Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in - - PDF document

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Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans Myung Jin Park 1 , Hwan Young Lee 1 , Ji-Eun Yoo 1 , Ukhee Chung 1,2 , Seon Yeong Lee 2 , Sang-Ho Cho 1,3 , Chong-Youl Kim 1,3 , Kyoung-Jin Shin 1,2,3 1 Department of

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Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans

Myung Jin Park1, Hwan Young Lee1, Ji-Eun Yoo1, Ukhee Chung1,2, Seon Yeong Lee2, Sang-Ho Cho1,3, Chong-Youl Kim1,3, Kyoung-Jin Shin1,2,3

1 Department of Forensic Medicine, College of Medicine, Yonsei University 2 Biometrics Engineering Research Center, Yonsei University 3 Human Identification Research Institute, Yonsei University

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Y-chromosomal STRs

Applications

forensic investigations genealogical purposes evolutionary studies

Advantages to Human Identity Testing

male component isolated without differential extraction paternal lineages

Needs

population studies to evaluate diversity of haplotypes robust assay for accurate characterization of Y markers

Y

STR Markers DYS19 DYS389I/II DYS390 DYS391 DYS392 DYS393 DYS385 DYS388 DYS434 DYS435 DYS436 DYS437 DYS438 DYS439

…..

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Y-STR Haplotype Reference Database http://www.ystr.org/asia 9 best studied Y STRs Percentage of unique haplotypes

n = 2576 7-locus Asian haplotypes, DYS385 excluded, logged in the database n = 2576 minimal Asian haplotypes logged in the database n = 850 European mt-DNA D-Loop sequences (from Legal Medicine Magdeburg, Germany) n = 551 extended Asian haplotypes logged in the database * ** *** ****

Minimal haplotype loci

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Previously study of Y-STRs

Forensic Science International 136 (2003) 89-91

Allele frequencies and haplotypes of six new Y- specific STR loci in Koreans

Hwan Young Lee, Ji-Eun Oh, Gil-Ro Han, Kyoung-Jin Shin International Journal of Legal Medicine 115 (2001) 109-117

Y-chromosome multiplexes and their potential for the DNA profiling of Koreans.

D. J. Shin, H. J. Jin, K. D. Kwak, J. W. Choi, M. S. Han, P. W. Kang, S. K. Cho,
W. Kim

DYS434, DYS435, DYS436 DYS437, DYS438, DYS438 DYS434, DYS435, DYS436 DYS437, DYS438, DYS438 Polymorphism and Haplotypes of 10 Y-STR Loci in Koreans

Zhe-Jia Zheng, Yong-Ji Zhang, Jin-Cheol Park, Hai-Yu Lin, S—Young Kim, Young-Tae Choi, Jung Bin Lee

Kor. J. Legal Med 27 (2003) 62-72

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Selection of new Y-STRs

Forensic Science International 130 (2002) 97-111

Forensic value of 14 novel STRs on the human Y chromosome

Alan J. Redd, Al B. Agellon, Veronica A. Kearney, Veronica A. Contreras, Tatiana Karafet, Hwayong Park, Peter de Knijff, John M. Butler, Michael F. Hammera

DYS464 DYS449 DYS446 0.926 0.880 0.763

DYS464 : four-copy locus DYS464 a/b/c/d

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Object

Usefulness of DYS464, DYS449, DYS446 Gene/haplotype diversity and discriminatory power

f 19 STR loci containing minimal

haplotype loci, DYS388, DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439 Assess of contribution of respective Y-STRs to the increase of haplotype diversity

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Materials and Methods

DNA samples

301 buccal swab samples from unrelated Korean population DNA was extracted using QIAamp DNA Mini Kit

Multiplex PCR

Total 10 µl PCR reaction: 1-2 ng of DNA, 1.4 -1.6 µl of Gold STR buffer,2.0 U of AmpliTaq Gold polymerase and primers Cycling condition: 95°C 11’; 94°C 1’ 55-59°C 1’ 72°C 1’ x 30; 60°C 45’

Detection Systems

ABI prism 310 genetic analyzer, Gene Scan software 3.1, and Genotyper 2.5 software (PE Applied Biosystems, CA, USA)

Statistical analysis

Gene, haplotype diversity and linkage disequilibrium values were calculated using Arlequin version 2.0 software.

