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PubMed2002

Extending STR markers in Y chromosome haplotypes.

Two multiplex reactions were developed to amplify 16 Y-STRs (DYS19, DYS385, DYS389 I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, GATA A7.1, GATA A7.2, GATA A10, GATA C4, GATA H4). Here we extend previous population studies done in a sample from northern Portugal for the GATA A7.1, GATA A7.2, GATA C4 and GATA H4 loci. A total of 199 different haplotypes identified by the 16 Y-STR markers were observed in a sample of 208 male individuals, of which 190 were unique and 9 were found twice. The overall haplotype diversity was 0.9996. The haplotype diversity of the Y-STR set composed of the 8 new markers is higher than the Y-STR core set included in the Y-STR haplotype reference database. Sequence structure of new alleles for GATA C4 and GATA H4 is reported. The usefulness of the inclusion of this new set of Y-STRs in forensic casework was also assessed. The increase in haplotype diversity with the addition of any new Y-STR marker to the 8 Y-STR core set is dependent not only on the gene diversity (positively) but also (negatively) on the degree of gametic association between the markers and the haplotypes previously defined. For instance, in our sample the addition of the DYS437, DYS438 and GATA A7.2 to a 13-locus set increased haplotype diversity only by 0.0001.

Base Sequence↗
PubMed2003

Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups.

This work presents a selection of 16 SNPs from the coding region of the human mitochondrial DNA. The selected markers are used for the assignment of individuals to one of the nine major European Caucasian mitochondrial haplogroups. The selected SNPs are targeted in two multiplex systems, via the application of the SNaPshot kit, a multiplex method based on the dideoxy single-base extension of unlabeled oligonucleotide primers. The method is conceived as a rapid screening technique prior to sequencing analysis, in order to eliminate multiple suspects from an inquiry or to discriminate between stains in a high volume casework example. Moreover, the ability to assign an unknown sample to an mtDNA type of known Caucasian origin could be of probative value in some investigations. A database of 277 Austrian Caucasians has been constructed, and the probability of a chance match between two unrelated individuals is calculated as 11.4%. This novel multiplex PCR amplification and typing system for mtDNA coding region SNPs promises to be a convenient and informative new DNA profiling system in the forensic field.

DNA, Mitochondrial↗
PubMed2003

Five highly informative X-chromosomal STRs in Koreans.

The five X-chromosomal short tandem repeats (STRs) GATA172D05, HPRTB, DXS8377, DXS101 and HumARA were analyzed in 150 males and 150 females from Korea. Markers were amplified in a quadruplex and a monoplex PCR reaction with fluorescently labeled primers. For accurate and reproducible STR typing, sequenced allelic ladders were constructed and a Genotyper macro was programmed. Some differences were found on comparing the allele frequencies of Koreans with those of other populations in DXS8377, DXS101 and HumARA. The forensic efficiency parameters showed that the five X-linked STRs are highly informative for forensic application in Koreans.

Chromosomes, Human, X↗
PubMed2004

Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians.

We have sequenced the entire mtDNA genome (mtGenome) of 241 individuals who match 1 of 18 common European Caucasian HV1/HV2 types, to identify sites that permit additional forensic discrimination. We found that over the entire mtGenome even individuals with the same HV1/HV2 type rarely match. Restricting attention to sites that are neutral with respect to phenotypic expression, we have selected eight panels of single nucleotide polymorphism (SNP) sites that are useful for additional discrimination. These panels were selected to be suitable for multiplex SNP typing assays, with 7-11 sites per panel. The panels are specific for one or more of the common HV1/HV2 types (or closely related types), permitting a directed approach that conserves limiting case specimen extracts while providing a maximal chance for additional discrimination. Discrimination provided by the panels reduces the frequency of the most common type in the European Caucasian population from approximately 7% to approximately 2%, and the 18 common types we analyzed are resolved to 105 different types, 55 of which are seen only once.

DNA, Mitochondrial↗
PubMed2000

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.

Africa, Northern↗
PubMed2000

A Korean population study of the nine STR loci FGA, VWA, D3S1358, D18S51, D21S11, D8S1179, D7S820, D13S317 and D5S818.

