. 2002 Sep 23;71(4):759–776. doi: 10.1086/342973

Table A.

Oligonucleotide Primer Sequences for the First- and Second-Round Amplification of 49 STRs^[Note]

Locus^a	Sequence (5′→3′)	Location	Nucleotide Position^b
*D6S291:
5o′	AGCTCAGAGGATGCCATGTC
5i′	GTCTAAAATATCCATCCGGC
3′	GGGGATGACGAATTATTCACTAACT	2.4 Mb centromeric to DPB1	Centromeric to DPB1
*D6S439:
5o′	GTCCACATTGCATGGGTCTG
5i′	GATGATTTAAGTTTCCTGTGGACC
3′	TTCAAGGACAGCCTCAGGG	.85 Mb centromeric to DPB1	Centromeric to DPB1
DPB2:
1720	TTACAGGAGGACATAAGTCC
2000	TTTAGGCAAGGTCAGCAACC	DPB2 intron 5	221554
DPB2A2:
5′	TGGGCTTGAGCTAAAGACTG
3i′	GGCAGGAGAATGGCATAAAC
3o′	TAGTGCCAGCTACTAGGAAG	Centromeric to DPB1	254315
DPB1:
14251	TGTCGTCTAAGTCTGCATTC
14528	TGCTGTGCACTGATTGTGTG	DPB1 3′ UTR	263644
DPB1tetra:
5o′	ATGCTGCCTGGGTAGAAATC
5i′	TCTTGGAGGGGGAAACATTC
3′	TGCATTCCAGACTTGGCAAC	DPB1	266072
DNA:
5200	CCTCAGTGGAGTCAGTCATG
5446	CCCAAGCAGTTCTTATGTGC	DN-A 3′ UTR	344577
DNRNGCA:
5o′	GGTGACATACATCAACTTGTG
5i′	AGGAATCTAGTGCTCTCTCC
3′	CTCTAGCAAAAGGAAGAGCC	Between HLA-DNA and RING3	355527
RING3CA:
5′	GCATACACTCTGAAGCAGCC
3i′	GATGGGAAGTTTCCAGAGTG
3o′	GAGGTAATGTCACAGGATGGG	RING3	375386
G3.64842:
5o′	GAGACAGAAGTAACAAAGGC
5i′	TGATGGCAGAAGTAATCCAG
3′	GTATAAGCCATTGCCACCAG	Between HLA-DMB and LMP2	461218
*TAP1CA:
5o′	CGCCATGTACTGTTCATATC
5i′	GCTTTGATCTCCCCCCTC
3′	GGACAATATTTTGCTCCTGAGG	TAP1	498684
2-7A:
5o′	GGGGAAGGATTCTAAATAGG
5i′	GTATTTCTGTATGACTCTGG
3′	AACCCAGCATTCTGGAGGTG	Between DQA2 and DQB3	601210
G4-96:
5o′	AGTCCCAGCTACTACTCAGG
5i′	TCACACCACTACACTCCATG
3′	CAACGGCATGTCAATTAGTGC	Between DQA2 and DQB3	612822
2-8:
5′	ATGAGATTGCACCACTGCAC
3i′	TACCTCCAACACTTTCTGGC
3o′	TATACGTCCCATGAGGACAG	Telomeric to DQB3	634333
G5-11525:
5o′	GGTAAAATTCCTGACTGGCC
5i′	ATTTGCCCTGAGGTCTATGC
3′	GACAGCTCTTCTTAACCTGC	Between DQB3 and DQB1	648774
*DQCARII:
5o′	TCTTGAGGACTGAGTCTGAG
5i′	GGGCAGCATTTGTAGATTTC
3′	GGCAAGAATCCAGCATTTTGG	Telomeric to DQB1	700000
DRB1CA:
5o′	TAGATTGTGGTACTATCAGG
5i′	TTTGAGTTAACTTCCACACG
3′	GAGCTAGTCATTCCTTATTC	DRB1	767929
DRA-CA:
5o′	ACATTATGTTCTGTTGCATG
5i′	TGGAATCTCATCAAGGTCAG
3′	TACTTTCCTAATTCTCCTCC	DRA	890718
2-10:
5o′	AGGTGACCTGGACCTTACTG
5i′	TTGTTGGAGGGGCAAAAGT
3′	ACACTATGCTAGTCTGTGCC	Between BTL-II and TSBP	952064
2-11:
5o′	TTCAGTATCCACTCACCAGG
