Table 2. Detailed results of targeted sequencing on the maternal plasma analysis with Illumina platform and comparison with CVS.
| rs3834466_IIe (−/t) | rs968857_3′ψβ (c/t) | rs10768683_AvaIIβ (g/c) | rs7480526_II74 (c/a) | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample no | Replicate no | No. of reads | Fetal fraction (%) a | Maternal genotype | Predicted genotype (mat. plasma) | CVS | No. of reads | Fetal fraction (%) a | Maternal genotype | Predicted genotype (mat. plasma) | CVS | No. of reads | Fetal fraction (%) a | Maternal genotype | Predicted genotype (mat. plasma) | CVS | No of reads | Fetal fraction (%) a | Maternal genotype | Predicted genotype (mat. plasma) | CVS | ||||
| Maternal allele | Fetal allele | FETAL allele detected?d | Maternal allele | Fetal allele | Fetal allele detected?d | Maternal allele | Fetal allele | Fetal allele detected?d | Maternal allele | Fetal allele | Fetal allele detected?d | ||||||||||||||
| 1 | 1 | 2073484 | 896 | 0.09 | mo:t/t | −/tb | t/t | 1548746 | 10277 | 1.32 | mo:c/c | c/c | c/c | 1897149 | 499 | 0.05 | mo:g/g | g/g | g/g | 1045459 | 1385449 | 113.99 | mo:c/a | NA | NA |
| 2 | 1957152 | 56566 | 5.62 | Yes | 1295375 | 7582 | 1.16 | No | 1694464 | 543 | 0.06 | No | 1329232 | 1214239 | 95.48 | NA | |||||||||
| 3 | 1819521 | 63366 | 6.73 | 1387503 | 7757 | 1.11 | 1884040 | 563 | 0.06 | 1351923 | 815548 | 75.25 | |||||||||||||
| 2 | 4 | 2357978 | 1100 | 0.09 | mo:t/t | t/t | t/t | 1160722 | 34820 | 5.82 | mo:c/c | c/t | c/c | 1825846 | 569 | 0.06 | mo:g/g | g/c | g/g | 1298378 | 1241940 | 97.78 | mo:c/a | NA | NA |
| 5 | 1750844 | 12450 | 1.41 | No | 1051814 | 42483 | 7.76 | Yes | 1910171 | 36498 | 3.75 | Yes | 969808 | 1519854 | 122.09 | NA | |||||||||
| 6 | 1728292 | 666 | 0.08 | 1324234 | 24515 | 3.64 | 1666173 | 120973 | 13.54 | 1436671 | 2150903 | 119.91 | |||||||||||||
| 3 | 7 | 2240645 | 65379 | 5.67 | mo:−/− | −/t | −/t | 1703340 | 41536 | 4.76 | mo:t/t | c/t | c/t | 2208515 | 811 | 0.07 | mo:g/g | g/g | g/g | 1872489 | 16531 | 1.75 | mo:c/c | c/c | c/c |
| 8 | 1944017 | 22796 | 2.32 | Yes | 1872737 | 96027 | 9.76 | Yes | 1894954 | 680 | 0.07 | No | 2254514 | 16372 | 1.44 | no | |||||||||
| 9 | 2296009 | 70803 | 5.98 | 1615333 | 26390 | 3.21 | 1971572 | 747 | 0.08 | 1963487 | 12282 | 1.24 | |||||||||||||
| 4 | 10 | 2219553 | 1792 | 0.16 | mo:t/t | t/t | −/t | 1429699 | 10218 | 1.42 | mo:c/c | c/t | c/t | 2095634 | 688 | 0.07 | mo:g/g | g/g | g/g | 341939 | 1511662 | 163.11 | mo:c/a | NA | NA |
| 11 | 1960695 | 1636 | 0.17 | No | 1037324 | 37577 | 6.99 | Yes | 1832665 | 698 | 0.08 | No | 644981 | 1342593 | 135.10 | NA | |||||||||
| 12 | 2103371 | 1491 | 0.14 | 1335824 | 56647 | 8.14 | 1865159 | 696 | 0.07 | 651981 | 965476 | 119.38 | |||||||||||||
| 5 | 13 | 1053614 | 896692 | 91.95 | mo:−/t | NAc | NA | 1344138 | 35877 | 5.20 | mo:c/c | c/t | c/t | 2104022 | 826 | 0.08 | mo:g/g | g/g | g/g | 2321198 | 22757 | 1.94 | mo:c/c | c/c | c/c |
