Y-chromosome STR Loci Research Articles

A Colombian Caribbean population study of 16 Y-chromosome STR loci

Allelic frequencies and haplotypic composition of 305 male unrelated individuals from the Caribbean Colombian states of Atlántico, Bolívar, Cesar, Córdoba, Guajira, Magdalena and Sucre, were determined using 16 Y-chromosome STR loci. Two hundred and ninety three (293) haplotypes were identified, of which 283 were unique and the other 10 were found twice or thrice in the Caribbean population tested. Haplotypic diversity surpassed the values obtained in other populations, ranging from 99.66% in the population of Sucre to 99.99% in the population of Córdoba. We also calculated the overall haplotypic diversity (99.97%) and the discrimination power of these haplotypes (96.1%) in these groups. Analysis of molecular variance (AMOVA) for 10 Colombian and Spanish populations (3139 haplotypes) reveals low differentiation between the Colombian populations of mainly European descent and large distance to Afroamerican populations living in Colombia.

The Y‐chromosome short tandem repeats variation within haplogroup E3b: Evidence of recurrent mutation in SNP

Haplogroup E3b is defined by a single nucleotide mutation (SNP) in locus M35 and is found at high frequency (more than 35%) in populations from North Africa with a heterogeneous distribution. On the basis of compilation of 553 Y-chromosomes from Europe and 633 from sub-Saharan Africa we selected 130 individuals belonging to haplogroup E3b and characterized subhaplogroups according to the Y-Chromosome Consortium nomenclature. Y-chromosome haplotypes can be defined using short tandem repeats (STR). The use of STRs makes it possible to measure diversity and estimate age coalescence. Significant differences on frequencies of Y-chromosome STR loci were found among the E3b subhaplogroups and the same was observed when haplotype frequencies were considered. Some mutations in SNPs were detected when comparing E3b subhaplogroups with the correspondent STR haplotypes. These results show that the mutation rate for some SNPs could be higher than previously thought and also that it is important to associate both haplotype and haplogroup in Y-chromosome studies.

Evaluation of haplotype discrimination capacity of 35 Y-chromosomal short tandem repeat loci

The haplotype discrimination capacity of the 9 Y-chromosomal short tandem repeat (Y-STR) loci comprising the so called minimal haplotype together with additional 26 recently described single-copy Y-STRs was evaluated within 391 males from Germany, The Netherlands, and Turkey. The aim of this study was to identify the minimum number of Y-STRs needed in addition to the recommended 9 minimal haplotype loci or the 11 SWGDAM loci for individualizing male lineages. Highest gene diversities were shown for DYS385 loci, DYS449, DYS481, DYS570, DYS447, DYS576, DYS389-II, and DYS390 ( D = 0.7518–0.8746). The five Y-STRs DYS447, DYS449, DYS481, DYS570, and DYS576 comprised the smallest set of loci in addition to the previously recommended standard Y-STRs leading to the individualization of all males from each single population group. Complete resolution of the pooled population was achieved by the additional genotyping of two further loci, DYS446 or DYS505 and DYF406S1 or DYS522.

Allele frequencies and population data for 17 Y-chromosome STR loci in a Serbian population sample from Vojvodina province

Seventeen Y-chromosomal STR (short tandem repeat) loci were analyzed in a group of 185 healthy unrelated male individuals ( n = 185) from the population of Serbian province of Vojvodina. After minimal haplotype STR loci analysis we observed 129 different haplotypes. The most frequent haplotype was found in 13 copies, and total haplotype diversity was 99.11%. After analysis of additional eight Y-STR loci (DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and YGATAH4) there were 176 different haplotypes observed, out of which 168 appeared in single copies, and 7 haplotypes appeared twice. The most frequent haplotype was found in three copies. The haplotype diversity (99.94%) and discrimination capacity (95.13%) were calculated. Comparisons were made with previously published haplotype data on neighbouring population samples and significant differences were demonstrated at DYS19, DYS389II and DYS393 loci. Pairwise comparison of populations revealed that our sample was significantly different only from Hungarian sample (RST = 23.98%, p = 0.0091).

