Genetic polymorphism study at 15 autosomal locus in central Indian population

A deep population reference panel of tandem repeat variation

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations

The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.

A deep population reference panel of tandem repeat variation

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3,550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

Forensic and genetic characterizations of diverse southern Thai populations based on 15 autosomal STRs

Southern Thailand is home to various populations; the Moklen, Moken and Urak Lawoi’ sea nomads and Maniq negrito are the minority, while the southern Thai groups (Buddhist and Muslim) are the majority. Although previous studies have generated forensic STR dataset for major groups, such data of the southern Thai minority have not been included; here we generated a regional forensic database of southern Thailand. We newly genotyped common 15 autosomal STRs in 184 unrelated southern Thais, including all minorities and majorities. When combined with previously published data of major southern Thais, this provides a total of 334 southern Thai samples. The forensic parameter results show appropriate values for personal identification and paternity testing; the probability of excluding paternity is 0.99999622, and the combined discrimination power is 0.999999999999999. Probably driven by genetic drift and/or isolation with small census size, we found genetic distinction of the Maniq and sea nomads from the major groups, which were closer to the Malay and central Thais than the other Thai groups. The allelic frequency results can strength the regional forensic database in southern Thailand and also provide useful information for anthropological perspective.

Population genetic data of 22 autosomal STR loci for the Scheduled Caste population of Rajasthan India

AIM

To study the genetic structure of the Scheduled Caste population of Rajasthan and its relationship with Indian and global populations using expanded 20 CODIS STR loci (autosomal) markers.

SUBJECTS AND METHODS

Blood samples of 226 healthy, unrelated adult individuals of the Scheduled Caste population of the Indian state of Rajasthan were taken from the routine casework of authors after obtaining written informed consent. Autosomal STR markers included in PowerPlex^® Fusion 5 C and GlobalFiler™ PCR amplification kits were used to explore the genetic diversity of the studied population. Amplicons were separated using Genetic Analyser 3500XL as per the recommended protocol.

RESULTS

Observed heterozygosity for the studied population ranged from 0.681(CSF1PO) to 0.881 (D1S1656).Combined Discrimination Power and Combined Exclusion Power were observed as 1 and 0.9999999852, respectively. The highest Discrimination Power was observed for the locus D1S1656. In the population comparison test, Nei's Da distance-based Neighbor-Joining (NJ) dendrogram revealed two significant clusters of geographically close Indian and East Asian populations along with a few small groups of outlier populations.

CONCLUSION

The matching probability for 20 STR markers was observed as 7.02 × 10^-24 and paternity index as 5.55 × 10⁷. These values play a key role in forensic applications.The studied population showed a higher genetic affinity with geographically closer populations than the distant ones. This caste-based population data is expected to play an important role in forensic DNA applications and genetic studies.

The Heart of Silk Road "Xinjiang," Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy-Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

An evaluation of inter and intra population structure of Uttar Pradesh, inferred from 24 autosomal STRs

Aim: Present study was designed to explore the STR diversity and genomic history of the inhabitants of the most populous subdivision of the country. A set of 24 hyper variable autosomal STRs was used to estimate the genetic diversity within the studied population. A panel of 15 autosomal STRs, which is most common in the previously reported data sets, was used to estimate the genetic diversity between the studied population and obtained unique relations were reported here.Method: The genetic diversity and polymorphism among 636 individuals of different ethnic groups, residing in Bareilly, Pilibhit, Shahjahanpur, Gorakhpur, Jhansi and Varanasi regions of Uttar Pradesh, India was investigated. This investigation was carried out via 24 autosomal STRs.Result: Studied 24 loci showed the highest value of combined power of discrimination (CPD =1), combined power of exclusion (CPE =0.99999999985), combined paternity index (CPI =6.10x10⁹) and lowest combined matching probability (CPM =7.90x10^-31).Conclusion: Studied population showed the genetic closeness with the population of Uttarakhand, Jats of Delhi, Jat Sikh (Punjab) and population of Rajasthan. The locus SE33 and Penta E was found to be most useful in the terms of highest discrimination power, lowest matching probability, highest power of exclusion and highest polymorphism information content for Uttar Pradesh population among the tested loci.

Genomic polymorphism in tribal population of Tripura: Signifying their closer affinity with the Nepalese and Tibetan populations

BACKGROUND

India is the second most populous country in the world, which is aligned into various community segments.

AIM

To evaluate the genetic diversity of the tribal population of Tripura, we carried out this study.

SUBJECTS AND METHODS

15 autosomal STR markers were used for investigation of genomic diversity, inter- and intra- population relationships among the studied population, and other reported neighbouring tribal and caste populations.

