Table 2 Comparison between the observed prevalence of known SNPs in the 17 studied breast cancer samples and Exome Sequencing Project – presented are the top 50 variants showing higher prevalence among the 17 samples. The variants are sorted according descending chi-square value. High Polyphen score indicates high probability of the variant to alter the protein function
From: Novel Insights into Breast Cancer Genetic Variance through RNA Sequencing
17 Breast cancer samples | ESP | Chi-Square Test | HapMap | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | #Samples | #Var Alleles | #Ref allelels | Var/Ref alleles | #Var Alleles | #Ref allelels | Var/Ref alleles | FREQ 17/FREQ ESP | value | P | Yates value | Yates P | Afr | Eur | Asia | rsID | AA change | Polyphen Score |
HOOK2 | 3 | 6 | 28 | 0.21 | 8 | 12136 | 0.001 | 325.1 | 912 | 0 | 766 | 0 | 0 | 0 | 7.3 | 2305376 | G10R | 0.99 |
ANTXR1 | 3 | 3 | 31 | 0.10 | 21 | 12903 | 0.002 | 59.5 | 138 | 0 | 95 | 0 | NA | NA | NA | 28365986 | R7K | 0.009 |
MCOLN1 | 3 | 4 | 30 | 0.13 | 46 | 12960 | 0.004 | 37.6 | 115 | 0 | 88 | 0 | NA | NA | NA | 73003348 | T261M | 0.614 |
C3orf17 | 3 | 4 | 30 | 0.13 | 65 | 12925 | 0.005 | 26.5 | 82 | 0 | 62 | 0 | NA | NA | NA | 115971253 | V297I | 0.117 |
TNKS1BP1 | 5 | 6 | 28 | 0.21 | 182 | 12808 | 0.014 | 15.1 | 63 | 0 | 52 | 0 | NA | NA | NA | 34448143 | A100P | 0.194 |
PLEC | 4 | 6 | 28 | 0.21 | 185 | 12391 | 0.015 | 14.4 | 59 | 0 | 49 | 0 | NA | NA | NA | 3135103 | R569Q | 0.993 |
DDX18 | 3 | 4 | 30 | 0.13 | 93 | 12913 | 0.007 | 18.5 | 56 | 0 | 42 | 0 | NA | NA | NA | 61755349 | V371I | 0.011 |
AP1M2 | 3 | 3 | 31 | 0.10 | 52 | 12238 | 0.004 | 22.8 | 54 | 0 | 37 | 0 | NA | NA | NA | 34276903 | Y85C | 0.998 |
GEMIN4 | 3 | 6 | 28 | 0.21 | 297 | 12201 | 0.024 | 8.8 | 33 | 0 | 27 | 0 | NA | NA | NA | 191778127 | H873Q | 0 |
LY75 | 5 | 8 | 26 | 0.31 | 658 | 12348 | 0.053 | 5.8 | 24 | 0 | 20 | 0 | NA | NA | NA | 35941588 | T1393I | 0.435 |
TXNDC5 | 4 | 5 | 29 | 0.17 | 289 | 10583 | 0.027 | 6.3 | 18.8 | 0.00001 | 14.4 | 0.0001 | NA | NA | NA | 183777097 | P49S | 0 |
HIST1H1B | 6 | 6 | 28 | 0.21 | 512 | 12494 | 0.041 | 5.2 | 16.7 | 0.00004 | 13.3 | 0.0003 | 0 | 7.5 | 0 | 34144478 | A211T | 0.404 |
IMPACT | 8 | 11 | 23 | 0.48 | 1602 | 11404 | 0.140 | 3.4 | 12.5 | 0.0004 | 10.8 | 0.001 | 4.3 | 16.9 | 2.2 | 582234 | D125E | 0.001 |
