scholarly journals Evaluation of a Custom SNP Panel for Identifying and Rectifying of Misjudged Paternity in Deficiency Cases

2021 ◽  
Vol 12 ◽  
Author(s):  
Liao Chang ◽  
Huiyun Yu ◽  
Xinyao Miao ◽  
Siqi Wen ◽  
Bao Zhang ◽  
...  
Keyword(s):  
Individual Identification ◽  
Close Relative ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Parentage Testing ◽  
Snp Panel ◽  
Custom Panel ◽  
Close Relatives ◽  
Short Tandem ◽  
Deficiency Cases

Parentage testing is routinely performed by genotyping short tandem repeat (STR) through capillary electrophoresis in the present. However, ambiguous or even misjudged paternity based on STRs happens from time to time in cases where only one putative parent is available. We analyzed STR data of 7,818,969 unrelated pairs and 75 close-relative pairs and found that although the probability of a random false match between non-relatives was 4.22 × 10–6, the incidence of false or ambiguous paternity results between children and first-degree relatives of their true parent was as high as 18.67%. These results highlight the risk of false inclusion of a relative or even non-relatives in parentage testing with STRs. We then validated all ambiguous STR results by targeted sequencing with a custom panel containing 4,830 individual identification single nucleotide polymorphisms (IISNP), found that the ratio of mismatch loci to total SNPs was 1.78–6.95% in close relatives compared with 10.93–13.49% in unrelated pairs. Last, we reported three real cases with undetermined paternity by STRs and rectified them by dissecting with our IISNP panel. These results suggested that high-density IISNP panel can be used to identify and rectify misjudged cases effectively.

scholarly journals Markers to Rapidly Distinguish Bacillus paralicheniformis From the Very Close Relative, Bacillus licheniformis

2021 ◽  
Vol 11 ◽  
Author(s):  
Atinuke M. Olajide ◽  
Shu Chen ◽  
Gisèle LaPointe
Keyword(s):  
Bacillus Licheniformis ◽  
Ribosomal Rna ◽  
Close Relative ◽  
Rrna Gene ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ionization Time ◽  
Bacillus Paralicheniformis ◽  
Rrna Gene Sequencing ◽  
Close Relatives

As close relatives, Bacillus paralicheniformis is often wrongly identified as Bacillus licheniformis. In this study, two genetic markers are presented based on fenC and fenD from the fengycin operon of B. paralicheniformis to rapidly distinguish it from B. licheniformis. The fengycin operon is one of the few present in B. paralicheniformis but absent in B. lichenformis up to date. Using these markers, two presumptive B. paralicheniformis isolates each were recovered from a set of isolates previously identified as B. licheniformis by Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) or identified only to genus level as Bacillus by 16S ribosomal RNA (rRNA) gene sequencing, respectively. Whole genome sequencing of the four isolates confirmed their identity as B. paralicheniformis having the closest similarity with B. paralicheniformis ATCC 9945a (GenBank: CP005965.1) with a 7,682 k-mer score and 97.22% Average Nucleotide Identity (ANI). ANI of 100% suggests that the four isolates are highly similar. Further analysis will be necessary to determine if finer differences exist among these isolates at the level of single nucleotide polymorphisms.

scholarly journals The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S84 ◽  
Author(s):  
John SK Kauwe ◽  
Sarah Bertelsen ◽  
Laura Bierut ◽  
Gerald Dunn ◽  
Anthony L Hinrichs ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

scholarly journals Evidence of adoption, monozygotic twinning, and low inbreeding rates in a large genetic pedigree of polar bears

2015 ◽  
Author(s):  
René M. Malenfant ◽  
David W. Coltman ◽  
Evan S. Richardson ◽  
Nicholas J. Lunn ◽  
Ian Stirling ◽  
...  
Keyword(s):  
Mating Systems ◽  
Parentage Analysis ◽  
Hudson Bay ◽  
Polar Bears ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Monozygotic Twinning ◽  
Close Relatives ◽  
Free Ranging ◽  
First Time

Multigenerational pedigrees have been developed for free-ranging populations of many species, are frequently used to describe mating systems, and are used in studies of quantitative genetics. Here, we document the development of a 4449-individual pedigree for the Western Hudson Bay subpopulation of polar bears (Ursus maritimus), created from relationships inferred from field and genetic data collected over six generations of bears sampled between 1966 and 2011. Microsatellite genotypes for 22-25 loci were obtained for 2945 individuals, and parentage analysis was performed using the program FRANZ, including additional offspring-dam associations known only from capture data. Parentage assignments for a subset of 859 individuals were confirmed using an independent medium-density set of single nucleotide polymorphisms. To account for unsampled males in our population, we performed half-sib/full-sib analysis to reconstruct males using the program COLONY, resulting in a final pedigree containing 2957 assigned maternities and 1861 assigned paternities with only one observed case of inbreeding between close relatives. During genotyping, we identified two independently captured two-year-old males with identical genotypes at all 25 loci, showing--for the first time--a case of monozygotic twinning among polar bears. In addition, we documented six new cases of cub adoption, which we attribute to cub misidentification or misdirected maternal care by a female bereaved of her young. Importantly, none of these adoptions could be attributed to reduced female vigilance caused by immobilization to facilitate scientific handling, as has previously been suggested.

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 IL-12 and IL-23—Close Relatives with Structural Homologies but Distinct Immunological Functions

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2184
Author(s):  
Doreen M. Floss ◽  
Jens M. Moll ◽  
Jürgen Scheller
Keyword(s):  
Protein Interactions ◽  
Intracellular Signaling ◽  
Signaling Cascades ◽  
Structural Knowledge ◽  
Nucleotide Polymorphisms ◽  
Protein Protein Interactions ◽  
Single Nucleotide ◽  
Mediated Effects ◽  
Protein Functions ◽  
Close Relatives

Cytokines of the IL-12 family show structural similarities but have distinct functions in the immune system. Prominent members of this cytokine family are the pro-inflammatory cytokines IL-12 and IL-23. These two cytokines share cytokine subunits and receptor chains but have different functions in autoimmune diseases, cancer and infections. Accordingly, structural knowledge about receptor complex formation is essential for the development of new therapeutic strategies preventing and/or inhibiting cytokine:receptor interaction. In addition, intracellular signaling cascades can be targeted to inhibit cytokine-mediated effects. Single nucleotide polymorphisms can lead to alteration in the amino acid sequence and thereby influencing protein functions or protein–protein interactions. To understand the biology of IL-12 and IL-23 and to establish efficient targeting strategies structural knowledge about cytokines and respective receptors is crucial. A highly efficient therapy might be a combination of different drugs targeting extracellular cytokine:receptor assembly and intracellular signaling pathways.

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.

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