5i′	CTGCCTATAGATGTTCCCTC
3′	TGTTGAGTTCTGGAGATAGG	Between TSBP and NOTCH4	959038
3-3A:
5o′	AAGATCACCCTACCACACTC
5i′	AGAGTGAGAGACTCTGTCTC
3′	AGGGAGAAGGATAGATAAGG	Between TSBP and NOTCH4	995315
3-2A:
5′	GGCAAAGTCAAGAACTTTCC
3i′	AGCTGAATAGTATTCCACTAC
3o′	CCAGGTTCATCCATGTTGTC	Between TSBP and NOTCH4	1049652
3-1:
5′	AAGCAACTGCTCTCGTAGAG
3i′	CCCAACACCTGCTCATTTTC
3o′	TTCAGTGACTTTGCTCTCAGC	Between NOTCH4 and G18	1111584
3-1A:
5′	AAAGGCCTCTACACCCAGAG
3i′	TGACAGACTGGGACTCCATC
3o′	AGGAGGTGAAGGTTGCAGTG	Between NOTCH4 and G18	1114474
3-3:
5′	CCTGACCACAAAGCTTTCTC
3i′	GGCAACAGAGCTCAAAAAAC
3o′	AAAGGTTGCAGTGAGCCAAG	Between TNXB and CYP21A2	1247950
3-4:
5o′	AGTTCGCACCACTGTAGTCC
5i′	ATAGAGTGAGACCCTGTCTC
3′	ATGAGGATACCCACTCTACC	Between BF and C2	1354878
3-4d:
5o′	ACAAAGTTCTGGCGAGGAAC
5i′	ACCAGTGGCTTCCAAACTTC
3′	GAGATCACGCCATTGCACTC	Between BF and C2	1358331
3-5:
5o′	CATGGAGAGAGCATGTGTTC
5i′	CTGATTGTGAGGTCACTGTG
3	AGATTGTGCCACTGCACTCC	Between HSPA1L and G7b	1483675
*D6S273:
5o′	CTTGCTAAATCAAATAAAGTC
5i′	GGAGAAGTTGAGTATTTCTGC
3′	ACCAAACTTCAAATTTTCGG	Between G6d and G6e	1577288
BAT2CA:
5o′	AAAGCTCCCTTCACTTTATC
5i′	TACAAGGGCTTTAGGAGGTC
3′	AGCCTGGATAACAGAACGAG	Telomeric to BAT2	1683589
3-7:
5o′	AGATTTCATCCAGCCACAGG
5i′	GCCTTTAAAGGTCGTCAGAG
3′	ATCCAATCACCTCTGCTCAC	Between LTA and NFKBIL1	1725566
MICB-CA:
5o′	ATGGGCAAGACTTCAATGGC
5i′	CCACAACGAGATACCACTTC
3′	CTACCTCCTTGCCAAACTTG	MICB	1789221
3-11:
5′	TAGCTGGGACTACAGACTGG
3i′	ACAAAGCAAGACCCAGTCTC
3o′	AAGTTCAAGACCAGCATGGG	Between MICA and HLA-B	1895528
*MIB:
5o′	CCCATGCTGAATTAGCTGAC
5i′	GCTTCACCCGATCAGTAGAAGAC
3′	CGTACCACAGTCTCTATCAGTCCAG	Between MICA and HLA-B	1909387
HLABC-CA:
5o′	CCCAGTAGTAAGCCAGAAGC
5i′	TGGGCAATGAGTCCTATGAC
3′	TGCCATTTGGCCCTAAATGC	Between HLA-B and HLA-C	1999074
1-1k:
5o′	CCAAGATTGTGCCATTGCAC
5i′	GCGACAAGAGAGAAACTCTG
3′	GGTGTTGGTTTTGTAACTCC	Telomeric to CDSN	2183701
1-1g:
5o′	TACTCGGAAAGCTGAGGCAC
5i′	CTGAGATCGCACTACTGCAC
3′	GTCTTTCCCCTGAACCAAAC	Telomeric to CDSN	2189182
1-2A:
5o′	TATTGTCCTATGACCCTGCC
5i′	CTCTGCGAGAAACACCCAAG
3′	CAGCGGAAAAATTCAGATCG	Centromeric to P52	2307351
1-3:
5o′	AACCTAAGCCTTCACCTCTC
5i′	CTCAGCAGGAACCAGACAAC
3′	TTGGGACTACAGGTGTGAGC	Between DDR and IER3	2419106
1-3A:
5′	CAGCAGACCTACCCTAAAAG
3i′	TGAGATCCTGCTTCTACACG
3o′	AGGAGTTTGAGAGTAGCCTG	Between DDR and IER3	2420460
