Short Tandem Repeat Haplotypes Research Articles

Y-chromosomal STR haplotypes in Inuit and Danish population samples

Nineteen Y-chromosomal short tandem repeats (STRs), DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS460, DYS461 and DYS462 were typed in Inuit ( n=70) and Danish ( n=62) population samples.

Comparative analysis of short tandem repeats and single nucleotide polymorphisms on the Y-chromosome in Germans, Chinese and Thais

We have typed genomic DNA samples from 95 individuals from Western Germany, 78 individuals from Bangkok/Thailand and 56 individuals from Chengdu/China for 11 Y-chromosomal diallelic polymorphisms and eight short tandem repeat (STR) systems. For single nucleotide polymorphism (SNP) analysis, a rapid method was applied using the single base extension technology (minisequencing) in combination with capillary electrophoresis. PCR products for SRY-8299, Tat, SRY2627, 92R7, SRY1532, M9, M13, M17/M19 and M20 were pooled and used as templates for the commercially available SNaPshot kit. In addition to these ten SNPs we also tested the Y-chromosomal diallelic Alu repeat insertion DYS287 (YAP) by agarose gel electrophoresis as well as the Y-chromosomal STR systems DYS19, DYS389I+II, DYS390, DYS391, DYS392, DYS393 and DYS385 by fluorescent multiplex fragment analysis. Among the 11 diallelic SNP/Alu systems, only six were found to be polymorphic in the three population samples. From these a total number of seven different haplogroups could be identified in the three populations. Of these, five haplogroups were present in Germans, five in Thais, and only two in Chinese. These haplogroup trees clearly represent population-specific structures. Haplogroup 26 is represented at a high frequency in the Thai and Chinese populations whereas it is absent in Germans. The Y-STR data confirm a haplogroup-specific distribution of Y-STR haplotypes. Only a few cases of identical STR haplotypes in the same SNP haplogroups were detected in each of the three populations studied.

Y-chromosome STR haplotypes in a population from Northeast Spain

The aim of this study is to present the distribution of haplotype frequencies for six Y-chromosome short tandem repeat (STR) loci (DYS19, DYS385, DYS389II, DYS390, DYS391 and DYS393) in a population sample of 100 Caucasoid unrelated individuals living in Northeast Spain. A total of 73 different haplotypes were observed among which 67 were unique and 6 were found at least two times. The most common haplotype occurred 12 times. The overall discrimination capacity of the six loci haplotypes analysed was 73%, and the gene diversity was 96.88%. This database study is an essential prerequisite for using Y-chromosomal STR in routine practice.

Y-chromosomal STR haplotypes in an Albanian population sample

Eight Y-chromosomal short tandem repeats (STRs), DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385, were typed in a population sample ( n=101) of first-generation Albanian immigrants living in Italy.

Online Y-chromosomal Short Tandem Repeat Haplotype Reference Database (YHRD) for U.S. Populations

We describe here an online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations, which represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001. This database is available online (http://www.ystr. org/usa/), free to access and was generated in order to supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Pairwise R(ST)-statistics derived from the Y-STR haplotypes indicate no significant substructure among African-American populations from different regions of the U.S., nor (usually) among European-American and Hispanic populations. Thus, pooling of Y-STR haplotype data from regional populations within these three major groups is appropriate in order to obtain larger sample sizes. However, pooling of different major populations is generally not recommended due to statistically significant differences between African-American populations and all European-American/Hispanic populations, as well as between some European-American and Hispanic populations.

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

Abstract Whole blood samples were obtained from 106 unrelated male individuals living in Metro Manila, Philippines, through the Department of Health, Manila. DNA was extracted by isopropanol fractionation-sodium iodide precipitation (4) and quantified by spectrophotometry. Nine Y-chromosomal short tandem repeats (STR's) were analyzed from a population sample of 106 unrelated males by means of a quadruplex PCR (DYS393, DYS19, DYS392, DYS385-I/II) and a triplex PCR (DYS390, DYS389-I/II, and DYS391).

Short tandem repeat (STR) haplotypes in HLA: an integrated 50-kb STR/linkage disequilibrium/gene map between the RING3 and HLA-B genes and identification of STR haplotype diversification in the class III region.

