Copyright
©The Author(s) 2015.
World J Gastroenterol. Apr 14, 2015; 21(14): 4136-4149
Published online Apr 14, 2015. doi: 10.3748/wjg.v21.i14.4136
Published online Apr 14, 2015. doi: 10.3748/wjg.v21.i14.4136
Table 1 Clinical characteristics and family histories of 23 early-onset and familial colorectal cancer patients
Patient ID | Gender | Patient's history | Family history |
43-1A | Female | RC at 37 yr | Brother RC at 53 yr |
43-2A | Male | RC at 53 yr | Sister RC at 37 yr |
49-4A | Male | CC at 30 yr | Brother CC at 43 yr; sister CC at 23 yr |
49-5A | Female | CC at 23 yr | Brother CC at 43 yr; brother CC at 30 yr |
50-11A | Male | CC at 34 yr and relapse at 36 | Father CRC at 35 yr and death at 52 yr; brother CC at 34 yr and death at 36 yr |
54-2A | Female | RC at 44 yr | Sister CRC; Brother CC at 76 yr and death |
66-1-1A | Female | CC at 47 yr | Sister CC at 51 yr |
71A | Female | RC at 57 yr | Sister RC at 53 yr |
77-1A | Female | CRC at 38 yr | Father EC at 64 yr and death; uncle CRC at 68 yr and death |
102-1A | Male | RC at 25 yr | |
103-1A | Male | CC at 53 yr | Brother CC at 36 yr and death at 48 yr; mother IO at 63 yr and death |
106-2A | Male | JC at 34 yr, CC at 39 yr, KC at 44 yr and PC at 45 yr | Father EC and death; mother RC at 42 yr and death; Sister CP |
108-1A | Male | RC at 33 yr | |
110-1A | Male | CC at 36 yr | |
116-1A | Female | CC at 31 yr and HC at 57 yr | Brother intussusception and death at 40 yr; Brother CC at 50 yr, RC and SMT at 58 yr; brother IC at 50 yr, CC at 53 yr and RC at 61 yr; sister GC at 56 yr |
120-1A | Female | RC at 36 yr | |
142-1A | Male | RC at 34 yr | |
149-1A | Male | CRC at 31 yr | Father EC and death, mother GC at 56 yr |
154-1A | Female | CRC at 40 yr | Father HC, RC and death at 57 yr |
156-1A | Female | CRC at 54 yr | Sister CP at 54 yr; sister CP; mother CC at 48 yr; grandfather EC and death. |
164-1A | Male | CC at 30 yr | Uncle colonitls at 42 yr |
165-1A | Male | CRC at 43 yr | Sister RC at 31 yr and death; grandmother RC at 65 yr and death. |
180-1 | Male | CRC at 40 yr | Sister CP at 46 yr |
Table 2 Alignment and coverage statistics for 23 early-onset and familial colorectal cancer patients
Sample ID | Total reads | Total mapped | Reads mapped to genome | Covered≥4× | Covered≥10× | Covered≥20× | Average target coverage |
43-1A | 62997602 | 52130593 | 45528212 | 93.30% | 85.80% | 74.30% | 55.88× |
43-2A | 57099664 | 50367772 | 43924906 | 93.60% | 86.40% | 75.00% | 54.94× |
49-4A | 67025248 | 51978393 | 45418701 | 93.30% | 85.70% | 74.10% | 55.30× |
49-5A | 60632336 | 51598017 | 45450431 | 92.60% | 85.00% | 73.40% | 55.49× |
50-11A | 68991044 | 58507454 | 51033221 | 94.00% | 87.20% | 76.80% | 60.71× |
54-2A | 68459832 | 57860336 | 50820626 | 93.40% | 86.50% | 76.10% | 61.71× |
66-1-1A | 69759994 | 58838035 | 51472112 | 94.10% | 87.60% | 77.50% | 61.82× |
71A | 68055130 | 58181783 | 51012277 | 94.00% | 87.60% | 77.70% | 61.50× |
77-1A | 65956248 | 56894265 | 49817369 | 93.80% | 87.30% | 77.10% | 61.06× |
102-1A | 64702600 | 57086284 | 49672873 | 94.40% | 87.90% | 77.70% | 59.92× |
103-1A | 66004146 | 55109962 | 48218769 | 93.80% | 86.90% | 76.40% | 59.28× |
106-2A | 61956558 | 54367359 | 47567033 | 93.80% | 86.80% | 76.00% | 57.97× |
108-1A | 64764180 | 56469665 | 49473520 | 94.00% | 87.20% | 76.50% | 57.52× |
110-1A | 68883264 | 56962439 | 49975545 | 94.10% | 87.30% | 76.90% | 59.31× |
116-1A | 68975484 | 60681318 | 53305706 | 93.70% | 86.70% | 75.60% | 55.86× |
