Y-chromosome STR Loci Research Articles

Погребальный памятник афанасьевской культуры Бертек-33 на плато Укок (Горный Алтай): результаты палеогенетического исследования

В статье представлены результаты палеогенетического исследования останков семи взрослых индивидов из погребального памятника афанасьевской культуры Бертек-33 (плато Укок, Республика Алтай, Россия) и их интерпретация с учетом археологического и палеоантропологического контекста. Проведен анализ четырех систем генетических маркеров: митохондриальной ДНК, полиморфного фрагмента гена амелогенина, аутосомных STR-локусов и STR-локусов Y-хромосомы. Полученные результаты свидетельствуют о доминировании в исследуемой группе населения западно-евразийских гаплогрупп митохондриальной ДНК (T, J, U5a, K, H) и однородности мужского генофонда, представленного вариантами гаплогруппы R1b Y-хромосомы. Данные по митохондриальной ДНК, Y-хромосоме, отдельным аутосомным маркерам указывают на западно-евразийский вектор генетических связей этой группы. Исследованная серия укладывается в рамки внутрипопуляционного разнообразия генофонда митохондриальной ДНК и Y-хромосомы афанасьевского населения Южной Сибири. В статье рассмотрены возможные родственные связи между индивидами, захороненными в курганах памятника Бертек-33. Обсуждаются вопросы корректного сопоставления и интерпретации данных о генетических характеристиках погребенных и особенностях материальной культуры исследуемого населения.

Genetic analysis of 27 Y-chromosomal STR loci in a Zimbabwean Shona ethnic group.

Buccal swabs from 200 unrelated Zimbabwean males were collected from voluntary participants located in Harare province. The 5-dye SureID® 27Y Human STR Identification Kit was used to perform multiplex polymerase chain reactions (PCR) and generate Y-chromosomal DNA profiles. This kit targets markers DYS456, DYS576, DYS570, DYS481, DYF387S1, DYS627, DYS393, DYS391, DYS390, DYS635, DYS449, DYS533, DYS438, DYS389I, DYS448, DYS389II, DYS19, GATA_H4, DYS518, DYS458, DYS460, DYS437, DYS439, DYS392, and DYS385, similar to the Yfiler® Plus Amplification Kit. A total of 161 haplotypes were generated with the PowerPlex® Y system, whereas 159 complete haplotypes were generated for the Yfiler® Plus system. Haplotype Discrimination Capacity (DC) with the Yfiler® Plus system was determined to be 0.9686, while the Genetic Diversity (GD) of the targeted loci ranged from 0.03748 at DYS392 to 0.867239 at DYS449. One haplotype contained the triallelic pattern 37, 38, and 39 at DYS387S1. In addition, marker DYS387S1 and marker DYS385 had 13 counts of microvariant alleles overall, while 9 null allele counts were noted at marker DYS448. Genetic distances between our population data and 22 other data sets from African countries and people of African descent were estimated and results showed significant genetic variation.

Validation of the AGCU Expressmarker 16 + 22Y Kit: a new multiplex for forensic application.

Genotyping by targeting short tandem repeats (STRs) has been widely used in forensic applications. However, most commercial kits detect autosomal STRs or Y-STRs alone, which waste both time and opportunity. The AGCU Expressmarker 16 + 22Y Kit includes 16 autosomal and 22 Y-chromosomal STR loci and is designed for the forensic science field and obtaining quicker results. Here, we conducted the validation study according to Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Validation of PCR-based studies, species specificity, sensitivity, DNA mixture studies, inhibitors, precision, and sizing accuracy were performed. Furthermore, this system was also tested in 346 random male samples from Han, Hui, Tibetan, and Zhuang populations in China, showing its high power for forensic discrimination in the Chinese population. In addition, this system was able to deal with AMELY deletion cases, which can correctly identify sex in forensic criminal investigations. Our results suggested that the AGCU Expressmarker 16 + 22Y Kit is a useful tool for rapid criminal investigation.

Population genetic analysis of 36 Y-chromosomal STRs yields comprehensive insights into the forensic features and phylogenetic relationship of Chinese Tai-Kadai-speaking Bouyei.

