Table 3.
Summary of polygenic risk score genotyping results with noticeably deviating allele frequencies (AFs) of centers of the German Consortium for Hereditary Breast and Ovarian Cancer.
| rs ID | Locus (hg19) | Allele frequencies | gnomAD | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| log OR | IMGAG (WGS) | ICG (MGP) | DMG (MGP) | CFBOC (MGP) | IHG (MGP) | deviating | |||||||||
| BCAC | BRIDGES | Expected | DRAGEN | FB | GATK | FB | GATK | DRAGEN | GATK | FB | GATK | CLC | AF | ||
| rs56168262 | 1-51467096-CT-C | 0.0374 | 0.0374 | 0.4856 | 0.4468 | 0.4025 | 0.4653 | 0.4846 | 0.4907 | 0.1193 | 0.3496 | 0.4922 | 0.4940 | 0.2211 | Yes |
| rs56097627 | 1-110198129-CAAA-C | 0.0458 | 0.0458 | 0.7779 | 0.0560 | 0.0599 | – | 0.4299 | 0.1692 | 0.0284 | 0.2368 | 0.3898 | 0.4880 | 0.1992 | Yes |
| rs12406858 | 1-118141492-A-C | 0.0452 | 0.0452 | 0.2654 | 0.2874 | 0.3096 | 0.2846 | 0.2846 | 0.2523 | 0.2523 | 0.2658 | 0.2670 | 0.2550 | 0.2948 | No |
| rs143384623 | 1-145604302-C-CT | −0.0399 | −0.0399 | 0.3490 | 0.3578 | 0.3628 | – | 0.3904 | 0.4941 | 0.3651 | 0.3467 | 0.3010 | – | – | Yes |
| rs11463354 | 1-172328767-T-TA | −0.0435 | −0.0435 | 0.3264 | 0.3305 | 0.3142 | 0.2637 | 0.3880 | 0.4496 | 0.3211 | 0.2694 | 0.2427 | 0.3127 | 0.3167 | No |
| rs11268668 | see caption | −0.0321 | −0.0321 | 0.7983 | 0.8233 | 0.5433 | 0.8009 | 0.4803 | 0.7917 | 0.7917 | 0.8070 | 0.4769 | 0.7908 | 0.7709 | No |
| rs553796823 | 2-39699510-C-CT | −0.0420 | −0.0420 | 0.4647 | 0.5603 | 0.4865 | 0.5000 | 0.3641 | 0.4956 | 0.0972 | 0.3710 | 0.3856 | 0.4602 | 0.3247 | Yes |
| rs11693806 | 2-218292158-C-G | −0.0757 | −0.0757 | 0.7289 | 0.7457 | 0.7443 | 0.7675 | 0.7675 | 0.7358 | 0.7358 | 0.7112 | 0.7112 | 0.4980 | – | No |
| rs371314787 | 3-49709912-C-CT | −0.0367 | −0.0367 | 0.2847 | 0.2917 | 0.2809 | 0.2305 | 0.2274 | 0.4889 | 0.2376 | 0.2476 | 0.2354 | 0.4980 | 0.2490 | No |
| rs34207738 | 3-141112859-CTT-C | 0.0551 | 0.0551 | 0.4205 | 0.3980 | 0.3929 | 0.4265 | 0.3316 | 0.4566 | 0.4248 | 0.4238 | 0.3800 | 0.3805 | 0.3745 | No |
| rs774021038 | 4-84370124-TA-T | −0.0464 | −0.0464 | 0.5353 | 0.4871 | 0.4840 | 0.5420 | 0.5214 | 0.0000 | – | 0.4757 | 0.4539 | 0.4741 | 0.4741 | Yes |
| rs147399132 | 4-126752992-A-AAT | −0.0377 | 0.5123 | 0.4842 | 0.5092 | 0.4909 | 0.3880 | No | |||||||
| rs199562199 | 5-52679539-C-CA | 0.0571 | 0.0571 | 0.1001 | 0.1049 | 0.1142 | 0.1527 | 0.4376 | 0.1829 | 0.0642 | 0.1262 | 0.1711 | 0.3924 | 0.1195 | No |
| rs113803968 | 5-55662540-C-CT | −0.0458 | −0.0458 | 0.3657 | 0.4066 | 0.3603 | 0.3018 | 0.2957 | 0.4919 | 0.3422 | 0.3350 | 0.2864 | 0.2948 | 0.3028 | No |
| rs113778879 | 5-58241712-C-T | −0.0434 | 0.5762 | 0.0000 | 0.0000 | 0.0000 | 0.0015 | – | |||||||
