Genetic Characteristics of 22 Y-STR loci in Koreans

Transcription

1 Genetic Characteristics of 22 Y-STR loci in Koreans Myung Jin Park, Hwan Young Lee, Na Young Kim, Jeong Eun Sim, Woo Ick Yang, Sang-Ho Cho, Kyoung-Jin Shin Department of Forensic Medicine, Yonsei University College of Medicine Human Identification Research Center, Yonsei University Establishment of a Korean Y-STR database for 22 Y-STRs 22 Y-STRs DYS9, DYS385, DYS388, DYS389I/II, DYS390, DYS39, DYS392, DYS393, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635 and GATA H4. 3 multiplex PCR systems 708 unrelated Korean males Haplotype alleles analysis and characterization of atypical

2 Schematic of 3 multiplex PCRs for 22 Y-STRs 00 bp 50 bp 200 bp 250 bp 300 bp I I II II H III DYS385 was included in each multiplex to detect sample switching Small amplicon was designed for DYS385 in multiplex III ( bp vs bp) Y-STR analysis in 708 Koreans Y-STR haplotype No. of haplotype Haplotype diversity Discriminatory power Minimal Haplotype loci Y-filer loci haplotype Y-STRs haplotype Atypical alleles Intermediate alleles at DYS447, DYS449, DYS458 and DYS464 Duplicated alleles at DYS9, DYS390 and DYS447 Different allele designation at DYS385 depending on the primer binding site Null allele at DYS448

3 Microvariant and intermediate alleles in DYS447, DYS449, DYS458 and DYS464 Locus Allele Sequence structure N DYS447 8 (TAATA) 7 TAAAA (TAATA) 0 TAAAA(TAATA) n 2 9 (TAATA) 7 TAAAA (TAATA) TAAAA(TAATA) n 4 DYS (25)* (TTTC) 2 -tctc-n0-n32-cttc-(tttc) 4 30 (30.)* (TTTC) 6 -tctc-n0-n32-ctttc-(tttc) 4 33 (42)* (TTTC) 5 -tctc-n0-[n32-cttc] 2 -(TTTC) 8 DYS458 DYS (TTTC) 3 TC(TTTC) 0 -tctc-n0-n32-cttc-(tttc) (TTTC) 3 TT(TTTC) -tctc-n0-n32-cttc-(tttc) (TTTC) 3 TC(TTTC) 0 -tctc-n0-n32-cttc-(tttc) (TTTC) 6 -tctc-n0-n32-cttc- (TTTC) 0 TT(TTTC) (GAAA) 4 G 7.2 (GAAA) 5 AA(GAAA) (CCTT) 7 CTT(CCTT) (CCTT) 3 CTT(CCTT) 5 * Ostensible alleles at DYS449 Duplicated alleles at DYS9, DYS390 and DYS447 Locus Allele Sequence structure DYS9 6,7 (TAGA) 3 tagg(taga) 3,4 DYS390 22,23 (TCTG) 8 (TCTA) 9,0 (TCTG) (TCTA) 4 DYS447 23,24 (TAATA) 7 TAAAA(TAATA) 7,8 TAAAA(TAATA) 7

4 Different allele designation at DYS385 in multiplex I/II and multiplex III Multiplex I/II Multiplex III 3 samples different by 2 repeat 5 samples different by repeat Characterization of allele designation difference at DYS385 Due to the deletion mutation in 8 samples, DYS385 allele designation in multiplex I and II was differently observed from that in multiplex III. 8 bp deletion: (gagaaaaa)2 -N38-(aagg) 6 (GAAA) n 4 bp deletion: (gagaaaaa) 2 -N38- (aagg)6 5(GAAA) n F primer in multiplex I/II agcatgggtg acagagctag acaccatgcc aaacaacaac aaagaaaaga aatgaaattc agaaaggaag gaaggaagga gaaagaaagt aaaaaagaaa gaaagagaaa aagagaaaaa gaaagaaaga gaagaaagag aaagaggaaa F primer in multiplex III 8 bp deletion gagaaagaaa ggaaggaagg aaggaaggaa gggaaagaaa gaaagaaaga R primer in multiplex I/II aagaaagaaa gaaagaaaga aagagaaaaa gaaaggagga ctatgtaatt 4 bp deletion ggaatagata gattattttt taaaatattt ttattacctt tacagttttt R primer in multiplex III ttaaatgccg ccatttcaga aagaaatctg gtcagcagcc cttaccagct

5 Null allele at DYS448 In 6 samples, null allele at DYS448 were commonly observed using multiplex II and Y-filer Multiplex II AmpFlSTR Yfiler kit Multiplex PCR assay of AZFc markers Male control Female control sy20 sy29 ZFX/ZFY (control) sy206 sy9 sy6

6 Characterization of the null allele at DYS448 Schematic representation of Y-STRs and STS markers Null alleles at DYS448 were occurred with partial AZFc deletion. Frequencies of null allele at DYS448 in various ethnic groups Korean 6 in % Present study Japanese 0 in % Mizuno et al. FSI In press Nepalese 3 in % Parkin et al. FSI 2006 Malays, Chinese and Indian in Malaysia 3 in % Chang et al. FSI 2006 Kalmyk 7 in % Roewer et al. FSI In press Mexican in % Gutiérrez-Alarcón et al. Leg Med 2007 Spanish in % Sánchez et al. FSI In press Asian 2 in % AmpFlSTR Yfiler database African American 2 in % AmpFlSTR Yfiler database Caucasian (USA) 2 in % AmpFlSTR Yfiler database The The relatively high high frequencies of of the the DYS448 null null allele allele in in Asians suggest giving careful consideration to to the the use use of of DYS448 for for commercial genotyping and and further database construction in in Asians.

7 Mutation analysis of 22 Y-STRs Sequence information for 35 mutations observed at 6 among 22 Y-STRs

8 Electropherograms for DYS464 in five father-son pairs with mutation events Comparison on Y-STR mutation rates between the present study and previous literature summary

9 Numbers of haplotypes and haplotype diversities obtained by adding each marker to the extended SWGDAM haplotype Concluding remarks. 8 microvariant alleles at DYS449, 6 intermediate alleles at DYS464, 2 intermediate alleles at DYS458, and duplicated allele at DYS9, DYS390 and DYS447 have been discovered and characterized. 2. At DYS385, allele size differences were one or two repeats dependent on the primer set used for PCR amplification and two widely used commercial kits amplify DYS385 so as to include the mutable sites. 3. Arrangement analysis of sequence tagged sites demonstrated that the deletion patterns at DYS448 (and DYS464) were associated with arrangements of the AZFc gene and the DYS448 deletion appears relatively frequent in Asians. 4. The combined haplotypes of DYS447, DYS458, DYS635, GATA H4., and SWGDAM Y-STR loci was comparable to haplotypes of 7 loci in the AmpFlSTR Yfiler kit in Koreans.

10 22 nd Congress of the International Society for Forensic Genetics Copenhagen, Denmark, August Acknowledgement Funding National R&D program of Ministry of Science and Technology (MOST) Korea Science and Engineering Foundation (KOSEF) To our lab members Hwan Young Lee, Ph.D Myung Jin Park, MSc. Na Young Kim, MSc. Jeong Eun Sim, BSc.