scholarly journals Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes

2022 ◽  
Vol 12 ◽  
Author(s):  
Haoliang Fan ◽  
Yitong He ◽  
Shuanglin Li ◽  
Qiqian Xie ◽  
Fenfen Wang ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Tandem Repeats ◽  
Molecular Genetic ◽  
Population Data ◽  
Systematic Evaluation ◽  
The Novel ◽  
Nucleotide Polymorphisms ◽  
Kinship Analysis ◽  
Additional Information ◽  
Typing System

Insertion/deletion (InDel) polymorphisms, combined desirable characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are considerable potential in the fields of forensic practices and population genetics. However, most commercial InDel kits designed based on non-Asians limited extensive forensic applications in East Asian (EAS) populations. Recently, a novel 6-dye direct and multiplex PCR-CE-based typing system was designed on the basis of genome-wide EAS population data, which could amplify 60 molecular genetic markers, consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin in a single PCR reaction and detect by capillary electrophoresis, simultaneously. In the present study, the DNA profiles of 279 unrelated individuals from the Hainan Li group were generated by the novel typing system. In addition, we collected two A-InDel sets to evaluate the forensic performances of the novel system in the 1,000 Genomes Project (1KG) populations and Hainan Li group. For the Universal A-InDel set (UAIS, containing 44 A-InDels) the cumulative power of discrimination (CPD) ranged from 1–1.03 × 10–14 to 1–1.27 × 10–18, and the cumulative power of exclusion (CPE) varied from 0.993634 to 0.999908 in the 1KG populations. For the East Asia-based A-InDel set (EAIS, containing 57 A-InDels) the CPD spanned from 1–1.32 × 10–23 to 1–9.42 × 10–24, and the CPE ranged from 0.999965 to 0.999997. In the Hainan Li group, the average heterozygote (He) was 0.4666 (0.2366–0.5448), and the polymorphism information content (PIC) spanned from 0.2116 to 0.3750 (mean PIC: 0.3563 ± 0.0291). In total, the CPD and CPE of 57 A-InDels were 1–1.32 × 10–23 and 0.999965, respectively. Consequently, the novel 6-dye direct and multiplex PCR-CE-based typing system could be considered as the reliable and robust tool for human identification and intercontinental population differentiation, and supplied additional information for kinship analysis in the 1KG populations and Hainan Li group.

scholarly journals mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Song ◽  
August E. Woerner ◽  
John Planz
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Genetic Markers ◽  
Software Package ◽  
Tandem Repeats ◽  
Population Data ◽  
Real Data ◽  
R Package ◽  
Nucleotide Polymorphisms ◽  
Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

scholarly journals Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Chong Chen ◽  
Xiaoye Jin ◽  
Xingru Zhang ◽  
Wenqing Zhang ◽  
Yuxin Guo ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Background ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Population Data ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy–Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.

scholarly journals A Multi-Level Strategy Based on Metabolic and Molecular Genetic Approaches for the Characterization of Different Coptis Medicines Using HPLC-UV and RAD-seq Techniques

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3090 ◽  
Author(s):  
Furong Zhong ◽  
Chan Shen ◽  
Luming Qi ◽  
Yuntong Ma
Keyword(s):  
High Performance ◽  
Molecular Genetic ◽  
Principal Component ◽  
Hierarchical Cluster ◽  
Chinese History ◽  
Nucleotide Polymorphisms ◽  
Additional Information ◽  
Multi Level ◽  
Coptis Herbs