Male-specifically inherited Y-STRs, harboring the features of haploidy and lack of crossing over, have gained considerable attention in population genetics and forensic investigations. Goldeneye® Y-PLUS kit was a recently developed amplification system focused on the genetic diversity of 36 Y-chromosomal short tandem repeats (Y-STRs) in East Asians. However, no population data and corresponding forensic features were reported in China. Here, 36 Y-STRs were first genotyped in 400 unrelated healthy Tai-Kadai-speaking Bouyei male individuals. A total of 371 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability and discrimination capacity values were 0.9999, 0.0026 and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Population comparisons between the Guizhou Bouyei and 80 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. The results showed that the population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our newly genotyped Bouyei samples show a close affinity with other Tai-Kadai-speaking groups in China and Southeast Asia. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.

Validation of a multiplex amplification system of 19 autosomal STRs and 27 Y-STRs

This article describes a newly devised autosomal short tandem repeat (STR) multiplex polymerase chain reaction (PCR) system for 19 autosomal loci (D12S391, D13S317, D16S539, D18S51, D19S433, D2S1338, D21S11, D3S1358, D5S818, D6S1043, D7S820, D8S1179, CSF1PO, FGA, TH01, TPOX, vWA, Penta D and Penta E), 27 Y-chromosome STR loci (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS635, DYS627, YGATAH4 and DYF387S1) and amelogenin with six-colour fluorescent labelling. Various parameters were evaluated, such as its accuracy, sensitivity, specificity, stability, ability to analysis of mixtures and effects of changes in the PCR-based procedures. All of the 47 selected STR loci were accurately and robustly amplified from 282 bloodstain samples. The species-specificity was high and some ability to inhibit Hematin was identified. The lowest detectable DNA amount was ≥0.125 ng. All of the male loci of the secondary component were revealed precisely when the control DNA was mixed at male/female and male/male ratios of 1:4 or more. We conclude that the present 19-plex autosomal STR and 27 Y-STR assay is both accurate and sensitive. It constitutes an additional powerful tool for forensic applications.

Mutation rates of six Y-chromosomal STR loci estimated from 210 pedigrees in Chinese Han population

The Y-chromosomal short tandem repeats (Y-STRs) with low mutation rates as slowly mutating (SM) Y-STRs could be used to refine the construction of phylogenetic trees in evolutionary research. Six Y-STR markers (DYS388, DYS426, DYS461, DYS485, DYS525 and DYS561) were from the previously published paper and considered as SM Y-STRs. Here, we investigated the six Y-STRs from 210 pedigrees in Chinese Han population in Henan province, covering an overall number of 8178 meiotic transfers. The number of mutations of the six Y-STRs ranged from 0 (DYS388 and DYS426) to 12 (DYS561), resulting the observed mutation rates spanned from 0 (95% credible interval [CI], 0∼2.196 × 10−3) to 8.804 × 10−3 (95% CI, 4.557 × 10−3∼1.533 × 10−2). According to the results, only DYS388 and DYS426 could be classified as SM Y-STRs in the Chinese Han population. Although these results will replenish the data of Y-STR mutations as well as be important for paternal genealogy identification, kinship analysis, and phylogenetic tree reconstruction, the mutation rates of the six Y-STRs were significantly different among different populations, which we need to pay attention to in future studies.

Is it reliable to use paraffin embedded tumor tissues as biological evidence in parentage cases?

Short tandem repeats (STR) are reliable markers used for forensic identification and paternity testing. In some cases, histological paraffin blocks containing malignant cells can be used for STR typing in identification and paternity. DNA profiling and result interpretation with these samples often becomes a challenging job. The malignant tissues may show preferential amplification, loss of heterozygosity, and microsatellite instability.Due to the suspected paternity case, two paraffin blocks were sent for DNA analysis by Court of Justice. Pathology report of the paraffin blocks have shown that they contain lung cancer tissues taken with bronchoscopy. After extracting DNA with silica based method from the samples taken from different parts of these two blocks, 21 autosomal STR loci and 17 gonosomal STR loci were studied.When we have compared the STR profiles of son and his alleged father, Y-chromosomal STR loci matched fully. But for 2 of the 21 autosomal STR loci were found mismatches in father-son comparing. These two mismatched loci have been homozygous in alleged father. Moreover, 10 of 21 autosomal loci have shown homozygosity, and at one locus D16S539 has three alleles. While increased homozygosity in FFPE sample of alleged father has increased the paternity index, mismatched loci have lessened it in our model with mutations but without dropout.These results suggest that great care and proper statistical model should be taken in the evaluation of the DNA typing results obtained from clinical cancerous specimens, in particular when no other reference samples containing normal tissue are available.

