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Syndromes Germline alterations Molecular methodology Sample size References Lynch syndrome PMS2 c.1376C>G, p.S459X, MLH1 c.1652A>C, p. N551T MSH2 c.2262-2267 delTTCTAC, p.T756-Y757 del MSH2 c.1226_1227delAG MSH2 c.1964.delT, p. V655fs MSH2 c.289C>T, Q97* MSH6 c.3475insT, p. Y1159fs MSH6 c.3475insT MMR protein by IHC, MSI, and BRAF mutation testing and deep sequencing 2.2% of all CRC (N=1207) 19,20 Lynch syndrome MSH2 c.737A>T, p.K246I MSH2 c. 2262_2267del, p.S755_T756del MSH2 c.367-? __1276+? Del MSH2 c.2089T>C, p.C697R MSH2 c. 2038C>T, p.R680* MLH1 c.62C>T, p.A21V MLH1 c.1961C>T, p.P654L MLH1 c.677G>A, p.R226Q MLH1 c.454-?_545+?del MMR protein by IHC, MSI, BRAF mutation testing, MLPA, deep sequencing, and Sanger sequencing 7.2% of all CRC (N=284) 21 Lynch syndrome Deletion of chromosomal regions: 2p21-2p16.3 (MSH2, MSH6, and EPCAM) 3p23-3p14.2 (MLH1) 7p22.1 (PMS2) 1p34.1-1p33 (MUTYH) Whole genome comparative genomic hybridization array N=12 (LS patients) 24 FAP syndrome PMS2 c.1376C>G, p.S459X WES One case report 19 FAP: familial adenomatous polyposis, MMR: mismatch repair, IHC: immunohistochemistry, MSI: microsatellite instability, BRAF: B-Raf, MLPA: multiplex ligation probe amplification, WES: whole-exome sequencing, CRC: colorectal cancer, LS: Lynch syndrome
Genetic loci Study approach Number of CRC cases Molecular methodologies Risk patterns References ABCC1 C218T Case-control N=51, 65 controls PCR-RFLP and DNA sequencing (Sanger) Increased CRC risk, OR=3.4 40 ADIPOQ G276T Case-control N=60, 60 controls PCR-RFLP Increased CRC risk, OR=2.64 41 CYP1A1wt/*2A Case-control N=92, 79 controls PCR-RFLP Increased CRC risk, OR=3.65 42 GSTM1 Case-control N=80, 78 controls Diplex PCR Increased CRC risk, OR=3.7 43 TP53 rs1042522 Case-control N=80, 78 controls TaqMan real-time PCR assays Increased CRC risk, OR=1.6 43 KIR 2DS1, 2DS2, 2DS3, 2DS5, and 3DS1 Case-control N=70, 70 controls PCR Increased CRC risk, OR=8.6-fold, 3-fold, 2.5-fold, 4.5-fold, and 16.25-fold 44 IL17A rs2275913: GA and AA genotypes Case-control N=117, 100 controls TaqMan allelic discrimination assay (PCR) Increased CRC risk, OR=2-fold and 2.8-fold 45 NOTCH3 rs1043994: G>A Case-control N=134, 139 controls TaqMan allelic discrimination assay (PCR) Increased CRC risk in males, OR=1.971 46 PARP1 K933N and K945N Case-control N=50, 50 controls PCR and Sanger sequencing Increased CRC risk OR=3.1429 for K933N G>T heterozygote; OR=2.5714 for K945N G>T heterozygote 47 PRNCR1 rs1456315: CC genotype Case-control N=144, 130 controls TaqMan assays Increased CRC risk, OR=2.09 48 RETN rs1862513 and rs375367 Case-control N=60, 60 controls PCR-RFLP Increased CRC risk, OR=2.48 (rs1862513); OR=6.5 (rs375367) 49 TDG rs4135113 Case-control N=100, 192 controls TaqMan genotyping Increased CRC risk, OR>3.6; OR=5 in those >57 years 50 TLR9 rs352139 Case-control N=115, 102 controls TaqMan allelic discrimination assay (PCR) Increased CRC risk for rectal cancers, OR=3.552 and 1.809 for GG genotype and G allele 51 TNFA rs361525 (G238A) Case-control N=100, 100 controls TaqMan allelic discrimination assay Increased CRC risk, OR=14.663 for AA genotype and 7.647 for the A allele 52 TSLP rs10043985 Case-control N=112, 108 controls TaqMan genotyping assay Increased CRC risk, OR=16.52 for AC genotype and 10.837 for the C allele 53 VDR1 ApaI rs797232 Case-control N=100, 100 controls PCR amplification, followed by Sanger sequencing Increased CRC risk, OR=1.778 in patients >57 years (rs797232 and C allele) 54 VDR1 TaqI rs731236 Case-control N=132, 124 controls PCR-RFLP Increased CRC risk, OR=6.18 55 XRCC1 A399G Case-control N=100, 100 controls PCR-RFLP and PCR-CTPP Increased CRC risk, OR=2.1 56 ABCB1 G2677T Case-control N=62, 100 controls PCR-RFLP Reduced CRC risk, OR=0.004 for heterozygotes GT and 0.005 homozygotes TT 57 ADIPOQ T45G Case-control N=60, 60 controls PCR-RFLP Reduced CRC risk, OR=0.41 for the G allele 41 CTNNB1 rs4135385 Case-control N=122, 110 controls TaqMan assays Reduced CRC risk, OR=0.092 for GG genotype 58 LRP6 rs2284396 Case-control N=122, 110 controls TaqMan assays Reduced CRC risk, OR=0.250 for the CC genotype in cases >57 years; OR=0.561 for the C allele 58 SFRP3 rs7775 Case-control N=122, 110 controls TaqMan assays Reduced CRC risk, OR=0.397 