RESULTS

Results indicated that the tribals of Tripura share their closer genetic affinity with the Trans-Himalayan (Nepalese, Bhutanese and Tibetan) populations. Locus D18S51 was found as the most discriminatory among all the studied loci with uppermost discrimination power (PD = 0.964) and lowest matching probability (Pm = 0.036) in the study. All the evaluated loci herein are useful, having the maximum value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999746), combined paternity index (CPI = 3 × 10⁵) and combined matching probability (CPm = 2.12 × 1 0 ^-7).

CONCLUSION

Population genetic analysis showed that the studied population has genetic relatedness with the compared Nepalese and Tibetan populations i.e., Kathmandu, Tibet, Newar, and Gorkhas, followed by eastern and central Indian populations.

Revealing genomic history and forensic features of Gurjars from western Uttar Pradesh and National Capital Region Delhi using 23 autosomal STRs

Here we report the genomic history of Gurjars and framed the useful set of autosomal STRs for Gujjar population. We designed this study with a total number of 215 Gurjars from district Saharanpur (previously known as Gujarat due to presence of many Gujjar zamindars), Moradabad, Bulandshahr, Ghaziabad, Meerut, Noida and NCR Delhi. Locus SE33 was found the most polymorphic and discriminating marker for Gujjar population while locus TPOX is the least. Ancestral information of Gurjars was revealed by comparing the Gujjar's population data with 19 neighbouring populations. In Neighbor Joining (NJ) tree Gurjars were found closer to Gujjars of Jammu region, population of Rajasthan and Uttarkhand, due to the same stock of gene pool.

Useful autosomal STR marker sets for forensic and paternity applications in the Central Indian population

BACKGROUND

Many countries have developed their core set of STR loci for forensic application and database generation, which India lacks.

AIM

To assess the usefulness of various combinations of autosomal STR marker sets for their superior use in the central Indian population for forensic and paternity applications.

SUBJECTS AND METHODS

19 STR marker sets were analysed on 200 central Indian populations and 20 paternity cases to assess their usefulness.

RESULTS

Two marker sets each comprising 19 STR markers are found to be superior to 20 expanded CODIS loci in the studied population. These marker sets also showed their effectiveness in 20 paternity cases having CPI values of 7.62 × 10¹¹ and 7.16 × 10¹¹. Three non-CODIS STR markers Penta E, Penta D, and SE33 showed amplification in 50 challenging samples with >0.80 heterozygosity.

CONCLUSION

Population-specific STR marker sets are useful in forensic and paternity applications, as well as database generation, and it is envisioned that Penta E, Penta D, and SE33 markers will be included in the list of core STR loci in the central Indian population.

Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside.

A study of genomic diversity in populations of Maharashtra, India, inferred from 20 autosomal STR markers

OBJECTIVE

This study was planned to evaluate the genetic diversity in the admixed and Teli (a Hindu caste) populations of Maharashtra, India using 20 autosomal Short Tandem Repeat (STR) genetic markers. We further investigated the genetic relatedness of the studied populations with other Indian populations.

RESULTS

The studied populations showed a wide range of observed heterozygosity viz. 0.690 to 0.918 for the admixed population and 0.696 to 0.942 for the Teli population. This might be due to the multi-directional gene flow. The admixed and Teli populations also showed a high degree polymorphism which ranged from 0.652 to 0.903 and 0.644 to 0.902, respectively. Their combined value of matching probability for all the studied loci was 4.29 × 10-25 and 5.01 × 10-24, respectively. The results of Neighbor-Joining tree and Principal Component Analysis showed that the studied populations clustered with the general populations of Jharkhand, UttarPradesh, Rajasthan and Central Indian States, as well as with the specific populations of Maharashtra (Konkanastha Brahmins) and Tamil Nadu (Kurmans). Overall, the obtained data showed a high degree of forensic efficacy and would be useful for forensic applications as well as genealogical studies.

Population genetic data of 22 autosomal STR loci for the Mong people in Vietnam

This study investigated 22 autosomal short tandem repeat (STR) loci in 156 unrelated individuals from the Mong ethnic minority in Ha Giang Province, Vietnam. Allele frequencies and forensic parameters were calculated, showing the combined Powers of Discrimination reaching 1.000000000000000000000000000000 and the combined Power of Exclusion greater than 0.999999986623. Phylogenetic analysis indicated that the Vietnamese Mong population has close genetic relationships with other Hmong-Mien populations.

Population genetic portrait of Pakistani Lahore-Christians based on 32 STR loci

Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFℓSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples. A total of 147 alleles were observed in 15 loci and allele 11 at the TPOX locus was the most frequent with frequency value (0.464). The data revealed that the Christian population has unique genetic characteristics with respect to a few unusual alleles and their frequencies relative to the other Pakistani population. Significant deviations from Hardy–Weinberg equilibrium were found at two loci (D13S317, D18S51) after Boneferroni’s correction (p ≤ 0.003). The combined power of discrimination, combined power of exclusion and cumulative probability of matching were 0.999999999999999978430815060354, 0.999995039393942 and 2.15692 × 10⁻¹⁷, respectively. On the bases of genetic distances, PCA, phylogenetic and structure analysis Lahore-Christians appeared genetically more associated to south Asian particularly Indian populations like Tamil, Karnataka, Kerala and Andhra Pradesh than rest of global populations.