RETRACTED: Population genetics of 24 Y‐STR loci in Chinese Han population from Jilin Province, Northeast China

BackgroundIt is meaningful to expand the available population information on forensic medicine and to investigate the genetic characteristics of Han population from Jilin Province, Northeast China.MethodsIn this study, we investigated the genetic characteristics of 24 Y‐chromosomal short tandem repeat (STR) loci in 1,088 unrelated Chinese Han male individuals from Jilin Province, using DNATyperTM Y24 amplification kit. Additionally, we performed the population comparison between the Jilin population and the other nine reported populations based on the Y‐STR genotyping haplotypes.ResultsA total of 1,067 different haplotypes were found from 1,088 unrelated individuals, of which 1,046 were unique and 21 were shared by two individuals. The gene diversity values of 22 loci ranged from 0.3870 (DYS391) to 0.9668 (DYS385ab). The random match probability was 0.0010 with the discrimination capacity of 0.9807. Population comparison showed that there were minor differences compared to Beijing Chinese Han, China Manchu, Gansu Chinese Han, and Jiangsu Chinese Han, but major differences with respect to the populations of Guangdong Chinese Han, Yunnan Chinese Han, China Hui, China Korean, and China Tibetan.ConclusionOur results showed that the 24 Y‐STR loci in Jilin Han population are valuable for forensic application and human genetics.

Population genetics of 25 Y-STR loci in Chinese Han population from Liaoning Province, Northeast China

In this study, we investigated the genetic characteristics of 25 Y-chromosomal short tandem repeat loci in 305 unrelated Chinese Han male individuals from Liaoning Province, using AmpFISTR® Yfiler® Plus amplification kit. A total of 293 different haplotypes were observed at the 25 Y-STR loci; among them, 281 were unique and 12 were occurred twice. The overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. The gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Population relationships between our data and other published populations were measured by Rst and visualized in two multi-dimensional scaling plots. The results showed that the 25 Y-STR loci in Liaoning Han population are valuable for forensic application and human genetics.

Genetic structure and forensic characteristics of Saraiki population from Southern Punjab, Pakistan, revealed by 20 Y-chromosomal STRs.

Pakistan harbors more than 18 major ethnic groups which speak 60 different languages. People speaking Saraiki languages are known as Saraiki or Multani. They are mainly residents of Southern Punjab including Multan, Dear Ghazi Khan, Rajanpur, and Rahim Yar khan. Here, we reported the data of 20 Y-chromosomal short tandem repeats (Y-STRs) genotyped with the Goldeneye® 20Y kit in 154 unrelated Saraiki individuals. We observed 141 different haplotypes on 20 Y-STR loci and the gene diversity (GD) ranged from 0.6566 (DYS448) to 0.9538 (DYS385a, b). The overall haplotype diversity was 0.9989 at 20 Y-STRs loci. Furthermore, we performed population genetic analyses by including data from 26 other South Asian populations. The presented haplotype data was recently included in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

Genetic analysis of 50 Y-STR loci in Dong, Miao, Tujia, and Yao populations from Hunan.