1-3B:
5′	AGAGCGAGACTCCTTCTAAG
3i′	TTGCACTTACTGGACCCCTG
3o′	TTTCTGACTCCACCTCACAG	Between DDX16 and PPP1R10	2554452
1-3F:
5o′	ATTACTTGAACCCAGGAGGC
5i′	CTGGCAACAGAGTAAGACTC
3′	CTTCACAGGGTTATTAGGGG	Between PPP1R10 and ABCF1	2623029
1-6:
5′	CTGAGGTCTGTGGTCATAAC
3i′	ATATTTTCCTGCTGCTGCCC
3o′	TCCCATGATCCTTACAGCAG	Between RANBP1 and GT257	2776550
1-7A:
5′	TACATTCTGTAGGCATTTTCAAGC
3i′	GGGCAACAAGATCAAAACTC
3o′	ATTGTGGTAAGCCGAGATTG	Between CAT75X and ZNF173	2947999
1-8:
5′	CTTACATGAATCGCAGAGGG
3i′	AATTTGGACCCACTCCGCTG
3o′	TTCTGGGTAATTCGAGACGC	Between ZNFB7 and RNF9	3052507
1-8A:
5o′	TGTAAGGATTGCTCATCGGG
5i′	CCCTCCTACGGTCCCAAATC
3′	TCTTGCCTTCTCCCCGCTAC	Between ZNFB7 and RNF9	3053094
1-8e:
5′	CGTGCAAGCCGAAAGTCTTC
3i′	CACTGTCCCTGGTTTATAGC
3o′	ACCACAACCTCACTTGATCC	Between HCG1 and ZNRD1	3121184
*D6S265:
5′	AGTCACCCTACTGTGCTATC
3i′	ATCGAGGTAAACAGCAGAAAG
3o′	AAAGGTTGATCTAATCGAGG	Between HTEX4 and HCGVIII-1	3164186
1-9:
5o′	CCATCCTGAGTCTTGTGATC
5i′	TTAAAGATTTGCACAATGAG
3′	GGAAGCTTAAAAACCAGCAG	Between HCGIV-6 and HCGII-7	3300981
1-9d:
5′	AGTCTATCATGGGACTTCTC
3i′	GCCTCCATAATTGTGTGAGC
3o′	ATCAGTGATACTATGACAGG	Between HCGII-7 and HLA-G	3375510
*RF:
5′	CTGTCCTATTTCATATGCTCAGG
3i′	CTGAGAATGAAGGTCTAGAG
3o′	ATGAACTTGTCCTGAGAATGAAG	HLA-F	3490957
*MOG-CA:
5o′	GAAATGTGAGAATAAAGGAGA
5i′	CACTCTCTAAGATCTCTTCC
3′	GATAAAGGGGAACTACTACA	Telomeric to HLA-F	3541259

Note.— Three oligonucleotide sequences are provided in the 5′-to-3′ orientation per locus. The first round of PCR amplification utilizes the 5′ or 3′ primer (shown in boldface italic type) matched with the outer 3′ or 5′ primer designated as “o” (e.g., D6S291 5o′ and 3′). The second (nested) round of amplification utilizes the same 5′ or 3′ primer matched with the internal 3′ or 5′ primer designated as “i” (e.g., D6S291 5i′ and 3′).

The three underlined loci are SNPs genotyped by SSCP analysis in select samples, as previously described by Cullen et al. (1997). The asterisk (*) preceding nine loci indicates a previously published STR amplified using the newly designed oligonucleotide primers listed.

The location of each marker is given as the nucleotide position centromeric to the tapasin gene (TAPBP), located at the centromeric end of the MHC.