Sub-Saharan Africa descendents in Rio de Janeiro (Brazil): population and mutational data for 12 Y-STR loci

A male sample of 135 African descendents from the Rio de Janeiro population were typed for the 12 Y-chromosome short tandem repeat (STR) loci included in the PowerPlex Y System. A high haplotype diversity was observed (0.9971), with 91% of haplotypes being unique, demonstrating the usefulness and informative power of this Y-STR set in male lineage identification. Samples with shared haplotypes were additionally typed with the Yfiler kit, which includes five extra markers. The haplotype diversity when using the 17-Yfiler loci increased to (0.9998) with 97% unique haplotypes. The same set of Y-STRs was also typed in 135 father/son pairs and three single-step mutations were observed: one at DYS19 and two at DYS385. Genetic distance analysis showed highly significant differences in all pairwise comparisons between this sample of African descendents and the general population from Rio de Janeiro, as well as with Iberian and African samples from Portugal, Mozambique, Angola and Equatorial Guinea. Comparisons with samples from other regions in Brazil showed that heterogeneity does exist, indicating that a Y-haplotype database for the whole country should take into account the population sub-structure. Moreover, a strong European influence was detected, and thus, a Y-chromosome STR profile proves a rather poor indicator for the ethnic origin of an individual in Rio de Janeiro.

Data for Y-chromosome haplotypes in Fang and Bubi populations from Bioko (Equatorial Guinea)

Haplotype frequencies for 16 Y-chromosomal short tandem repeat (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448) loci, included in the AmpFLSTR ® YfilerTM PCR Amplification Kit, were analysed in 110 Fang and 133 Bubi individuals from Bioko Island, Equatorial Guinea. The diversity was higher in Fang population, probably since they were originally from the mainland, with which they maintain tribal village and family links, and to which they travel frequently. Comparisons were made with previously published haplotype data on European and African populations, and significant differences were found between them.

Genetic polymorphism of Y-chromosomal STR loci in South Korean population

Y-chromosomal STRs loci were analyzed from a sample of 355 healthy unrelated male individuals of South Korean population. Allele and haplotype frequencies for DYS441, DYS442, DYS443, DYS444, DYS445, DYS446, DYS452 and DYS456 were determined by the general PCR and silver staining methods. The gene diversity values for the Y-STRs loci ranged from 0.4902 (DYS465) to 0.7883 (DYS446). A total of 263 haplotypes were identified in the Y-STR loci, among which 225 were unique, while 38 occurred more than once. And the combined haploytpes diversity was 0.9958.

Haplotype frequencies of 16 Y-chromosome STR loci in the Barcelona metropolitan area population using Y-Filer™ kit

Haplotype frequencies for 16 Y-chromosomal short tandem repeat (STR) loci, included in the Y-Filer™ kit, were determined in 247 unrelated healthy individuals from the Barcelona metropolitan area (Catalonia, NE Spain). After PCR amplification and denaturing PAGE electrophoresis, DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4.1, DYS437, DYS438 and DYS448 loci were typed. The aim of this study is to evaluate the performance in our population of the 16 loci of the Y-chromosome present in the new Y-Filer™ commercial identification kit, and acquire haplotype frequencies for mathematic processing of the forensic diagnosis in our geographical working area. In this sample, all haplotypes were unique. From the forensic point of view, the combined polymorphisms of the Y-Filer™ kit provide a high diagnostic efficiency.

Genetic data for 16 Y-chromosomal STR loci in Japanese

Allele frequencies and haplotypes for 16 Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y GATA H4, and DYS385a/b, were determined in 161 unrelated Japanese males using AmpF lSTR ® Yfiler™ PCR Amplification Kit. This population was demonstrated 153 haploytpes, of which 146 were unique, six were found in two individuals, and one was found in three individuals. The haplotypes diversity calculated from the 16 Y-STR loci was 0.9994 and the discrimination capacity was 0.9503.

Mother-child double incompatibility at vWA and D5S818 loci in paternity testing

In a paternity dispute case, 17 autosomal short tandem repeats (STR) were examined and signified a possible paternal mismatch at vWA locus and a maternal mismatch at D5S818 locus in the child under investigation. Seventeen autosomal, 17 Y-chromosome and six X-chromosome repeat loci were used in parentage analysis. The mutated vWA and D5S818 alleles were amplified, cloned and sequenced to analyze the repeat structure. The vWA locus genotype in the mother, questioned child and suspected father were 18/19, 16/18 and 14/18, and were 13/15, 11/12 and 11/14, respectively, for the D5S818 locus. A complete match with the mother at six X-chromosome STR loci and with the father at 17 Y-chromosome STR loci was observed. Nucleotide sequence analysis of the family at vWA alleles indicated the maternal loss of the repeat motif TCTA by two repeat units and a loss of AGAT repeat by one unit in the D5S818 locus leading to an allele mismatch in the child. The probability of maternity and paternity were 0.999999 and 0.999999, respectively. This is the first study of a maternally transmitted microsatellite mutation in the loci D5S818 and vWA in paternity DNA testing. The results convincingly established that the mother and suspected father are the biological parents of the questioned child.

