Table 3

SNPs showing significant genotypic association with PFS

GeneSymbolSNP
Reference allele (dbSNP)N*HR95% CIP
Dominantly acting alleles         
    Sec23 homolog B SEC23B H489Q — C 93 0.60 0.45-0.81 .001† 
    Leukocyte immunoglobulin-like receptor, subfamily A member 4 LILRA4 P27L‡ rs2241384 C 285 1.44 1.12-1.85 .004† 
    Chondroitin sulfate galnact-2 GALNACT-2 P479S‡ rs2435381 C 237 0.70 0.55-0.89 .004† 
    Cubilin (intrinsic factor-cobalamin receptor) CUBN S253F rs1801222 C 151 1.42 1.11-1.83 .006† 
    Killer cell lectin-like receptor subfamily C, member 4 KLRC4 S29I‡ rs1841958 G 195 0.72 0.57-0.91 .007† 
    Phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP R94Q rs6597801 G 344 1.49 1.11-1.99 .008 
    Melanoma inhibitory activity 2 MIA2 D547H rs10134365 G 269 1.39 1.09-1.78 .008 
    ARP10 protein ARP10 K121N rs139299 G 114 1.47 1.11-1.95 .008† 
    Dystonin DST Q1634R rs4712138 A 153 1.39 1.08-1.79 .011† 
    Myosin binding protein C, cardiac MYBPC3 V158M‡ rs3729986 G 350 1.47 1.09-1.99 .012† 
    Sema domain, immunoglobulin domain, short basic domain, secreted SEMA3C V337M‡ rs1527482 G 419 3.15 1.28-7.75 .013 
    Zinc finger protein 169 ZNF169 Q583H‡ rs12350212 G 344 1.46 1.08-1.97 .013† 
    Serologically defined colon cancer antigen 3-like SDCCAG3L I437T rs2000746 T 218 0.74 0.58-0.94 .013 
    Phospholipase A2, group VII PLA2G7 A379V rs1051931 C 281 0.72 0.56-0.94 .014† 
    Apolipoprotein E APOE R176C‡§ rs7412 C 352 1.46 1.08-1.98 .015† 
    BRCA1-associated RING domain 1 BARD1 S378R‡ rs2229571 C 154 0.75 0.59-0.95 .019† 
    General transcription factor IIE, polypeptide 1, alpha 56 kDa GTF2E1 P366S rs3732401 C 387 0.56 0.34-0.91 .02† 
    X-ray repair complementing defective repair in Chinese hamster cells 2 XRCC2 R188H rs3218536 G 354 1.44 1.06-1.95 .02 
    Excision repair cross-complementing rodent repair deficiency, complementation group ERCC6 G399D rs2228528 G 299 1.35 1.05-1.73 .021 
    Low-density lipoprotein receptor–related protein 4 LRP4 G1554S‡ rs2306029 G 133 1.37 1.05-1.78 .021† 
    Erbb2 interacting protein ERBB2IP S274L‡ rs3213837 C 291 1.34 1.04-1.72 .022 
    Low-density lipoprotein–related protein 2 LRP2 L4210I‡ rs4667591 C 262 1.32 1.04-1.68 .024 
    Cancer susceptibility candidate 5 CASC5 M598T rs11858113 T 139 0.75 0.59-0.96 .025† 
    Tyrosinase TYR S192Y‡ rs1042602 C 159 0.76 0.60-0.97 .027 
    Thrombospondin 1 THBS1 N700S‡§ rs17632786 A 325 0.72 0.54-0.96 .027† 
    Excision repair cross-complementing rodent repair deficiency, complementation group ERCC5 H1104D rs17655 C 256 1.32 1.03-1.69 .028 
    Transmembrane protease, serine 4 TMPRSS4 G206V rs1941635 G 395 1.57 1.05-2.35 .028† 
    E2F transcription factor 2 E2F2 G205R rs3218170 G 412 1.98 1.08-3.62 .028 
    Laminin, alpha 2 LAMA2 V1138M rs2306942 G 378 1.51 1.04-2.18 .028 
    Interleukin-16 (lymphocyte chemoattractant factor) IL16 P434S rs4072111 C 334 0.72 0.53-0.97 .031† 
