Sequence polymorphism of the mitochondrial DNA control region in the Slovenian population

The forensic application of mitochondrial DNA (mtDNA) typing requires large and regionally well-defined databases. To expand the database for forensic identification purposes in Slovenia, the mtDNA control region sequences of the hypervariable regions HVI and HVII were determined in a population of 129 maternally unrelated Slovenians, using a fluorescent-based capillary electrophoresis sequencing method. A total of 111 different haplotypes resulting from 124 polymorphic positions (80 polymorphic positions in HVI and 44 in HVII) were found. Of these, 101 mtDNA types were unique, 6 haplotypes were shared by 2 individuals, 1 haplotype by 3 individuals, 2 haplotypes by 4 individuals, and the most common haplotype was found in 5 individuals. The most frequent haplotypes in the Slovenian population ,263(G), 315.1(C) and 263(G), 309.1(C), 315.1(C) are also the most common in other European populations. The data support the concept that these haplotypes may represent a common European mtDNA sequence types. The sequence poymorphisms were compared to the databases of west Austria and central Italy and the HVI and HVII sequence matching probabilities within and between populations were calculated. It is 1.1–4.5 times more likely to find a sequence match in a random pair of Slovenians than in a random Slovenian-Italian pair and in a random Slovenian-Austrian pair. The length heteroplasmy in the homopolymeric C-stretch regions located at nucleotide positions 16184–16193 in HVI and at positions 303–315 in HVII was observed in 17% and 8% of individuals, respectively. A statistical estimate of the results for this population showed the random match probability and the genetic diversity of 1.16% and 0.996, respectively.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00414-003-0394-3     

Mitochondrial DNA hypervariable region 1 polymorphism in Singapore Chinese population

Sequence polymorphisms of hypervariable region 1 were analyzed in 100 unrelated Singaporean Chinese. Ninety-five different haplotypes resulting from 113 variable sites were found between nucleotide positions 16045 and 16364. Single nucleotide polymorphism at nucleotide positions 16223, 16045, 16129, 16362 and 16189 was amongst the five highest frequencies observed in the sequences, whilst the most frequent haplotype was 16045-16223. Based on polymorphic sites observed at HV1, haplogroups A, F1a, M7b1, B5a and D4b were the most commonly observed clusters. The haplotype, nucleotide diversity and the average number of nucleotide differences were found to be 0.999, 0.028 and 9.082, respectively. The cytosine-stretch region located around nucleotide position 16189 was observed in 22% of this population sample. Transitions were found to be more predominant than transversions.     

The results of an mtDNA study of 1200 inhabitants of a German village in comparison to other Caucasian databases and its relevance for forensic casework

Mitochondrial DNA control region sequences were determined in 1200 male volunteers from one village area of Lower Saxony for the hypervariable region 1 (HV1). The 154 variable positions found resulted in 460 different haplotypes with a haplotype diversity value of 0.98165. The number of different haplotypes showed a nearly linear increase with the number of individuals typed. The haplotype diversity approached saturation level at a value of approximately 0.981 after typing 400 individuals. Furthermore, the number of different haplotypes and the haplotype diversity were calculated for four short amplicons of HV1 in order to establish the most variable section with a high efficiency for forensic casework. Received: 29 January 2000 / Accepted: 24 April 2000     

Mitochondrial DNA sequence variation in Jewish populations

Sequence analysis of HVRI and HVRII mitochondrial DNA was carried out on 107 Jewish samples from Ashkenazi, Oriental, North African, and Sephardic origins. Control region sequences were assigned to a haplogroup by means of the analysis of the RFLP motif -7025 AluI or by using sequence motifs. A total of 88 different haplotypes were observed with a lower incidence of unique haplotypes (68.2%) than in other populations. Four individuals with one position of sequence heteroplasmy at nucleotides 16093, 16134, 16169, and 235, respectively, were detected. The mean pairwise difference in the Jewish population was 9.7 nucleotides. The gene diversity was 0.996, and the random match probability was 1.3%. When the data were compared with the autosomal and Y-chromosome markers previously studied in these populations, sex-specific differences could be observed in the Jewish populations. This fact must be taken into account for choosing suitable databases to correctly weigh the value of the evidence of a mtDNA and/or Y profile match.Electronic Supplementary Material Supplementary material, including all sequencing electropherograms, is available for this article at     

