Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The SNPforID Assay as a Supplementary Method in Kinship and Trace Analysis.

ABSTRACT: OBJECTIVE: Short tandem repeat (STR) analysis using commercial multiplex PCR kits is the method of choice for kinship testing and trace analysis. However, under certain circumstances (deficiency testing, mutations, minute DNA amounts), STRs alone may not suffice. METHODS: We present a 50-plex single nucleotide polymorphism (SNP) assay based on the SNPs chosen by the SNPforID consortium as an additional method for paternity and for trace analysis. The new assay was applied to selected routine paternity and trace cases from our laboratory. RESULTS AND CONCLUSIONS: Our investigation shows that the new SNP multiplex assay is a valuable method to supplement STR analysis, and is a powerful means to solve complicated genetic analyses.

SUBMITTER: Schwark T

PROVIDER: S-EPMC3375134 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The SNPforID Assay as a Supplementary Method in Kinship and Trace Analysis.

Schwark Thorsten T Meyer Patrick P Harder Melanie M Modrow Jan-Hendrick JH von Wurmb-Schwark Nicole N

Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie 20120511 3

OBJECTIVE: Short tandem repeat (STR) analysis using commercial multiplex PCR kits is the method of choice for kinship testing and trace analysis. However, under certain circumstances (deficiency testing, mutations, minute DNA amounts), STRs alone may not suffice. METHODS: We present a 50-plex single nucleotide polymorphism (SNP) assay based on the SNPs chosen by the SNPforID consortium as an additional method for paternity and for trace analysis. The new assay was applied to selected routine pa ...[more]

PMID: 22851934

Similar Datasets

An unbiased kinship estimation method for genetic data analysis.

Project description:Accurate estimate of relatedness is important for genetic data analyses, such as heritability estimation and association mapping based on data collected from genome-wide association studies. Inaccurate relatedness estimates may lead to biased heritability estimations and spurious associations. Individual-level genotype data are often used to estimate kinship coefficient between individuals. The commonly used sample correlation-based genomic relationship matrix (scGRM) method estimates kinship coefficient by calculating the average sample correlation coefficient among all single nucleotide polymorphisms (SNPs), where the observed allele frequencies are used to calculate both the expectations and variances of genotypes. Although this method is widely used, a substantial proportion of estimated kinship coefficients are negative, which are difficult to interpret. In this paper, through mathematical derivation, we show that there indeed exists bias in the estimated kinship coefficient using the scGRM method when the observed allele frequencies are regarded as true frequencies. This leads to negative bias for the average estimate of kinship among all individuals, which explains the estimated negative kinship coefficients. Based on this observation, we propose an unbiased estimation method, UKin, which can reduce kinship estimation bias. We justify our improved method with rigorous mathematical proof. We have conducted simulations as well as two real data analyses to compare UKin with scGRM and three other kinship estimating methods: rGRM, tsGRM, and KING. Our results demonstrate that both bias and root mean square error in kinship coefficient estimation could be reduced by using UKin. We further investigated the performance of UKin, KING, and three GRM-based methods in calculating the SNP-based heritability, and show that UKin can improve estimation accuracy for heritability regardless of the scale of SNP panel.

| S-EPMC9727941 | biostudies-literature

Kinship analysis on single cells after whole genome amplification.

Project description:Short Tandem Repeat (STR-) and Single Nucleotide Polymorphism (SNP-) genotyping have been extensively studied within forensic kinship analysis. Nevertheless, no results have been reported on kinship analysis after whole genome amplification (WGA) of single cells. This WGA step is a necessary procedure in several applications, such as cell-based non-invasive prenatal testing (cbNIPT) and pre-implantation genetic diagnosis (PGD). In cbNIPT, all putative fetal cells must be discriminated from maternal cells after enrichment from whole blood. This study investigates the efficacy and evidential value of STR- and SNP-genotyping methods for the discrimination of 24 single cells after WGA, within three families. Formaldehyde-fixed and unfixed cells are assessed in offspring-parent duos and offspring-mother-father trios. Results demonstrate that both genotyping methods can be used in all tested conditions and scenarios with 100% sensitivity and 100% specificity, with a similar evidential value for fixed and unfixed cells. Moreover, sequence-based SNP-genotyping results in a higher evidential value than length-based STR-genotyping after WGA, which is not observed using high-quality offspring bulk DNA samples. Finally, it is also demonstrated that the availability of the DNA genotypes of both parents strongly increases the evidential value of the results.

