: Chinese Academy of Medical Sciences and Peking Union Medical College
Zhi Xie: Sun Yat-sen University
Wenqing Qiu: Fudan University
Yun Liu: Fudan University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

Date: 2023
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DOI: 10.1038/s41467-022-35389-w

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