Autosomal STR Loci Research Articles

The Paleogenetic Study of Bertek-33, an Afanasyevo Cemetery on the Ukok Plateau, the Altai Mountains

We present the results of a paleogenetic analysis of bone samples representing seven adult individuals from Bertek-33—an Afanasyevo cemetery on the Ukok plateau, in the Altai Republic, Russia. The fi ndings are interpreted with reference to archaeological and anthropological data. Four systems of genetic markers were analyzed: mitochondrial DNA, polymorphic fragment of the amelogenin gene, autosomal STR-loci, and Y-chromosomal STR-loci. Genetic results indicate the dominance of Western Eurasian mtDNA haplogroups (T, J, U5a, K, H) and the homogeneity of the male gene-pool represented by variants of the Y-chromosomal haplogroup R1b. Data on mtDNA, Y-chromosome, and individual autosomal markers attest to the Western Eurasian affi nities of this group. The sample falls within the mtDNA and Y-chromosomal diversity of the Afanasyevo population of southern Siberia. Possible kinship between the individuals buried at Bertek-33 is discussed. Also, we address theoretical issues such as the accuracy of comparisons and the interpretation of genetic data with regard to cultural features.

Peopling of Rajasthan, India: Evaluating the gene flow from east and west

Rajasthan is a state located in the north-western part of India and it has been cited as a major route of human migration since ancient times. The present study was conducted to find out the genetic affinity of Rajasthani population with the population living in its east as well as the west. In particular, we compared them with the population of Pakistan which shares the common geographical boundary with the Rajasthan while also having a look at their inter and intra population affinities with the population belonging to other Indian states. We investigated the genetic structure and population parameters of Rajasthani populations obtained for twenty polymorphic autosomal STR loci from 669 unrelated individuals belonging to its three population groups including Mina, Gujjar and the admixed population of Rajasthan. The studied populations showed a wide range of genetic diversity and besides the genetic structure of the studied populations, it was found that the average heterozygosity value was highest among the populations of Rajasthan, possibly, because of gene flow from different directions. Various statistical analyses suggested that the Rajasthani populations had a higher affinity with the North Indian populations rather than with the Pakistani population.

Genetic Polymorphism of 15 Autosomal STR loci in Population of Madhya Pradesh

We report here an autosomal STR DNA database of Population of Madhya Pradesh and evaluation ofautosomal STR diversity in the context of population genetics and forensic efficiency parameters. In thisstudy, Allele frequencies of 15 autosomal STR loci were investigated in 123 unrelated individuals (57 Female& 66 Male) from the various geographical regions of Madhya Pradesh using PowerPlex® 16 HS System.All the studied loci appeared the high degree of genetic polymorphism with observed Heterozygosity (Ho=observed heterozygosity) ranged from 0.911 (D21S11) to 0.659 (TPOX). Locus PENTA E showed the highestpower of discrimination (0.978) and the highest polymorphism (PIC = 0.90). The combined probability ofmatch (CPM) and combined paternity Index (CPI) for all the 15 STR loci was found to be 2.8 x 10-18 and 1.2x106, respectively. The combined discrimination power (CPD) and combined exclusion power (CPE) for allthe tested 15 Loci was observed 1 and 0.9999989 respectively, assign that all the loci are highly polymorphicand have the potential for forensic application.

Strategy for STR typing of bones from the Second World War combining CE and NGS technology: A pilot study

The genetic identification of skeletal remains found in Second World War mass graves is complicated because of the poor quality of the samples. The aim of this study was to set up a workflow for STR typing of such samples combining PCR/CE and PCR/NGS technologies. To this end, 57 DNA samples from an equal number of 75-year-old femurs were studied. After a first round of PCR typing using GlobalFiler CE, 42 samples yielded a full profile and were therefore submitted to our standard workflow. The 15 samples that yielded no or a limited number (2–17/21) of autosomal STR markers as well four bone control samples that provided a full profile with the conventional PCR/CE test were typed in duplicate by the GlobalFiler NGS kit. Despite the degradation of the samples, which resulted in lower coverage and a lower % of on-target reads, reliable sequencing data were obtained from 16/19 samples. The use of a threshold of 30× for the locus call led to a consensus profile (cp) of 20–31/31 STR autosomal loci in 10 samples and to a cp of 8–10/31 loci in two samples, whereas the four control samples yielded a cp of 26–31/31 loci. Finally, the data of the NGS typing were combined with those of the CE typing. This last task allowed us to recover (on average) three alleles per sample and to increase the number of the heterozygous patterns in 37 cases. In total, the combined approach proposed here made possible the genetic typing of 65–100% of the autosomal STR markers in 10/15 (66.6 %) skeletal remains that yielded no or very poor results with the conventional PCR/CE approach. However, because several artefacts (such as allelic drop-out and allelic drop-in) were scored, the risk of mistyping cannot be neglected.

