Search results for "SNP genotyping"
showing 10 items of 20 documents
Development and implementation of high-throughput SNP genotyping in barley
2009
Abstract Background High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based…
Forensic typing of autosomal SNPs with a 29 SNP-multiplex--results of a collaborative EDNAP exercise.
2008
We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot …
A multiplex SNP typing approach for the DNA pyrosequencing technology
2006
Abstract We have developed a multiplex Pyrosequencing assay which enables the simultaneous analyses of 23 single nucleotide polymorphisms (SNPs) from the human genome selected by the SNPforID Consortium. In our investigations we have studied the multiplex capacity of the PSQ™ 96MA instrument (Biotage AB). To test the reliability of SNP typing by Pyrosequencing the SNPs were analysed in parallel by using the SNaPshot minisequencing technique as reference method.
Mixture analysis using SWaP™ SNPs and non-biallelic SNPs
2006
Abstract Improved analysis of degraded samples, increased throughput, and a wider choice of typing platforms are some of the significant advantages offered by single nucleotide polymorphism (SNP) genotyping over established short tandem repeat (STR)-based systems. However, DNA mixtures present a considerable problem to SNP analysis as there is currently no generally accepted technique that allows recognition of the presence of a mixed profile or identification of the individual contributors. We present the first demonstration of SNP mixture analysis with an approach based upon the use of two rare subsets of SNPs: SWaP™ SNPs and non-biallelic SNPs and discuss their value for forensic mixture…
Genome-Wide SNP-Genotyping Array to Study the Evolution of the Human Pathogen Vibrio vulnificus Biotype 3
2014
Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains Of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae , horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism …
Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping
2021
The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of six years (2006-2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities, and repeatability within and across lactations were estimated, fitting parity, litter size, season of lambing, and fortnights in milk, as fixed; and additive genetic, permanent environment within and across …
Metodo per la tracciabilità/autenticazione di prodotti lattiero-caseari mono-razza
2016
Il brevetto consiste in un metodo per l’autenticazione e la tracciabilità genetica delle produzioni lattiero-casearie mono-razza su base molecolare con approccio statistico-probabilistico. Il metodo si basa sull’impiego di tecniche di analisi ad elevata processività (in particolare SNPs genotyping su Bead Chip Illumina) su pool di DNA e sull’applicazione di metodi computazionali innovativi. Il metodo è già stato validato su produzioni lattiero-casearie ovine quali la Vastedda della Valle del Belice (DOP), sia su prodotti lattiero caseari a DOP ottenuti in laboratorio, che su prodotti a DOP reperibili sul mercato. Il metodo può comunque essere esteso, su richiesta, a qualsiasi altro prodotto…
Analysis of Illumina BovineSNP50 BeadChip data in different Italian cattle breeds to identify useful markers for breed authentication of dairy and be…
2013
The identification of the breed of origin of cattle derived products has recently assumed particular relevance since the increasing interest in marketing mono-breed labelled cheese and beef. These products are usually sold at a higher price creating financial incentives to substituting them with lower value products coming from undifferentiated or common breeds or crossbred animals. Frauds can damage these valuable niche markets that, indirectly, may help to preserve genetic diversity through the economic incentive on raising local breeds, derived by the high value products, that are usually less productive. DNA analysis can help to identify fraudulent behaviour as we already demonstrated f…
Copulation duration, but not paternity share, potentially mediates inbreeding avoidance in Drosophila montana
2014
Studying the incidence of inbreeding avoidance is important for understanding the evolution of mating systems, especially in the context of mate choice for genetic compatibility. We investigated whether inbreeding avoidance mechanisms have evolved in the malt fly, Drosophila montana, by measuring mating latency (a measure of male attractiveness), copulation duration, days to remating, offspring production, and the proportion of offspring sired by the first (P1) and second (P2) male to mate in full-sibling and unrelated pairs. SNP markers were used for paternity analysis and for calculating pairwise relatedness values (genotype sharing) between mating pairs. We found 18 % inbreeding depressi…
Incidence and dynamics of active cytomegalovirus infection in allogeneic stem cell transplant patients according to single nucleotide polymorphisms i…
2014
Single nucleotide polymorphisms (SNPs) in genes involved in the activation or regulation of innate and adaptive immune responses may modulate the susceptibility to and the natural history of certain chronic viral infections. The current study aimed to investigate whether donor and recipient SNPs in the chemokine receptor 5 (rs1800023), monocyte chemoattractant protein 1 (rs13900), interleukin-10 (rs1878672), and Toll-like receptor 9 (rs352140) genes would exert any influence on the rate of incidence and features of CMV DNAemia in the allogeneic stem cell transplantation setting. This was a retrospective observational multicenter study. The cohort consisted of 102 non-consecutive allogeneic …