Coptis plants (Ranunculaceae) to have played an important role in the prevention and treatment human diseases in Chinese history. In this study, a multi-level strategy based on metabolic and molecular genetic methods was performed for the characterization of four Coptis herbs (C. chinensis, C. deltoidea, C. omeiensis and C. teeta) using high performance liquid chromatography-ultraviolet (HPLC-UV) and restriction site-associated DNA sequencing (RAD-seq) techniques. Protoberberine alkaloids including berberine, palmatine, coptisine, epiberberine, columbamine, jatrorrhizine, magnoflorine and groenlandicine in rhizomes were identified and determined based on the HPLC-UV method. Among them, berberine was demonstrated as the most abundant compound in these plants. RAD-seq was applied to discover single nucleotide polymorphisms (SNPs) data. A total of 44,747,016 reads were generated and 2,443,407 SNPs were identified in regarding to four plants. Additionally, with respect to complicated metabolic and SNP data, multivariable statistical methods of principal component analysis (PCA) and hierarchical cluster analysis (HCA) were successively applied to interpret the structure characteristics. The metabolic variation and genetic relationship among different Coptis plants were successfully illustrated based on data visualization. Summarily, this comprehensive strategy has been proven as a reliable and effective approach to characterize Coptis plants, which can provide additional information for their quality assessment.

INTERVERTEBRAL DISC DEGENERATION LINKED TO STRUCTURAL GENE VARIATIONS

2019 ◽  
Author(s):  
Saeeda Baig
Keyword(s):  
Intervertebral Disc ◽  
Disc Degeneration ◽  
Intervertebral Disc Degeneration ◽  
English Language ◽  
Tandem Repeats ◽  
Lumbar Disc ◽  
Disease Process ◽  
Nucleotide Polymorphisms ◽  
Structural Protein ◽  
Lumbar Disc Degeneration

During the recent past focus has shifted from identifying intervertebral disc degeneration as being caused by physical exposure and strain to being linked with a variety of genetic variations. The objective of this review is to provide an up to date review of the existing research data regarding the relation of intervertebral disc degeneration to structural protein genes and their polymorphisms and thus help clearly establish further avenues where research into causation and treatment is needed. A comprehensive search using the keywords “Collagen”, “COL”, “Aggrecan”, “AGC”, “IVDD”, “intervertebral disc degeneration”, and “lumbar disc degeneration” from PubMed and Google Scholar, where literature in the English language was selected spanning from 1991 to 2019. There are many genes involved in the production of structural components of an intervertebral disc. The issues in production of these components involve the over-expression or under-expression of their genes, and single nucleotide polymorphisms and variable number of tandem repeats affecting their structures. These structural genes include primarily the collagen and the aggrecan genes. While genetic and environmental factors all come into play with a disease process like disc degeneration, the bulk of research now shows the significantly larger impact of hereditary over exposure. While further research is needed into some of the lesser studied genes linked to IVDD and also the racial variations in genetic makeup, the focus in the near future should be on establishment of genetic testing to identify individuals at greater risk of disease and deliberation regarding the use of gene therapy to prevent disc degeneration.

New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

2020 ◽  
Vol 36 (6) ◽  
pp. 49-54
Author(s):  
A.A. Nalbandyan ◽  
T.P. Fedulova ◽  
I.V. Cherepukhina ◽  
T.I. Kryukova ◽  
N.R. Mikheeva ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Flowering Time ◽  
Molecular Genetic ◽  
Bioinformatic Analysis ◽  
Early Flowering ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Time Control ◽  
Flowering Time Control ◽  
Exon 10

The flowering time control gene of various sugar beet plants has been studied. The BTC1 gene is a regulator for the suppressor (flowering time 1) and inducer (flowering time 2) genes of this physiological process. The F9/R9 primer pair was used for polymerase chain reaction; these primers are specific to the BTC1 gene region containing exon 9, as well as intron and exon 10. For the first time, nucleotide substitutions in exon 10 of BTC1 gene were identified in bolting sensitive samples (HF1 and BF1), which led to a change in the amino acid composition of the coded polypeptide chain. Based on the results of bioinformatic analysis, it can be assumed that certain nucleotide polymorphisms in the BTC1 gene may determine with a high probability the predisposition of sugar beet genotypes to early flowering. The use of the Geneious Prime tool for the analysis of the BTC1 gene sequences may allow the culling of genotypes prone to early flowering at early stages of selection. sugar beet, flowering gene, BTC1, genetic polymorphism, PCR, molecular genetic markers, selection

scholarly journals EVOLUTION OF DNA SEQUENCING METHODS AND PROSPECTS FOR THEIR USE IN FORENSIC DNA EXAMINATION

2020 ◽  
Vol 11 (87) ◽  
Author(s):  
Zhanna Bazyliuk ◽  
Keyword(s):  
Dna Sequencing ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Snp Markers ◽  
Degraded Dna ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Biological Origin ◽  
Genetic Traits ◽  
Str Loci