Human Y-chromosomal STR haplotypes in a Kurdish population sample

In an Iraqi Kurdish population sample (n = 101), seven polymorphic STR loci of the Y-chromosome (DYS19, 389, 390, 391, 392, 393, and DXYS156-Y) were typed, with DYS389 being subtyped for its four segments. The haplotype diversity was 97.83% and 82 different haplotypes were observed. The Kurds shared some Y-types with neighbouring south Turks but strikingly few with Germans: it is 20–30 times more likely to find a sequence match in a random pair of Kurds than in a random Kurd-German pair. Received: 25 September 1998 / Received in revised form: 4 November 1998 / Accepted: 5 November 1998     

Molecular characterization of the canine mitochondrial DNA control region for forensic applications

The canine mitochondrial DNA (mtDNA) control region of 133 dogs living in the area around Innsbruck, Austria was sequenced. A total of 40 polymorphic sites were observed in the first hypervariable segment and 15 in the second, which resulted in the differentiation of 40 distinct haplotypes. We observed five nucleotide positions that were highly polymorphic within different haplogroups, and they represent good candidates for mtDNA screening. We found five point heteroplasmic positions; all located in HVS-I and a polythymine region in HVS-II, the latter often being associated with length heteroplasmy. In contrast to human mtDNA, the canine control region contains a hypervariable 10 nucleotide repeat region, which is located between the two hypervariable regions. In our population sample, we observed eight different repeat types, which we characterized by direct sequencing and fragment length analysis. The discrimination power of the canine mtDNA control region was 0.93, not taking the polymorphic repeat region into consideration. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Mitochondrial DNA D-loop hypervariable regions: Czech population data

In order to identify polymorphic sites and to find out their frequencies and the frequency of haplotypes, the complete D-loop of mitochondrial DNA (mtDNA) from 93 unrelated Czech Caucasians was sequenced. Sequence comparison showed that 85 haplotypes were found and of these 78 were unique, 6 were observed twice and 1 was observed three times. Genetic diversity (GD) was estimated at 0.999 and the probability of two randomly selected sequences matching (random match probability, RMP) at 1.2%. Additionally these calculations were carried out for hypervariable regions 1, 2 (HV1, HV2), for the area between HV1 and HV2 and for the area of the hypervariable region HV3. The average number of nucleotide differences (ANND) was established to be 10.2 for the complete D-loop. The majority of sequence variations were substitutions, particularly transitions. Deletions were found only in the region where HV3 is situated and insertions in the same place and in poly-C tracts between positions 303 and 315 in HV2. A high degree of length heteroplasmy was found especially in the regions of poly-C tracts between positions 16184 and 16193 in HV1 and between positions 303 and 315 in HV2. Position heteroplasmies were found in two cases.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00414-003-0407-2     

Genetic polymorphism of 17 Y chromosomal STRs in the Rusyn population sample from Vojvodina Province,Serbia

Seventeen short tandem repeats on the Y chromosome were analyzed in the sample of 200 males of Rusyn origin from the Vojvodina Province, Serbia. We observed 180 different haplotypes; 163 of which were unique and 17 occurred between two and four times. The haplotype diversity was 0.9988, and the discrimination capacity was 0.9. Data are available in the Y chromosome haplotype reference database under accession number YA003631. The obtained results were compared to haplotypes from geographically and linguistically close populations.     

Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography

Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1 by 3 individuals. The probability of drawing a HV1 sequence match within the north west Germans or within published sets of south Germans and west Austrians is similar (within a factor of 2) to drawing a sequence match between any two of these three population samples. Furthermore, HV1 sequences of 700 male inhabitants of one village in Lower Saxony were generated and these showed a nearly linear increase of the number of different haplotypes with increasing number of individuals, demonstrating that the commonly used haplotype diversity measure (Nei 1987) for population samples tends to underestimate mtDNA diversity in the actual population. Received: 14 January 1999 / Accepted: 15 February 1999     