Forensic application and genetic diversity of 21 autosomal STR loci in five major population groups of Pakistan.

Investigation of genetic diversity of the 21 autosomal STR loci included in the GlobalFilerTM PCR Amplification Kit in 529 Pakistani individuals belonging to the Punjabi, Pashtun, Sindhi, Saraiki, and Baloch ethnic groups. Population genetic parameters and forensic informative metrics for each group were evaluated. SE33 showed the greatest power of discrimination in all populations studied. The combined match probability ranged from 8.06E-27 (Saraiki) to 1.05E-26 (Baloch), and the combined power of exclusion ranged from 0.99999999902 (Punjabi) to 0.99999999964 (Pashtun). D12S391 in the Baloch population and D2S441 in the Saraiki population showed deviation from Hardy-Weinberg equilibrium. Significant genetic distances were observed between the Punjabi, Pashtun, and Baloch populations. This study supports the utilization of the GlobalFilerTM STR kit for forensic applications in Pakistan.

Genetic variation of 20 autosomal STRs in Jats belonging to Delhi, India.

The present study based on 20 autosomal STR polymorphism reveals the genetic diversity of the Jat population of Delhi, India (n = 120). A total of 240 alleles were observed for this study. The allele frequency ranged from 0.004 to 0.508. The studied loci followed the Hardy-Weinberg equilibrium (HWE), and the heterozygosity ranged from 0.658 to 0.908. The locus Penta-E was found the most polymorphic and discriminating in the studied population with the value 0.910 and 0.981, respectively, whereas the locus TPOX was found least polymorphic and discriminating with the value 0.612 and 0.833, respectively. The combined paternity index (CPI) was 1.46 × 109, and the probability of match (CPm) was 2.68 × 10-25 for all 20 autosomal STR loci. The generated data adds to the Indian population database. It will be used for forensic purposes and in other population-based genetic studies.

Genetic polymorphism of 15 autosomal STR loci in population of Chhattisgarh, India

This study presents a database related to autosomal STR DNA of population of Chhattisgarh, India and evaluates diversity of autosomal STR in the context of forensic applications and genetics.In this piece of study, allele distribution at 15 autosomal STR loci were investigated for the randomly selected 445 unrelated healthy individuals (205 females and 240 males) from various geographical regions of Chhattisgarh using AmpFlSTR(R) Identifiler(R) Plus PCR Amplification Kit. High degree of genetic polymorphism have been indicated by all the loci with observed Heterozygosity (Hobs) obtained in the range from 0.661 (TH01) to 0.852 (D2S1338). Locus FGA was observed as the most discriminatory and polymorphic with the value of 0.965 and 0850 respectively among all the studied loci. The paternity index and cumulative matching probability for the examined loci were found to be 3.7 × 105 and 3.8 × 10−18 respectively. The cumulative power of discrimination and exclusion were detected to be 1 and 0.99999764 respectively, a sign that all the loci are exceptionally polymorphic and conceivably significant in forensic applications.

Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics.

Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10-29 , which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution.

Estimating genetic polymorphism in Bhuiyan population of eastern India using 20 autosomal STR loci.

We conducted a study of 182 unrelated adult individuals belonging to Bhuiyan population resident of Eastern India in order to estimate genetic polymorphism by using 20 autosomal STR loci. The results obtained from this study were compared with the published data of Indian and neighbouring countries' populations. This research study is expected to contribute significantly to forensic investigations for human identification and parentage testing.