    Carboxypeptidase A4 CPA4 G303C‡ rs2171492 G 153 0.76 0.6-0.98 .032 
    RAD18 homolog RAD18 Q302R rs373572 A 223 1.29 1.02-1.64 .034 
    Cytochrome P450, family 39, subfamily A, polypeptide 1 CYP39A1 P23R rs12192544 C 258 1.3 1.02-1.65 .034† 
    Keratin 1 KRT1 A454S‡ rs17678945 G 395 1.59 1.03-2.44 .035 
    Polymerase (DNA-directed), beta POLB P242R‡ rs3136797 C 409 1.87 1.04-3.36 .036† 
    Breast cancer 2, early onset BRCA2 T1915M rs4987117 C 393 1.59 1.03-2.44 .036 
    PMS2 postmeiotic segregation increased 2 PMS2 M622I rs1805324 G 411 0.39 0.16-0.95 .037 
    Ubiquitin specific protease 47 USP47 V75G‡ rs11022079 T 205 1.28 1.01-1.63 .039 
    Zinc finger protein 311 ZNF311 K511Q rs6456880 A 168 1.29 1.01-1.65 .039 
    Zinc finger CCCH-type containing 3 ZC3H3 G452S rs4874147 G 245 1.30 1.01-1.66 .040 
    Protein tyrosine phosphatase, nonreceptor type 13 PTPN13 Y2062D rs989902 T 146 0.78 0.61-0.99 .041† 
    Homeodomain interacting protein kinase 4 HIPK4 R302Q‡ rs11670988 G 347 1.37 1.01-1.87 .042† 
    RAD1 homolog (Saccharomyces pombe) RAD1 E281G rs1805327 A 357 0.71 0.50-0.99 .042 
    Cytochrome P450, family 2, subfamily C, polypeptide 9 CYP2C9 I359L‡ rs1057910 A 370 1.42 1.01-2.00 .042† 
    Forkhead box N1 FOXN1 R69C‡ rs2071587 C 350 1.37 1.01-1.85 .042 
    Ectonucleotide pyrophosphatase/phosphodiesterase 5 ENPP5 V171I rs6926570 G 117 0.76 0.58-0.99 .043 
    FRAS1-related extracellular matrix protein 2 FREM2 F1070S rs2496425 T 231 1.28 1.01-1.62 .044 
    Serine/threonine kinase 6 STK6 I31F rs2273535 A 261 0.78 0.61-0.99 .045† 
    O-6-methylguanine-DNA methyltransferase MGMT L84F rs12917 C 327 0.75 0.56-0.99 .045 
    Carbonyl reductase 3 CBR3 V244M rs1056892 G 186 1.28 1.00-1.63 .046 
    Zinc finger protein 527 ZNF527 H181R‡ rs4452075 A 295 0.76 0.59-1.00 .047 
Recessively acting alleles         
    Interleukin-19 IL19 S213F rs2243191 C 16 2.53 1.46-4.38 .001† 
    Cadherin 11, type 2, OB-cadherin CDH11 T255M rs35195 C 47 1.73 1.22-2.45 .002† 
    Cathepsin B CTSB L26V rs12338 C 71 0.57 0.40-0.82 .002† 
    CD5 antigen (p56–62) CD5 V471A‡ rs13328900 T 104 1.50 1.16-1.96 .002† 
    Extra spindle poles–like 1 (S cerevisiae) ESPL1 R614S‡ rs1318648 A 58 1.60 1.15-2.22 .006 
    Ectonucleotide pyrophosphatase/phosphodiesterase 5 ENPP5 V171I rs6926570 G 86 0.64 0.46-0.88 .006† 
    Glypican 1 GPC1 G500S rs2228331 G 32 0.48 0.28-0.81 .006† 
    Matrix metalloproteinase 10 (stromelysin 2) MMP10 G65R‡ rs17293607 G 8 2.92 1.36-6.27 .006† 
    Dual specificity phosphatase 13 DUSP13 C206Y‡ rs3088142 G 77 0.63 0.45-0.88 .007 
    Sucrase-isomaltase (alpha-glucosidase) SI A231T rs9283633 G 71 1.51 1.12-2.05 .008 
    Neural precursor cell–expressed, developmentally down-regulated 4 NEDD4 Q260R rs2303580 A 15 0.35 0.16-0.79 .012† 
    Reticulon 3 RTN3 A6E rs11551944 C 9 2.44 1.19-5.00 .015† 
    Carnitine palmitoyltransferase II CPT2 M647V‡ rs1799822 A 27 1.74 1.11-2.73 .016† 
