Table 3.
52 candidate genes (58 SNPs) exhibiting extreme (θ ≥ 2) ASE in familial pancreatic cancer (NFPTR) samples
| Heterozygous NFPTR individuals | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Locus | RefSNP | MAF | SNP | Function | Class± | Tested | # extreme ASE |
% extreme ASE |
Extreme θ† |
Background θ† |
| Nonsynonymous SNPs | |||||||||||
| MUTYH | 1p34.3-p32.1 | rs3219484 | 0.1 | 198G>A | 22Val>Met | a | 12 | 1 | 8 | 3 | 1.58 |
| TNFRSF1B | 1p36.3-p36.2 | rs1061622 | 0.26 | 676T>G | 196Met>Arg | b | 36 | 2 | 6 | 2.4 | 1.53 |
| EPHX1 | 1q42.1 | rs1051740 | 0.32 | 612T>C | 113Tyr>His | b | 34 | 1 | 3 | 2.07 | 1.41 |
| CASP8 | 2q33-q34 | rs1045485 | 0.13 | 1192G>C | 302Asp>His | b | 8 | 1 | 13 | 2.63 | 1.68 |
| BARD1 (1)* | 2q34-q35 | rs2229571 | 0.4 | 1207G>C | 378Arg>Ser | b | 42 | 1 | 2 | 2.27 | 1.37 |
| PTCH1 (2) | 9q22.3 | rs357564 | 0.33 | 4132C>T | 1315Pro>Leu | b | 9 | 3 | 33 | 2.98 | 2.12 |
| ZWINT | 10q21-q22 | rs2241666 | 0.38 | 596A>G | 187Arg>Gly | b | 38 | 1 | 3 | 4 | 1.51 |
| BAG3 | 10q25.2-q26.2 | rs2234962 | 0.21 | 757T>C | 151Cys>Arg | a | 3 | 1 | 33 | 2.26 | 1.72 |
| GSTP1 | 11q13 | rs947894 | 0.34 | 342A>G | 105Ile>Val | a | 42 | 1 | 2 | 2.44 | 1.38 |
| MMP7 | 11q21-q22 | rs10502001 | 0.2 | 277G>A | 77Arg>His | b | 31 | 2 | 6 | 2.32 | 1.51 |
| FLT3 | 13q12 | rs1933437 | 0.36 | 738C>T | 227Thr>Met | a | 24 | 1 | 4 | 2.07 | 1.61 |
| BRCA2 (3) | 13q12.3 | rs144848 | 0.33 | 1341A>C | 372Asn>His | a | 46 | 1 | 2 | 2.33 | 2.33 |
| TEP1 | 14q11.2 | rs1760904 | 0.49 | 3624T>C | 1195Ser>Pro | b | 43 | 1 | 2 | 2.52 | 1.31 |
| CARD15 (4) | 16q12 | rs2066842 | 0.28 | 907C>T | 268Pro>Ser | a | 40 | 1 | 3 | 5.79 | 1.83 |
| FANCA | 16q24.3 | rs2239359 | 0.37 | 1543G>A | 501Gly>Ser | b | 49 | 3 | 6 | 2.38 | 1.56 |
| PLAUR | 19q13 | rs2302524 | 0.17 | 889A>G | 220Lys>Arg | b | 25 482 |
2 23 |
8 5 |
2.32 2.74 (6.7)‡ |
1.58 1.63 (3.1)‡ |
| Synonymous SNPs | |||||||||||
| FRAP1 (5) | 1p36.2 | rs11121705 | 0.3 | 1516T>C | 479Asp | b | 42 | 4 | 10 | 2.57 | 1.57 |
| FRAP1 (5) | 1p36.2 | rs1057079 | 0.27 | 4810G>A | 1577Ala | b | 34 | 3 | 9 | 2.57 | 1.54 |
| DST | 6p12-p11 | rs2230862 | 0.5 | 4176G>A | 1358Lys | a | 54 | 1 | 2 | 2.37 | 1.17 |
| DDR1 | 6p21.3 | rs1049623 | 0.19 | 2130T>C | 599Val | b | 55 | 2 | 4 | 2.14 | 1.42 |
| MET | 7q31 | rs41736 | 0.4 | 4045C>T | 1286Asp | a | 16 | 1 | 6 | 2.1 | 1.49 |
| EPHA1 | 7q34 | rs10952549 | 0.21 | 1924C>T | 613Leu | a | 5 | 1 | 20 | 2.39 | 2.1 |
| PTK2B | 8p22-p11.2 | rs1030526 | 0.4 | 978G>A | 110Thr | b | 38 | 1 | 3 | 2.19 | 1.37 |
| TEK | 9p21 | rs639225 | 0.48 | 2110A>G | 654Ser | a | 17 | 1 | 6 | 2.16 | 1.36 |
| PTCH1 (2) | 9q22.3 | rs2066836 | 0.22 | 1874C>T | 562Ala | b | 39 | 3 | 8 | 2.67 | 1.68 |
| CYP2E1 | 10q24.3-qter | rs2515641 | 0.13 | 1296T>C | 421Phe | b | 17 | 1 | 6 | 2.33 | 1.96 |
| PDE1B | 12q13 | rs1249950 | 0.45 | 1642T>C | 492Asn | a | 46 | 1 | 2 | 2.06 | 1.44 |
| BRCA2 (3) | 13q12.3 | rs1799955 | 0.21 | 7469A>G | 2414Ser | b | 32 | 1 | 3 | 2.8 | 1.57 |
| TCF4 | 18q21.1 | rs6567211 | 0.39 | 2123G>A | 643Ser | b | 42 | 1 | 2 | 4.92 | 4.92 |