To investigate the genetic polymorphism of Y chromosome short tandem repeat (Y-STR) loci in Dong, Miao, Tujia, and Yao minority populations from Hunan Province, China. Fifty Y-STRs (DYS392, DYS389I/II, DYS447, DYS438, DYS527, DYS645, DYS596, DYS391, DYS456, DYS19, DYS593, DYS448, DYS627, DYS557, DYS437, DYS481, DYS533, DYS390, DYS385, DYF387S1, DYS460, DYS393, Y_GATA_H4, DYS439, DYS635, DYS444, DYS643, DYS549, DYS576, DYS570, DYS458, DYS449, DYS518, DYS531, DYS630, DYS622, DYS552, DYS510, DYS459a/b, DYS446, DYS443, DYS587, Y_GATA_A10, DYS520, DYS522) were analyzed for 2553 unrelated healthy male individuals from Hunan (643 Dong males, 666 Miao males, 633 Tujia males, 611 Yao males) using AGCU Y37 and AGCU Y SUPP STR amplification system. There were 624 different haplotypes in 643 unrelated Dong males, 662 in 666 unrelated Miao males, 627 in 633 unrelated Tujia males, and 587 in 611 unrelated Yao males. The haplotype diversities of Dong, Miao, Tujia, and Yao were determined as 0.999879, 0.999982, 0.999970, and 0.999860, respectively. Analysis of molecular variance (AMOVA) tests demonstrated that genetic distance between Miao and Tujia was the smallest (0.0003), while the genetic distance between Dong and Yao was the largest (0.0252). The 50 Y-STR loci in the four minority populations from Hunan Province revealed a highly polymorphic genetic distribution, which showed a high potential for population genetics and forensic practice.

Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449.

In forensic casework, Y-chromosome short tandem repeats (Y-STRs) are essential for differentiating between unrelated males and resolving the male component of admixed biological evidence. While the majority of Y-STRs are adequate for discriminating between different paternal lineages, rapidly mutating Y-STRs are necessary for improving discrimination between males within populations of low Y-chromosome diversity and between paternal relatives. Alternatively, sequencing of Y-STRs may also improve the discrimination between isometric Y-STR alleles by identifying variation in the repeat unit pattern arrangements and by identifying SNPs in the flanking region or within the STR repeat unit itself. In this report, a total of 153 DNA sequences are presented across the Y-STR loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. A total of 94 Y-STR sequences provided herein are reported for the first time, of which 37 sequences represent alleles showing size homoplasy, 34 sequences of known alleles for which sequence data has been unavailable and a total of 23 novel allele sequences across loci DYS644, DS447, DYS710 and DYS504. This study further encountered a rare sequence variant in the 5' flanking region of DYS385 and a total of two SNPs in the repeat structure at DYS481 and DYS449.

Alleles dropout patterns of Y-short tandem repeats in infertile males with Y chromosome microdeletions

Y chromosomal short tandem repeat (Y-STR) typing is the most commonly used genetic technique in forensic studies. However, there may be a limit to the application of Y-STR in forensic science as Y-STR loci are subject to loss or variation caused by the higher chromosomal structures' spontaneous mutation rate. Located in the long arm of the Y chromosome, azoospermia factor (AZF) have been shown to participate in spermatogenesis and its deletion could cause infertility. However, little is known about the Y-STR dropout pattern in individuals with Y chromosome microdeletions. In this study, 85 infertile males with Y chromosome interstitial deletion were identified and special Y-STR allele dropout patterns were analyzed by employing a Y-STR Commercial Kit and a Y chromosome Deletion Kit. Results demonstrate that AZF a region deletion are related to DYS439-DYS389I-DYS389II alleles dropout, while AZF b region or c region deletions correlate to DYS448 allele dropout. Null DYS385-DYS392-DYS448 alleles were observed in AZF b+c+d region deletion individuals. While null DYS390-Y-GATA-H4-DYS385-DYS392-DYS448 alleles were observed in AZF a+b+c+d large region deletion individuals. Our data suggest that Y chromosome microdeletions may indicate specific Y-STR locus dropout patterns.