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Schematic of multiplex PCR

Multiplex I (minimal haplotype)

100 bp 250 bp 200 bp 150 bp 300 bp 6FAM (blue) DYS392 10 16 DYS389I 11 16 DYS389II 26 32 DYS19 13 18 GS500-internal lane standard ROX (red) HEX (green) DYS393 10 16 DYS391 7 11 DYS390 21 27 9 22 DYS385 100 bp 250 bp 200 bp 150 bp 300 bp 6FAM (blue) DYS434 8 11 DYS436 11 14 DYS438 9 14 HEX (green) DYS437 14 16 DYS435 10 13 DYS439 10 14 DYS388 10 15 GS500-internal lane standard ROX (red)

Multiplex II (DYS388+previously studied 6 Y-STRs) Multiplex III (DYS464, DYS449, DYS446 and DYS385)

240 bp 360 bp 320 bp 280 bp 390 bp GS500-internal lane standard ROX (red) 6FAM (blue) 10 19 DYS464 11 19 DYS446 HEX (green) 9 22 DYS385 26 35 DYS449

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Allelic structure

(CCTT)3CTT(CCTT)11(CCTT)2N33(CCTT)3N8(CCTT)4N4(CCTT)2N5(CCTT)2-

14.3

(CCTT) n(CCTT)2N33(CCTT)3N8(CCTT)4N4(CCTT)2N5(CCTT)2-

Repeat

DYS464

Microvariant allele

DYS449

N106 (TTTC)15N14[(TTTC)2N4(TTTC)2N16]2(TTTC)18N88-

Mutant (407bp)

N106(TTTC)16N14(TTTC)2N4(TTTC)2N16(TTTC)10TT(TTTC)4N88-

30.2 (361bp)

(TTTC)xN14(TTTC)2N4(TTTC)2N16(TTTC)y-

Repeat

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Single locus analysis

67 11 9 5 51 6 7 4 7 7 6 6 #Allele seen 0.9590 9-18 ― 19-20

GAAA

DYS385 0.9668 12 ― 14-15-16-17

CCTT

DYS464 0.8433 26-30, 30.2, 31 ― 35

TTTC

DYS449 0.7873 11 ― 19

TCTCT

DYS446 0.5083 10, 12 ― 15

ATT

DYS388 0.6338 10, 12 ― 16

AGAT

DYS393 0.6931 10 ― 16

TAT

DYS392 0.2924 7, 9 ― 11

TCTA

DYS391 0.6689 21 ― 27

(TCTA)(TCTG)

DYS390 0.7257 26 ― 32

(TCTG)(TCTA)

DYS389II 0.6659 11 ― 16

(TCTG)(TCTA)