Population data of 22 autosomal STR loci in Chinese Han individuals from Hebei Province in northern China

Population data of 22 autosomal STR loci in Chinese Han individuals from Hebei Province in northern China

A newly devised multiplex assay of novel polymorphic non-CODIS STRs as a valuable tool for forensic application

DNA profiling that relies on sets of highly polymorphic autosomal STR markers is widely used in the forensic field for human identification and paternity testing. However, the number of markers that are included in the STR kits that are currently available is insufficient to conclusively prove or disprove a relationship between individuals, especially when complex family scenarios are suspected or indirect analyses are required. In these cases, it becomes necessary to increase the number of loci under analysis to reach an adequate likelihood ratio (LR). In this study, we discovered 18 new autosomal non-CODIS STR loci (D1S1616, D1S1608, D2S437, D3S2457, D4S2406, D4S3249, D5S2843, D5S2501, D6S1010, D8S1039, D12S1301, D14S586, D15S815, SHGC-145653, CHLC.GATA14D12, D1S1603, HUMUT7148, and CHLC.GATA84D07) by web scanning and experimental screening. On the basis of this discovery, we developed a novel multiplex typing system named the “SiFaSTR 21plex_NCII Typing System” comprising 1) the 18 non-CODIS autosomal STRs mentioned above, 2) a CODIS locus of D2S1338, and 3) Amelogenin and DYS391. A forensic developmental validation, including sensitivity, species specificity, concordance, reproducibility, sample suitability, testing stability, and mixture testing, was performed following SWGDAM. The results of the validation studies indicated that this system is accurate, reliable and suitable for human DNA profiling. The sensitivity study of the system demonstrated that a full profile was obtainable with DNA as low as 125 pg. Species specificity was proven by the lack of cross-reactivity with a series of common animal species. The stability study demonstrated that 1 ng of control DNA could be fully genotyped with concentrations of haematin ≤ 150 μM, indigotin ≤ 5000 ng/μl, urea ≤ 16000 ng/μl, nigrosine ≤ 100 ng/μl and humic acid ≤ 20 ng/μl. In the mixture test, all of the minor alleles could be called at mixed ratios of 1:1, 1:3 and 3:1. We also investigated the allelic frequencies and forensic parameters of the included markers in 259 Chinese Han individuals. The forensic efficiency parameters, including the total power of discrimination (TDP) and the combined exclusion power in duos (CPEduos) and in trios (CPEtrios) of the system were calculated to be greater than 0.9999999, 0.9997347 and 0.9999997, respectively. This result proved that the system is suitable for human identification and paternity testing. The 18 newly discovered non-CODIS STRs and the developed system will be a valuable supplementary tool for the forensic community and will help solve complex paternity cases, evolutionary studies and population investigations.

Polymorphisms of 19 Autosomal STR Loci in Sichuan Han Population and Their Forensic Application.

Objective To investigate the allele distribution, population genetics parameters and genetic analysis of neighboring populations of 19 autosomal STR loci in Sichuan Han population, and to evaluate their forensic application value. Methods The Goldeneye?? DNA ID system 20A was used to perform multiplex PCR amplification and allelic gene typing of 19 STR loci in 1 201 unrelated Han individuals from Sichuan Province. Allele frequencies and population genetics parameters were calculated. The Nei's genetic distances between Sichuan Han population and 12 previously reported populations were analyzed. Multidimensional scaling and principal component analysis were carried out and phylogenetic trees were also constructed. Results The heterozygosity of 19 STR loci ranged from 0.617 0 to 0.915 1, their discrimination power ranged from 0.777 4 to 0.986 5, matching probability ranged from 0.013 5 to 0.222 6, polymorphism information content ranged from 0.546 4 to 0.910 5, probability of exclusion ranged from 0.311 8 to 0.826 3 （triplet） and from 0.197 9 to 0.712 1 （biplet）, and no significant deviations from Hardy-Weinberg equilibrium were observed. Based on the results of multidimensional scaling, principal component analysis and phylogenetic trees of the genetic distances between Sichuan Han population and the other 12 populations, Sichuan Han population was closest to Hubei Han population and was farthest to Xinjiang Uygur population. Conclusion The 19 autosomal STR loci showed a high polymorphism and discriminating ability in Sichuan Han population, which can provide a data foundation for personal identification, paternity test and population genetics study.

