Y-chromosome STR haplotypes in a Bangladeshi population

Y-chromosome STR haplotypes in a Bangladeshi population

Legal Medicine 7 (2005) 122–126 www.elsevier.com/locate/legalmed Announcement of population data Y-chromosome STR haplotypes in a Bangladeshi popula...

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Legal Medicine 7 (2005) 122–126 www.elsevier.com/locate/legalmed

Announcement of population data

Y-chromosome STR haplotypes in a Bangladeshi population Yuji Dobashia, Akira Kidob,*, Noboru Fujitanic, Rie Susukidab, Masaaki Harad, Masakazu Oyab a

Scientific Crime Detection Laboratory, Yamanashi Prefectual Police Headquaters, Yamanashi 406-0036, Japan b Department of Legal Medicine, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan c Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Japan d Department of Forensic Medicine, Saitama Medical School, Saitama 350-0451, Japan Received 25 May 2004; received in revised form 11 August 2004; accepted 11 August 2004 Available online 11 November 2004

Abstract Allele frequencies and haplotypes for 10 Y-chromosome STR loci, DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438 and DY439, were determined in 72 unrelated Bangladeshi males using Y-PLEXe5 and Y-PLEXe6 Amplification Kits. This population demonstrated 71 haplotypes, of which 70 were unique. The haplotype diversity calculated from the 10 Y-STR loci was 0.9996 and the discrimination capacity was 0.9861. q 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosome; STR; Haplotype; Population genetics; Bangladeshi population

1. Population

2. Extraction

Blood samples were obtained from 72 unrelated Bangladeshi males living in Dhaka (capital of Bangladesh).

Genomic DNA was isolated from the blood samples using the phenol-chloroform method.

3. PCR

* Corresponding author. Tel.: C81-55-273-9548; fax: C81-55273-6753. E-mail address: [email protected] (A. Kido).

The five Y-STR loci (DYS389I, DYS389II, DYS392, DYS438 and DYS439) were amplified using the Y-PLEXe5 Kit (ReliaGene Technologies, New Orleans, LA, USA) and the six Y-STR loci (DYS19, DYS385, DYS389II, DYA390, DYS391

1344-6223/$ - see front matter q 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2004.08.005

Table 1 Allele frequencies and gene diversity values at 10 Y-STR loci in Bangladeshis Allele

G

DYS 19

DYS 389I

DYS 389II

DYS 390

DYS 391 0.0278 0.7917 0.1805

0.0278 0.2361 0.4306 0.2639 0.0417

0.1111 0.5278 0.3472 0.0139

0.0278 0.0694 0.2917 0.2917 0.2639 0.0417 0.0139

0.6965

0.5967

0.7633

DYS 392

0.0833 0.7222 0.0417 0.0556 0.0833 0.0139

DYS 393

0.0417 0.3194 0.4444 0.1528 0.0278 0.0139

DYS 438 0.0139 0.2778 0.1944 0.4722 0.0417

DYS 439 0.0139 0.3056 0.3472 0.1667 0.1389 0.0278

0.2361 0.2500 0.2083 0.2500 0.0278 0.0278

0.7852

0.3447

0.4661

0.6840

0.6694

0.7483

Allele

DYS 385

9–12 9–16 9–18 11–14 11–15 11–16 11–17 11–19 12–12 12–13 12–14 12–16 12–18 12–19 13–13 13–17 13–18 13–20 13–21 14–14 14–16 14–17 14–19 14–20 15–16 15–17 15–18 15–19 15–21 15–22 16–16 16–17 16–19 16–20 17–19 17–20

0.0139 0.0139 0.0139 0.2361 0.0694 0.0139 0.0139 0.0139 0.0139 0.0139 0.0278 0.0139 0.0139 0.0139 0.0278 0.0278 0.0139 0.0278 0.0139 0.0139 0.0417 0.0139 0.0278 0.0139 0.0556 0.0556 0.0139 0.0139 0.0139 0.0139 0.0139 0.0556 0.0139 0.0139 0.0139 0.0139 0.9325