| S-EPMC7474072 | biostudies-literature

An Application of ITO Analysis in Secondary Kinship Identification.

Project description:ObjectiveAs the methods of the paternity and kinship testing have been developed, the second-degree and more distant relationships remain challenging in forensic science. Currently, the ITO method is the mainstream method to clarify the kinship between two individuals.MethodsIn this study, the ITO algorithm was used to calculate the uncle-nephew index based on 55 autosomal short tandem repeats (STRs) loci that were universally used for forensic identification. 19 STRs loci in Y chromosome were used for verification of the kinship.ResultsThe cumulative uncle-nephew index between A and B was calculated to 0.993 by the analysis of the genotyping results of 21 STRs. When genotyping results of the other 34 STRs were added to the calculation algorithm, the cumulative uncle-nephew index between A and B was promoted to 227.928. Meanwhile, genotyping results of 17 Y-STRs loci showed that A and B shared the same Y-STRs haplotype that was in accord with the paternal inheritance law.ConclusionThe biological uncle-nephew relationship between A and B are identified by applying the statistical principles and genetic technologies.

| S-EPMC9270131 | biostudies-literature

Validation of an optimised microwave-assisted acid digestion method for trace and ultra-trace elements in indoor PM<sub>2.5</sub> by ICP-MS analysis.

Project description:Three microwave-assisted digestion procedures, followed by analysis of digestates employing inductively coupled mass spectrometry (ICP-MS) were evaluated for use in the determination of elements at trace and ultra-trace levels in PM2.5 samples. Digestion procedure 1 used 2.5 mL HNO3 (65%) at 200 °C. Procedure 2, consisted of a two-stage digestion step at 200 °C with 2.5 mL HNO3 (65%) and 3 μL HF (48%) followed by 24 μL H3BO3 (5%). A 10-fold increase in the amounts of HF and H3BO3 was used for procedure 3. The addition of HF/H3BO3 was carried out to aid the dissolution of silicate matrices and refractory compounds. The digestions were carried out using PTFE ultra-trace inserts which increased the sample throughput threefold. The addition of small quantities of HF resulted in the effective solubilisation of Na, Mg, Al, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, As, Sr, Cd, Sb and Pb. The optimal method using HNO3/HF/H3BO3 digestion as in procedure 3 showed recovery efficiency greater than 70% for all elements. The validated method was applied to quantify the elemental content of indoor and outdoor PM2.5 (with samples <0.5 mg) at an urban background site in Malta.

| S-EPMC9860410 | biostudies-literature

TRACE: An Unbiased Method to Permanently Tag Transiently Activated Inputs.

Project description:A fundamental interest in circuit analysis is to parse out the synaptic inputs underlying a behavioral experience. Toward this aim, we have devised an unbiased strategy that specifically labels the afferent inputs that are activated by a defined stimulus in an activity-dependent manner. We validated this strategy in four brain circuits receiving known sensory inputs. This strategy, as demonstrated here, accurately identifies these inputs.

| S-EPMC7243865 | biostudies-literature

Binding site prediction of galanin peptide using evolutionary trace method.

Project description:Galanin is a neuropeptide with aminoacid length ranging from 29 to 31 is widely distributed in central and peripheral nervous system. Galanin controls various psychological processes such as sensation of pain, learning, feeding, and sexual behaviour. The N-terminal region of this neuropeptide has highly conserved 15 amino acids, which is triggered by galanin receptors. We performed evolutionary trace analysis for galanin sequences to gather information about functional residues. The consensus pattern given by the evolutionary trace (ET) analysis is supported by CLUSTALW and WEBLOGO results. Our observations strongly suggest the presence of functional residues in the N-terminal region of galanin for agonist-receptor binding.

| S-EPMC1891676 | biostudies-literature

Floating sphere assay: A rapid qualitative method for microvolume analysis of gelation.