AKAP9 | 7 | 9 | 25 | 0.36 | 1229 | 11777 | 0.104 | 3.4 | 11.4 | 0.0007 | 9.5 | 0.002 | 1.7 | 15 | 0.6 | 35759833 | K2476R | 0.001 |
QRSL1 | 3 | 5 | 29 | 0.17 | 456 | 12550 | 0.036 | 4.7 | 12.5 | 0.0004 | 9.4 | 0.002 | 0 | 5 | 5.6 | 34221917 | N263S | 0.593 |
DSG2 | 6 | 7 | 27 | 0.26 | 759 | 11175 | 0.068 | 3.8 | 11.5 | 0.0007 | 9.2 | 0.002 | 0 | 9.9 | 0.2 | 2230234 | I293V | 0.99 |
HLA-DRB5 | 6 | 10 | 24 | 0.42 | 1288 | 10016 | 0.129 | 3.2 | 10.9 | 0.001 | 9.2 | 0.002 | NA | NA | NA | 112872773 | V209L | 0 |
JRK | 4 | 5 | 29 | 0.17 | 459 | 12219 | 0.038 | 4.6 | 11.9 | 0.0006 | 8.9 | 0.002 | NA | NA | NA | 34288113 | T30M | 0.988 |
LAPTM5 | 11 | 14 | 20 | 0.70 | 2541 | 10465 | 0.243 | 2.9 | 10.1 | 0.001 | 8.8 | 0.003 | 2.5 | 25.8 | 7.2 | 35351292 | R226K | 0.002 |
DDRGK1 | 8 | 11 | 23 | 0.48 | 1762 | 11244 | 0.157 | 3.1 | 10.2 | 0.001 | 8.7 | 0.003 | 0 | 19.2 | 0 | 11591 | A303T | 0.004 |
KIF20B | 7 | 12 | 22 | 0.55 | 2044 | 10952 | 0.187 | 2.9 | 9.8 | 0.001 | 8.4 | 0.004 | 2.5 | 26.9 | 37.9 | 1129777 | A50G | 0.918 |
GLB1 | 4 | 6 | 28 | 0.21 | 637 | 11695 | 0.054 | 3.9 | 10.7 | 0.001 | 8.3 | 0.004 | NA | NA | NA | 73826339 | S401G | 0.001 |
WDR55 | 5 | 7 | 27 | 0.26 | 873 | 12133 | 0.072 | 3.6 | 10.4 | 0.001 | 8.3 | 0.004 | NA | NA | NA | 35983033 | Y235C | 0.998 |
THUMPD3 | 8 | 10 | 24 | 0.42 | 1564 | 11442 | 0.137 | 3.0 | 9.7 | 0.001 | 8.1 | 0.004 | 4.3 | 18.9 | 7.8 | 1129174 | R459Q | 0.056 |
NLRP2 | 8 | 14 | 20 | 0.70 | 2629 | 10377 | 0.253 | 2.8 | 9.2 | 0.002 | 8 | 0.005 | NA | NA | NA | 34804158 | T529A | 0 |
XPO5 | 4 | 6 | 28 | 0.21 | 645 | 11467 | 0.056 | 3.8 | 10.1 | 0.001 | 7.9 | 0.005 | 0 | 14.2 | 0 | 34324334 | S241N | 0.002 |
RRS1 | 3 | 4 | 30 | 0.13 | 374 | 12560 | 0.030 | 4.5 | 9.4 | 0.002 | 6.6 | 0.01 | NA | 4.1 | 20.4 | 3739336 | R191L | 0.999 |
PLSCR1 | 6 | 6 | 28 | 0.21 | 770 | 12236 | 0.063 | 3.4 | 8.3 | 0.004 | 6.4 | 0.01 | 0 | 8.3 | 3.1 | 343320 | H262Y | 0.945 |
PTPN12 | 10 | 12 | 22 | 0.55 | 2252 | 10754 | 0.209 | 2.6 | 7.6 | 0.005 | 6.4 | 0.01 | 19.7 | 11.3 | 29.8 | 3750050 | T573A | 0.001 |
REV3L | 4 | 6 | 28 | 0.21 | 789 | 12215 | 0.065 | 3.3 | 7.9 | 0.004 | 6 | 0.01 | 3.8 | 4.1 | 0 | 458017 | Y1156C | 0.002 |
ERBB2IP | 7 | 9 | 25 | 0.36 | 1498 | 11506 | 0.130 | 2.8 | 7.4 | 0.006 | 6 | 0.01 | 0 | 17.8 | 8.1 | 3213837 | S274L | 0.024 |
