Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898

Lee, Hwan Young; Park, Myung Jin; Jeong, Chan Kwon; Lee, Seon Yeong; Yoo, Ji Eun; Chung, Ukhee; Choi, Jong Hoon; Kim, Chong Youl; Shin, Kyoung Jin

doi:10.1007/s00414-004-0456-1

Cited by 35 publications

(27 citation statements)

References 19 publications

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“…However, when dealing with haplotypes of closely linked loci, the fact that LD may vary in different populations has to be taken into account. Whilst our group observed a strong LD between DXS101 and DXS7424 [7], other authors [10] failed to indicate the same phenomenon in a Korean population.…”

Section: Discussionmentioning

confidence: 74%

DXS6797 contains two STRs which can be easily haplotyped in both sexes

et al. 2005

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DXS6797 is a complex X-chromosomal locus which contains two variable short tandem repeats (STRs) (motif ATCT) separated by 128 non-polymorphic nucleotides. The two STRs can be cleaved apart by Taq I digestion. Conventionally, DXS6797 is typed by measuring the overall amplicon length, providing only eight alleles [polymorphism information content (PIC) 0.733, mean exclusion chance (MEC) 0.712]. Separate amplification would increase the discrimination but obscure the haplotype constellation in females. Therefore, we proceed by amplifying the whole sequence containing both repeats (DXS6797 I and DXS6797 II) using a Fam-labelled forward primer and a Tamra-labelled reverse primer. We then measure the length of the entire double-labelled amplicon and a Taq-I-digested aliquot to infer, for both males and females, compound haplotypes consisting of DXS6797 I and DXS6797 II repeat length. This procedure has the potential to provide 42 DXS6797 haplotypes. If the crossover rate between both STRs is assumed to be <1.5x10(-6), DXS6797 haplotypes could be used for kinship testing like STR alleles. In our German sample (780 X chromosomes), we determined 27 haplotypes (PIC 0.842, MEC 0,834) and in 220 meioses, we found no new mutations.

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Section: Discussionmentioning

confidence: 74%

DXS6797 contains two STRs which can be easily haplotyped in both sexes

et al. 2005

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“…It is recognised that factors other than the physical distance between loci are involved [15,17]. Indeed, the X chromosome appears to be rather prone to recombination, and an absence of linkage has been reported in other studies, even when quite close markers were studied [8,18].…”

Section: Discussionmentioning

confidence: 93%

“…However, although frequencies from different continents have been published (for instance, see [2,[8][9][10]), it is unclear to which extent Xlinked markers display differences at the regional level. This is an important issue in order to decide which database is needed to interpret DNA results.…”

Section: Introductionmentioning

confidence: 97%

Study of six X-linked tetranucleotide microsatellites: population data from five Spanish regions

et al. 2005

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We studied six X-linked microsatellites in a large group of Spanish individuals (n=614) from five different regions located in northern, central and southern Spain. All the markers had tetranucleotide repeat units (DXS9895, DXS9898, DXS7130, DXS7132, GATA172D05 and DXS6789). They were amplified in two triplex PCR reactions. There were no significant sex- or region-related differences in allelic frequencies, suggesting that general national databases can be adequate as a reference for X-linked markers. The analysis of those six short tandem repeats combined in 316 males revealed 300 different "temporary haplotypes", 283 of which were found only once. There was no evidence for statistically significant linkage disequilibrium among the loci studied. Therefore these markers are quite polymorphic and useful for forensic purposes.

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“…Blood or buccal samples from 450 unrelated Koreans living in Seoul (300 men and 150 women), including 150 men and 150 women already typed for 9 X-STRs (13,14), were analyzed. Genomic DNA was extracted using a QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, and the DNA was quantitated using NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), following the manufacturer's recommendation.…”

Section: Materials and Methods Dna Samplesmentioning

confidence: 99%

Genetic Polymorphism and Haplotype Analysis of 4 Tightly Linked X-STR Duos in Koreans

Lim¹,

Lee²,

Sim³

et al. 2009

Croat Med J

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*The first two authors equally contributed to this workAim To investigate genetic polymorphism and haplotypes of tightly linked X-chromosomal short tandem repeat (X-STR) clusters in Koreans.Methods Four X-STR duos in the linkage group 1-4 (DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101, and DXS10134-DXS7423) were investigated in 450 unrelated Koreans (300 men and 150 women) using the Mentype Argus X-8 Polymerase Chain Reaction Amplification Kit.Results No significant deviation from Hardy-Weinberg equilibrium was observed in any of the 8 loci. DXS10135 was the most polymorphic X-STRs, with 25 alleles and DXS7423 was the least informative, with 5 alleles. Eleven off-ladder alleles and a triallelic pattern were observed, and these alleles were characterized by cloning and sequencing analysis. In 300 Korean men, 38 to 59 haplotypes were observed for each linkage duo with 91.6-96.6% of haplotype diversities. However, due to the low genetic diversity of DXS7423, the X-STR duo in linkage group 4 (DXS10134-DXS7423), in comparison with other linkage duos, had considerably lower haplotype diversity values (91.6%) with 3 common haplotypes (35-15, 36-15, and 37-15) observed in 44.3% of Koreans.Conclusion Four X-STR duos in the linkage group 1-4 will be able to provide a powerful tool for solving complex kinship cases in Koreans. However, to increase the haplotype diversity in the linkage group 4, it will be useful to discover a new marker for Asians that can serve as an adequate substitute for DXS7423 or at least complement the existing linkage duo of DXS10134-DXS7423.

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Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898

Cited by 35 publications

References 19 publications

DXS6797 contains two STRs which can be easily haplotyped in both sexes

DXS6797 contains two STRs which can be easily haplotyped in both sexes

Study of six X-linked tetranucleotide microsatellites: population data from five Spanish regions

Genetic Polymorphism and Haplotype Analysis of 4 Tightly Linked X-STR Duos in Koreans

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