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

Kumawat, R. K.; Shrivastava, Pankaj; Shrivastava, Divya; Mathur, G.K.; Dash, Hirak Ranjan; Chaubey, Gyaneshwer

doi:10.1016/j.genrep.2020.100990

Cited by 8 publications

(2 citation statements)

References 32 publications

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“…In this preliminary test, all the tested samples produced quality DNA profiles with both the reaction volumes and showed concordance. Our few previous studies have also reported use of 10 µl PCR reaction volume for an efficient reaction product, which further supported the reduction of final PCR reaction volume 42 , 43 . Direct amplification protocol was further validated for 10 µl reaction volume PCR reaction as per recommended PCR conditions of the particular multiplex kits.…”

Section: Resultssupporting

confidence: 67%

Direct PCR amplification from saliva sample using non-direct multiplex STR kits for forensic DNA typing

Shrivastava

Jain

Kumawat

2021

Sci Rep

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Due to its proficiency to provide the most discriminating results for forensic applications, medical research and anthropological studies, multiplex PCR based STR analysis has been established as the most efficient technique in the forensic DNA analysis. Several multiplex amplification kits based on 4, 5 and 6 dyes chemistry are commercially available and used in forensic DNA typing across the globe. These multiplex PCR systems are routinely used for amplification of multiple STR loci (Autosomal, Y and/or X STR’s) in the DNA extracted from various biological samples. In the routine forensic DNA testing, DNA profile obtained is compared with the DNA profile of the reference sample, which takes a certain turnaround time and employs costly lab resources. Successive development in forensic DNA typing have resulted in advent of improved multiplex kits which have reduced the effective analysis time, cost and minimized the number of steps required in comparison to conventional forensic DNA typing. Specialized direct amplification compatible multiplex kits are also available nowadays. These kits are relatively costlier but still require few pre-processing steps, which does not make them worth the hefty cost. Herein, this study, we have used non-direct multiplex STR kits to assess their efficacy for direct amplification. In the present study, 103 saliva samples were directly amplified without any pre-treatment of the samples using thirteen non-direct multiplex kits (4 dyes, 5 dyes and 6 dyes chemistry based) for forensic DNA typing. Here, we report a validated direct PCR amplification protocol from the reference saliva samples by omitting DNA extraction and quantification steps, which resulted in 80% reduction of the turnaround time. The developed protocol is cost effective, time efficient and it does not compromise with the quality of DNA profiles. To the best of our knowledge, this is the first report for direct amplification of DNA with the most commonly used non-direct multiplex STR kits without any pre-treatment of the sample. Complete DNA profiles matching all the essential quality parameters were obtained successfully from all the tested samples.

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Section: Resultssupporting

confidence: 67%

Direct PCR amplification from saliva sample using non-direct multiplex STR kits for forensic DNA typing

Shrivastava

Jain

Kumawat

2021

Sci Rep

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“…The inferred cluster k ranged from 2 to 10 with 20 repetitions after a 100,000 burn in period and 100,000 MCMC simulations for each k. Δk and estimated log probability data statistics were evaluated using Structure Harvester 63 for the selection of most suitable con gured K. Cluster 4 (K=4) was found in the informative shared ancestry component among the studied and compared populations. The ancestry component (Yellow color) was found most prevalent in the North-west Indian populations viz., Gujjar 64 , Meena 64 , Kahar population of Uttar Pradesh, admixed populations of Uttar Pradesh, Rajasthan 64 , Madhya Pradesh, Jharkhand similar to ANI 61,65 ; and Pakistani populations (Balochi, Brahui, Sindhi, Pathan, and Burusho)(Fig. 6).…”

Section: Structure Analysismentioning

confidence: 99%

Genomic Insight Into 21 Hypervariable Molecular Markers in The Population of Lower Himalayan Geographical Province Himachal Pradesh, India

Sharma

Srivast

Sahajpal

et al. 2021

Preprint

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A natural geographical barrier between Tibetan plateau and south Asian countries, the Himalayan Mountain range, serves as a natural barrier between these regions for genetic flow. This has lead to vast genomic divergence among the population residing in Indian Himalayan region..This study was designed with an aim to decipher the genomic diversity and molecular characterization of 21 hypervariable molecular markers in the population of geographical province of Himachal Pradesh in the lower Himalayan region. Randomly selected 401 unrelated individuals native of the lower Himalayan geographical region were included for this study. 21 hypervariable molecular markers included in the PowerPlex® 21 system were amplified and genotyped. A total of 246 alleles and 12.3 (SE 0.927) private alleles per locus were observed. Population differentiation analysis revealed that the studied population showed a genetic affinity with the population of North India, North-west India, Central India, and Uttar Pradesh rather than the population of East India, South India, East Asia, and West Asia. Heterozygosity at the studied loci was found in the range of 0.686 to 0.920. The unite discrimination power (PD) and exclusion power (PE) was found to be 1 and 0.999999998073765 respectively. The unite value of matching probability and typical paternity index was found to be 9.33x10-26 and 5.05x108 respectively for the studied population. All the tested loci were found in Hardy Weinberg Equilibrium (HWE) expectations. Overall the studied population exhibited a great extent of genomic diversity and had a greater genetic affinity with Indo-European speakers rather than Dravidian and Tibeto-Burman speakers.

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Revealing the genomic diversity of North-western Indian people through 20 hypervariable genetic markers

Arya,

Prakash,

Hirani

et al. 2024

Nucleus

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

Cited by 8 publications

References 32 publications

Direct PCR amplification from saliva sample using non-direct multiplex STR kits for forensic DNA typing

Direct PCR amplification from saliva sample using non-direct multiplex STR kits for forensic DNA typing

Genomic Insight Into 21 Hypervariable Molecular Markers in The Population of Lower Himalayan Geographical Province Himachal Pradesh, India

Revealing the genomic diversity of North-western Indian people through 20 hypervariable genetic markers

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