Highlights
- •A sequenced based nomenclature was established for eight STR-loci located on chromosome 6 (6p21.3).
- •Sequenced reference DNA samples enable the construction of allelic ladders.
- •Sequence and length polymorphism was studied in an Austrian population sample.
- •The loci cover the HLA-coding region from HLA-A to HLA-DQB1 can be used for clinical, genetic and forensic applications.
Abstract
Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem
repeat (STR) polymorphisms and consistent results across instrument platforms. For
eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based
nomenclature was established according to international recommendations. Publicly
available reference DNA samples were sequenced enabling interested laboratories to
construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one
trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273)
were investigated. Apart from the very complex sequence structure at the DQIV locus,
three loci showed a compound and four loci a simple repeat pattern. In the flanking
regions of some loci additional single nucleotide and insertion/deletion polymorphisms
occurred as well as sequence polymorphisms within the repeat region of alleles with
the same length. In an Austrian Caucasoid population sample (n = 293) between eight and 22 alleles were found. No significant deviation from Hardy–Weinberg
expectations was observed, the power of discrimination ranged from 0.826 to 0.978.
The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a
better definition of HLA haplotypes for population and disease association studies,
recombination point mapping, haematopoietic stem cell transplantation as well as for
identity and relationship testing.
Keywords
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Article info
Publication history
Published online: October 18, 2014
Accepted:
October 13,
2014
Received in revised form:
September 23,
2014
Received:
April 22,
2014
Identification
Copyright
© 2014 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