    Monoacylglycerol O-acyltransferase 1 MOGAT1 S162P rs1868024 T 21 1.91 1.13-3.23 .016 
    Extra spindle poles–like 1 (S cerevisiae) ESPL1 D25A rs6580942 A 44 1.58 1.09-2.29 .017 
    Topoisomerase (DNA) II binding protein 1 TOPBP1 S730L rs17301766 C 18 1.89 1.12-3.19 .018† 
    Zinc finger protein 643 ZNF643 C13Y rs2272994 G 16 0.45 0.23-0.87 .019 
    SET domain, bifurcated 2 SETDB2 G117E rs7998427 G 64 1.45 1.05-2.00 .023† 
    Zinc finger protein 573 ZNF573 A166G‡ rs3752365 C 24 1.71 1.08-2.70 .024 
    A kinase (PRKA) anchor protein (yotiao) 9 AKAP9 M463I rs6964587 G 65 1.43 1.05-1.97 .025 
    BCL2-like 13 (apoptosis facilitator) BCL2L13 P360S rs9306198 C 6 2.68 1.09-6.60 .032† 
    Dynein, axonemal, heavy polypeptide 9 DNAH9 N2195S rs3744581 A 23 1.68 1.03-2.72 .037 
    A kinase (PRKA) anchor protein 10 AKAP10 R249H rs2108978 G 63 1.41 1.02-1.94 .038† 
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 DDX27 G206V rs11908296 G 22 1.70 1.03-2.80 .038 
    Inhibin, beta C INHBC R322Q‡ rs2229357 G 22 1.75 1.02-2.98 .041 
    Sterile alpha motif and leucine zipper containing kinase AZK ZAK S531L rs3769148 C 95 0.75 0.56-1.00 .047 
    Eosinophil peroxidase EPX Q122H rs11652709 G 35 0.64 0.41-0.99 .047 
    Four and a half LIM domains 5 FHL5 S243R‡ rs9373985 C 43 0.65 0.42-1.00 .049 
GeneSymbolSNP
Reference allele (dbSNP)N*HR95% CIP
Dominantly acting alleles         
    Sec23 homolog B SEC23B H489Q — C 93 0.60 0.45-0.81 .001† 
    Leukocyte immunoglobulin-like receptor, subfamily A member 4 LILRA4 P27L‡ rs2241384 C 285 1.44 1.12-1.85 .004† 
    Chondroitin sulfate galnact-2 GALNACT-2 P479S‡ rs2435381 C 237 0.70 0.55-0.89 .004† 
    Cubilin (intrinsic factor-cobalamin receptor) CUBN S253F rs1801222 C 151 1.42 1.11-1.83 .006† 
    Killer cell lectin-like receptor subfamily C, member 4 KLRC4 S29I‡ rs1841958 G 195 0.72 0.57-0.91 .007† 
    Phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP R94Q rs6597801 G 344 1.49 1.11-1.99 .008 
    Melanoma inhibitory activity 2 MIA2 D547H rs10134365 G 269 1.39 1.09-1.78 .008 
    ARP10 protein ARP10 K121N rs139299 G 114 1.47 1.11-1.95 .008† 
    Dystonin DST Q1634R rs4712138 A 153 1.39 1.08-1.79 .011† 
    Myosin binding protein C, cardiac MYBPC3 V158M‡ rs3729986 G 350 1.47 1.09-1.99 .012† 
    Sema domain, immunoglobulin domain, short basic domain, secreted SEMA3C V337M‡ rs1527482 G 419 3.15 1.28-7.75 .013 
    Zinc finger protein 169 ZNF169 Q583H‡ rs12350212 G 344 1.46 1.08-1.97 .013† 
    Serologically defined colon cancer antigen 3-like SDCCAG3L I437T rs2000746 T 218 0.74 0.58-0.94 .013 
    Phospholipase A2, group VII PLA2G7 A379V rs1051931 C 281 0.72 0.56-0.94 .014† 
    Apolipoprotein E APOE R176C‡§ rs7412 C 352 1.46 1.08-1.98 .015† 
    BRCA1-associated RING domain 1 BARD1 S378R‡ rs2229571 C 154 0.75 0.59-0.95 .019† 
    General transcription factor IIE, polypeptide 1, alpha 56 kDa GTF2E1 P366S rs3732401 C 387 0.56 0.34-0.91 .02† 