Genomic diversity of the Muslim population from Telangana (India) inferred from 23 autosomal STRs

AIM

This study aimed to investigate the genomic diversity and population structure in the Muslim community of Telangana, India, using 23 autosomal microsatellite genetic markers. We also examined genetic relatedness between Muslim and non-Muslim populations of India.

SUBJECTS AND METHODS

A sample of 184 randomly selected unrelated healthy Muslim individuals from the Telangana state were included in this study. The genotyping of 23 autosomal STR markers included in PowerPlex^® Fusion 6 C multiplex system (Promega)was done.

RESULTS

A total of 273 alleles were observed in the studied population, and locus SE33 showed 37 observed alleles, which is the highest number of observed alleles among all the studied loci. Among all the studied loci the most polymorphic and discriminatory locus was SE33, with the values of polymorphic information content (PIC) = 9.411E-01 and power of discrimination (PD) = 9.865E-01. Observed heterozygosity ranged from 6.630E-01 (D22S1045) to 9.239E-01 (SE33). Discrimination power, exclusion power, matching probability and paternity index for all the studied loci were 1.00E + 00, 1.00E + 00, 2.01E-28, and 5.68E + 09, respectively. The studied Muslim population showed genetic relatedness with non-Muslim populations i.e. populations of central India, Jharkhand, and Uttar Pradesh, suggesting the conversion of Hindus during the Muslim invasion.

CONCLUSION

Neighbor-joining (NJ) tree and principal component analysis (PCA) revealed that the studied population showed genetic affinity with communities of Jharkhand, Madhya Pradesh and Uttar Pradesh states. The genetic data of this study may be useful for forensic, medical, and anthropological studies.

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.

Genetic variation and differentiation among a native British and five migrant South Asian populations of the East Midlands (UK) based on CODIS forensic STR loci

BACKGROUND

Short Tandem Repeats (STRs) are widely used in population and forensic genetic studies.

AIM

The objective of this study was to document the level and extent of genetic variation of the FBI Combined DNA Index System (CODIS) STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX and CSF1PO) in 6 populations (British, Indian (Punjabis and Gujaratis), Pakistani, Bangladeshi and Sri Lankan) of the East Midlands (UK). There is a lack of genetic research on the migrant South Asian populations.

SUBJECTS AND METHODS

DNA samples (N = 603) were analysed for 13 autosomal forensic STR loci along with the amelogenin locus following standard protocols. Data were analysed for genetic variation and a range of forensic indices.

RESULTS

All loci were polymorphic in all populations with a variable degree of variation. Average observed heterozygosity was highest in Bangladeshi (0.803) and lowest in Punjabi (0.761). FGA locus had the highest power of discrimination (PD) in most populations.

CONCLUSION

FGA locus was most polymorphic and discriminatory among migrant populations demonstrating it as the marker with the highest potential in forensic analyses. These results could be useful for population and forensic genomic studies.

The genomic ancestry of Jat Sikh population from Northwest India inferred from 15 autosomal STR markers using capillary electrophoresis

BACKGROUND

Autosomal STR typing using capillary electrophoresis is a reliable method for establishing parentage and for deciphering genomic ancestry.

AIM

This study was planned to show the genetic diversity of the Jat Sikh population, which is a widespread community of the Punjab region, and to assess its genetic relationship with existing Indian populations.

SUBJECTS AND METHODS

Blood samples of unrelated healthy individuals of the Jat Sikhs (n = 123) were used in this study. Fifteen autosomal STR markers along with the sex determination genetic marker Amelogenin were amplified using AmpFlSTR^®Identifiler^® Plus kit, and genetic analyser 3100 was used for genotyping.

RESULTS

A total of 246 alleles were observed with allele frequencies ranging from 0.004 to 0.447. The heterozygosity ranged from 0.659 to 0.886, and all studied loci were in Hardy-Weinberg Equilibrium (HWE). Fibrinogen A alpha (Aα) chain (FGA) was found to be the most polymorphic and also the most discriminating locus in the studied population. Neighbor-joining (NJ) tree, principal component analysis (PCA) plot, and Nei's Distance matrix revealed genetic affinity with the previously reported Jatt Sikh (Punjab) population and showed the outlier nature of this population compared with other Indian populations.

CONCLUSION

The data generated by this study enhance the database of Indian populations to be used in civil and forensic cases and also in other population-based genetic studies.