120-1A | 64307066 | 56593051 | 49900259 | 94.20% | 87.30% | 75.90% | 53.02× |
142-1A | 72999930 | 65321752 | 57822754 | 94.70% | 87.60% | 76.20% | 53.19× |
149-1A | 69636008 | 59789305 | 52641740 | 93.90% | 87.20% | 76.90% | 61.19× |
154-1A | 80632788 | 63934448 | 56196297 | 94.40% | 88.30% | 78.90% | 64.69× |
156-1A | 94340904 | 82125696 | 73199086 | 94.20% | 87.10% | 76.10% | 56.48× |
164-1A | 67813680 | 58837471 | 51779826 | 93.60% | 86.50% | 75.80% | 58.83× |
165-1A | 68657326 | 59845292 | 52561646 | 94.30% | 87.80% | 77.70% | 60.99× |
180-1 | 65727112 | 57908057 | 50742938 | 94.40% | 87.90% | 77.50% | 59.01× |
Average | 68190354 | 58321250 | 51197211 | 93.90% | 87.03% | 76.35% | 58.51× |
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) |
Table 4 Identification of germline mutations in known colorectal cancer predisposing genes
Sample ID | Gene name | Gene ID | Genomic change | cDNA change | Protein change | Pathogenicity |
43-1A | MLH1 | NM_000249 | g.chr3:37053590G>A | c.677G>A1 | p.Arg226Glna | Yes[38,44] |
106-2A | MLH1 | NM_000249 | chr3:g.37048555G>T | c.453+1G>T | SSM | Yes[42] |
116-1A | MLH1 | NM_000249 | g.chr3:37042445G>A | c.208-1G>A | SSM | Yes[43] |
180-1 | MUTYH | NM_001128425 | g.chr1:45797972G>A | c.799C>T | p.Gln267* | Yes[39] |
180-1 | MUTYH | NM_001128425 | g.chr1:45797914C>T | c.857G>A | p.Gly286Glu | Yes[40] |
49-4A | MLH1 | NM_000249 | g.chr3:37067252_37067253insT | c.1163_1164insT | p.Arg389Profs*6 | NR |
49-5A | MLH1 | NM_000249 | g.chr3:37067252_37067253insT | c.1163_1164insT | p.Arg389Profs*6 | NR |
49-4A | MSH6 | NM_000179 | g.chr2:48027422C>G | c.2300C>G | p.Thr767Ser | NR |
50-11A | MSH2 | NM_000251 | g.chr2:47641406A>T | c.793-2A>T | SSM | NR |
Table 5 Characteristics of 24 variants identified in 19 novel genes likely to play a role in colorectal cancer development
Sample ID | Gene name | Gene/pathway involved | cDNA change | Protein change | rs ID in dbSNP138 | MAF (700 Chinese exomes) | MAF (NHLBI ESP) | MAF (1000 genome) |
102-1A | ATM | Cancer gene, DNArep | c.1402_1403del | p.Lys468Glufs*18 | NR | NR | NR | NR |
66-1-1A | PARP1 | DNArep | c.758dup | p.Lys254Glufs*6 | NR | NR | 0.000077 | NR |
66-1-1A | MAX | Cancer gene | c.181del | p.Leu61Serfs*15 | NR | NR | NR | NR |
106-2A | BUB1 | Cancer gene | c.46C>T | p.Gln16* | NR | NR | NR | NR |
149-1A | BUB1 | Cancer gene | c.2844del | p.Gln949Argfs*3 | NR | NR | NR | NR |
165-1A | LIG3 | DNArep | c.218del | p.Phe73Serfs*41 | NR | NR | NR | NR |
54-2A | MCC | Transposon studies | c.1355+1_1355+2ins14 | SMM | NR | NR | NR | NR |
49-4A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
71A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
103-1A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
108-1A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
120-1A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
154-1A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
164-1A | EIF2AK4 | GWAS related | c.2214_2215insCGACGA | p.Glu738_Asp739insArgArg | NR | NR | NR | NR |
77-1A | LRP5 | WNT | c.2156A>G | p.Tyr719Cys | NR | NR | NR | NR |
43-1A | LRP5 | WNT | c.3536G>A | p.Arg1179His | NR | NR | 0.000077 | NR |
54-2A | LRP5 | WNT | c.3919C>T | p.Arg1307Trp | NR | NR | 0.000077 | NR |
110-1A | RPS6KB2 | PI3K/AKT | c.331A>G | p.Lys111Glu | NR | 0.00075 | NR | NR |
43-1A | RPS6KB2 | PI3K/AKT | c.683C>A | p.Thr228Asn | rs183360785 | NR | NR | 0.001 |
43-1A | RYR2 | Somatic mutation gene | c.2701G>A | p.Gly901Ser | NR | NR | NR | NR |
