Genetic variations of 15 autosomal and 17 Y-STR markers in Sindhi population of Pakistan

Perveen, Rukhsana; Shahid, Ahmad Ali; Shafique, Muhammad; Shahzad, Muhammad; Husnain, Tayyab

doi:10.1007/s00414-017-1544-3

Cited by 11 publications

(6 citation statements)

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“…Significant differences were observed after Boneferroni’s correction ( p ≤ 0.0002) at 15/15 loci with Mongol, 14/15 African American 26 , 27 , Caucasian (12/15) 27 , Uganda Yousafzai and Kashmiri (11/15) 16 , 18 , 28 , Balochi, Punjabi, central India (7/15) 14 , 23 , 38 . While differences at small numbers of loci for Nepalese, Sindhi (3/15), Karnataka and Bangladeshi (2/15) 21 , 24 , 25 , 39 were observed. However, there were no significant differences at any loci for the Tamil, Balmiki, and Kerala populations 19 , 20 , 22 .…”

Section: Resultsmentioning

confidence: 94%

“…We have provided evidence that the Christian population in Lahore, Pakistan, forms a sub-population among Asian groups and has some unique genetic characteristics 14 , 39 , 49 . Results of inter-population differentiations, PCA, phylogenetic and structure analysis revealed that Lahore Christians have relatively close genetic relationships with south Asians particularly Indians.…”

Section: Discussionmentioning

confidence: 98%

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

Rubab

Shafique

Javed

et al. 2020

Sci Rep

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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.

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Section: Resultsmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 98%

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

Rubab

Shafique

Javed

et al. 2020

Sci Rep

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“…We compared our current results with previously published work on populations from Pakistan with Yfiler and RM Y-STRs. On Yfiler 17 Y-STRs, British Pakistanis [ 22 ], Punjabi population [ 23 ], Kashmiri population [ 23 ], Hazara population [ 9 ], Sindhi population [ 24 ], Youszai population [ 25 ] and Pathan population [ 26 ] showed discrimination capacities (DCs) of 99.24%, 87.23%, 68.3%, 76.47%, 86.40%, 71.92% and 73.7%, respectively. The samples studied with RM Y-STRs showed HD values ranging from 1 to 0.9921 for Pathan [ 19 ], Brahui [ 19 ], Punjabi [ 19 ], Sindhi [ 19 ], Araein [ 27 ], Pakistani [ 6 ], Punjabi [ 20 ] and Sindhi [ 20 ] populations.…”

Section: Resultsmentioning

confidence: 99%

Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan

Nazir

Adnan

Rehman

et al. 2022

Genes

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Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1–20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father–son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.

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“…Short tandem repeats show enough variations from individual to individual which make them suitable for personal identification, paternity testing cases, population genetics and evolutionary research (Adnan, Rakha, Oscar, & Kayser, ; Adnan et al, ; Adnan, Ralf, Rakha, Kousouri, & Kayser, ; Adnan, Zhan, Zhan, Kasim, Rakha, & Xin, ; Zhan et al, ). In the present study, we examined the polymorphisms of 15 hypervariable autosomal STR loci in 181 individuals from interior Sindh of Pakistan and compared them with already published data taken from different studies (Barni et al, ; Bentayebi, Abada, Ihzmad, & Amzazi, ; Chen et al, ; Di Cristofaro, Julie, Temori, & Chiaroni, ; Demeter, Kelemen, Székely, & Popescu, ; Perveen, Shahid, Shafique, Shahzad, & Husnain, ; Shafique et al, ; Shan et al, ; Shrivastava, Jain, & Trivedi, ; Tie, Wang, & Oxida, ; Yao & Wang, ; Yoo et al, ; Zhang, , ; Zhang, Zhao, Guo, Liu, & Wang, ; Zhu et al, ).…”

Section: Introductionmentioning

confidence: 99%

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

Adnan

Rakha

Nazir

et al. 2019

Int J Immunogenetics

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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.

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Genetic variations of 15 autosomal and 17 Y-STR markers in Sindhi population of Pakistan

Cited by 11 publications

References 5 publications

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

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

Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan

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

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