DNA typing was performed on 379 randomly selected unrelated Koreans using the nine short tandem repeat loci FGA, VWA, D3S1358, D18S51, D21S11, D8S1179, D7S820, D13S317 and D5S818 present in the AmpF/STR Profiler Plus PCR amplification kit. Allele frequencies, heterozygosity, power of discrimination, mean exclusion chance, and polymorphism information content of each locus were calculated by statistical analysis. All nine loci were in Hardy-Weinberg equilibrium. The combined discrimination index and the combined mean exclusion chance in Koreans was 2.31 x 10(-12) and 0.99983, respectively. By evaluation of 297 children from 128 families, 2 mutations were found at the FGA locus and 1 each at the D18S51 and D13S317 loci. This study demonstrates that this multiplex system is a useful and convenient tool for forensic identification and parentage testing in Korea.

Adolescent↗
PubMed2001

Tibetan population data on the PCR-typed loci D16S539, D7S820, D13S317, HUMF13A01, FESFPS, vWA, HUMTH01, TPOX and CSF1PO.

Frequency data for nine tetrameric short tandem repeat loci (D16S539, D7S820, D13S317, HUMF13A01, FESFPS, vWA, HUMTH01, TPOX and CSF1PO) were investigated in a population sample of 107 unrelated Tibetan individuals by using a multiplex polymerase chain reaction (PCR), followed by 4% polyacrylamide gel electrophoresis (PAGE) and silver staining. All loci met the Hardy-Weinberg expectations. The forensically relevant parameters were calculated. This is the first time that Chinese Tibetan population data on DNA loci have been reported that are of forensic importance.

Alleles↗
PubMed1999

D20S161 data for three ethnic populations and forensic validation.

In order to evaluate the forensic applicability of the STR locus D20S161 and construct a preliminary database, the genotype distributions and allele frequencies in five populations from three main ethnic groups were investigated, including Germans, Slovakians, African Americans, Japanese and Chinese. A total of 512 samples from unrelated individuals and 85 confirmed father/mother/ child triplets were analyzed by PCR and allele determination was carried out by comparison with a sequenced human allelic ladder. The results showed that D20S161 typing was both precise and reliable. A total of 7 alleles was found in these populations and no evidence of deviation from Hardy-Weinberg equilibrium was observed. Pairwise comparisons between populations showed that there were significant differences in the distributions of the allele frequencies among the three main ethnic groups. No mutation events were observed from the confirmed father/mother/child triplets. With a maximum likelihood method, the mutation rate was indirectly estimated as 2.5 x 10(-5). These results suggest that D20S161 is a useful marker for forensic casework and paternity analysis.

Asian People↗
PubMed1998

A study on the short tandem repeat systems HumCD4, HumTH01 and HumFIBRA in population samples from Yemen and Egypt.

The short tandem repeat systems (STRs) HumCD4 (CD4), HumTH01 (TH01) and HumFIBRA (FGA) were amplified by the polymerase chain reaction (PCR) on blood samples from 100 unrelated Yemenians and 100 unrelated Egyptians. PCR products were separated on native horizontal discontinuous gel electrophoresis followed by silver staining. The distribution of observed phenotypes did not deviate from Hardy-Weinberg equilibrium. While significant differences between both Arab populations and an European population from Austria were found at all loci, differences between the Egyptian and the Yemenian samples were found only for CD4. In a number of verified Austrian families (TH01: 426 meioses, CD4: 275 meioses, FGA: 144 meioses) no mutations were found. The observation of a TH01 allele consisting of 4 repeats was confirmed by sequencing. Moreover we report the structure of a TH01 allele 6.3 observed in a Hungarian Caucasian population.

Alleles↗
PubMed1999

The polymorphisms of DYS388 and DYS392 on the Y chromosome in Japanese and German populations.

The analysis of a genotype survey in Japanese and German populations at the loci DYS388 and DYS392 located on the Y chromosome is reported. The gene diversities of DYS388 were 0.34 and 0.30 in the Japanese and German males, respectively, and six alleles were found in both groups. The gene diversities of DYS392 were 0.65 and 0.64 and the number of alleles was 8 and 9, respectively in the two populations. The distribution of DYS388 alleles in the Japanese population was different from the German population. The allele distribution of DYS392 showed significant differences among Asian populations.

Asian People↗
PubMed2000

Mitochondrial heteroplasmy among maternally related individuals.

