TARGET-C genotyping data

The TARGET-C study is a large-scale, multicenter CRC screening randomized controlled trial (RCT) conducted in 6 cities of 5 provinces in China, which aiming to compare the feasibility, participation, yield and cost of colonoscopy, fecal immunochemical test (FIT), and risk-adapted strategies for CRC screening. This study was approved by the Ethics Committee of the National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, and registered in the Chinese Clinical Trial Registry (registration number: ChiCTR1800015506). All participants provided written informed consent.In the present study, we included participants who underwent colonoscopy at the baseline screening phase and provided qualified plasma samples (N=3173). Eligible subjects were genotyped using the Infinium™ Chinese Genotyping Array Bead Chip. 1000 Genomes Project Phase 3 data was used as reference for imputation. We first pre-phased the genotypes with SHAPEIT2 and then performed imputation using IMPUTE21. As for quality control (QC), SNPs were excluded based on the SNPs (i) on sex chromosomes, (ii) with call rates < 95%, (iii) with P value for Hardy Weinberg equilibrium (HWE) < 1.0 × 10-6, (iv) with minor allele frequency < 0.01. For QC of samples, we excluded those (i) with sample call rates < 95%, (ii) deviate ±3 standard deviation (SD) from the samples' heterozygosity rate mean value, (iii) with relatedness above a pi-hat threshold of 0.25, (iv) ±4 SD outliers identified by principal component analysis. Finally, a total of 7,895,576 SNPs and 2821 samples were included.