Project description:A huge, unprecedented demand for gelatin coupled with its implications on global sustainability has resulted in the need to discover novel proteins with gelling attributes for applications in the food industry. Currently used gelation assays require large sample volumes and thus the screening for novel gelling proteins is a formidable technical challenge. In this paper, we report the 'Floating Sphere Assay' which is a simple, economical, and miniaturized assay to detect minimum gelling concentration with volumes as low as 50 μl. Results from the Floating Sphere Assay are consistent with currently used methods for gelation tests and accurately estimate the Minimum Gelling Concentrations (MGCs) of gelatin, κ-carrageenan and gellan gum. The assay was also able to differentiate the strengths of strong and weak gellan gum gels prepared at pH 3.5 and pH 7.0 respectively. The Floating Sphere Assay can be utilized in high-throughput screens for gelling proteins and can accelerate the discovery of gelatin substitutes.

| S-EPMC9269766 | biostudies-literature

A multi-residue method for trace analysis of pesticides in soils with special emphasis on rigorous quality control.

Project description:A multi-residue trace analytical method is presented to accurately quantify 146 currently used pesticides in (agricultural) soils with varying soil properties. Pesticides were extracted using an optimized quick, easy, cheap, effective, rugged, and safe (QuEChERS) approach and chemical analysis was carried out by liquid chromatography coupled to tandem mass spectrometry (triple quadrupole). Quantification was based on matrix-matched internal standards calibration, using 95 isotopically labeled analyte analogues. In contrast to the common approach of method validation using soils freshly spiked with analytes shortly before the extraction, our method is additionally validated via an in-house prepared partly aged soil, which contains all target pesticides and via agricultural field soils with native pesticide residues. The developed method is highly sensitive (median method limit of quantification: 0.2 ng/g), precise (e.g., median intra-day and inter-day method precision both ~ 4% based on field soils), and true ((i) quantified pesticide concentrations of the partly aged soil remained stable during 6 months, were close to the initially spiked nominal concentration of 10 ng/g, and thus can be used to review trueness in the future; (ii) median freshly spiked relative recovery: 103%; and (iii) participation in a ring trial: median z-scores close to one (good to satisfactory result)). Its application to selected Swiss (agricultural) soils revealed the presence of in total 77 different pesticides with sum concentrations up to 500 ng/g. The method is now in use for routine soil monitoring as part of the Swiss Action Plan for Risk Reduction and Sustainable Use of Plant Protection Products.

| S-EPMC10556155 | biostudies-literature

How to estimate kinship.

Project description:The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next-generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker-based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.

| S-EPMC6220858 | biostudies-literature

Kinship composition in mammals.

Project description:Understanding the evolution of group-living and cooperation requires information on who animals live and cooperate with. Animals can live with kin, non-kin or both, and kinship structure can influence the benefits and costs of group-living and the evolution of within-group cooperation. One aspect of kinship structure is kinship composition, i.e. a group-level attribute of the presence of kin and/or non-kin dyads in groups. Despite its putative importance, the kinship composition of mammalian groups has yet to be characterized. Here, we use the published literature to build an initial kinship composition dataset in mammals, laying the groundwork for future work in the field. In roughly half of the 18 species in our sample, individuals lived solely with same-sex kin, and, in the other half, individuals lived with related and unrelated individuals of the same sex. These initial results suggest that it is not rare for social mammals to live with unrelated individuals of the same sex, highlighting the importance of considering indirect and direct fitness benefits as co-drivers of the evolution of sociality. We hope that our initial dataset and insights will spur the study of kinship structure and sociality towards new exciting avenues.

| S-EPMC10354477 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data