Table 1.
Proposed biallelic SNPs for distinguishing the cfDNA of two individuals.
| SNP ID | Alleles | Chr: position (GRCh38.p12) | European MAF | Global MAF | Position in relation to genes |
|---|---|---|---|---|---|
| rs1935037 | A, T | 1:223323387 | T = 0.4602 | T = 0.4942 | SUSD4 intron |
| rs10168994 | T, C | 2:193486802 | C = 0.4026 | C = 0.4754 | / |
| rs745581 | C, T | 2:2729334 | T = 0.4881 | T = 0.4984 | / |
| rs6546954 | C, G | 2:75182348 | C = 0.4702 | G = 0.4585 | TACR1 and LOC105374811 intron |
| rs1707473* | T, G | 3:146133737 | T = 0.4950 | G = 0.4930 | PLOD2 intron |
| rs6775401 | A, G | 3:183462906 | G = 0.4682 | G = 0.4718 | / |
| rs7431017* | A, C | 3:76502252 | A = 0.4811 | C = 0.4559 | ROBO2 intron |
| rs9289628* | C, T | 3:98548445 | T = 0.4901 | C = 0.4896 | / |
| rs7687645* | T, C | 4:70350352 | T = 0.4523 | C = 0.4970 | / |
| rs615954 | G, C | 5:123144242 | C = 0.4761 | C = 0.4884 | PRDM6 intron |
| rs10078699 | C, T | 5:155125342 | T = 0.4940 | T = 0.4507 | / |
| rs153749 | A, G | 5:171754251 | G = 0.4205 | G = 0.4764 | / |
| rs2561182 | G, C | 5:69437818 | C = 0.4911 | C = 0.4784 | MARVELD2 intron |
| rs7746234 | C, T | 6:138498373 | C = 0.4066 | T = 0.4930 | NHSL1 intron |
| rs2517471 | G, C | 6:31084321 | G = 0.4254 | C = 0.4952 | / |
| rs9656097 | T, C | 7:104526571 | C = 0.4076 | C = 0.4708 | LHFPL3 intron |
| rs751966 | G, A | 7:135879129 | A = 0.4871 | A = 0.4679 | / |
| rs2691527* | C, T | 7:78173386 | C = 0.4881 | T = 0.4647 | MAGI2 intron |
| rs6557883 | T, C | 8:26127967 | C = 0.4811 | C = 0.4992 | LOC105379335 non-coding transcript |
| rs4733016 | C, T | 8:26991085 | T = 0.4722 | T = 0.4806 | / |
| rs2974298 | C, T | 8:42518957 | T = 0.5000 | T = 0.4850 | SLC20A2 intron |
| rs7011817 | G, C | 8:60212109 | G = 0.4771 | C = 0.4667 | CA8 intron |
| rs2246293 | C, G | 9:104928557 | G = 0.4871 | G = 0.4892 | LOC105376196 intron; ABCA1 upstream transcript |
| rs10901532 | T, C | 10:126136495 | C = 0.4414 | C = 0.4591 | ADAM12 intron |
| rs7117897 | T, C | 11:129853970 | C = 0.4632 | C = 0.4561 | TMEM45B intron |
| rs1166235 | G, A | 12:126874295 | A = 0.4563 | A = 0.4888 | LINC02372 intron; LOC105370061 upstream transcript |
| rs10843022 | C, G | 12:27904982 | G = 0.4414 | G = 0.4503 | / |
| rs7972248 | C, T | 12:3515931 | C = 0.4980 | T = 0.4579 | PRMT8 intron |
| rs4770602 | C, G | 13:24136006 | G = 0.4901 | G = 0.4617 | SPATA13 intron |
| rs7321093 | T, C | 13:28573704 | C = 0.4831 | C = 0.4872 | LOC105370135 upstream transcript |
| rs2799341 | T, C | 13:53072591 | C = 0.4036 | C = 0.4501 | / |
| rs3784165 | G, C | 14:31088123 | C = 0.4135 | C = 0.4696 | AP4S1 intron |
| rs8014321 | T, C | 14:91501322 | C = 0.4751 | C = 0.4916 | PPP4R3A intron |
| rs10148348 | T, C | 14:92866186 | T = 0.4732 | C = 0.4950 | / |
| rs1420530* | C, T | 16:52524817 | T = 0.4821 | T = 0.4892 | TOX3 intron |
| rs1392494 | G, A | 16:59678252 | A = 0.4781 | A = 0.4894 | / |
| rs1384366 | G, A | 17:78733702 | A = 0.4553 | A = 0.4665 | CYTH1 intron |
| rs4789798 | C, G | 17:82573767 | G = 0.4254 | G = 0.4603 | FOXK2 intron |
| rs12605230 | G, C | 18:38219647 | C = 0.4871 | G = 0.4996 | / |
| rs6075029 | C, T | 20:16200100 | T = 0.4980 | T = 0.4573 | / |
| rs6050798 | C, T | 20:2641352 | T = 0.4891 | T = 0.4681 | TMC2 3' UTR; LOC105372505 intron |
| rs6070149* | C, T | 20:57554682 | T = 0.4791 | C = 0.4732 | / |
| rs243593 | G, A | 21:17783905 | A = 0.4831 | A = 0.4802 | C21orf91-OT1 intron |
SNPs marked with asterisk (*) were selected for assay design and evaluation of minor allele quantification performance. The European and global minor allele frequencies (MAF) of the SNPs were derived from the 1,000 Genomes Project (18).