Volume 31, No 12, Dec 2021

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 31 Issue 12, December 2021: 1308-1310   |  Open Access

LETTERS TO THE EDITOR

The ChinaMAP reference panel for the accurate genotype imputation in Chinese populations

Lin Li^1,2,† , Peide Huang^3,† , Xiaohui Sun^2,† , Siyu Wang^2,† , Min Xu¹ , Sha Liu¹ , Zhimin Feng¹ , Qing Zhang^1,2 , Xiaoji Wang⁴ , Xiaole Zheng³ , Mengyao Dai² , Yufang Bi¹ , Guang Ning^1,2 , Yanan Cao^1,2,* , Weiqing Wang^1,*

¹Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, National Clinical Research Centre for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
²National Research Center for Translational Medicine, National Key Scientific Infrastructure for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
³BGI, BGI-Shenzhen, Shenzhen, Guangdong, China
⁴SJTU-BGI Innovation Research Center, Shanghai, China
^†These authors contributed equally: Lin Li, Peide Huang, Xiaohui Sun, Siyu Wang
Correspondence: Yanan Cao(caoyanan@vip.sina.com)Weiqing Wang(wqingw61@163.com)

Dear Editor,

The genotype imputation is an efficient and pivotal approach to estimate the unobserved genotypes in the genomic data from the single nucleotide polymorphism (SNP) genotyping arrays or whole-genome sequencing (WGS). The fine mapping of variants in the genome-wide association study (GWAS) could be critically improved by the imputation with an optimal reference panel based on the population-specific haplotypes.1 The significant progresses of imputation were recently achieved by large high-resolution reference panels, such as the 1KGP3 (1000 Genomes Project Phase 3, n = 2504),2 the UK10K (10,000 UK Genome Sequences, n = 3781),3 the HRC (Haplotype Reference Consortium, n = 32,470),4 TOPMed (Trans-Omics for Precision Medicine, n = 97,256)5 and the GAsP (The GenomeAsia 100 K Project, n = 1654)6 (Supplementary information, Table S1). The multi-ethnic 1KGP3 reference panel is most commonly used for the genetic studies of Asian populations. However, the European ancestry-dominant reference panels exhibited poor performance in the genotype imputation for Chinese and other East Asian populations.7,8,9 The number of well-imputed variants and imputation accuracy depend on the characteristics of the reference panel dataset, including the sample size, sequencing data quality and population composition. The limited Chinese samples restrict the imputation quality with current reference panels in Chinese population studies. Additionally, the insufficient sequencing depth of construction datasets could undermine the detection capacity of rare variants for the imputation. Therefore, a population-specific reference panel constructed by a large-scale, in-depth WGS dataset of Chinese populations could be essential for the accurate and comprehensive imputation of the genotyping array and sequencing data from Chinese individuals.9,10

https://doi.org/10.1038/s41422-021-00564-z

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