Y chromosome genetic data defined by 23 short tandem repeats in a Serbian population on the Balkan Peninsula

Background: Serbs mainly live in the territory of the recently re-established state of Serbia. However, the turbulent history in the Balkan Peninsula has led to settlement of Serbs not only within present day Serbia, but also in different parts of neighbouring countries.Aim: To define polymorphisms of 23 Y-chromosomal short tandem repeat (STR) loci in a modern Serbian population from the central part of the Balkan Peninsula.Subjects and methods: The reference sample consisted of 303 men declared as Serbs over three generations. Localities of the collected materials include the territories of Serbia, Bosnia and Herzegovina, Croatia and Montenegro. DNA samples were typed using the PowerPlex®Y23 amplification kit.Results: The highest locus diversity was observed for DYS385 and DYS481. In this study the most abundant haplogroups were I2a, E1b1b, R1a and I1. The largest genetic distances between the Serbs and other close Southern Slavs were for the Macedonians and Slovenians.Conclusion: This study is the first one to define STR polymorphism of Serbian people not only from Serbia but also from other parts of the Balkan Peninsula. The presented genetic data may be useful in further examinations of the genesis and genetic structuring of the present-day Serbian gene pool.

Forensic characteristics and phylogenetic analysis of 23 Y-STR loci in the Miao population from Guizhou province, southwest China

Background: Investigation of haplotype/allele frequency data of Y-STR loci in ethnically diverse populations is essential for forensic reference database construction and genetic application. However, the population genetic characteristics of the Chinese Miao minority from Guizhou Province remain uncharacterised.Aim: To assess forensic characteristics for 23 Y-Chromosomal STR loci in Guizhou Miao and explore population genetic relationships with geographically neighbouring populations.Subjects and methods: Twenty-three Y-Chromosomal STRs were genotyped using the Powerplex® Y23 system in 103 unrelated Chinese Miao males from Guizhou Province, southwest China. Haplotypes and forensic parameters were obtained. Population relationships of Guizhou Miao with others were revealed using AMOVA and an MDS plot.Results: A total of 96 haplotypes were identified with overall haplotype diversity (HD) and discrimination capacity (DC) of 0.9985 and 0.9320, respectively. Genetic differentiation was observed with most of the comparison populations, prominently for Guizhou Shui.Conclusion: The 23 Y-STR loci were highly polymorphic and discriminating in the Guizhou Miao population and could be used for forensic practice and population genetic studies. Population relationship analysis revealed Guizhou Miao had a close genetic relationship with geographically close Guizhou Gelao, as well as Han majorities derived from different regions.

Profile interpretation of extremely long alleles at DYF387S1 and DYS447 migrated into allele range of adjacent loci

Two rare cases of long alleles at Y-chromosome short tandem repeat (Y-STR) loci (DYF387S1 and DYS447) were identified when two father–son pairs were analyzed by multiplex amplification. “Null alleles” were observed at DYF387S1 and DYS447, and duplicated alleles were displayed at DYS533 and DYS19. We secondly amplified DYF387S1, DYS533, DYS447, and DYS19 loci by singleplex polymerase chain reaction (PCR) and sequence analysis of the long alleles at DYF387S1 and DYS447 loci. The results showed that alleles from DYF387S1 (allele 55) and DYS447 (allele 41) were longer than their common sizes in the allelic ladder ranges (33–42 for DYF387S1 and 18–30 for DYS447) and located in the neighboring loci (DYS533 and DYS19, respectively). Therefore, to identify these cases involving this unusual phenomenon, not only re-amplification using the same kit but also additional amplification (using alternative multiplex kits with different adjoining markers or additional singleplex PCR amplification) should be performed to avoid misinterpreting Y-STR profiles.

Population genetics of 19 Y-STR loci in Yanbian Korean samples from China.

China harbors 56 ethnic groups, including Korean, with a population size of approximately 1.92 million at the 2010 census. Most of the Koreans live in Northeastern parts of China, including Jilin (59.64%), Heilongjiang (20.21%), and Liaoning (12.55%) provinces, and the rest are spread to other parts of China. Koreans across China share a common culture, which is similar to Korea. We have explored the genetic characteristics of 20 Y-chromosomal short tandem repeat (Y-STR) loci in 252 unrelated Chinese Korean male individuals from Jilin Province, using a Goldeneye 20Y amplification kit. Moreover, phylogenetic analysis was performed between the Korean population and other relevant populations based on the Y-STR haplotypes. We have found 237 different haplotypes among 252 unrelated individuals. The haplotype frequencies ranged from 0.0238 to 0.0040, while gene diversity ranged from 0.9666 (DYS385a/b) to 0.2260 (DYS391). The random match probability was 0.0048, the haplotype diversity was 0.9992 ± 0.0006 and discrimination capacity was 0.9405. Population comparison revealed that Korean populations are lining up together with other Korean populations from East Asia. Our results showed that the 20 Y-STR loci in the Yanbian Korean population are valuable for forensic application and human genetics. The Yanbian Koreans have lined up with other Korean population from China and Korea while showing significant differences from other East Asian populations.