| MAP3K9 | 14q24.3-q31 | rs3829955 | 0.17 | 2676C>T | 892Asn | a | 32 | 1 | 3 | 3.08 | 1.52 |
| CARD15 (4) | 16q12 | rs2066843 | 0.28 | 1482C>T | 459Arg | a | 41 | 2 | 5 | 3.16 | 2 |
| CDH1 | 16q22.1 | rs1801552 | 0.41 | 2200T>C | 692Ala | b | 27 | 2 | 7 | 2.91 | 1.74 |
| TOB1 | 17q21 | rs4626 | 0.29 | 992A>G | 319Lys | b | 41 | 1 | 2 | 2.06 | 1.24 |
| RIPK4 | 21q22.3 | rs3746893 | 0.38 | 1524G>A | 492Ala | b | 9 587 |
2 29 |
22 5 |
4.18 2.70 (6.5)‡ |
2.35 1.80 (3.5)‡ |
| Untranslated region SNPs | |||||||||||
| BARD1 (1) | 2q34-q35 | rs1129804 | 0.31 | 44C>G | exon1 | b | 46 | 6 | 13 | 2.21 | 1.64 |
| COL4A3 | 2q36-q37 | rs2070735 | 0.14 | 5490C>A | exon52 | a | 16 | 1 | 6 | 2.78 | 1.7 |
| FANCD2 | 3p25.3 | rs7647987 | 0.21 | 4556G>A | intron43 | b | 29 | 1 | 3 | 2.06 | 1.37 |
| TNFSF10 | 3q26 | rs1131542 | 0.34 | 1297C>A | exon5 | b | 49 | 1 | 2 | 2.77 | 1.58 |
| SPARC | 5q31.3-q32 | rs1059829 | 0.47 | 2120T>C | exon10 | b | 54 | 2 | 4 | 2.14 | 1.46 |
| FRK | 6q21-q22.3 | rs495565 | 0.38 | 2566G>A | exon8 | b | 46 | 1 | 2 | 2.56 | 1.41 |
| SLC22A2 | 6q26 | rs3127594 | 0.13 | 2198T>A | exon11 | a | 9 | 3 | 33 | 2.45 | 2.02 |
| SERPINE1 | 7q21.3-q22 | rs1050813 | 0.23 | 2176G>A | exon9 | a | 28 | 2 | 7 | 2.11 | 1.6 |
| Untranslated region SNPs | |||||||||||
| SMO | 7q32.3 | rs1061285 | 0.13 | 3660C>A | exon12 | b | 18 | 1 | 6 | 2.32 | 1.5 |
| NBN | 8q21 | rs1063045 | 0.31 | 212T>C | exon2 | b | 42 | 1 | 2 | 3.07 | 3.07 |
| NOTCH1 | 9q34.3 | rs6563 | 0.48 | 9010G>A | exon34 | b | 46 | 1 | 2 | 2.4 | 1.55 |
| DNMT2 | 10p15.1 | rs10904889 | 0.16 | 2082G>T | exon11 | b | 19 | 3 | 16 | 2.23 | 1.64 |
| CCKBR | 11p15.4 | rs1042048 | 0.33 | 1974G>A | exon5 | a | 6 | 2 | 33 | 2.3 | 2 |
| LRRC32 | 11q13.5-q14 | rs3781701 | 0.32 | 3312T>C | exon34 | a | 17 | 1 | 6 | 2.26 | 1.47 |
| MMP1 | 11q22.3 | rs5854 | 0.33 | 1750T>C | exon10 | a | 16 | 1 | 6 | 2.13 | 1.4 |
| KRAS(6) | 12p12.1 | rs13096 | 0.5 | 3636G>A | exon5 | b | 47 | 1 | 2 | 2.31 | 1.4 |
| KRAS(6) | 12p12.1 | rs1801539 | 0.5 | 4534G>A | exon5 | b | 49 | 1 | 2 | 2.14 | 2.14 |
| HDAC7A | 12q13.1 | rs9859 | 0.21 | 3798C>A | exon24 | b | 31 | 1 | 3 | 3.64 | 1.49 |
| THBS1 | 15q15 | rs1051442 | 0.15 | 3771T>C | exon22 | b | 9 | 1 | 11 | 2.32 | 1.73 |
| LRRK1 | 15q26.3 | rs1048326 | 0.14 | 4704T>C | exon20 | b | 28 | 1 | 4 | 2.36 | 1.52 |
| IMPACT | 18q11.2-q12.1 | rs1053474 | 0.33 | 3452G>A | exon11 | b | 40 | 1 | 3 | 2.41 | 1.37 |
| GNG7 | 19p13.3 | rs3752174 | 0.26 | 808T>C | exon5 | b | 39 | 1 | 3 | 2.14 | 1.45 |
| JAG1 | 20p12 | rs7828 | 0.36 | 5201T>G | exon26 | b | 48 | 1 | 2 | 2.22 | 1.64 |
| TFF2 | 21q22.3 | rs225334 | 0.4 | 513G>A | exon4 | b | 12 744 |
1 36 |
8 5 |
2.13 2.39 (5.3)‡ |
1.45 1.65 (3.1)‡ |
*
Numbers in parentheses identify SNPs marking the same gene.
±
Class a/b identifies SNPs showing ASE exclusively in NFPTR and those common to CEPH and NFPTR, respectively.
†
The extreme and background θ are calculated from those showing ASE and all heterozygotes, respectively.
‡
Values in parentheses represent average fold change calculated from the average θ.