DYS389I 0.7167 13 ― 18

TAGA

DYS19 Gene diversity # Repeat unit Motif Marker

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Haplotype analysis

12,13,14,15 34 13 11 11 15 12 11 9 10 13,20 12 14 10 24 28 12 14 1 H29 13,14,15 32 15 12 11 14 12 11 9 10 13,20 12 14 10 24 28 12 14 1 H28 12,13,14 34 13 12 11 15 11 11 9 10 13,20 12 14 10 24 28 12 14 1 H27 12,14,15 31 12 12 11 15 14 11 9 10 13,18 12 14 10 24 28 12 14 1 H26 11,13,15 32 13 12 11 15 12 11 9 10 13,13 12 14 10 24 28 12 14 1 H25 12,13,15 32 11 12 11 15 14 11 9 10 15,20 12 14 10 23 28 12 14 1 H24 13,14,15 33 13 11 11 15 12 11 9 10 13,20 12 14 10 23 28 12 14 1 H23 13 31 13 13 11 15 12 11 9 10 13,18 12 14 10 24 27 12 14 1 H22 13,15 29 13 13 11 15 12 11 9 10 13,18 12 14 10 24 27 12 14 1 H21 13,15,16 31 13 12 11 15 12 11 9 10 13,18 12 14 10 24 27 12 14 1 H20 12,14,15 34 14 11 11 15 12 11 9 10 13,18 13 14 10 24 27 12 14 1 H19 12,13,14,15 32 13 11 11 15 12 11 9 10 13,18 12 14 10 24 27 12 14 1 H18 13,15 34 13 12 11 14 12 11 9 10 13,18 12 14 10 24 27 12 14 1 H17 12,13,14,15 32 13 11 11 14 12 11 9 10 13,18 12 14 10 24 27 12 14 1 H16 12,13,14,15 32 14 11 11 15 12 11 9 10 12,19 12 14 10 24 27 12 14 1 H15 13,14 34 13 12 11 15 12 11 9 10 13,19 12 10 10 24 27 12 14 1 H14 12,13,14,15 33 14 11 11 15 12 11 9 10 13,20 12 14 10 23 27 12 14 1 H13 12,13,14,15 32 13 12 11 15 12 11 9 10 13,19 12 14 10 23 27 12 14 1 H12 13,14,15 32 13 12 11 15 12 11 9 10 13,18 12 14 10 24 26 12 14 1 H11 12,13,15 34 13 12 11 15 12 11 9 10 13,19 12 14 10 25 28 11 14 1 H10 12,13,14 33 13 12 11 15 12 11 9 10 15,19 12 14 10 23 27 11 14 1 H9 15,16 31 15 11 12 14 13 11 9 12 15,22 14 14 9 24 31 14 13 1 H8 15,16 31 15 11 12 14 13 11 9 12 15,21 14 14 9 24 31 14 13 1 H7 15,16 30 15 11 12 14 13 11 9 12 19,19 14 14 9 24 30 14 13 1 H6 15,16 30 14 11 12 14 13 11 9 12 15,20 14 14 9 24 30 14 13 1 H5 14,15 30 14 11 12 14 13 11 9 12 16,20 14 15 9 24 29 14 13 1 H4 14,15 30 14 11 12 14 13 11 9 12 15,20 14 15 9 23 29 14 13 1 H3 15,16 31 14 11 12 14 13 11 9 12 15,22 14 14 9 24 30 13 13 1 H2 13,14,16 33 13 12 11 15 13 11 9 12 12,16 12 12 10 23 28 12 13 1 H1 DYS- 464 DYS- 449 DYS- 446 DYS- 439 DYS- 438 DYS- 437 DYS- 436 DYS- 435 DYS- 434 DYS- 388 DYS- 385 DYS- 393 DYS- 392 DYS- 391 DYS- 390 DYS- 389II DYS- 389I DYS- 19 N Haplotypes 12,13,14 28 14 12 10 14 12 11 8 13 11,12 13 14 10 23 31 14 14 1 H61 13 31 14 10 10 14 12 11 8 12 11,12 13 14 10 22 31 14 14 1 H60 13 29 15 11 10 15 12 11 8 12 11,13 13 13 10 22 31 14 14 1 H59 14,14.3 28 18 11 11 14 12 11 8 12 11,13 14 16 11 23 30 14 14 1 H58 14,14.3 28 17 10 11 14 12 11 8 12 11,13 14 16 11 23 30 14 14 1 H57 13 26 13 14 10 14 12 11 8 13 11,12 13 15 11 23 30 14 14 1 H56 15,16 30 18 10 10 14 12 11 8 12 11,13 13 14 11 23 30 14 14 1 H55 12,13,14 28 14 11 10 14 12 11 8 13 11,12 13 14 11 23 30 14 14 1 H54 12 28 14 11 10 14 12 11 8 13 11,12 13 14 10 23 30 14 14 1 H53 14,15,16,17 30 14 12 13 14 12 11 9 12 10,21 13 13 10 22 30 14 14 1 H52 12,14,15 34 13 12 11 15 12 11 9 10 13,17 12 14 11 25 29 14 14 1 H51 13,14,15 33 16 12 11 15 12 12 9 12 13,18 13 13 11 25 30 13 14 1 H50a 13 30 14 11 10 14 12 11 8 12 11,14 13 15 10 21 30 13 14 1 H49 13 29 14 11 10 14 12 11 8 12 11,14 13 15 10 21 30 13 14 1 H48 12,14,15 35 13 12 11 15 12 11 9 10 13,17 12 14 11 25 29 13 14 1 H47 13,14,16,17 31 15 13 10 14 12 11 8 12 12,12 13 16 11 24 29 13 14 1 H46 12,13,14 28 13 11 10 14 12 11 8 13 11,12 13 14 11 23 29 13 14 1 H45 13 30 16 10 10 14 12 11 8 13 11,14 13 15 10 21 29 13 14 1 H44 10,14,16 29 16 11 10 14 12 12 9 12 11,17 13 14 10 24 