We present a dense STR/linkage disequilibrium(LD)/gene map between the RING3 and HLA-B loci, reference allelic sizes on the most prevalent HLA haplotypes and their allelic frequencies in pedigree founders. This resource will facilitate LD, evolution and gene mapping studies, including comparisons of HLA and STR haplotypes and identification of HLA recombinants. The map was constructed by testing novel and previously reported STRs using a panel of 885 individuals in 211 families and 60 DNA samples from cell lines and bone marrow donors homozygous in the HLA-A, -B and -DR loci selected from over 15 000 entries into the registry of Swedish bone marrow donors. We have also analysed the variability of STR alleles/haplotypes on the most prevalent HLA haplotypes to identify STRs useful for fine mapping of disease genes in the region previously implicated in susceptibility to many disorders. The analysis of 40 HLA-A*01, B*0801, DRB1*03011, DQB1*0201 haplotypes in homozygous donors showed a surprising stability in 23 STRs between the class II recombination hot spot and HLA-B, with the average of 1.9% (16/838) variant alleles. However, 40% variant alleles were found at the D6S2670 locus in intron 19 of the tenascin-X gene both in the families and homozygous donors. The nucleotide sequence analysis of this STR showed a complex polymorphism consisting of tetra- (CTTT)(8-18) and penta-nucleotide (CTTTT)(1-2) repeats, separated by an intervening non-polymorphic sequence of 42 bp. The HLA-A1, B*0801, DRB1*03011, DQB1*0201 haplotypes had five (CTTT)(14-18)/(CTTTT)(2) variants with a predominant (CTTT)(16) allele, implicating the tetranucleotide component as the source of this ancestral haplotype diversification, which may be due to the location of D6S2670 in the region of the highest GC content in the human MHC.

Y chromosome STR haplotypes in four populations from northwest Africa.

The eight short tandem repeat (STR) polymorphic systems mapping on the male-specific region of the human Y chromosome, DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393, were typed in four populations from northwest (NW) Africa (Moroccan Arabs, southern Moroccan Berbers, Saharawis and Mozabites). Allele frequency distributions showed statistically significant differences for all loci among all the populations except for DYS19. Complete typing was obtained for 185 chromosomes, which showed 74 different haplotypes. The two most frequent haplotypes were found in 16.2% and 15.1% of the individuals, although the latter was almost exclusively found in the Mozabites. Locus and haplotype informativeness were measured by means of the gene diversity (D). The haplotype diversity ranged from 0.856 (Mozabites) to 0.967 (southern Moroccan Berbers). For some loci, allele frequencies in NW Africans were clearly different from those in Europeans. The most common NW African haplotype was found only in one individual out of a total of 494 Europeans typed for the whole STR set. Thus, NW African and European Y chromosomes are clearly differentiated.

An Asian-Native American paternal lineage identified by RPS4Y resequencing and by microsatellite haplotyping.

Human paternal population history was studied in 9 populations [three Native American, three Asian, two Caucasian and one African-derived sample(s)] using sequence and short tandem repeat haplotype diversity within the non-pseudoautosegmal region of the Y chromosome. Complete coding and additional flanking sequences (949 base pairs) of the RPS4Y locus were determined in 59 individuals from three of the populations, revealing a nucleotide diversity of 0.0147%, consistent with previous estimates from Y chromosome resequencing studies. One RPS4Y sequence variant, 711C > T, was polymorphic in Asian and Native American populations, but not in African and Caucasian population samples. The RPS4Y 711C > T variant, a second unique sequence variant at DYS287 and nine Y chromosome short tandem repeat (YSTR) loci were used to analyze the evolution of Y chromosome lineages. Three unambiguous lineages were defined in Asian, Native American and Jamaican populations using sequence variants at RPS4Y and DYS287. These lineages were independently supported by the haplotypes defined solely by YSTR alleles, demonstrating the haplotypes constructed from YSTRs can evaluate population diversity, admixture and phylogeny.

A single polymorphic STR system in the human phenylalanine hydroxylase gene permits rapid prenatal diagnosis and carrier screening for phenylketonuria.

Phenylketonuria (PKU) is an autosomal recessive genetic disorder caused by phenylalanine hydroxylase (PAH) deficiency. Individuals afflicted with PKU develop irreversible mental retardation that can be largely prevented by the administration of a low-phenylalanine diet. A number of restriction fragment-length polymorphisms (RFLPs) have been identified in the PAH gene. Combinations of RFLPs constitute unique haplotypes that can be used to identify mutant PAH chromosomes for prenatal diagnostic purpose in PKU families. Unfortunately, the utility of haplotype analysis is limited in populations with a single predominant haplotype. We have identified a novel short tandem repeat (STR) within the PAH gene that has an average level of heterozygosity of about 75% in Orientals and about 80% in European Caucasian populations. This single marker is as informative as haplotype analysis in Europeans and nearly twice as informative as haplotype analysis in Orientals. Although there is statistically significant disequilibrium between STR alleles and RFLP-based haplotypes, there is a relatively low degree of disequilibrium between STR alleles and certain RFLP sites. Nevertheless, the combined use of the STR and RFLP haplotype systems increases the informativity of linkage-based tests for prenatal diagnosis and carrier screening in PKU families.