| 1 | CAS Array:design and assessment of a genotyping array for Chinese biobanking显示文摘Background:Chronic diseases are becoming a critical challenge to the aging Chinese population.Biobanks with extensive genomic and environmental data offer opportunities to elucidate the complex gene-environment interactions underlying their aetiology.Genome-wide genotyping array remains an efficient approach for large-scale genomic data collection.However,most commercial arrays have reduced performance for biobanking in the Chinese population.Materials and methods:Deep whole-genome sequencing data from 2641 Chinese individuals were used as a reference to develop the CAS array,a custom-designed genotyping array for precision medicine.Evaluation of the array was performed by comparing data from 384 individuals assayed both by the array and whole-genome sequencing.Validation of its mitochondrial copy number estimating capacity was conducted by examining its association with established covariates among 10162 Chinese elderly.Results:The CAS Array adopts the proven Axiom technology and is restricted to 652429 single-nucleotide polymorphism(SNP)markers.Its call rate of 99.79% and concordance rate of 99.89% are both higher than for commercial arrays.Its imputation-based genome coverage reached 98.3% for common SNPs and 63.0% for low-frequency SNPs,both comparable to commercial arrays with larger SNP capacity.After validating its mitochondrial copy number estimates,we developed a publicly available software tool to facilitate the array utility.Conclusion:Based on recent advances in genomic science,we designed and implemented a high-throughput and low-cost genotyping array.It is more cost-effective than commercial arrays for large-scale Chinese biobanking. | Zijian Tian Fei Chen Jing Wang Benrui Wu Jian Shao Ziqing Liu Li Zheng You Wang Tao Xu Kaixin Zhou | 2023 | Precision Clinical Medicine2023，6，1： | 0 |
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