28 13 14 1 H43 13,14,16 32 14 13 11 15 12 11 9 10 13,18 12 14 10 23 28 13 14 1 H42 13,14,16 29 17 11 10 14 12 11 11 12 11,17 14 11 10 23 28 13 14 1 H41 12,13,15 32 14 12 11 15 12 11 9 10 13,19 12 14 10 25 30 12 14 1 H40 12,13,15 31 13 13 11 15 12 11 9 10 12,18 12 15 10 25 29 12 14 1 H39 12,13,15 32 13 12 11 15 12 11 9 10 13,19 12 14 10 25 29 12 14 1 H38 11,12,13,15 32 13 14 11 15 12 11 9 10 13,18 12 15 10 25 28 12 14 1 H37 12,13,15 32 13 13 11 15 12 11 9 10 12,18 12 15 10 25 28 12 14 1 H36 12,13,15 33 16 12 11 15 12 11 9 10 13,19 12 14 10 25 28 12 14 1 H35 12,13,14 33 13 12 11 15 12 11 9 10 13,17 12 14 10 25 28 12 14 1 H34 12,13,14,15 33 14 13 11 15 12 11 9 10 13,18 12 13 10 25 28 12 14 1 H33 13,14,15 32 13 12 11 15 12 11 9 10 13,21 12 14 10 24 28 12 14 1 H32 12,14,16 32 11 13 10 15 12 12 9 13 14,20 13 13 10 24 29 13 17 1 H283 13,14,15,17 31 13 12 13 14 12 11 9 12 10,18 13 14 10 23 28 13 17 1 H282 13,15,16,17 33 14 12 13 14 12 11 9 12 10,18 13 13 10 23 28 13 17 1 H281 13,14,15,16 31 11 11 10 14 12 12 9 13 14,20 12 13 11 24 30 12 17 1 H280 12,14,15,16 30 11 11 10 14 12 12 9 13 15,21 12 13 10 24 30 12 17 1 H279 13,15,17 31 12 11 10 14 12 12 9 12 13,21 12 13 11 25 29 12 17 1 H278 12,14,16 31 11 11 10 15 12 12 9 13 14,20 12 14 10 24 29 12 17 1 H277 12,14,17 30 12 13 11 15 12 11 9 10 12,19 12 14 10 25 28 12 17 1 H276 12,13,14,16 28 12 12 11 15 12 11 9 10 12,19 12 14 10 25 28 12 17 1 H275 13,15,16 28 12 11 10 14 12 11 11 12 12,20 12 13 10 25 28 12 17 1 H274 12,14,15,16 30 12 12 10 14 12 12 9 12 12,20 12 13 10 24 28 12 17 1 H273 13,15,18 27 12 12 10 14 12 12 9 12 14,18 13 13 11 25 27 12 17 1 H272 13,15,18 27 12 12 10 14 12 12 9 13 14,19 12 13 10 25 27 12 17 1 H271 13,15,18 27 12 12 10 14 12 12 9 12 14,18 12 13 10 24 27 12 17 1 H270 13,15,18 27 12 12 10 14 12 12 9 12 14,17 12 13 10 24 27 12 17 1 H269 13,14,16,17 32 13 11 13 14 12 11 9 12 10,18 13 13 10 22 31 16 16 1 H268 12,15,16 32 12 12 10 15 12 12 9 12 15,15 12 12 10 24 31 14 16 1 H267 12,14,16 30 16 11 10 14 12 11 11 13 11,17 14 11 10 23 31 14 16 1 H266 12,16 30 13 12 10 14 12 12 9 12 13,20 12 13 7 23 31 14 16 1 H265 13,15,16 33 13 10 11 14 12 11 9 12 11,14 13 11 10 25 30 14 16 1 H264 12,16 29 15 12 12 15 12 11 9 14 9,19 13 13 11 24 30 14 16 1 H263 13,16 31 14 12 12 14 12 11 9 12 9,19 13 13 11 24 30 14 16 1 H262 12,14,16 31 16 11 10 14 12 11 11 12 10,20 15 11 10 24 30 14 16 1 H261 13,16 29 14 12 12 14 12 11 9 12 9,20 13 13 11 23 30 14 16 1 H260 13,14,16,17 32 13 12 13 14 12 11 9 12 10,19 13 13 10 23 30 14 16 1 H259 14,16,17 30 13 11 13 14 12 11 9 13 10,18 13 13 10 23 30 14 16 1 H258 14,16,17 30 13 12 14 14 12 11 9 12 10,17 10 13 10 23 30 14 16 1 H257 12,14,16 32 15 12 10 16 12 11 11 12 1019 15 11 10 23 30 14 16 1 H256 12,13,15,16 30 16 12 10 14 12 11 10 13 13,18 14 11 10 22 30 14 16 1 H255 12,14,16 32 17 13 10 14 12 11 11 12 10,21 15 11 10 25 29 14 16 1 H254 12,15,16 31 11 11 10 15 12 11 9 13 14,14 12 13 10 24 29 12 18 1 H297 15,17 31 18 14 10 14 12 11 9 13 12,16 13 11 10 27 31 14 17 1 H296 13,14 34 14 12 10 14 12 11 9 12 11,20 12 13 9 25 31 14 17 1 H295 17 27 17 11 10 14 12 11 9 12 13,16 13 11 10 24 31 14 17 1 H294 12,15,16,17 32 12 12 10 15 12 11 9 12 15,19 12 12 10 24 30 14 17 1 H293 13,14,17 33 13 11 13 14 12 11 9 12 10,17 13 13 11 23 29 14 17 1 H292 13,14,17 31 13 12 13 14 12 11 9 12 10,19 13 13 10 23 29 14 17 1 H291 DYS- 464 DYS- 449 DYS- 446 DYS- 439 DYS- 438 DYS- 437 DYS- 436 DYS- 435 DYS- 434 DYS- 388 DYS- 385 DYS- 393 DYS- 392 DYS- 391 DYS- 390 DYS- 389II DYS- 389I DYS- 19 N Haplotypes

