scholarly journals Construction and forensic application of 20 highly polymorphic microhaplotypes

2020 ◽  
Vol 7 (5) ◽  
pp. 191937
Author(s):  
Aliye Kureshi ◽  
Jienan Li ◽  
Dan Wen ◽  
Shule Sun ◽  
Zedeng Yang ◽  
...  
Keyword(s):  
South Asian ◽  
Forensic Genetics ◽  
Individual Identification ◽  
Nucleotide Polymorphisms ◽  
Important Research ◽  
Effective Number ◽  
Forensic Application ◽  
Research Focus ◽  
Single Nucleotide ◽  
1000 Genomes

Microhaplotype markers have become an important research focus in forensic genetics. However, many reported microhaplotype markers have limited polymorphisms. In this study, we developed a set of highly polymorphic microhaplotype markers based on tri-allelic single-nucleotide polymorphisms. Eleven newly discovered microhaplotypes along with nine previously identified in our laboratory were studied. The microhaplotype genotypes of unrelated individuals and familial samples were generated on the MiSeq PE300 platform. These 20 loci have an average greater than 3.5 effective number of alleles. Over the whole set, the cumulative power of discrimination was 1–3.3 × 10 −18 , the cumulative power of exclusion was 1–1.928 × 10 −7 and the theoretical probability of detecting a mixture was 1–1.427 × 10 −6 . Differentiation comparisons of 26 populations from the 1000 Genomes Project distinguished among East Asian, South Asian, African and European populations. Overall, these markers enrich the current microhaplotype marker databases and can be applied for individual identification, paternity testing and biogeographic ancestry distinction.

scholarly journals Screening of Three Different Alleles of mtDNA (G709A, G3496T, A3537G) in Subpopulation of UKM Students

2018 ◽  
Vol 5 (1) ◽  
pp. 37-40
Author(s):  
Seri Mirianti Ishar ◽  
Jeyaganesan Pillay a/l Balaraman ◽  
Muhammad Jefri Mohd Yusof ◽  
Khairul Osman ◽  
Lee Loong Chuen
Keyword(s):  
Uv Light ◽  
Forensic Genetics ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Documentation System ◽  
Single Nucleotide ◽  
National University ◽  
Pcr Products ◽  
Malay Population ◽  
Mutation Allele

Human DNA consists of nucleus DNA (nDNA) and mitochondrial DNA (mtDNA). Both are valuable in medicine and forensic genetics but in this project, single nucleotide polymorphisms (SNPs) in mtDNA are used to trace the mutation occurred. Mutations in the sequence of alleles can lead to haplogroup variation and also certain diseases. The purpose of this study is to screen of mutations on alleles G709A, G3496T, and A3537G in Malay population of The National University of Malaysia (UKM) students. These SNPs lie in the ND1 (nitrogen dehydrogenase subunit 1) coding region, and the reports state that these three alleles are prone to mutate. From MitoMap Web site, the mutations of these alleles are reported to have potential in causing several diseases with the collaboration of other SNPs mutation. Allele G709A is reported to have an association with hearing loss and Leber Hereditary Optic Neuropathy (LHON) while allele G3496T is associated to LHON only. Allele A3537G is related to diabetes. A total of 100 DNA samples were collected from Malay students of UKM and preserved on FTA card to be purified later. The concentration of the DNA on the purified FTA card was between 10μM to 20μM. An attempt was made by amplifying those three loci from the genomic DNA. The amplified product was detected and separated using 1% gel electrophoresis. Before sequencing, the PCR products were visualized under UV light using gel documentation system. All PCR products were sequenced to detect the mutation on every single position chosen. From the alignment of sequencing results, allele G709A and allele G3496T showed no mutation. Meanwhile four samples from alleles A3537G has the mutation. From the results obtained, it seems that mutations are rare in all selected alleles. It is recommended to increase the sample size and alleles selected in the future to increase the strength of the study. This study also should be applied to other populations in Malaysia such as Chinese and Indian.  

scholarly journals Ancestral Spectrum Analysis With Population-Specific Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Gang Shi ◽  
Qingmin Kuang
Keyword(s):  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
1000 Genomes Project ◽  
Specific Population ◽  
High Coverage ◽  
Single Nucleotide ◽  
Target Populations ◽  
1000 Genomes ◽  
Sequencing Studies ◽  
Best Linear Unbiased