SHARPIN | 4 | 4 | 30 | 0.13 | 401 | 12255 | 0.033 | 4.1 | 8.1 | 0.004 | 5.6 | 0.02 | NA | NA | NA | 34674752 | P294S | 0.447 |
KIAA1755 | 10 | 19 | 15 | 1.27 | 4605 | 8401 | 0.548 | 2.3 | 6.2 | 0.01 | 5.4 | 0.02 | 10.8 | 47.5 | 38.8 | 3746471 | R1045W | 0.003 |
SEC63 | 3 | 4 | 30 | 0.13 | 427 | 12579 | 0.034 | 3.9 | 7.6 | 0.006 | 5.2 | 0.02 | NA | NA | NA | 17854547 | V556I | 0.203 |
LAMC2 | 4 | 6 | 28 | 0.21 | 848 | 12158 | 0.070 | 3.1 | 6.9 | 0.009 | 5.2 | 0.02 | 0 | 9.9 | 0.2 | 11586699 | T124M | 0.999 |
ZNF880 | 4 | 7 | 27 | 0.26 | 376 | 4190 | 0.090 | 2.9 | 6.7 | 0.009 | 5.2 | 0.02 | NA | NA | NA | 14048 | V12M | 0.999 |
IGFBP7 | 7 | 8 | 26 | 0.31 | 640 | 5676 | 0.113 | 2.7 | 6.6 | 0.01 | 5.2 | 0.02 | NA | NA | NA | 11573021 | L11F | 0.005 |
PHF3 | 3 | 3 | 31 | 0.10 | 255 | 12751 | 0.020 | 4.8 | 8.2 | 0.04 | 5.1 | 0.02 | NA | NA | NA | 34288820 | V525I | 0.972 |
KIAA0232 | 3 | 4 | 30 | 0.13 | 395 | 11489 | 0.034 | 3.9 | 7.5 | 0.006 | 5.1 | 0.02 | NA | NA | NA | 116439703 | P1138S | 0.22 |
PJA1 | 7 | 11 | 23 | 0.48 | 1742 | 8821 | 0.197 | 2.4 | 6.2 | 0.01 | 5.1 | 0.02 | 12.5 | 24.6 | 12.5 | 11539157 | E606D | 0.992 |
PRCP | 3 | 3 | 31 | 0.10 | 265 | 12741 | 0.021 | 4.7 | 7.8 | 0.005 | 4.8 | 0.03 | NA | NA | NA | 2228312 | T465S | 0.021 |
MXRA5 | 14 | 23 | 11 | 2.09 | 5006 | 5557 | 0.901 | 2.3 | 5.6 | 0.02 | 4.8 | 0.03 | 22 | 27.6 | 34.9 | 1974522 | P1665S | 0.689 |
PARP14 | 7 | 7 | 27 | 0.26 | 1022 | 10826 | 0.094 | 2.7 | 6.1 | 0.01 | 4.7 | 0.03 | 4 | 7.6 | 10.9 | 13093808 | A561E | 0.972 |
EML4 | 12 | 15 | 19 | 0.79 | 3414 | 9592 | 0.356 | 2.2 | 6.6 | 0.02 | 4.7 | 0.03 | 11.7 | 26.7 | 43.9 | 28651764 | K398R | 0.003 |
ACOX1 | 13 | 24 | 10 | 2.40 | 6616 | 6390 | 1.035 | 2.3 | 5.3 | 0.02 | 4.5 | 0.03 | 13.6 | 34.9 | 29 | 1135640 | I312M | 0.007 |
SP110 | 3 | 6 | 28 | 0.21 | 928 | 12078 | 0.077 | 2.8 | 5.6 | 0.01 | 4.16 | 0.04 | 0 | 9 | 4 | 11556887 | A128V | 0.999 |
PPL | 12 | 20 | 14 | 1.43 | 5261 | 7733 | 0.680 | 2.1 | 4.7 | 0.03 | 4 | 0.05 | 0 | 47.5 | 30.4 | 2037912 | Q1573E | 0.994 |
TBL2 | 3 | 4 | 30 | 0.13 | 489 | 12517 | 0.039 | 3.4 | 5.9 | 0.01 | 3.9 | 0.05 | NA | 3.1 | NA | 35607697 | V345I | 0.969 |
ZBTB45 | 3 | 4 | 30 | 0.13 | 491 | 12511 | 0.039 | 3.4 | 5.9 | 0.01 | 3.9 | 0.05 | NA | NA | NA | 35430780 | D293E | 0 |
TMEM106C | 4 | 6 | 28 | 0.21 | 962 | 12044 | 0.080 | 2.7 | 5.1 | 0.02 | 3.8 | 0.05 | 0 | 11.2 | 40.4 | 2286025 | S175F | 0.985 |