    X-ray repair complementing defective repair in Chinese hamster cells 2 XRCC2 R188H rs3218536 G 354 1.44 1.06-1.95 .02 
    Excision repair cross-complementing rodent repair deficiency, complementation group ERCC6 G399D rs2228528 G 299 1.35 1.05-1.73 .021 
    Low-density lipoprotein receptor–related protein 4 LRP4 G1554S‡ rs2306029 G 133 1.37 1.05-1.78 .021† 
    Erbb2 interacting protein ERBB2IP S274L‡ rs3213837 C 291 1.34 1.04-1.72 .022 
    Low-density lipoprotein–related protein 2 LRP2 L4210I‡ rs4667591 C 262 1.32 1.04-1.68 .024 
    Cancer susceptibility candidate 5 CASC5 M598T rs11858113 T 139 0.75 0.59-0.96 .025† 
    Tyrosinase TYR S192Y‡ rs1042602 C 159 0.76 0.60-0.97 .027 
    Thrombospondin 1 THBS1 N700S‡§ rs17632786 A 325 0.72 0.54-0.96 .027† 
    Excision repair cross-complementing rodent repair deficiency, complementation group ERCC5 H1104D rs17655 C 256 1.32 1.03-1.69 .028 
    Transmembrane protease, serine 4 TMPRSS4 G206V rs1941635 G 395 1.57 1.05-2.35 .028† 
    E2F transcription factor 2 E2F2 G205R rs3218170 G 412 1.98 1.08-3.62 .028 
    Laminin, alpha 2 LAMA2 V1138M rs2306942 G 378 1.51 1.04-2.18 .028 
    Interleukin-16 (lymphocyte chemoattractant factor) IL16 P434S rs4072111 C 334 0.72 0.53-0.97 .031† 
    Carboxypeptidase A4 CPA4 G303C‡ rs2171492 G 153 0.76 0.6-0.98 .032 
    RAD18 homolog RAD18 Q302R rs373572 A 223 1.29 1.02-1.64 .034 
    Cytochrome P450, family 39, subfamily A, polypeptide 1 CYP39A1 P23R rs12192544 C 258 1.3 1.02-1.65 .034† 
    Keratin 1 KRT1 A454S‡ rs17678945 G 395 1.59 1.03-2.44 .035 
    Polymerase (DNA-directed), beta POLB P242R‡ rs3136797 C 409 1.87 1.04-3.36 .036† 
    Breast cancer 2, early onset BRCA2 T1915M rs4987117 C 393 1.59 1.03-2.44 .036 
    PMS2 postmeiotic segregation increased 2 PMS2 M622I rs1805324 G 411 0.39 0.16-0.95 .037 
    Ubiquitin specific protease 47 USP47 V75G‡ rs11022079 T 205 1.28 1.01-1.63 .039 
    Zinc finger protein 311 ZNF311 K511Q rs6456880 A 168 1.29 1.01-1.65 .039 
    Zinc finger CCCH-type containing 3 ZC3H3 G452S rs4874147 G 245 1.30 1.01-1.66 .040 
    Protein tyrosine phosphatase, nonreceptor type 13 PTPN13 Y2062D rs989902 T 146 0.78 0.61-0.99 .041† 
    Homeodomain interacting protein kinase 4 HIPK4 R302Q‡ rs11670988 G 347 1.37 1.01-1.87 .042† 
    RAD1 homolog (Saccharomyces pombe) RAD1 E281G rs1805327 A 357 0.71 0.50-0.99 .042 
    Cytochrome P450, family 2, subfamily C, polypeptide 9 CYP2C9 I359L‡ rs1057910 A 370 1.42 1.01-2.00 .042† 
    Forkhead box N1 FOXN1 R69C‡ rs2071587 C 350 1.37 1.01-1.85 .042 
    Ectonucleotide pyrophosphatase/phosphodiesterase 5 ENPP5 V171I rs6926570 G 117 0.76 0.58-0.99 .043 
    FRAS1-related extracellular matrix protein 2 FREM2 F1070S rs2496425 T 231 1.28 1.01-1.62 .044 
    Serine/threonine kinase 6 STK6 I31F rs2273535 A 261 0.78 0.61-0.99 .045† 
    O-6-methylguanine-DNA methyltransferase MGMT L84F rs12917 C 327 0.75 0.56-0.99 .045 
    Carbonyl reductase 3 CBR3 V244M rs1056892 G 186 1.28 1.00-1.63 .046 