The study of the human genome makes it possible to use genetic information to identify individual traits, diagnosis of diseases and forecasting and prevention of their development, promotes a personal approach when choosing treatment methods; population research, ethnogenesis and evolutionary processes. Introduction of DNA sequencing methods in domestic genetic fingerprinting will contribute to a more informative establishment of human genetic traits. The main purpose of molecular genetic research is to establish the genetic features of missing people, their relatives, to conduct paternity, to identify traces of biological origin and their identification. This article talks about the gradual development of DNA sequencing technology, which is conventionally divided into three types. The first type includes sequencing using capillary electrophoresis and pyrosequencing. The second type is high-throughput pyrosequencing, semiconductor, cyclic ligase, and the use of fluorescently labeled precursors, based on the sequencing of millions of DNA fragments simultaneously. The third stage includes methods that do not require prior sample preparation. These are methods of nanoporous sequencing, sequencing of one molecule, one-molecular sequencing. Today, each of the sequencing methods is aimed at performing different tasks. A number of methods are promising in the field of molecular-genetic examination. In world jurisprudence, sequencing is implemented mainly with the help of devices - Illumina’s, MiSeq FGx, Ion Torrent PGM from ThermoFisher and Ion S5. Research in forensic expertise of single nucleotide polymorphisms (SNP), sequencing of STR-loci and mitochondrial DNA, STR-loci and SNP-markers of the Y chromosome, will provide a high level of information, determination of human phenotypic traits, the possibility of establishing genetic traits from significantly degraded DNA. This article deals with modern problems of identification of human genetic traits and the prospect of introduction of the newest methods of sequencing for their qualitative and complete establishment.

scholarly journals Genomic analysis of family data reveals additional genetic effects on intelligence and personality

2017 ◽  
Author(s):  
W. David Hill ◽  
Ruben C. Arslan ◽  
Charley Xia ◽  
Michelle Luciano ◽  
Carmen Amador ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Molecular Genetic ◽  
Copy Number Variants ◽  
Twin Studies ◽  
Genomic Analysis ◽  
Heritability Estimate ◽  
Genetic Effects ◽  
Genetic Differences ◽  
Substantial Contribution ◽  
Nucleotide Polymorphisms

AbstractPedigree-based analyses of intelligence have reported that genetic differences account for 50-80% of the phenotypic variation. For personality traits these effects are smaller, with 34-48% of the variance being explained by genetic differences. However, molecular genetic studies using unrelated individuals typically report a heritability estimate of around 30% for intelligence and between 0% and 15% for personality variables. Pedigree-based estimates and molecular genetic estimates may differ because current genotyping platforms are poor at tagging causal variants, variants with low minor allele frequency, copy number variants, and structural variants. Using ∼20 000 individuals in the Generation Scotland family cohort genotyped for ∼700 000 single nucleotide polymorphisms (SNPs), we exploit the high levels of linkage disequilibrium (LD) found in members of the same family to quantify the total effect of genetic variants that are not tagged in GWASs of unrelated individuals. In our models, genetic variants in low LD with genotyped SNPs explain over half of the genetic variance in intelligence, education, and neuroticism. By capturing these additional genetic effects our models closely approximate the heritability estimates from twin studies for intelligence and education, but not for neuroticism and extraversion. We then replicated our finding using imputed molecular genetic data from unrelated individuals to show that ∼50% of differences in intelligence, and ∼40% of the differences in education, can be explained by genetic effects when a larger number of rare SNPs are included. From an evolutionary genetic perspective, a substantial contribution of rare genetic variants to individual differences in intelligence and education is consistent with mutation-selection balance.

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