US forensic Y-chromosome short tandem repeats database

A forensic Y-STR database generated in the US was compiled with profiles containing a portion or complete typing of 16 STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4. There were 17,447 samples in the version of database in which 77% and 20% were collected in North America and Asia, respectively. The database was separated into six general populations, African American, Asian, Caucasian, Hispanic, Indian, and Native American. Each population was further classified into subgroups according to geographic regions. Some subgroups were tested, found to be homogenous and merged together. Allele and haplotype frequencies, as well as sample sizes were summarized. Of the full haplotypes (i.e., 16 STRs without missing data), 93.7% in total population were distinct, 92.9% were population specific, and 89.3% were only observed once. The majority of shared haplotypes were found among North American populations as a result of admixture lasting the past few hundred years. The power of discrimination (PD), coancestry coefficient (F_st), and coefficient of gene differentiation (G_st) at locus and haplotype levels were also calculated. The most polymorphic marker was DYS385; this marker contains a tandem duplication and actually is composed of two loci. Both G_st and F_st estimates were very small with haplotypes composed of a high number of STRs haplotypes (e.g., 10–16 markers), although G_st is slightly more conservative for these extended haplotypes. With Native American removed from the total population data set, the G_st and F_st estimates reduce further. PD was 0.9998 for the total population dataset for all 16 Y-STR markers. Three measures of Y-STR profile frequency were calculated: (1) unconditional haplotype frequency, (2) population substructure adjusted frequency, and (3) binomial upper bound of the haplotype frequency. The binomial upper bound is the most conservative estimate for most forensic applications. Estimates of the weight of a Y-STR haplotype can be estimated using population specific or total population databases.     

Haplotype analysis of the polymorphic 24 Y-STR markers in six ethnic populations from China

Twenty-four Y-STR loci were analysed in 1446 males from the following six Chinese ethnic populations: Guangxi Han (n=600), Gin (n=161), Maonan (n=135), Miao (n=186), Zhuang (n=226) and Yao (n=138) using the AGCU Y24 STR amplification kit. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.4006), DYS438 (0.4300), and DS388 (0.4907), and the greatest diversity corresponds to markers DYS385a/b (0.9636) and DYS527a/b (0.9439). Moreover, there were 1331 different haplotypes identified from the 1446 total samples, of which 1233 were unique. Notably, we observed shared haplotypes between the four ethnic populations (Maonan, Miao, Zhuang, Yao ethnic population), except between the Guangxi Han and Gin population. The estimated overall haplotype diversity (HD) was 0.9997. A multidimensional scaling (MDS) plot based on the genetic distances between populations demonstrates the genetic similarity of the Maonan, Miao and Zhuang populations with genetic distance below 3.0. No substructure correction is required to estimate the rarity of a haplotype comprising 24 markers. In summary, the results of our study indicate that the 24 Y-STRs have a high level of polymorphism in these six Chinese ethnic populations and could therefore be a powerful tool for forensic applications and population genetic studies.     

Polymorphism of the mitochondrial DNA control region in Italians

Mitochondrial DNA sequences of the hypervariable regions HVI and HVII were analysed in 83 Caucasians living in central Italy to expand the database for forensic identification purposes, and 75 different haplotypes resulting from 62 polymorphic positions in HVI and 44 in HVII were observed. The most frequent haplotype (263G, 309.1C, 315.1C) was shared by 7 individuals, 2 haplotypes were shared by 2 individuals, and 72 were unique. The genetic diversity was found to be 0.99 and the random match probability 1.9%. A condition of sequence heteroplasmy was found in only one case at nt 16311, whereas a length heteroplasmy was found in the homopolymeric stretch of cytosines 303–315. Our results indicate that in direct sequencing beyond the poly-cytosine stretch, the overlap is due to length heteroplasmy, whereas the blurred signal occurs when the stretch is composed of more than 10 cytosines. Received: 14 February 2000 / Accepted: 23 May 2000     

Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control

We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users.     

Mitochondrial DNA sequence analysis of a native Bolivian population

Mitochondrial DNA analysis is very useful for the interpretation of the history of human migration and to estimate the frequency of a haplotype in the forensic context. From a human settlement perspective, La Paz area is greatly interesting since the first planned city of the region is located there. Samples from 110 individuals from La Paz were studied analysing the polymorphisms in the D-loop, hypervariable region I (HVI) and hypervariable region II (HVII) in order to verify the genetic diversity. The aim of this study was to start the creation of a population database in order to obtain the genetic interpopulation variability and classify haplotypes into characteristic haplogroups of South America. A total of 97 different haplotypes were identified, 90 being unique, expressed by 122 polymorphic nucleotide positions. Nucleotide and sequence diversity were estimated to be 0.015 ± 0.0075 and 0.996, respectively. Haplogroup distribution in the samples was 57.27% B4, 19.09% C1, 10.00% A2, 3.64% D1, 2.73% D4h3, 1.82% H, and 0.91% for each of the haplogroups A4, B4c1a, CZ, D4J, M7a and M8/N9b. The rate of length heteroplasmy was 36.36% in HVI and 52.73% in HVII. Phylogenetic analysis reveals proximity to the Korean, Chilean aboriginal, Japanese and Australian populations. The estimated genetic variability of the studied population was high, suggesting an early settlement.     

