Table 1.
Primer sequences and plex level and composition for the KIR/MALDI genotyping assay
| Well number | SNP assay name | 5′ Capture primer (5′ 10-mer tag not shown) | 3′ Capture primer (5′ 10 mer tag not shown) | Extend primer |
|---|---|---|---|---|
| W1 4 plex | 2DS3.D1.G | CTGTGATCACGATGTCCAG | AAGGCCAACTTCTCCATCGG | CACTCCCCCTATCAGTT |
| 2DL2.D2.S | GAGCTCCTATGACATGTACC | GCCTGGAATGTTCCGTTGACCTTG | CCCTGCAGAGAACCTAC | |
| 3DL3.D1.G | GATGACTAAGGACCCCTTGC | TCATGGGACCCATGGAATAG | AATAGTTGACCTGGGAACCC | |
| 3DL3.D2.G | AGAATGTGACCTTGTCCTGC | CAGTGAGCCTAAGTTCACCG | GGATAGATGGTAAATGTCAAA | |
| W2 3 plex | 2DL4.DO.G | TGCCGACCACTCAGTGGG | CCCTGAGCTCTACAACAGAA | TGGAACAGTTTCCTCAT |
| 3DL2.TC.G | GATGAACAAGACCCTCAGGAGGTG | TACACGCTGGTATCTGTT | GCCTCTGAGAAGGGCGA | |
| 3DS1.3DL1.D1.S | CAAGGCCAATTTCTCCATCG | GGGAGCTGACAACTGATAGG | CTGTAGGTCCCTGCAAGGGCA | |
| W3 4 plex | 2DL5.D2.G | TGACAGAAACAAGCAGTGGG | GACTTTCCTCTGGGCCCTG | CCACGGAGGGACCTACA |
| 2DL5.TC.G | CTTGGGCCTCTGAGAAGGG | CAAGACCCTCAGGAGGTGAC | CACTGCGTTTTCACACAGA | |
| 2DS4.D1.G | AGAGACAGTCATCCTGCAATG | ATGGAGAAGTTGGCCTTGGA | GAAGTGCTCAAACATGACATC | |
| 3DL2.D1.G | GGAGCTGACAACTGATAGGG | CCAAGGCCAACTTCTCCATC | CTTGCAGGAACCTACAGATG | |
| W4 3 plex | 2DL1.D2.G.no004 | GACTTTGACCACTCGTAT | CAGGGCCCAAGGTCAACG | ATGCTTCGGCTCTTTCC |
| 2DL4.TC.G | ATCTGTTGAGGGTCTCTTGC | AGGTGACATACGCACAGTTG | CACAGTTGGATCACTGC | |
| 2DL2.004.TC.G | GGCCGAGGAGTACCTACCT | GTAATGGACCAAGAGTCTGC | GAAACAGAACAGCGAATA | |
| W5 2 plex | 2DS2.D1.G | AGAAGTTGGCCTTGGAGACC | CCTGCAATGTTGGTCAGATG | GCACAGAGAGGGGAAGT |
| 3DL1.TC.S | ATGGGCAGGAGACAACTTTG | CACTGCGTTTTCACACAGAG | GAGGCCCAAGACACCCCC | |
| W6 2 plex | 2DS5.D2.G | AGGCCCATGAACGTAGGCTCC | AAGAGCCGAAGCATCTGTAG | CTCCGTGGGTGGCAGGG |
| 2DL1.no005.2DL2. 004.TC.S | GTAATGGACCAAGAGTCTGC | CGGGCCGAGGAGTACCTACCT | CGCTATTCGCTGTTCTGTT | |
| W7 uniplex | 2DL3.2DL2.D1.S | GAGTCCACAGAAAACCTTCCCTCC | AGTGTCCTTAAACTTCCCTTCTC | CTTCTGATTTCACCAGG |
| W8 2 plex | 2DS3.D2.S | AGGTCAACGGAACATTCCAGGCCG | AAGAGCCGAAGCATCTGTAG | CATCTGTAGGTTCCTCC |
| 3DS1.TC.G.INT | AACTGCTATGATTAGCTTC | GATGAAGGAGAAAGAAGAGGAGGA | GAATGTGCAGGTGTCTG | |
| W9 5 plex | 3DP1.D2.G | GAGCTGCAGGACAAGGTCAC | TGGGAAACCTTCTCTCTCAGCC | CTCTCTCAGCCCAGCCG |
