Summary of the data sets included in the Han Chinese Genomes Database

Population samples

In the Han Chinese Genomes Database version 2.0 (PGG.Han 2.0), we designedly select and include only individuals of Han Chinese ancestry, particularly for imputation and GWAS in the Han Chinese population. All the participants are 18 years of age or older and contributed DNA to the project. The ancestry of participants is determined based on self-reported data and their genetic profiles. In the current release of the PGG.Han 2.0 database, we collect data of 137,012 individuals in total, including high coverage WGS data (n = 17,546), low coverage WGS data (n = 11,878), high coverage WES data (n = 5,002) and genotyping or partially imputed data (n = 102,586) With these more than 100K Han Chinese samples being whole-genome sequenced to high coverage (~30 – 80×), or medium coverage (~13.7×), low-coverage ~1.7, or whole-exome sequenced (>100×), or high-density genome-wide SNP genotyped or imputed, we constructed the multiple reference panels specific to the Han Chinese population, a.k.a., Han100K. See the description below and table 1 for more detailed information.

Available Data

Totally near 30,000 Han Chinese individuals with whole genomes sequenced using next-generation sequencing are archived in PGG.Han, including deep-sequencing data sets (~30 – 80×) (n=11,767) and a low-pass sequencing data sets (~1.7×, n=11,878). The deep-sequencing datasets include Han Chinese samples from 30 administrative divisions representing 28 dialects across China were collected; 2,780 samples were sequenced at a median depth (~13.7×) and obtained from the previous study (Wu et al., 2019). Moreover, 5,002 samples with whole-exomes were obtained from a previous study (Hao et al., 2021).

Whole-genome low-pass sequencing data

The genomes of 11,878 women Han Chinese were sequenced by the CONVERGE project as a control group for the investigation of major depressive disorders (Chiang et al., 2017). Although in a much lower coverage (~1.7×), this data set provides a catalog of 25,057,223 variants for the Han Chinese population and is also included in the PGG.Han.

Genome-wide SNP data

The high-density genome-wide SNP genotyped data of 102,586 samples are contributed by the collaborators of PGG.Han (see for the list of collaborators), which were collected from previous GWAS projects, only non-patient (control) are retained. Using all the whole-genome sequencing data of Han Chinese samples as reference data, the 102,586 samples are carefully imputed so that the final data set retained 8,056,973 genome-wide SNPs.

Whole exome sequencing

Data of 5,002 samples were provided by the HuaBiao project with high depth of target region (>100×) (Hao et al., 2021). Finally, 121,773,740 biallelic SNVs were left after quality control.

The fine-scale genetic structure of the Han Chinese population

The 100K Han Chinese individuals formed a distinct cluster from the surrounding groups including minority groups in China and other neighboring countries, suggesting the identity of Han Chinese people in terms of overall genetic make-up. On the other hand, genetic differentiation within the Han Chinese population is discerned and 6 sub-groups are identified, i.e., Northwest Han (NWH), Northeast Han (NEH), Central China Han (CCH), Southwest Han (SWH), Southeast Han (SEH), and South coast Han (SCH) (Gao et al., 2020). Overall, the main difference is between northern and southern subgroups, consistent with previous observations (Chen et al., 2009; Qin et al., 2014; Xu et al., 2009), while southern subgroups show higher divergence than northern subgroups. We further screened nested AIMs panels for detecting population structure and controlling population stratification in association studies. We provided high-quality individual-level variant data for future genotype imputation, population genetics a,nalysis and association studies. The reference panel provided here is expected to greatly facilitate current and future GWAS or candidate-gene based association studies in Han Chinese and related Asian populations.

Table 1. Summary of the data sets included in PGG.Han

Data Source Data Type Sample Size Sequencing Coverage Geographical Coverage Language Coverage References
The Han Chinese Genomes ProjectGenotyping102,586NA34 divisions28 dialectsXu et al., 2009
Gao et al., 2020
The Han Chinese Genomes ProjectWGS11,767~30×30 divisions28 dialectsPGG.Han
HuaBiaoProject WES5,002>100×31 divisions5 dialects(Hao et al., 2021)
CONVERGEWGS11,878~1.7×24 divisionsNA(Chiang et al., 2018)
SG10KWGS2,780~13.7×NANA(Wu et al., 2019)
NyuWaWGS2,999~26.2×23NA(Zhang et al., 2021)

WGS: Whole Genome Sequencing; NA: Not available.


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Research citing our database

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