With the advance of sequencing technology, an increasing number of populations have been sequenced to study the histories of worldwide populations, including their divergence, admixtures, migration, and effective sizes. The variants detected in sequencing studies are largely rare and mostly population specific. Population-specific variants are often recent mutations and are informative for revealing substructures and admixtures in populations; however, computational methods and tools to analyze them are still lacking. In this work, we propose using reference populations and single nucleotide polymorphisms (SNPs) specific to the reference populations. Ancestral information, the best linear unbiased estimator (BLUE) of the ancestral proportion, is proposed, which can be used to infer ancestral proportions in recently admixed target populations and measure the extent to which reference populations serve as good proxies for the admixing sources. Based on the same panel of SNPs, the ancestral information is comparable across samples from different studies and is not affected by genetic outliers, related samples, or the sample sizes of the admixed target populations. In addition, ancestral spectrum is useful for detecting genetic outliers or exploring co-ancestry between study samples and the reference populations. The methods are implemented in a program, Ancestral Spectrum Analyzer (ASA), and are applied in analyzing high-coverage sequencing data from the 1000 Genomes Project and the Human Genome Diversity Project (HGDP). In the analyses of American populations from the 1000 Genomes Project, we demonstrate that recent admixtures can be dissected from ancient admixtures by comparing ancestral spectra with and without indigenous Americans being included in the reference populations.

scholarly journals The population genetics characteristics of a 90 locus panel of microhaplotypes

2021 ◽  
Vol 140 (12) ◽  
pp. 1753-1773
Author(s):  
Andrew J. Pakstis ◽  
Neeru Gandotra ◽  
William C. Speed ◽  
Michael Murtha ◽  
Curt Scharfe ◽  
...  
Keyword(s):  
Individual Identification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Web Based ◽  
Geographical Regions ◽  
Forensic Case ◽  
Biogeographic Regions ◽  
Ancestry Inference ◽  
Public Repositories ◽  
Genomic Regions

AbstractSingle-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.

scholarly journals An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Tao Jin ◽  
Ming Sun ◽  
Lizhu Jia ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Single Nucleotide Polymorphisms ◽  
Disease Risk ◽  
Software Tool ◽  
Mature Mirnas ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
1000 Genomes ◽  
Mirna Sequencing

MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease/phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual’s samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs. Using matpred2, we identified isomiRs and then verified them by searching within individual miRNA sequencing data. Our approach yielded biomarkers for biological experiments, mined functions of miRNAs and SNPs, improved disease risk assessment, and provided a way to achieve individualized precision medicine.

Potential relationship between single nucleotide polymorphisms used in forensic genetics and diseases or other traits in European population

2015 ◽  
Vol 129 (3) ◽  
pp. 435-443
Author(s):  
Maria Pombar-Gomez ◽  
Elixabet Lopez-Lopez ◽  
Idoia Martin-Guerrero ◽  
Africa Garcia-Orad Carles ◽  
Marian M. de Pancorbo
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Forensic Genetics ◽  
European Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Potential Relationship

scholarly journals Selection in the dopamine receptor 2 gene: New candidate SNPs for disease-related studies

2015 ◽  
Author(s):  
Tobias Göllner ◽  
Martin Fieder
Keyword(s):  
Dopamine Receptor ◽  
Balancing Selection ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
1000 Genomes ◽  
Selection Processes ◽  
Flanking Region ◽  
A Minor

Dopamine is a major neurotransmitter in the human brain and is associated with various diseases. Schizophrenia, for example, is treated by blocking the dopamine receptors type 2. In 2009, Shaner, Miller and Mintz stated that schizophrenia was the low fitness variant of a highly variable mental trait. We therefore explore whether the dopamine receptor 2 gene (DRD2) underwent any selection processes. We acquired genotype data of the 1000 Genomes project (phase I), which contains 1093 individuals from 14 populations. We included only single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) of over 0.05 in the analysis. This is equivalent to 151 SNPs for DRD2. We used two different approaches (an outlier approach and a Bayesian approach) to detect loci under selection. The combined results of both approaches yielded nine candidate SNPs under balancing selection. While directional selection strongly favours one allele over all others, balancing selection favours more than one allele. All candidates are in the intronic region of the gene and only one (rs12574471) has been mentioned in the literature. Two of our candidate SNPs are located in specific regions of the gene: rs80215768 lies within a promoter flanking region and rs74751335 lies within a transcription factor binding site. We strongly encourage research on our candidate SNPs and their possible phenotypic effects.

A SNaPshot assay for genotyping 44 individual identification single nucleotide polymorphisms

2010 ◽  
Vol 32 (3-4) ◽  
pp. 368-378 ◽  
Author(s):  
Chunguang Lou ◽  
Bin Cong ◽  
Shujin Li ◽  
Lihong Fu ◽  
Xiaojing Zhang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Individual Identification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
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