| 3DS1.DO.S | TCATGCTATACAAAGAAGAC | TGTGTAGTTCCCTGCATGTG | AGGGCTCATGTTGAAGC | |
| 2DL5sub5 | GATCTTGGCTTAGCATTTGG | CTGCGTTTTCACACAGAC | CTTCTCAGAGGCCCAAG | |
| 2DL5sub4 | CCACGGAGGGACCTACAC | GTGACAGAAACAAGCAGTGG | GTGAGTCATGGAGAGAGC | |
| 2DL5sub1 | AGGACAAGCCCTTGCTGTCT | CAAGACGAGAGCGACACA | GTCCTCCTCGAGGCACCACAG | |
| W10 2 plex | 2DS5.D1.G | ACACTTTGCGCCTCATTGGAG | GTGAGTAACAGAACCGTAG | GACCGATGGAGAAGTTG |
| 2DP1.D0.G | GGGTTTAACAACTTCAGTCTGT | TGTGCTGGGGTCACAGGGCC | ATTCTGTTGTAGAGCTCAG | |
| W11 2plex | 2DS2.D2.G | GTCTATATGAGAAACCTTC | GGACAAGGTCACGCTCTCTC | CACGCTCTCTCCTGCCA |
| 2DL1.2DS1.D1.S.tri | AAGGCCAACTTCTCCATCA | GTGAGTAACAGAACCGTAGC | GGTCCCTGCCAGGTCTTGC | |
| W12 2 plex | 2DL5sub3 | GACATGAGTCCTCTGACCTG | CCCTGAGCTCTACAACAA | GCAACCCCCTGGTGATC |
| 2DL5sub2 | GACATGAGTCCTCTGACCTG | CCCTGAGCTCTACAACAA | CGCTCCCCCATTGAGTGGTC | |
| W13 2 plex | 2DS4del.sub | TTGACCACTCGTAGGGAGC | CGGTTCAGGCAGGAGAGAAT | CCTTGTCCTGCAGCTCC |
| 2DL5sub6 | TAAGGTGGCGCCTCCTTCTC | CAAGACGAGAGCGACACA | AGCAAGGGCTTGTCCTG | |
| W14 2plex | 2DS4.D2.S | GAGCTCTGTGACGGAAACAA | GCATCAACGGAACATTCCAGGCC | TCGGCTCTTTCCGTGAC |
| 2DL3.TC.S.INT | CTGCTTCGTGAGACTTACTT | GTAACCCCAGACACCTGCATG | TCTCCTTCATCGCTGGTGCT | |
| W15 uniplex | 2DL2.001.2.3.D1.G | GGAGCTGACAACTGATAGGG | CCTGCAATGTTGGTCAGATG | CATGATGGGGTCTCCAA |
| W16 uniplex | 2DS1.D2.G | ACTTGACTTTGACCACTCGT | CCTATGACATGTACCATCTA | CAACGGAACATTCCAGGCC |
The assays are named according to the following convention: “Targeted Locus.Targeted Domain.Specificity (G or S).comment.” If more than one locus is targeted, the convention is “Targeted Locus. 2nd Targeted Locus.Targeted Domain.Specificity (G or S)”. A “universal” 10-mer tag (ACGTTGGATG) is added to the 5′ end of each of the capture primers to keep the capture primers out of the “mass window” where the extension primers are measured.
W Well, e.g., W1 well no. 1; INT intronic; G generic, i.e., primers are designed to capture more than the targeted locus; S specific, i.e., primers were designed to exclude most of the KIR genes; D0 domain 0; D1 domain 1; D2 domain 2; Trans/Cyt transmembrane/cytoplasmic domain; sub subtyping primer; tri triallelic choice