103-1A | RYR2 | Somatic mutation gene | c.6457A>G | p.Lys2153Glu | NR | NR | NR | NR |
102-1A | RYR3 | Somatic mutation gene | c.13507G>A | p.Val4503Met | NR | NR | NR | NR |
71A | ETV4 | Cancer gene | c.991G>A | p.Glu331Lys | NR | NR | NR | NR |
103-1A | PRDM1 | Cancer gene | c.1499A>G | p.Gln500Arg | rs201512476 | NR | NR | 0.001 |
164-1A | TSC2 | Cancer gene, PI3K/AKT | c.5200G>A | p.Asp1734Asn | NR | NR | NR | NR |
71A | MTOR | PI3K/AKT | c.5857G>T | p.Val1953Leu | NR | 0.000714 | NR | NR |
154-1A | DAAM1 | WNT | c.667G>A | p.Val223Met | NR | NR | NR | NR |
71A | FZD10 | WNT | c.1341C>G | p.Phe447Leu | NR | NR | NR | NR |
164-1A | TCF7 | WNT | c.572G>T | p.Arg191Met | NR | NR | NR | NR |
71A | MAST2 | Transposon studies | c.3482A>G | p.Asn1161Ser | NR | NR | 0.000077 | NR |
Table 6 In silico functional prediction of 16 missense variants
Sample ID | Gene name | Gene/pathway involved | cDNA change | Protein change | Domain | PhyloP score | Grantham score | Align GVGD | SIFT score | SIFT prediction | Polyphen2 score | Polyphen2 prediction |
77-1A | LRP5 | WNT | c.2156A>G | p.Tyr719Cys | LDLR class B repeat | 4.751 | 194 | C65 | 0.000 | D | 0.999 | PrD |
43-1A | LRP5 | WNT | c.3536G>A | p.Arg1179His | LDLR class B repeat | 3.712 | 29 | C25 | 0.000 | D | 0.953 | PrD |
54-2A | LRP5 | WNT | c.3919C>T | p.Arg1307Trp | LDLR class A repeat | 3.172 | 101 | C35 | 0.000 | D | 0.948 | PrD |
110-1A | RPS6KB2 | PI3K/AKT | c.331A>G | p.Lys111Glu | Protein kinase, catalytic domain | 4.639 | 56 | C55 | 0.000 | D | 0.535 | PoD |
43-1A | RPS6KB2 | PI3K/AKT | c.683C>A | p.Thr228Asn | Protein kinase, catalytic domain | 5.062 | 65 | C55 | 0.001 | D | 0.994 | PrD |
43-1A | RYR2 | Somatic mutation gene | c.2701G>A | p.Gly901Ser | Ryanodine receptor | 6.081 | 56 | C55 | 0.010 | D | 1.000 | PrD |
103-1A | RYR2 | Somatic mutation gene | c.6457A>G | p.Lys2153Glu | Intracellular calcium-release channel | 5.067 | 56 | C0 | 0.020 | D | 0.615 | PoD |
102-1A | RYR3 | Somatic mutation gene | c.13507G>A | p.Val4503Met | Ryanodine Receptor TM 4-6 | 6.012 | 21 | C15 | 0.000 | D | 1.000 | PrD |
71A | ETV4 | Cancer gene | c.991G>A | p.Glu331Lys | PEA3-type ETS-domain transcription factor, N-terminal | 6.424 | 56 | C55 | 0.001 | D | 0.862 | PoD |
103-1A | PRDM1 | Cancer gene | c.1499A>G | p.Gln500Arg | Zinc finger, C2H2 | 4.875 | 43 | C0 | 0.050 | D | 0.570 | PoD |
164-1A | TSC2 | Cancer gene, PI3K/AKT | c.5200G>A | p.Asp1734Asn | Rap/ran-GAP | 5.538 | 23 | C0 | 0.000 | D | 0.998 | PrD |
71A | MTOR | PI3K/AKT | c.5857G>T | p.Val1953Leu | PIK-related kinase | 5.634 | 32 | C0 | 0.001 | D | 0.827 | PoD |
154-1A | DAAM1 | WNT | c.667G>A | p.Val223Met | Diaphanous GTPase-binding | 6.347 | 21 | C0 | 0.000 | D | 0.998 | PrD |
71A | FZD10 | WNT | c.1341C>G | p.Phe447Leu | Frizzled protein | 4.229 | 22 | C15 | 0.000 | D | 0.984 | PrD |
164-1A | TCF7 | WNT | c.572G>T | p.Arg191Met | High mobility group, HMG1/HMG2 | 4.202 | 91 | C65 | 0.000 | D | 0.999 | PrD |
71A | MAST2 | Transposon studies | c.3482A>G | p.Asn1161Ser | PDZ/DHR/GLGF | 4.854 | 46 | C0 | 0.000 | D | 0.999 | PrD |
- Citation: Zhang JX, Fu L, de Voer RM, Hahn MM, Jin P, Lv CX, Verwiel ET, Ligtenberg MJ, Hoogerbrugge N, Kuiper RP, Sheng JQ, Geurts van Kessel A. Candidate colorectal cancer predisposing gene variants in Chinese early-onset and familial cases. World J Gastroenterol 2015; 21(14): 4136-4149
- URL: https://www.wjgnet.com/1007-9327/full/v21/i14/4136.htm
- DOI: https://dx.doi.org/10.3748/wjg.v21.i14.4136