| 14 | 936608 | 878892 | 96.82 | NA | 1236671 | 13578 | 2.17 | Yes | 1796659 | 777 | 0.09 | No | 2083631 | 17684 | 1.68 | No | |||||||||
| 15 | 854173 | 1171199 | 115.65 | 1060075 | 22627 | 4.18 | 1883374 | 798 | 0.08 | 1774714 | 12425 | 1.39 | |||||||||||||
| 6 | 16 | 2171601 | 3513 | 0.32 | mo:−/− | −/− | −/t | 1349070 | 24017 | 3.50 | mo:t/t | c/t | c/t | 1045257 | 696087 | 79.95 | mo:g/c | NA | NA | 676750 | 19252 | 5.53 | mo:a/a | c/a | c/a |
| 17 | 2200687 | 3182 | 0.29 | No | 1053813 | 24517 | 4.55 | Yes | 942509 | 909284 | 98.21 | NA | 851481 | 14683 | 3.39 | Yes | |||||||||
| 18 | 1937523 | 2728 | 0.28 | 1304525 | 17539 | 2.65 | 950240 | 893454 | 96.92 | 701110 | 14476 | 4.05 | |||||||||||||
| 7 | 19 | 2026011 | 1100 | 0.11 | mo:t/t | t/t | t/t | 1208208 | 40848 | 6.54 | mo:c/c | c/t | c/c | 1934519 | 611 | 0.06 | mo:g/g | g/g | g/g | 2093685 | 19675 | 1.86 | mo:c/c | c/c | c/c |
| 20 | 2190300 | 955 | 0.09 | No | 1124971 | 21212 | 3.70 | Yes | 2006072 | 759 | 0.08 | No | 2158817 | 16864 | 1.55 | No | |||||||||
| 21 | 2038383 | 903 | 0.09 | 959038 | 32842 | 6.62 | 1713765 | 543 | 0.06 | 1884662 | 12393 | 1.31 | |||||||||||||
| 8 | 22 | 2033758 | 30848 | 2.99 | mo:t/t | −/t | −/t | 1260241 | 46185 | 7.07 | mo:c/c | c/t | c/t | 1652465 | 427 | 0.05 | mo:g/g | g/g | g/g | 2102837 | 22228 | 2.09 | mo:c/c | c/c | c/c |
| 23 | 2225247 | 36166 | 3.20 | Yes | 1094286 | 45367 | 7.96 | Yes | 1675197 | 503 | 0.06 | No | 2294171 | 20870 | 1.80 | No | |||||||||
| 24 | 2158341 | 591 | 0.05 | 1369524 | 60658 | 8.48 | 1546598 | 409 | 0.05 | 1839280 | 14216 | 1.53 | |||||||||||||
| 9 | 25 | 2051763 | 36353 | 3.48 | mo:t/t | −/t | −/t | 1321919 | 11531 | 1.73 | mo:c/c | c/c | c/t | 1792980 | 719 | 0.08 | mo:g/g | g/g | g/g | 793248 | 9537 | 2.38 | mo:a/a | a/a | a/a |
| 26 | 1944390 | 1179 | 0.12 | Yes | 1241992 | 9361 | 1.50 | No | 1870102 | 784 | 0.08 | No | 871091 | 9846 | 2.24 | No | |||||||||
| 27 | 2298786 | 83406 | 7.00 | 1106279 | 7763 | 1.39 | 1762583 | 711 | 0.08 | 598521 | 6544 | 2.16 | |||||||||||||
| 10 | 28 | 2482264 | 1325 | 0.11 | mo:t/t | t/t | t/t | 1569485 | 12349 | 1.56 | mo:c/c | c/c | c/c | 993793 | 826316 | 90.80 | mo:g/a | NA | NA | 2277314 | 37611 | 3.25 | mo:c/c | c/c | c/c |
| 29 | 1886618 | 939 | 0.10 | No | 1430534 | 10039 | 1.39 | No | 850463 | 780507 | 95.71 | NA | 2070000 | 21045 | 2.01 | No | |||||||||
| 30 | 2323991 | 1027 | 0.09 | 1272596 | 8017 | 1.25 | 1160267 | 834042 | 83.64 | 1754158 | 15404 | 1.74 | |||||||||||||
Abbreviation: CVS, chorionic villus sampling. NA, not applicable.
a
f = 2*fetal/(mat+fetal).
b
Highlighted genotypes indicate disconcordance of maternal plasma analysis with CVS analysis.
c
Mother heterozygous, father heterozygous for the SNP.
d
Fetal allele is detected if f ≥2.5 for at least two out of three replicates.