| rs10074269 | 5-169591460-T-C | 0.0412 | 0.0412 | 0.3393 | 0.3463 | 0.3507 | 0.3538 | 0.3538 | 0.3349 | 0.3349 | 0.3398 | 0.3398 | 0.2709 | 0.2709 | No |
| rs543824204 | 6-20537845-CA-C | −0.0391 | −0.0391 | 0.4741 | 0.2802 | 0.2904 | 0.4412 | 0.5000 | 0.5027 | 0.3119 | 0.4022 | 0.4951 | 0.5000 | 0.2649 | Yes |
| rs574103382 | 6-82263549-AAT-A | 0.0477 | 0.4240 | 0.3391 | 0.3564 | 0.3193 | 0.3880 | Yes | |||||||
| rs73754909 | 6-87803819-T-C | 0.0383 | 0.0383 | 0.2809 | 0.0000 | 0.0004 | 0.0000 | 0.0148 | 0.0734 | 0.2615 | 0.0000 | 0.0350 | 0.0020 | – | – |
| rs55941023 | 6-130341728-C-CT | 0.0472 | 0.0472 | 0.7113 | 0.7414 | 0.7099 | 0.7154 | 0.7154 | 0.6899 | 0.6899 | 0.7197 | 0.7197 | 0.7809 | 0.7809 | No |
| rs57589542 | see caption | 0.0137 | 0.0137 | 0.6130 | 0.3908 | 0.3723 | 0.3488 | 0.3632 | 0.3940 | 0.2954 | 0.3400 | 0.3204 | 0.3506 | 0.2928 | Yes |
| rs10644978 | 7-91459189-A-ATT | 0.0452 | 0.0452 | 0.3332 | 0.3520 | 0.3585 | 0.3134 | 0.3274 | 0.4623 | 0.3514 | 0.3325 | 0.3313 | 0.3566 | 0.3685 | Yes |
| rs111963714 | 7-99948655-T-G | 0.0420 | 0.0420 | 0.2083 | 0.1494 | 0.2113 | – | – | 0.1002 | 0.1523 | 0.1493 | 0.2027 | 0.1793 | 0.0339 | Yes |
| rs5887960 | 7-139943702-CT-C | 0.0582 | 0.0582 | 0.5378 | 0.4468 | 0.4330 | 0.4700 | 0.4752 | 0.4804 | 0.3890 | 0.5085 | 0.4757 | 0.4801 | 0.4084 | Yes |
| rs62485509 | 7-144048902-G-T | −0.0563 | −0.0563 | 0.2289 | 0.1595 | 0.2255 | 0.2265 | 0.2256 | 0.2229 | 0.1092 | 0.2354 | 0.2354 | 0.2490 | 0.1753 | No |
| rs3988353 | 8-17787610-CT-C | −0.0377 | −0.0377 | 0.6217 | 0.5460 | 0.5479 | 0.4345 | 0.4214 | 0.5089 | 0.2495 | 0.3568 | 0.4187 | 0.4960 | 0.1534 | Yes |
| rs1511243 | 8-76230943-A-G | 0.0755 | 0.0755 | 0.8289 | 0.8348 | 0.8376 | 0.8333 | 0.8333 | 0.8376 | 0.8376 | 0.8374 | 0.8374 | 0.6175 | 0.8486 | No |
| rs10975870 | 9-6880263-A-G | 0.0348 | 0.0348 | 0.2900 | 0.3132 | 0.2848 | 0.2975 | 0.2975 | 0.3018 | 0.3018 | 0.2532 | 0.2524 | 0.2968 | 0.1972 | No |
| rs3057314 | 9-21964882-CAAAA-C | 0.0550 | 0.0550 | 0.3210 | 0.2011 | 0.2043 | 0.1803 | 0.1923 | 0.3105 | 0.1101 | 0.1667 | 0.0595 | 0.4183 | 0.0896 | Yes |
| rs4880038 | 9-36928288-T-C | 0.0249 | 0.0249 | 0.5427 | 0.5431 | 0.5440 | 0.5026 | 0.5026 | 0.5165 | 0.5165 | 0.5388 | 0.5376 | 0.4024 | 0.5080 | No |
| rs542275778 | 10-22477776-ACC-A | 0.1687 | 0.1687 | 0.0214 | 0.0187 | 0.0294 | 0.0318 | 0.0256 | 0.0435 | 0.0294 | 0.1535 | 0.0317 | 0.1474 | 0.0299 | No |
| rs2384736 | 10-38523626-C-A | 0.0404 | 0.0404 | 0.3740 | 0.0014 | 0.3996 | 0.0009 | 0.3521 | 0.0000 | 0.1817 | 0.0000 | 0.0836 | 0.0020 | 0.0020 | Yes |
| rs111833376 | 10-71335574-C-T | −0.4040 | −0.4040 | 0.3122 | 0.0417 | 0.0443 | 0.2681 | 0.2684 | 0.2561 | 0.1128 | 0.0181 | 0.3051 | 0.0558 | 0.2231 | Yes |