Y. Dobashi et al. / Legal Medicine 7 (2005) 122–126

8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

G, gene diversity. 123

124

Table 2 Haplotypes of 10 Y-STR loci in Bangladeshis DYS 19

DYS 385

DYS 389I

DYS 389II

DYS 390

DYS 391

DYS 392

DYS 393

DYS 438

DYS 439

N

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

13 13 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

12–16 14–20 9–12 11–14 11–19 12–18 13–13 13–17 13–17 13–18 13–20 13–20 13–21 14–14 14–16 14–19 15–16 15–19 16–20 9–18 11–14 11–14 11–14 11–14 11–14 11–14 11–14 11–15 12–12 12–13 12–14 12–19 13–13 14–16 14–16 15–16 15–17 15–17 15–17 15–18 15–21

14 13 13 14 14 12 13 12 12 15 12 12 14 13 12 14 13 13 13 13 13 13 14 14 14 14 14 14 13 14 13 14 13 13 14 13 14 14 14 14 13

30 29 29 30 31 27 31 28 28 31 28 28 30 30 27 30 29 30 29 29 30 31 30 31 31 32 33 32 30 32 29 30 31 31 30 28 30 30 31 31 29

22 23 24 24 23 24 23 22 22 23 23 24 23 24 24 23 24 23 23 22 25 25 25 25 25 25 26 26 24 27 24 23 23 23 23 22 23 23 22 23 24

10 10 10 11 10 10 10 10 10 10 10 10 10 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 10 9 10 10 10 10 10 10 10 10

14 10 12 13 10 11 11 14 14 11 14 14 10 10 11 11 11 11 11 14 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11 11 11 13

13 14 13 12 14 13 13 11 11 14 12 12 14 13 14 13 13 12 13 12 13 13 13 13 13 13 13 13 14 13 12 13 14 15 12 12 12 12 12 12 15

11 11 10 12 11 10 9 10 10 11 12 11 11 9 10 9 10 9 9 10 11 11 11 11 11 11 11 11 11 11 10 11 11 10 9 8 9 9 9 9 10

11 10 13 12 10 9 11 12 14 11 11 11 13 11 13 11 12 11 11 12 10 10 10 10 14 10 10 10 11 10 13 10 13 11 11 11 11 12 12 12 13

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

Y. Dobashi et al. / Legal Medicine 7 (2005) 122–126

H

15 15 15 15 15 15 15 15 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 17 17

15–22 16–16 16–17 16–17 16–17 16–19 17–19 17–20 11–14 11–14 11–14 11–14 11–14 11–14 11–15 11–15 11–15 11–15 11–16 11–17 12–14 14–17 14–19 15–16 15–16 15–17 16–17 9–16 11–14 11–14

14 13 13 14 14 13 13 13 12 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 14 13 13 14 12 14

30 29 29 30 31 29 30 29 29 29 30 31 31 31 29 30 30 31 31 31 31 29 29 29 29 29 29 30 29 31

25 22 22 22 22 22 22 25 24 27 24 24 25 25 25 25 25 25 24 25 25 22 23 22 22 22 22 23 24 25

10 10 10 9 10 10 10 11 11 10 10 11 10 11 11 11 11 10 10 11 10 10 11 10 10 10 10 10 11 10

13 11 11 11 11 11 11 13 12 11 11 11 11 11 11 11 11 11 11 12 11 11 10 11 11 11 11 15 11 11

16 12 12 13 12 12 12 14 13 13 13 13 13 13 13 13 13 13 13 14 14 11 12 12 12 12 12 12 14 13

10 9 9 9 9 9 10 10 11 11 11 11 12 11 11 11 11 11 11 11 11 9 11 9 9 9 9 10 11 11

13 11 11 10 11 11 12 12 10 10 11 11 10 13 10 10 11 10 11 11 10 12 10 11 12 12 11 13 13 10

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

Y. Dobashi et al. / Legal Medicine 7 (2005) 122–126

42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71

H, haplotype number; and N, individuals observed for each haplotype.