Y-chromosomal microsatellite mutation rates in a population sample from northwestern Germany

To estimate Y-chromosomal short tandem repeat (Y-STR) mutation rates, 15 loci (i.e., DYS19, DYS389 I/II, DYS390, and DYS393; DYS437, DYS438, DYS439, and DYS385; DYS391, DYS392, YCA II, and DXYS156) were analyzed in a sample of 1,029 father/son pairs from Westphalia, northwestern Germany. Among 15,435 meiotic allele transfers, 32 mutations were observed; thus, the mutation rate across all 15 Y-STR loci was 2.1 x 10(-3) per locus (95% C.I.: 1.5-3.0 x 10(-3)). With the exception of a three-repeat mutation at DYS385, all remaining mutations were single repeat mutations. Repeat losses were more frequent than gains (20:12), and the mutation rate appeared to increase with age. The Y haplogroups that were detected in the individuals showing a mutation reflect the haplogroup distribution in the Westphalian population. Additionally, the correlation of surnames and haplotypes was tested: Only 49 surnames occurred more than once, and only two men with the same rare surname shared the same haplotype. All other men with identical surnames carried different haplotypes.

Allele frequencies and haplotypes of 12 Y-STR loci for the local Chinese population in Hong Kong

Haplotype frequencies were established for 12 Y-chromosome STR loci, including all loci recommended by Scientific Working Group on DNA Analysis Methods Y-STR Subcommittee (DYS391, DYS389I/II, DYS439, DYS393, DYS390, DYS385a/b, DYS438, DYS19 and DYS392) plus DYS437, in the local Chinese population in Hong Kong. In a sample of 481 unrelated males, it was possible to define 424 different haplotypes of which 388 were unique, 26 was found in two individuals, 2 were shared in three individuals, 5 were shared in four individuals and 3 were shared in five individuals. The allele diversity values for each locus ranged from 0.4273 (DYS438) to 0.9555 (DYS385a/b). The observed haplotype diversity value and discrimination capacity were 0.9992 and 0.8815, respectively. In a genetic study of these unrelated males, triple alleles were found at the DYS358 locus in six individuals. The combined Y-chromosome STR polymorphisms provide a powerful discrimination tool for routine forensic applications.

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

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).

Population study and evaluation of 20 Y-chromosome STR loci in Germans

The nine European minimal haplotype (EMH) loci, the two SWGDAM loci and five further single-copy Y-chromosomal short tandem repeats (Y-STRs) DYS446, DYS447, DYS448, DYS449, DYS463, and the multicopy loci DYS464 were evaluated in the German population groups Dresden, Hamburg, Rostock, Munich, and the Sorbs who are a Slavic-speaking minority in Lusatia. Highest gene diversities in all populations were shown for DYS464, DYS385, and DYS449 (D=0.8559-0.9486). The haplotype diversity for the European minimal haplotype loci ranged between 0.9852 for Sorbs and 0.9983 for the Hamburg population showing that there is a significant portion of haplotypes which could not be resolved. Advanced typing using DYS446, DYS447, DYS448, DYS449, DYS463, and DYS464 discriminated all non-related individuals of the Dresden, Hamburg, and Rostock populations. Evaluation of the Y-STRs was accomplished by sequence analysis of all allelic fragments of the allelic ladders and microvariant alleles of DYS385 and the determination of the amounts of stutter products of the loci.

Identification of a novel A1v‐O1v hybrid allele with G829A mutation in a chimeric individual of AelBel phenotype

Many A and B suballeles responsible for ABO subgroup formation have been identified. Some of these minor alleles have mutations in the ABO gene coding sequence. Most of these mutations are due to single-nucleotide substitution and lead to amino acid alteration. Several alleles at the ABO locus appear to be caused by crossing over between dissimilar alleles. Blood samples were collected from an individual with AelBel phenotype and her family members. Sequencing of the seven ABO exons was performed on these samples. The following was performed for the samples from the AelBel proposita: cloning and sequencing of the genomic DNA of the ABO gene, reverse transcription-polymerase chain reaction (PCR) analysis of cDNA transcript of the ABO gene, sequence-specific priming (SSP)-PCR analysis and direct sequencing of the ABO gene, SSP-PCR DNA typing of generic HLA-ABC and HLA-DRB, and short-tandem repeat (STR)-PCR typing on 15 autosomal, 2 X-chromosomal, and 6 Y-chromosomal loci. The proposita with AelBel phenotype has blood group chimerism with a major group of A1v-O1v/O1(O01) and a minor group of B(B101)/O1v(O02). Additional haplotypes on HLA-ABC, HLA-DR-B, STR loci, and Y-chromosome STR loci were present on the proposita. The paternal genotype is B(B101)/O1(O01) and the maternal genotype is A1v(A102)/O1v(O02). No other siblings have the A1v-O1v hybrid allele. Parentage was confirmed with the paternity STR-PCR test. Full-length cDNA transcripts of the B(B101) allele and alternately spliced cDNA transcripts of the hybrid A1v-O1v, O(1), and O1v alleles were cloned from the proposita. The A1v-O1v hybrid gene contains two missense mutations: C467T and G829A, resulting in Pro156Leu and Val277Met substitution. Formation of the A1v-O1v hybrid allele appears to result from de novo recombination in the germ line of the mother during meiosis. G829A with Val277Met appears to be responsible for the decrease in A-transferase activity and Ael phenotypic expression in the proposita. The chimeric minor population of B(B101)/O1v is responsible for Bel phenotypic expression in the proposita.

