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Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas.

Parkin EJ, Kraayenbrink T, Opgenort JR, van Driem GL, Tuladhar NM, de Knijff P, Jobling MA - Forensic Sci. Int. (2006)

Bottom Line: We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%).Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan.Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.

ABSTRACT
Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

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Haplotype diversity for (a) all 26 STRs and the 20plex, and (b) the extended and minimal haplotypes. Histograms show the frequency distributions of haplotypes present more than once in the dataset.
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fig1: Haplotype diversity for (a) all 26 STRs and the 20plex, and (b) the extended and minimal haplotypes. Histograms show the frequency distributions of haplotypes present more than once in the dataset.

Mentions: Haplotype diversity (equivalent to power of discrimination, PD) was calculated, omitting chromosomes carrying alleles and duplications. This provided a sample size of 741. For the full set of 26 Y-STRs, there are 437 unique haplotypes (59.0%), and PD is 0.9970. The corresponding values for the 20plex [7], extended (11-locus) haplotype and minimal (9-locus) haplotype are shown in Fig. 1.


Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas.

Parkin EJ, Kraayenbrink T, Opgenort JR, van Driem GL, Tuladhar NM, de Knijff P, Jobling MA - Forensic Sci. Int. (2006)

Haplotype diversity for (a) all 26 STRs and the 20plex, and (b) the extended and minimal haplotypes. Histograms show the frequency distributions of haplotypes present more than once in the dataset.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2627361&req=5

fig1: Haplotype diversity for (a) all 26 STRs and the 20plex, and (b) the extended and minimal haplotypes. Histograms show the frequency distributions of haplotypes present more than once in the dataset.
Mentions: Haplotype diversity (equivalent to power of discrimination, PD) was calculated, omitting chromosomes carrying alleles and duplications. This provided a sample size of 741. For the full set of 26 Y-STRs, there are 437 unique haplotypes (59.0%), and PD is 0.9970. The corresponding values for the 20plex [7], extended (11-locus) haplotype and minimal (9-locus) haplotype are shown in Fig. 1.

Bottom Line: We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%).Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan.Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.

ABSTRACT
Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

Show MeSH