Candidate colorectal cancer predisposing gene variants in Chinese early-onset and familial cases

Table 3 Prioritization scheme for exome data analysis of all 23 patients

Type of prioritization filter	Remaining variants (n)
All variants	1106642
Coding region and canonical splice site variants after quality filtering (total ≥ 10 reads, ≥ 5 variant reads and ≥ 20% variant reads)	13819
Non-synonymous variants, canonical splice site variants	9833
Variants that result in alterations in protein function (protein truncation, splice site defects and missense mutations at highly conserved (phyloP ≥ 3.0) nucleotide positions.Not in in-house database and MAF ≤ 0.001 in dbSNPv138	44321
	2883
Variants in known CRC predisposing genes and genes likely to play a role in CRC development (MAF ≤ 0.001 in ESP and 700 control Chinese exome data sets)	61
Variants/genes validated by Sanger sequencing	39 (32 different variants in 23 genes)

¹Including 172 nonsense variants, 188 frame shift variants, 943 canonical splice site variants, 237 in-frame deletions, 191 in-frame insertions and 2701 missense variants with highly conserved (phyloP ≥ 3.0); In-house database: 1302 in-house analyzed exomes, mostly from European ancestry. MAF: Minor allele frequency; ESP: Exome Sequencing Project database (6503 exomes, http://evs.gs.washington.edu/EVS/); 700 control Chinese exome data sets: Chinese subjects with Han ancestry (Juan Tian and Zhi-Min Feng, BGI, personal communication).