125

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Y. Dobashi et al. / Legal Medicine 7 (2005) 122–126

and DYS393) were amplified using the Y-PLEXe6 Kit (ReliaGene Technologies) according to the manufacturer’s recommended protocols. DYS389II was common to both kits. 4. Typing The amplified products were separated by denaturing polyacrylamide capillary electrophoresis in an automated ABI PRISMw 310 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). Fragment sizes were determined using GeneScanw Analysis v3.1 Software (Applied Biosystems) and the alleles were typed using Genotyperw v2.5 Software (Applied Biosystems).

5. Results The results are shown in Tables 1 and 2.

6. Analysis of data Gene and haplotype diversities were calculated according to Nei [1].

7. Other remarks Allele frequencies and gene diversity values at the 10 Y-STR loci in Bangladeshis are shown in Table 1. Three alleles for DYS391, four alleles for DYS389I, five alleles for DYS19 and DYS438, six alleles for DYS390, DYS392, DYS393 and DYS439, seven alleles for DYS389II and 36 alleles for DYS385 were observed in Bangladeshis. The most common allele for each locus was: DYS19, allele 15; DYS389I, allele 13; DYS398II, alleles 29 and 30; DYS390, alleles 23 and 25; DYS391, allele 10; DYS392, allele 11; DYS393, allele 13; DYS438, allele 11; DYS439, allele 11; DYS385, alleles 11–14. The highest gene diversity value was found at DYS385 (0.9325), followed by DYS390 (0.7852) and DYS389II (0.7633); the lowest gene diversity value was at

DYS391 (0.3447). Allele frequency distributions of the 10 loci in Bangladeshis were compared with those in Japanese [2] and Chinese [3] as well as the distributions of eight loci other than DYS438 and DYS439 in Bangladeshis were compared with those in Koreans [4] and Filipinos [5] using the R!C contingency test. The majority of the allele frequency distributions in Bangladeshis were significantly different (P!0.05) from those of these four Asian populations. The exceptions were found in DYS19, DYS389II, DYS390 and DYS391 in Japanese, DYS19 and DYS391 in Chinese, DYS19, DYS391 and DYS393 in Koreans and DYS19, DYS391 and DYS393 in Filipinos. Haplotypes of the 10 Y-STR loci in Bangladeshis are shown in Table 2. A total of 72 unrelated individuals demonstrated 71 haplotypes, of which 70 were unique and one was found in two individuals. The haplotype diversity calculated from the 10 Y-STR loci was 0.9996 and the discrimination capacity was 0.9861. The combination of the 10 Y-STR loci included in the Y-PLEXe5 and Y-PLEXe6 Kits is a powerful tool for the investigation of sexual crimes and paternity tests of male offspring in Bangladeshis.

References [1] Nei M. Molecular evolutionary genetics. New York: Columbia University Press; 1987. [2] Kido A, Hara M, Kameyama H, Yamamoto Y, Susukida R, Oya M. Y-chromosom STR loci data in Japanese using the YPLEXe5 and Y-PLEXe6 PCR amplification kits. J Forensic Sci 2004;49:849–51. [3] Li W, Hu L, Chen S, Qiu N. 10 Y-STRs haplotypes in Chinese. Forensic Sci Int 2004;139:85–8. [4] Shin DJ, Jin HJ, Kwak KD, Choi JW, Han MS, Kang PW, Choi SK, Kim W. Y-chromosome multiplexes and their potential for the DNA profiling of Koreans. Int J Legal Med 2001;115:109–17. [5] Miranda JJ, Benecke M, Hidding M, Schmitt C. Y-chromosomal short tandem repeat haplotypes at the loci DYS393, DYS19, DYS392, and DYS385-I/II, DYS390, DYS389-I/II, and DYS391 in a Filipino population sample. J Forensic Sci 2001;46:1250–3.