    Zinc finger protein 527 ZNF527 H181R‡ rs4452075 A 295 0.76 0.59-1.00 .047 
Recessively acting alleles         
    Interleukin-19 IL19 S213F rs2243191 C 16 2.53 1.46-4.38 .001† 
    Cadherin 11, type 2, OB-cadherin CDH11 T255M rs35195 C 47 1.73 1.22-2.45 .002† 
    Cathepsin B CTSB L26V rs12338 C 71 0.57 0.40-0.82 .002† 
    CD5 antigen (p56–62) CD5 V471A‡ rs13328900 T 104 1.50 1.16-1.96 .002† 
    Extra spindle poles–like 1 (S cerevisiae) ESPL1 R614S‡ rs1318648 A 58 1.60 1.15-2.22 .006 
    Ectonucleotide pyrophosphatase/phosphodiesterase 5 ENPP5 V171I rs6926570 G 86 0.64 0.46-0.88 .006† 
    Glypican 1 GPC1 G500S rs2228331 G 32 0.48 0.28-0.81 .006† 
    Matrix metalloproteinase 10 (stromelysin 2) MMP10 G65R‡ rs17293607 G 8 2.92 1.36-6.27 .006† 
    Dual specificity phosphatase 13 DUSP13 C206Y‡ rs3088142 G 77 0.63 0.45-0.88 .007 
    Sucrase-isomaltase (alpha-glucosidase) SI A231T rs9283633 G 71 1.51 1.12-2.05 .008 
    Neural precursor cell–expressed, developmentally down-regulated 4 NEDD4 Q260R rs2303580 A 15 0.35 0.16-0.79 .012† 
    Reticulon 3 RTN3 A6E rs11551944 C 9 2.44 1.19-5.00 .015† 
    Carnitine palmitoyltransferase II CPT2 M647V‡ rs1799822 A 27 1.74 1.11-2.73 .016† 
    Monoacylglycerol O-acyltransferase 1 MOGAT1 S162P rs1868024 T 21 1.91 1.13-3.23 .016 
    Extra spindle poles–like 1 (S cerevisiae) ESPL1 D25A rs6580942 A 44 1.58 1.09-2.29 .017 
    Topoisomerase (DNA) II binding protein 1 TOPBP1 S730L rs17301766 C 18 1.89 1.12-3.19 .018† 
    Zinc finger protein 643 ZNF643 C13Y rs2272994 G 16 0.45 0.23-0.87 .019 
    SET domain, bifurcated 2 SETDB2 G117E rs7998427 G 64 1.45 1.05-2.00 .023† 
    Zinc finger protein 573 ZNF573 A166G‡ rs3752365 C 24 1.71 1.08-2.70 .024 
    A kinase (PRKA) anchor protein (yotiao) 9 AKAP9 M463I rs6964587 G 65 1.43 1.05-1.97 .025 
    BCL2-like 13 (apoptosis facilitator) BCL2L13 P360S rs9306198 C 6 2.68 1.09-6.60 .032† 
    Dynein, axonemal, heavy polypeptide 9 DNAH9 N2195S rs3744581 A 23 1.68 1.03-2.72 .037 
    A kinase (PRKA) anchor protein 10 AKAP10 R249H rs2108978 G 63 1.41 1.02-1.94 .038† 
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 DDX27 G206V rs11908296 G 22 1.70 1.03-2.80 .038 
    Inhibin, beta C INHBC R322Q‡ rs2229357 G 22 1.75 1.02-2.98 .041 
    Sterile alpha motif and leucine zipper containing kinase AZK ZAK S531L rs3769148 C 95 0.75 0.56-1.00 .047 
    Eosinophil peroxidase EPX Q122H rs11652709 G 35 0.64 0.41-0.99 .047 
    Four and a half LIM domains 5 FHL5 S243R‡ rs9373985 C 43 0.65 0.42-1.00 .049 

HRs adjusted for age, sex, stage of disease, and treatment.

db SNP indicates database of single nucleotide polymorphisms.

*

Number of patients with at-risk genotype.

†

Significant after adjustment for IgVH mutation status.

‡

Predicted to be intolerant/potentially intolerant, damaging/probably damaging, or radical/moderately radical based on SIFT/POLYPHEN/Grantham scores.

§

Established to be functional.

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