for the Gly allele in female gender 58 CYP19A1 rs4774585 rs4775936 Case-control N=100, 100 controls TaqMan genotyping by real-time PCR Reduced CRC risk, OR=0.28 for rs4774585 AA genotype in the male gender; OR=0.37 for rs4775936 CT genotype in the female 59 IL7R rs1053496 Case-control N=112, 108 controls TaqMan genotyping assay Reduced CRC risk, OR=0.529, 0.467 and 0.644 for the CT and TT genotypes, and the T allele 53 PARP1 rs8679 Case-control N=183, 190 controls TaqMan assay Reduced CRC risk, OR=0.566 for the TC genotype and 0.695 for the C allele 60 TDG rs1866074 rs3751209 Case-control N=100, 192 controls TaqMan genotyping Reduced CRC risk, OR=0.501 for rs1866074 GG genotype; OR=0.407 for rs3751209 GA genotype in the male gender 50 TLR4 rs10759931 rs2770150 Case-control N=115, 102 controls TaqMan allelic discrimination assay Reduced CRC risk, OR=0.052, 0.018 and 0.085 for rs10759931 GA and AA genotypes, and A allele, respectively; OR=0.074, 0.194, 0.188 for rs2770150 TC and CC genotypes, and C allele only in the female gender 61 TLR9 rs187084 rs352144 Case-control N=115, 102 controls TaqMan allelic discrimination assay (PCR) Reduced CRC risk, OR=0.527 for rs187084 T allele in the female gender; OR=0.067 for rs352144 AC genotype for rectal tumours 51 VDR1 BsmI rs1544410 Case-control N=100, 100 controls PCR amplification, followed by Sanger sequencing OR=0.217 for rs1544410 AA genotype and 0.442 for A allele in the female gender 54 PCR-RFLP: polymerase chain reaction-restriction fragment length polymorphism, CRC: colorectal cancer, OR: odds ratio
Genes Mutation rates (mutation type) Sample sizes Molecular methodologies References KRAS 56.0% (point) 150 PCR followed by amplicon hybridization 68 28.6% (point) 755 PCR and DNA sequencing 69 30.1% (point) 498 PCR and DNA sequencing 70 50.0% (point) 194 Biocartis IdyllaTm 71 45.2% (point) 93 NGS 72 42.2% (point) 83 PCR followed by amplicon hybridization 73 49.6% (point) 248 Biocartis IdyllaTm 74 35.0% (point) 99 Ion PGM sequencing 75 32.5% (point) 80 Sanger sequencing 76 42.85% (point) 56 HRM analysis, Sanger sequencing, and shifted termination assays 77 42.0% (point) 300 LCD-array 78 43.0% (point) 51 Ion AmpliSeq NGS Panel 79 25.0% (point) 99 Ion AmpliSeq™ 80 NRAS 2.2% (point) 93 NGS 72 2.0% (point) 248 Biocartis IdyllaTm 74 BRAF 2.5% (point) 757 PCR and DNA sequencing 69 2.4% (point) 498 PCR and DNA sequencing 70 2.2% (point) 93 NGS 72 0.4% (point) 248 Biocartis IdyllaTm 74 PIK3CA 19.0% (point) 99 Ion PGM Sequencing 75 12.2% (point) 418 Sanger sequencing 81 HER2 (ERBB2) 0.0% (gene amplification) 114 FISH 82 51.0% (point) 99 Ion AmpliSeq™ 80 CCND1 1.9% (gene amplification) 114 FISH 82 EGFR 11.0% (point) 99 Ion PGM Sequencing 75 1.1% (gene amplification) 114 FISH 82 40.0% (point) 99 Ion AmpliSeq™ 80 C-MYC 9.0% (gene amplification) 114 FISH 82 MSI 11.2% 741 Microsatellite analysis by multiplex fluorescent PCR 69 10.9% 494 Microsatellite analysis by multiplex fluorescent PCR 70 20.2% 388 Microsatellite analysis by multiplex fluorescent PCR 81 9.7% 992 Microsatellite analysis by multiplex fluorescent PCR 83 11.6% 284 Pentaplex MSI analysis system 84 11.3% 807 Microsatellite analysis by multiplex fluorescent PCR and immunohistochemistry assessment 20 TP53 65.0% (point) 99 Ion PGM sequencing 75 33.7% (point) 386 Sanger sequencing 81 19.0% (point) 99 AmpliSeq comprehensive 80 APC 36.0% (point) 99 Ion PGM sequencing 75 66.0% (point) 99 AmpliSeq comprehensive cancer panel 80 SMAD4 11.0% (point) 99 Ion PGM sequencing 75 3.0% (point) 99 AmpliSeq comprehensive cancer panel 80 13.6% (point) 426 High depth capture sequencing 83 60.8% (SMAD4 gene and 18q deletion) 991 FISH 83 PTEN 13.0% (point) 99 Ion PGM sequencing 75 3.0% (point) 99 AmpliSeq comprehensive cancer panel 80 66.1% (point) 386 Sanger sequencing 81 CIMP CIMP-H=4.8%; CIMP-L=44.6%; CIMP-negative=50.6% 500 Real-time PCR (MethyLight) 70 MSI: microsatellite instability, CIMP: CpG island methylator phenotype, CIMP-H: CpG island methylator phenotype-high, CIMP-L: CpG island methylator phenotype-low, PCR: polymerase chain reaction, PGM: personal genome machine, FISH: fluorescence in situ hybridisation, HRM: high resolution melt, LCD: liquid-crystal display, NGS: next-generation sequencing
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