Preliminary population study at fifteen autosomal and twelve Y-chromosome short tandem repeat loci in the representative sample of multinational Bosnia and Herzegovina residents

We have selected 100 unrelated healthy individuals born in the Bosnia and Herzegovina, from three main ethnical groups for our study. For the autosomal STR analysis we choose 100 male and female individuals (Bosniaks=44%, Serbs=31%, Croats=17% and others=8%). Additionally, 100 males, voluntary donors [ Bosniaks: Muslim (35), Serbs (31), Croats (34)], have been investigated for the Y-STR analysis. Buccal swabs and blood samples (blood spots) have been used as the DNA source and Qiagen Dnaeasy™ Tissue Kit was employed for DNA extraction. The PowerPlex 16® System and PowerPlex® Y System (Promega Corp., Madison, WI, USA) have been used to amplify 15 autosomal and 12 Y-STR loci. Amplification was carried out as described previously. Electrophoresis of the amplification products was preformed on an ABI PRISM 377 genetic analyzer. We have compared three Bosniak ethnic group according to Y-STR data. Also, we have compared entire B&H autosomal STR data with data obtained from geographically closer (neighboring) European populations. These results will be used as guiding principle for our upcoming studies.

Evaluation of 12 single-copy and 2 multi-copy Y-chromosomal STR loci in five German populations

The European Minimal Haplotype loci and six further Y-chromosomal loci (one multi-copy) were evaluated with regard to their gene diversity (D) in five German population groups. The newly established ranking list showed DYS464 (D=0.7733–0.9446), DYS449 (D=0.7844–0.8511), and DYS385 (D=0.7511–0.8433) on the top. The need for further loci became obvious in one forensic case where the discrimination of two haplotypes was only successfully with DYS446.

Distribution of Y-chromosomal haplotypes in the Basque Country autochthonous population using a 17-locus multiplex PCR assay

Haplotype, allele frequencies and population data of 17 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (Y GATA C4) and Y GATA H4 were determined from a sample of 168 unrelated male individuals from the Basque Country. Individuals were considered autochthonous if the 8 surnames and birthplace of their grandparents were of Basque origin. The haplotype diversity (99.03%) and discrimination capacity (82.14%) were calculated. The combined polymorphism provides a powerful discrimination tool for routine forensic applications.

Haplotypes for 12 Y-chromosomal STR loci in a Korean population (the central region)

Haplotypes and allele frequencies of 12 STR loci included in the PowerPlex ® Y system (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390, and DYS385a/b) were obtained from a sample of 569 unrelated individuals living in the central region of Korea. A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. In DYS439, we found a new intermediate-sized allele that added an A at base 3 upstream from the repeat region's first GATA motif. The allele was named 11 (U3Ains) according to its sequence structure.

Y-chromosomes and the extent of patrilineal ancestry in Irish surnames

Ireland has one of the oldest systems of patrilineal hereditary surnames in the world. Using the paternal co-inheritance of Y-chromosome DNA and Irish surnames, we examined the extent to which modern surname groups share a common male-line ancestor and the general applicability of Y-chromosomes in uncovering surname origins and histories. DNA samples were collected from 1,125 men, bearing 43 different surnames, and each was genotyped for 17 Y-chromosome short tandem repeat (STR) loci. A highly significant proportion of the observed Y-chromosome diversity was found between surnames demonstrating their demarcation of real and recent patrilineal kinship. On average, a man has a 30-fold increased chance of sharing a 17 STR Y-chromosome haplotype with another man of the same surname but the extent of congruence between the surname and haplotype varies widely between surnames and we attributed this to differences in the number of early founders. Some surnames such as O'Sullivan and Ryan have a single major ancestor, whereas others like Murphy and Kelly have numerous founders probably explaining their high frequency today. Notwithstanding differences in their early origins, all surnames have been extensively affected by later male introgession. None examined showed more than about half of current bearers still descended from one original founder indicating dynamic and continuously evolving kinship groupings. Precisely because of this otherwise cryptic complexity there is a substantial role for the Y-chromosome and a molecular genealogical approach to complement and expand existing sources.