A genomic exploration of 15 autosomal STR loci for establishment of a DNA profile database of the population of Himachal Pradesh.

In order to create an autosomal STR loci population database for Himachal Pradesh, 259 blood samples were taken from people residing in various regions of the state and AmpFlSTR® Identifiler® Plus PCR amplification kit was used for evaluation of 15 autosomal STR markers. A total of 149 alleles were investigated in this study with a mean allele number of 9.933 per locus. The locus D2S1338 was most informative in our data, as it had the highest discrimination power (PD-0.967) and the highest polymorphic information content (PIC-0.86). The matching probability and typical paternity index for all the studied loci were observed as 2.9x10-18 and 4.7x105, respectively. Discrimination power (CPD) and exclusion power (CPE) for all the studied loci were observed as 1 and 0.999998.

Forensic parameters and ancestral fractions in the Kedayan population inferred using 21 autosomal STR loci

Few population groups in Borneo (Sabah and Sarawak) have been genetically characterized. No study has ever been done on the Kedayan population. In this project, genetic polymorphism was measured at 21 autosomal STR loci in 200 unrelated Kedayan individuals living in Sabah and Sarawak, Malaysia and their forensic statistics calculated. We also compared these new data with those from elsewhere in Southeast Asia, Europe and Africa. A PCO plot showed that Austronesian populations in the Asia-Pacific region plot closely together and well separated from the unrelated reference populations. Our statistics show that these 21 STR loci are highly informative for population studies and fully suitable for use in forensic DNA analyses.

Updated population genetic data of 15 autosomal STR loci in a Shandong Han population from East China and genetic relationships among 26 Chinese populations

Background The population genetics investigation of STR loci in specific populations is the basic premise for forensic practice, and the AmpFlSTRTM IdentifilerTM Plus kit is still widely used in most forensic DNA laboratories. Aim To obtain more reliable and accurate population genetic data of 15 autosomal STRs in the Shandong Han population and explore the genetic relationship with 25 neighbouring Chinese populations. Subjects and methods A total of 5356 unrelated Chinese Han individuals from Shandong Province were genotyped using the IdentifilerTM Plus Kit. Allele frequencies and corresponding forensic statistical parameters were calculated. Population comparisons were further explored through the neighbour-joining tree and multidimensional scaling analysis. Results A total of 217 alleles were calculated, the allele frequencies spanned from 0.0001 to 0.5340. The combined discrimination power (CDP) and the combined probability of paternity (CPE) of 15 STR loci were 0.99999999999999998755 and 0.999994524, respectively. Population comparisons demonstrated that Shandong Han have genetic homogeneity with most Sino-Tibetan populations. Conclusions Our study updates the Shandong Han population database with a large sample size. These 15 STR loci in the Shandong Han population are more polymorphic and discriminatory than shown in previous data, which could be more applicable to personal identification and paternity testing, as well other population genetics studies.

Genetic polymorphism analysis of 23 STR loci in the Tujia population from Chongqing, Southwest China.

To evaluate the applicability of 23 autosomal STR loci (D10S1248, D11S4463, D12ATA63, D14S1434, D17S1301, D18S853, D1GATA113, D1S1627, D6S1017, D20S1082, D20S482, D17S974, D22S1045, D1S1677, D2S1776, D2S441, D3S4529, D4S2408, D9S1122D5S2500, D6S474, D18S51, D9S2157) included in DNA Typer™ 25 Kit for individual identification and parentage testing, allele frequencies and forensic efficiency parameters were first obtained from healthy, unrelated 506 Chongqing Tujia individuals. A total of 1012 alleles were identified in 23 STR loci, and allele frequencies ranged from 0.001 to 0.5761. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the 23 STR loci were 0.999999999999999999999753 and 0.99999967, respectively. These results suggested that 23 autosomal STR loci could be used as an effective tool for forensic application in Chongqing Tujia population. Comprehensive comparisons were conducted based on the analysis of genetic distance, principal component analysis (PCA), multidimensional scaling plot (MDS), and phylogenetic tree to explore the interpopulation genetic relationship. Our results revealed that Chongqing Tujia keeps the more relatively genetic similarity with Hunan Han, Hubei Tujia, and Sichuan Han, which could be interpreted by that those populations were originated from the same ethnic ancestor or genetic communication were happened in adjacent areas.