Genetic characterization of Y-chromosomal STRs in Hazara ethnic group of Pakistan and confirmation of DYS448 null allele.

Pakistan harbors 18 major ethnic groups and Hazara is one of the distinct but smaller groups comprising 0.090% of the total population. Hazara individuals have typical Mongolian facial features and they claim to be descendants of Genghis Khan's army in the first quarter of the thirteenth century AD. In this study, we genotyped 153 unrelated males living in Quetta, Baluchistan, Pakistan, for a total of 26 (n = 153) to 30 (n = 47) Y-chromosomal STR loci. One hundred forty unique haplotypes were developed for Hazara population using the PowerPlex Y23 loci. The Y-STR locus showed a genetic diversity ranging from 0.2384 to 0.7918, and an overall discrimination capacity (DC) of 91.5%. The Hazara population samples were profiled for three additional Y-STRs (DYS388, DYS449 and DYS460), which increased the number of unique haplotypes to 144 while the DC increased to 94.11% in Hazara Population of Pakistan. Interestingly, null alleles were observed at DYS448 in 25 individuals of Hazara population. The Hazaras showed significant differences from other local populations of Pakistan as well as neighboring populations, but had considerable genetic affinities to Kazakhs and Mongols.

Mutation analysis of 13 RM Y-STR loci in Han population from Beijing of China.

Two five-color fluorescence multiplex amplification systems of 13 Y chromosome short tandem repeat (Y-STR) loci (DYF387S1, DYF399S1, DYF403S1a/b, DYF404S1, DYS449, DYS518, DYS526a/b, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) have been designed. A study was conducted measuring the mutation rates of the 13 Y-STRs in 501 father-son pairs of Han origin in Beijing, China. Among 7515 allele transmissions in 501 father-son pairs, 75 single-step and 2 two-step mutations were observed. Two father-son pairs had mutations at two different loci in 13 Y-STRs. The estimated mutation rates ranged from 2.00 × 10-3 (95% CI 1.00 × 10-4 to 1.11 × 10-2) for the DYF387S1, DYF403S1b, DYS526a, and DYS449 loci to 4.59 × 10-2 (95% CI 2.93 × 10-2 to 6.81 × 10-2) for the DYF399S1 locus. The average mutation rate is 1.02 × 10-2 (95% CI 8.10 × 10-3 to 1.28 × 10-2). Among these Y-STR markers, only DYF399S1, DYS627, DYF403S1a, DYS547, DYS612, and DYS626 had mutation rates higher than 1.00 × 10-2.

Genetic variation for three Y-STR loci: DYS390, DYS518, and DYS643.

Y chromosome short tandem repeats (Y-STRs) are commonly used to analyze male-specific DNA. Although biallelic patterns due to duplication events have been detected at some loci, Y-STRs generally appear as a single peak except for DYS385 because the Y chromosome is haploid. STR loci in regions of segmental duplication by homologous recombination on the Y chromosome exhibit double allelic peaks, rather than single peaks. In this study, we report a bi- and triallelic pattern observed simultaneously in DYS390, DYS518, and DYS643. A bi- and triallelic pattern has not previously been observed simultaneously for these three loci. We also identified the copy number variation in the region including these loci by the microarray-based analysis. Given the peak balance pattern, the copy number variation, and the close position of these three loci on the Y chromosome, we consider that this phenomenon is caused by a segmental duplication in the euchromatin region. By ruling out mixed samples, a common interpretation of multiple peaks, these results have practical implications for the interpretation of Y-STR results in forensics analyses.