Interpreting Y chromosome STR haplotype mixture

Mixture interpretation is a challenging problem in forensic DNA analyses. The interpretation of Y short tandem repeat (STR) haplotype mixtures, due to a lack of recombination, differs somewhat from that of the autosomal DNA markers and is more complex. We describe approaches for calculating the probability of exclusion (PE) and likelihood ratio (LR) methods to interpret Y-STR mixture evidence with population substructure incorporated. For a mixture sample, first, all possible contributor haplotypes in a reference database are listed as a candidate list. The PE is the complement of the summation of the frequencies of haplotypes in the candidate list. The LR method compares the probabilities of the evidence given alternative hypotheses. The hypotheses are possible explanations for the mixture. Population substructure may be further incorporated in likelihood calculation. The maximum number of contributors is based on the candidate list and the computing complexity is polynomial. Additionally, mixtures were simulated by combining two or three 16 Y-STR marker haplotypes derived from the US forensic Y-STR database. The average PE was related to the size of database. With a database comprised of 500 haplotypes an average PE value of at least 0.995 can be obtained for two-person mixtures. The PE decreases with an increasing number of contributors to the mixture. Using the total sample population, the average number of candidate haplotypes of two-person mixtures is 3.73 and 95% mixtures have less than or equal to 10 candidate haplotypes. More than 98.7% of two-person mixtures can only be explained by the haplotype combinations that mixtures are composed. These values are generally higher for three-person mixtures. A small proportion of three-person mixture can also be explained by only two haplotypes.     

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. Electronic Supplementary Material Supplementary material is available for this article at     

Human Y-chromosomal STR types in north Thailand

A north Thai Y-haplotype database consisting of the loci DYS19, DXYS156-Y, DYS390, DYS391, DYS392, DYS393, and the four subsegments of DYS389 is presented. We observed 44 Y-types in 50 unrelated Thais, and the haplotype diversity was calculated to be 97.36%. No Y-types were shared with a sample of 55 Japanese, but 3 matches were found in a sample of 61 Han Chinese, and there was one Thai-German match in a larger west German sample (n = 179).     

Polish population study on Y chromosome haplotypes defined by 18 STR loci

Polymorphism of 18 STR loci specific to the human Y chromosome (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS426, DYS437, DYS438, DYS439, DYS460, GATA H4.1, DYS385 a/b, and YCAII a/b) was evaluated by means of a multiplex (octadecaplex) PCR reaction and capillary electrophoresis in a Polish population sample of 208 unrelated males. A total of 192 different haplotypes and 183 unique haplotypes were identified. The observed haplotype diversity was 0.998, while discrimination capacity was 92.3%. DYS389 was shown to be the most valuable in discrimination of similar haplotypes, whereas DYS388, DYS393, DYS426, and DYS438 did not affect the discrimination power of the multiplex.Electronic Supplementary Material Supplementary material is available for this article at .     

Population genetic polymorphisms for 17 Y-chromosomal STRs haplotypes of Chinese Salar ethnic minority group

We studied and established a DNA database of 17 Y-STRs in a population sample of 133 unrelated individuals of Salar ethnic minority group, in order to investigate haplotype frequencies of Salar population, evaluate their usefulness in forensic applications, and enrich Chinese population genetic informational resources. Out of a total of 133 individuals 123 showed different haplotypes, while six haplotypes occurred more than once. The overall haplotype diversity for the Y-STRs loci was 0.9983, and the discrimination capacity was 0.9248.     

Haplotype diversity of 23 Y-chromosomal STRs in a population sample from the Federal District (Brazil)—a territory that arose from nothing

In this study, the genetic variations of 23 short tandem repeats on the Y-chromosome were analyzed in a sample of 201 males from the Federal District (Brazil). The Federal District (Brazil) was built in 1960 in Brazil’s Central West region, where there was no previous population. In 2010, the population of this artificially founded district consisted of 2,500,000 inhabitants. We observed 200 different haplotypes, 199 of which were unique and one of which occurred two times. The haplotype diversity was 0.9999, and the discrimination capacity was 0.995. The data are available in the Y chromosome haplotype reference database under accession number YA003843. The results were compared to the haplotypes from other Brazilian macroregions.