Population data of 21 autosomal STR loci in Malaysian populations for human identification.

The use of 21 autosomal STR loci for human identification has been gaining popularity throughout the world. It has been indicated that the forensic statistical parameters for supporting the use of 21 STR loci varied among different populations. Hitherto, such data for the diverse Malaysian populations remain unreported, rendering doubts in the court of law about its real ability for human identification in Malaysian population. Using the GlobalFiler™ Express PCR Amplification Kit, complete DNA profiles of 21 STR loci from buccal swabs of convicted Malaysian criminal (n = 570; 190 each for Malays, Chinese, and Indians) (by the year 2016-2017) were analyzed for their allele frequencies, exact test of Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, power of exclusion, match probability, and polymorphism information content. Most of the loci were found to be in the Hardy-Weinberg equilibrium after the Bonferroni correction. Being the most informative locus, SE33 demonstrated the highest power of discrimination and power of exclusion, indicating its usefulness to discriminate individuals. In contrast, TPOX had the lowest power of discrimination and power of exclusion, as well as being the less informative genetic locus for all Malaysian population studied here. The probabilities that two individuals would share the same DNA profiles among the Malaysian Malays, Chinese, and Indians, as well as in general Malaysian population, were 1.3713 × 10-25, 2.8822 × 10-25, 7.5668 × 10-26, and 1.0385 × 10-26, respectively. The results obtained here were found comparable with similar studies reported in other populations. Hence, its robustness for forensic human identification among the Malaysian populations is, therefore, statistically supported.

Genomic portrait of Odisha, India drawn by using 21 autosomal STR markers.

In order to find out the genetic diversity in the eastern Indian population of Odisha consisting of various linguistic and ethnic groups, we undertook a study on 508 unrelated healthy individuals belonging to Odisha, India. We assessed genetic variation and compared the data with published literature of Indian population consisting of different ethnic groups from different geographical areas using 21 autosomal STR markers. The most polymorphic and discriminatory STR locus in the studied population was found to be SE33 with the calculated values of 0.94 and 0.991 respectively for both the parameters. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were found to be 1 and 0.999999999704865 respectively. The combined probability of match (CPm) and combined paternity index (CPI) for all 21 autosomal STR loci were found to be 8.01 × 10-26 and 3.45 × 109 respectively. Though, the studied eastern Indian population of Odisha shared its closest genetic affinity with nearest Indian geographical regions, i.e., the population of Jharkhand which is geographically located in eastern India as well as the Central Indian population.

Genomic blueprint of population of Rajasthan based on autosomal STR markers

Aim: Genetic diversity and forensic efficacy of 20 autosomal STR genetic markers were investigated in a highly diverse population of Rajasthan, a state in north-western India.Subjects and methods: In this study, 317 blood samples from unrelated healthy individuals were directly amplified using the PowerPlex® 21 multiplex system (Promega). Amplified products were separated by capillary electrophoresis using a Genetic Analyser –3500 XL (Thermo Fisher Scientific). The data thus obtained was statistically analysed using population genetic software.Results: The studied population showed genetic affinity with the geographically close populations. The locus Penta-E was found to be the most polymorphic with a value of 0.90 in the studied population. The combined discrimination power (CPD) and combined power of exclusion (CPE) were observed as >0.999999999 and 0.999999997, respectively, for all the studied 20 autosomal STR loci. The combined probability of match (CPm) was 1.39 × 10−25 and combined paternity index (CPI) was 3.66 × 108 for all the studied loci.Conclusion: The results conclusively support the hypothesis that the studied autosomal STR loci are polymorphic in nature and, besides being useful in forensic applications they can also be applied in anthropological and other population genetic studies. This study supports the ‘isolation-by-distance’ model. Genetic data obtained from this study will enrich the population data bank.

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.