Search results for " Polymorphism."
showing 10 items of 1006 documents
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models
2015
The discovery of single nucleotide variants (SNVs) from next-generation sequencing (NGS) data typically works by aligning reads to a given genome and then creating an alignment map to interpret the presence of SNVs. Various approaches have been developed to call whether germline SNVs (or SNPs) in normal cells or somatic SNVs in cancer/tumor cells. Nonetheless, efficient callers for both germline and somatic SNVs have not yet been extensively investigated. In this paper, we present SNVSniffer, an integrated caller for germline and somatic SNVs from NGS data based on Bayesian probabilistic models. In SNVSniffer, our germline SNV calling models allele counts per site as a multinomial condition…
Genotype frequencies of the +874T→A single nucleotide polymorphism in the first intron of the interferon-γ gene in a sample of Sicilian patients affe…
2002
In the light of the key role played by interferon (IFN)-gamma in the control of tuberculosis, in the present paper we have evaluated the distribution of the functional +874T --> A IFN-gamma single nucleotide polymorphism (SNP) in Sicilian patients affected by tuberculosis. Our aim was to determine whether there is an association between the TT genotype, which has been suggested to be linked to an increased production of IFN-gamma, and resistance to chronic tuberculosis. DNA samples were obtained from 45 patients and 97 healthy controls. Polymorphism at +874 was identified using amplification refractory mutational system methodology. The +874T SNP was less frequent in patients than in contro…
Study of β-defensin polymorphisms in Valle del Belice dairy sheep
2009
The aim of this work was to sequence the exons of β-defensin 1 and 2 genes (SBD1 and SBD2) in Valle del Belice dairy sheep in order to identify polymorphisms. The study was conducted on 60 samples from three flocks. Six SNPs were identified: two in SBD1 and four in SBD2. Both genes consist of two exons and one intron. In SBD1 gene, SNPs were found only in the exon 2, whereas in SBD2, SNPs were detected in both exons. In both genes, SNPs were located in the coding regions and in the 3'-UTR. The SNP in SBD2 located at position 1659 determined a change in the protein sequence. Further studies will be necessary to investigate if the amino acid change modifies the biological function of the…
Development and characterization of 11 microsatellite markers in the rock sparrow, Petronia petronia
2006
Eleven polymorphic microsatellite loci were isolated in the passeriform Petronia petronia using the enrichment protocol FIASCO (fast isolation by AFLP of sequences containing repeats). We detected three to 13 alleles per locus in 25 specimens collected from an Italian population. The level of expected heterozygosity ranged from 0.439 to 0.856. One locus is sex linked to the Z chromosome. The total exclusionary probabilities using these loci for the first and the second parent were 0.978 and 0.999, respectively. These are the first microsatellite loci characterized from the rock sparrow that can be used for estimating population structure and for large-scale parentage analysis.
Identification of yeasts by RFLP analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers
1999
The identification and classification of yeasts have traditionally been based on morphological, physiological and biochemical traits. Various kits have been developed as rapid systems for yeast identification, but mostly for clinical diagnosis. In recent years, different molecular biology techniques have been developed for yeast identification, but there is no available database to identify a large number of species. In the present study, the restriction patterns generated from the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene were used to identify a total of 132 yeast species belonging to 25 different genera, including teleomorphic and anamorphic a…
Inter- and intraspecific chromosome pattern variation in the yeast genusKluyveromyces
1998
The analysis of the electrophoretic chromosome patterns of the species of the genus Kluyveromyces, reveals a high polymorphism in size, number and intensity of bands. DiVerent sets of electrophoresis running conditions were used to establish species-specific patterns and also to detect intraspecific variation. According to their karyotypes, the species of this genus can be divided into two major groups. The first group includes the species K. africanus, K. bacillisporus, K. delphensis, K. lodderae, K. phaY, K. polysporus and K. yarrowii, composing the so-called ‘Saccharomyces cerevisiae-like’ group, because their karyotypes resemble that of the species S. cerevisiae. The second group compri…
Exploring diversity among Spanish strains of Erwinia amylovora and possible infection sources
2007
Aims: We have examined the intraspecific diversity of a collection of 63 Spanish strains of Erwinia amylovora, isolated from 1995 to 2001, to determine whether or not they could be grouped based on phenotypic or genotypic criteria and to investigate the sources of inoculum for fire blight dissemination in Spain. Methods and Results: Several biochemical and molecular techniques, such as miniaturized API 20E, API 50CH, ATB G-5 and API-ZYM tests, BIOLOG metabolic fingerprinting, PCR ribotyping, pulsed-field gel electrophoresis (PFGE), minisatellite-primed PCR (MSP-PCR), random amplified polymorphic DNA (RAPD) analyses and AFLP were used. We report the first identification in Spain of the PFG…
A genetic linkage map ofPhysocarpus, a member of the Spiraeoideae (Rosaceae), based on RAPD, AFLP, RGA, SSR and gene specific markers
2008
Physocarpus opulifolius is a deciduous shrub native to North America belonging to the Spiraeoideae subfamily of the Rosaceae. The cultivars 'Luteus' and 'Diabolo' are grown in gardens for their ornamental foliage, golden and purple respectively. We developed a linkage map of P. opulifolius with a view to detecting markers for the leaf colour genes, which are under major gene control. A total of 162 molecular markers (128 RAPDs, 27 AFLPs, three RGA, three STS markers and one SSR) and the leaf colour genes Pur and Aur were scored in the Physocarpus progeny and used to create a linkage map covering 586.1 cM over nine linkage groups. There was an average of 18.2 markers per linkage group and a …
Microduplications At 22q11.21 are Associated with Classic Bladder Exstrophy
2010
Purpose Classic exstrophy of the bladder (CBE) is part of the exstrophy-epispadias complex (EEC), a spectrum of urogenital anomalies in which part or all of the distal urinary tract fails to close. Familial occurrence has been observed, and previous studies have suggested an underlying multifactorial mode of inheritance. To date, no causative genetic or non-genetic factor has been unequivocally identified in humans. The present study aimed to identify microaberrations characterized by loss or gain of genomic material that contribute to the EEC at a genome-wide level. Material and Methods Molecular karyotyping, utilizing 549,839 single nucleotide polymorphisms (SNPs) with an average spacing …
Identification and prevention of genotyping errors caused by G-quadruplex- and i-motif-like sequences.
2009
Abstract Background: Reliable PCR amplification of DNA fragments is the prerequisite for most genetic assays. We investigated the impact of G-quadruplex– or i-motif–like sequences on the reliability of PCR-based genetic analyses. Methods: We found the sequence context of a common intronic polymorphism in the MEN1 gene (multiple endocrine neoplasia I) to be the cause of systematic genotyping errors by inducing preferential amplification of one allelic variant [allele dropout (ADO)]. Bioinformatic analyses and pyrosequencing-based allele quantification enabled the identification of the underlying DNA structures. Results: We showed that G-quadruplex– or i-motif–like sequences can reproducibly …