Allelic frequency database of 15 polymorphic autosomal STRs in the Malayalam-speaking population of Kerala, India

In this study, we assessed and established an allelic frequency database of Malayalam-speaking population of south western Indian state Kerala, using 15 polymorphic short tandem repeats (STRs) genetic markers. For this study, 464 unrelated healthy individuals were randomly selected following the ethical standards. The most polymorphic and most discriminating locus was D2S1338, with a value of 0.860 and 0.968, respectively. The range of heterozygosity extended from a minimum of 0.668 (TH01) to a maximum of 0.847 (D2S1338). The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999997861, respectively, for all 15 autosomal STR loci under study. The combined probability of match (CPM) and combined paternity index (CPI) for all 15 autosomal STR loci were found to be 9.85 × 10^-19 and 4.18 × 10⁵, respectively.

Genetic variation (population database) at 20 autosomal STR loci in the population of Rajasthan (north-western India)

To explore the genetic diversity and establish the allelic database of the population of Rajasthan, we assessed 571 randomly selected unrelated healthy individuals residing in the state. Blood samples of the selected individuals were collected with the compliance of ethical standards. Locus Penta E was observed to be the most polymorphic (0.908), whereas locus TPOX was observed to be the least polymorphic (0.639). The observed heterozygosity ranged from a minimum of 0.667 (TPOX) to a maximum of 0.925 (Penta E). The combined value of the power of discrimination (PD) and power of exclusion (PE) for all the studied 20 short tandem repeat (STR) loci were observed to be 1 and 0.999999997560235 respectively. The combined values of matching probability (PM) and paternity index (PI) for all the studied 20 STR loci were 7 × 10^-26 and 4 × 10⁸ respectively. The obtained genetic data are useful for forensic DNA applications and expected to enrich the genetic database of Indian populations.

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 (CP_m) 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.

Forensic effectiveness and genetic distribution of 23 autosomal STRs included in Verifiler PlusTM multiplex in a population sample from Madhya Pradesh, India

We report here the first ever global study on genetic polymorphism using a Verifiler Plus^TM autosomal STR multiplex system. The study evaluated genetic characteristics of 23 autosomal STRs in 200 unrelated residents of Guna district of Madhya Pradesh, India. Allele frequencies and forensic parameters are reported. Population comparison analysis was also performed using NJ tree and PCA plot. Penta E marker showed highest power of discrimination (0.938) among all 23 studied markers. The study also presents the first ever global forensic assessment in Indian population on D6S1043 marker (PD 0.937). The results demonstrated that all the 23 markers were highly polymorphic and the Verifiler Plus^TM kit is suitable for forensic purposes in Indian population.

Genetic characterization of 15 autosomal STRs in the interior Sindhi population of Pakistan and their phylogenetic relationship with other populations

Genetic structure of a population can be influenced by evolutionary processes and cultural histories which can alter the frequencies of different variants at particular genetic markers. These characteristics make DNA evidence suitable for forensic applications. Little relevant data are available from the interior Sindhi population; thus, in the current study, we have investigated 15 autosomal STRs in 181 unrelated individuals belonging to the interior parts of Sindh Pakistan, to establish its lineage and parameters of forensic interest. These STRs revealed a high power of discrimination (CPD), power of exclusion (CPE) and matching probability (CMP) are 0.9999999999999999968997, 0.99998612 and 3.1003 × 10^-18 respectively. The genetic distances, neighbour-joining (NJ) tree, interactivity test and principal component analysis (PCA) based on 15 autosomal STR loci showed that the interior Sindhi population had a closer genetic relationship with Pakistani populations and distant relationships with regional (India and Afghanistan) populations. The present findings exhibited that STRs included in AmpFLSTR Identifiler kit (Applied Biosystems) are genetically polymorphic in the interior Sindhi population of Pakistan. This study provides valuable population genetic data for the genetic information study, forensic human individual identification and paternity testing.

Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C™ Multiplex System

Performance of PowerPlex Fusion 6C kit (PP F6C) was assessed in 374 unrelated individuals belonging to Madhya Pradesh, an Indian state. The study evaluated the forensic parameters for the loci included in PP F6C Multiplex System. The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999999995, respectively, for all 23 autosomal STR loci. SE33 showed the greatest power of discrimination (0.990) in the studied population, whereas TPOX showed the lowest (0.843). The availability of three Y-STR loci in the Multiplex System is suitable for assessing male contribution and amelogenin deletion in a single Multiplex PCR simultaneously. The study also presents the first global report on polymorphism in the Indian population on SE 33 autosomal STR loci and PP Fusion 6C Multiplex System. The results revealed that the studied STR Multiplex System is highly polymorphic and suitable for forensic purposes.

Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic relationships with neighboring populations

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifiler PCR amplification kit. There was no evidence of departures from Hardy-Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the different populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China.