| rs140936696 | 10-95292187-CAA-C | −0.0512 | −0.0512 | 0.8177 | 0.7677 | 0.7742 | – | – | 0.4492 | 0.1853 | 0.8232 | 0.4746 | 0.4821 | 0.2590 | Yes |
| rs9421410 | 10-123095209-G-A | −0.0538 | −0.0538 | 0.3246 | 0.3247 | 0.3170 | 0.3068 | 0.3068 | 0.2761 | 0.2752 | 0.3058 | 0.3058 | 0.2590 | – | No |
| rs35054928 | 10-123340431-GC-G | −0.2408 | −0.2408 | 0.5971 | 0.5747 | 0.6028 | 0.5744 | 0.5744 | 0.5477 | 0.5477 | 0.5206 | 0.5206 | 0.5418 | 0.5438 | No |
| rs199504893 | 11-108267402-C-CA | −0.0022 | 0.4168 | 0.4526 | 0.4362 | 0.3877 | 0.3137 | No | |||||||
| rs11049431 | 12-28347382-C-T | −0.0521 | −0.0521 | 0.2151 | 0.1997 | 0.2053 | – | – | 0.2138 | 0.2128 | 0.1735 | 0.1735 | 0.1693 | 0.1175 | No |
| rs1027113 | 12-29140260-G-A | 0.0647 | 0.0647 | 0.9124 | 0.9109 | 0.9195 | 0.9162 | 0.9162 | 0.9284 | 0.9284 | 0.9163 | 0.9163 | 0.7649 | 0.9024 | No |
| rs144767203 | 15-100905819-A-C | −0.0608 | −0.0608 | 0.1072 | 0.0934 | 0.1043 | – | – | 0.1112 | 0.1046 | 0.1363 | 0.1371 | 0.0837 | 0.0199 | No |
| rs57920543 | 16-4008542-CAAAAA-C | 0.0550 | 0.0550 | 0.8194 | 0.7457 | 0.7011 | 0.4668 | 0.4658 | 0.4758 | 0.4064 | 0.7959 | 0.4830 | 0.4761 | 0.4442 | Yes |
| rs12709163 | 16-6963972-C-G | 0.0354 | 0.0354 | 0.7915 | 0.7572 | 0.7660 | 0.7846 | 0.7846 | 0.7982 | 0.7982 | 0.7791 | 0.7791 | 0.6932 | 0.7988 | No |
| rs9931038 | 16-85145977-T-C | −0.0211 | −0.0211 | 0.4851 | 0.5431 | 0.5110 | 0.4855 | 0.4855 | 0.4734 | 0.4734 | 0.4757 | 0.4757 | 0.4940 | 0.4940 | No |
| rs79461387 | 17-29168077-G-T | −0.0568 | −0.0568 | 0.2573 | 0.0000 | 0.2567 | 0.2504 | 0.2504 | 0.0257 | 0.2385 | 0.0000 | 0.2494 | – | – | – |
| rs71363517 | 17-43212339-C-CT | 0.0438 | 0.0438 | 0.2273 | 0.2256 | 0.2128 | – | – | 0.4975 | 0.2101 | 0.2017 | 0.2106 | 0.2928 | 0.2012 | No |
| rs2668667 | 17-44283858-G-A | −0.0540 | −0.0540 | 0.1919 | 0.0805 | 0.1872 | – | – | 0.1963 | 0.1413 | 0.1808 | 0.1808 | 0.1813 | 0.0876 | Yes |
| rs1111207 | 18-24125857-T-C | 0.0346 | 0.0346 | 0.4243 | 0.4267 | 0.4135 | 0.4282 | 0.4282 | 0.4321 | 0.4321 | 0.4345 | 0.4345 | 0.3267 | 0.4104 | No |
| rs140702307 | 19-19517054-C-CGGGCG | 0.0437 | 0.0437 | 0.3525 | 0.3405 | 0.3504 | 0.3735 | 0.3000 | 0.3450 | 0.3468 | 0.3410 | 0.2694 | 0.3386 | 0.3247 | No |
| rs66987842 | 22-40904707-CT-C | 0.1148 | 0.1148 | 0.1068 | 0.1207 | 0.1195 | 0.1160 | 0.1188 | 0.1820 | 0.1404 | 0.1141 | 0.1165 | 0.1414 | 0.1016 | No |
Noticeably deviating AFs are shown in bold. Loci (hg19-based) of rs11268668 and rs57589542 are 1-204502514-T-TTCTGAAACAGGG (hg19) and 6-152022664-CAAAAAAA-C (hg19), respectively.
WGS whole-genome sequencing, MGP multi-gene panel sequencing, FB freebayes.