0.9867 0.9999 297 19 Y-STRs haplotype 0.6645 0.9946 200 DYS385+DYS464 0.8937 0.9989 269 Multiplex III 0.2990 0.9509 90 Multiplex II 0.7641 0.9963 230 Multiplex I (minimal haplotype) Discriminatory power Haplotype diversity Number of haplotypes Y-STR marker

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Contribution of Y-STR loci to haplotype diversity

0.967 0.843 0.787 0.610 0.672 0.413 0.102 0.259 0.361 0.508 Gene diversity 0.9989 276 8 Minimal haplotype + DYS464 0.9985 258 8 Minimal haplotype + DYS449 0.9980 250 7 Minimal haplotype + DYS446 0.9980 255 6 Minimal haplotype + DYS439 0.9964 232 8 Minimal haplotype + DYS438 0.9968 236 7 Minimal haplotype + DYS437 0.9967 233 5 Minimal haplotype + DYS436 0.9966 234 6 Minimal haplotype + DYS435 0.9967 233 7 Minimal haplotype + DYS434 0.9968 239 7 Minimal haplotype + DYS388 0.9963 230 _ Minimal haplotype Haplotype diversity # of haplotype # of LD locia Y-STR marker

a Number of minimal haplotype core loci in significant linkage disequilibrium with each added Y-STR locus.

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Contribution of Y-STR loci to haplotype diversity

0.9989 0.9963

438 449

Minimal hapltype

446 464 439 388 437 434 435 436

0.9994 0.9999 0.9999 0.9999 0.9999 0.9998 0.9997 0.9997 0.9999 220 230 240 250 260 270 280 290 300 8 9 10 11 12 13 14 15 16 17 18 19

No. of adding loci
No. of cumulative haplotypes

DYS438, DYS437, DYS434, DYS435, DYS436 do not significantly contribute to increment of diversity of minimal haplotype DYS438, DYS437, DYS434, DYS435, DYS436 do not significantly contribute to increment of diversity of minimal haplotype

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Conclusions

Haplotype diversity of 19 Y-STR loci was 0.9999 and 297 different haplotypes was identified. DYS464 (0.9668), DYS385 (0.9590), DYS449 (0.8433) and DYS446 (0.7873), in order of those, are highly diverse in a Korean population DYS464, DYS449 and DYS446 are significantly increase the haplotype diversity

minimal haplotype. DYS434, DYS435, DYS436, DYS437, DYS438 did not significantly increase the number of different haplotypes and the haplotype diversity.