The second hypervariable segment of the human mtDNA control region contains a homopolymeric tract of cytidines between nucleotides (nt) 303 and 315, interrupted by a thymidine at position 310, according to the Cambridge reference sequence. By direct sequencing, some individuals show blurred sequence chromatograms in this region which are not caused by a sequencing artefact but by high levels of length heteroplasmy. With respect to this length heteroplasmy ten maternally related individuals and two unrelated probands were examined. The relative proportions of length variants in the homopolymeric tract in selected individuals were determined by cloning and sequencing of multiple independent clones. All ten family members examined were heteroplasmic while the proportions of each genotype varied widely in different individuals. The size of a possible mitochondrial bottleneck during embryonic development of the offspring is discussed with respect to the changes in mitochondrial haplotypes within mother-offspring pairs. Our data are consistent with both slow and rapid segregation of mtDNAs between the generations, which would implicate a tight as well as a wide bottleneck. Therefore, a common bottleneck size in all individuals from this lineage seems to be very unlikely.

Chromosome Segregation↗
PubMed2002

Statistical analysis for estimating heterogeneity of the Korean population in DNA typing using STR loci.

The coancestry coefficients for the Korean population are estimated by using 3 statistical methods for 17 loci (D3S1358, D21S11, D13S317, D18S51, D7S820, D8S1179, D5S818, FGA, VWA, F13A1, FES/FPS, THO1, TPOX, CSF1PO, D12S391, GABA and ACTBP2). The subpopulations were considered by last name and home origin, respectively. Our results show that the values for the coancestry coefficient for the Korean population are too large to ignore although they do not show substantial heterogeneity. These estimated values are also applied to simulated forensic cases.

Forensic Medicine↗
PubMed2000

Analysis of eight STR loci in two Hungarian populations.

A multiplex reaction for the eight STR loci D3S1358, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 was used to generate allele frequency databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. During the analysis two intermediate-sized alleles and a sequence variant allele were observed at the D7S820 locus. All three types of allelic variants were found to have modifications in the same block of a (T)9 stretch located within the 3' flanking region of each allele, which may indicate a possible higher mutation rate of this (T)9 block. For the loci D3S 1358 and D7S820 the Romany population database showed departures from Hardy-Weinberg equilibrium. The forensic efficiency values for the Romany population were slightly different from those found in the Hungarian Caucasian population. Comparing the allele frequency values by G-statistic, calculating the F(ST) indices and with the pair-wise comparisons of interpopulation variance, the two Hungarian populations could be distinguished using data from the eight STR loci.

Albania↗
PubMedDate not supplied

The phenotypic frequencies of group specific component and alpha-2-HS-glycoprotein in three ethnic groups. The use of these proteins as racial markers in forensic biology.

The phenotypic frequencies of group-specific component (Gc) and alpha-2-HS-glycoprotein (A2HS) were determined in White European, Asian and Afro-Caribbean populations. Typical allele frequencies were observed for Gc, with Gc 1S being the major allele for the first two groups and Gc 1F being the major allele for Afro-Caribbeans. For all groups the dominant A2HS allele was A2HS 1, although Asians had a significantly higher proportion of this allele than the White Europeans. Gc and A2HS either singly or in combination with other blood grouping systems provide good discriminating potential. The A2HS 10 allele was detected with a very low frequency in the White European group (A2HS 10 = 0.0013) and was not detected in the Asian group, while the Afro-Caribbean group had a relatively high frequency of this allele (A2HS 10 = 0.0966). The different distribution of the Gc 1F and A2HS 10 alleles in White Europeans and Asians compared with Afro-Caribbeans, can be used to determine the likelihood of blood coming from an Afro-Caribbean.

Africa, Western↗
PubMed1993

Analysis of a Danish Caucasian population sample of single locus DNA-profiles. Allele frequencies, frequencies of DNA-profiles and heterozygosity.

The frequency distributions of the length of restriction fragments (HinfI) revealed by RFLP-analysis (restriction fragment length polymorphism) of blood samples from 482 Danish Caucasians using the single locus VNTR (variable number of tandem repeats) probes MS1, MS31, MS43a and YNH24 are reported. From two blood samples three fragments were obtained with MS1. The consistency of the characteristic allele frequency distribution for each probe is exemplified by comparing the accumulated frequency curves obtained with MS43a in samples consisting of 50 and 920 bands, respectively. The distribution of the differences in migration distance for the two fragments of a bandpair was investigated. The results suggest that the high frequency of apparent homozygotes observed is due mainly to coalescence of close heterozygotes. The distribution of frequencies of 437 DNA-profiles is reported.

Bias↗