Table 1.
General characteristics of investigated arrays.
| Content | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Overall | SNPs/INDELs | CNVs | MT | ||||||||
| Distributor | Array | ShortNamea | Total | autosomal | X | Y | Exonic | Splice-site | |||
| Illumina | Exome V1.1 | Exome | 242,901 | 242,682 | 237,436 | 5107 | 139 | 225,826 | 2082 | 0 | 219 |
| Illumina | Immuno V2 | Immuno | 252,604 | 252,603 | 249,285 | 2115 | 1203 | 6840 | 280 | 0 | 1 |
| Illumina | Cyto12 | Cyto12 | 297,481 | 296,540 | 278,181 | 15,988 | 2371 | 5125 | 21 | 941 | 0 |
| Illumina | Core | Core | 298,930 | 298,725 | 288,675 | 8107 | 1943 | 33,327 | 5237 | 0 | 205 |
| Illumina | DrugDev | DrugDev | 475,233 | 475,035 | 459,659 | 13,405 | 1971 | 74,732 | 1025 | 0 | 198 |
| Illumina | Onco | Onco | 498,315 | 498,195 | 483,528 | 14,355 | 312 | 25,602 | 360 | 0 | 120 |
| Illumina | PsychArray | Psych | 570,100 | 569,789 | 554,577 | 13,890 | 1322 | 266,517 | 7451 | 0 | 311 |
| Affymetrix | Axiom_GW_ASI | Axiom_ASI | 630,191 | 629,957 | 610,467 | 17,268 | 2222 | 14,598 | 40 | 0 | 234 |
| Illumina | 660w-Quad | 660w-Quad | 652,132 | 587,527 | 573,493 | 14,015 | 19 | 11,189 | 37 | 64,484 | 121 |
| Affymetrix | Axiom_GW_CHB | Axiom_CHB | 657,615 | 657,520 | 632,267 | 24,273 | 980 | 10,283 | 282 | 0 | 95 |
| Affymetrix | Axiom_NL | Axiom_NL | 671,222 | 670,931 | 647,127 | 23,033 | 771 | 19,760 | 624 | 0 | 291 |
| Affymetrix | Axiom_GW_EUR | Axiom_EUR | 674,996 | 674,897 | 661,452 | 13,155 | 290 | 16,634 | 64 | 0 | 99 |
| Illumina | OmniExpress | OmniExpress | 715,322 | 715,322 | 695,789 | 18,166 | 1367 | 23,603 | 80 | 0 | 0 |
| Illumina | GSAv1 | GSAv1 | 618,540 | 618,406 | 601,120 | 16,100 | 1186 | 75,481 | 6231 | 0 | 134 |
| Illumina | GSAv3 | GSAv3 | 654,017 | 652,879 | 620,686 | 28,055 | 4138 | 75,481 | 2822 | 0 | 1138 |
| Affymetrix | Axiom_LAT | Axiom_LAT | 817,614 | 817,494 | 791,856 | 25,403 | 235 | 22,977 | 95 | 0 | 120 |
| Affymetrix | Axiom_UKB | Axiom_UKB | 845,485 | 845,131 | 823,234 | 21,084 | 813 | 137,657 | 4101 | 0 | 354 |
| Illumina | CytoSNP850K | Cyto850 | 850,078 | 850,078 | 818,101 | 30,859 | 1118 | 37,793 | 1025 | 0 | 0 |
| Illumina | OmniZhongHua | OmniZH | 899,502 | 899,381 | 873,429 | 23,935 | 2017 | 23,167 | 59 | 0 | 121 |
| Affymetrix | PMRA | PMRA | 920,744 | 920,520 | 883,265 | 37,246 | 9 | 77,781 | 6536 | 0 | 224 |
| Affymetrix | PMDA | PMDA | 921,664 | 920,950 | 857,925 | 62,577 | 448 | 51,811 | 3337 | 0 | 714 |
| Affymetrix | Affy6.0 | Affy6.0 | 933,122 | 932,711 | 893,949 | 37,902 | 860 | 8966 | 33 | 0 | 411 |
| Illumina | MultiEthnic-AMR/AFR | Multi_AFR | 1,426,177 | 1,425,533 | 1,380,255 | 42,918 | 2360 | 357,838 | 4922 | 0 | 644 |
| Illumina | MultiEthnic-EUR/ASN | Multi_EUR | 1,474,463 | 1,473,819 | 1,432,449 | 39,772 | 1598 | 358,382 | 5062 | 0 | 644 |
| Illumina | MultiEthnic-Global | Global | 1,768,335 | 1,767,356 | 1,707,340 | 56,079 | 3937 | 399,721 | 10,325 | 0 | 979 |
| Affymetrix | Axiom_GW_PanAFR | Axiom_AFR | 2,268,172 | 2,267,890 | 2,199,268 | 65,975 | 2647 | 21,954 | 100 | 0 | 282 |
| Illumina | Omni2.5 | Omni2.5 | 2,435,293 | 2,435,200 | 2,376,441 | 57,178 | 1581 | 70,425 | 201 | 0 | 93 |
| Illumina | Omni5 | Omni5 | 4,082,393 | 4,082,109 | 3,965,887 | 113,724 | 2498 | 128,327 | 5298 | 17 | 267 |
aManufacturers’ array names were shortened to improve readability, mostly by compressing population names, or removing version names if irrelevant or superfluous. Four arrays have an acronym as name: the Global Screening Array (GSA, both version), the Precision Medicine Research Array (PMRA), and the Precision Medicine Diversity Array (PMDA).