Search results for "Polymorphism"

A report of an international collaborative experiment to demonstrate the uniformity obtainable using DNA profiling techniques

1992

This paper describes a collaborative exercise intended to demonstrate whether uniformity of DNA profile results could be achieved between different European laboratories. It was shown that this goal can be obtained provided that a common protocol is followed (specifically the use of a common electrophoretic buffer as being the most important parameter). Generally, lower molecular weight loci (with lower molecular weight fragments) such as YNH24 perform better than higher molecular weight loci such as MS43a. The results of the exercise are discussed in relation to the objectives of the European DNA profiling group (EDNAP).

Rapid evolving RNA gene HAR1A and schizophrenia

2008

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.

Polymorphism and chromosomal localization of the porcine signal transducer and activator of transcription 5B gene (STAT5B).

2006

Signal transducers and activators of transcription (STATs) are a family of transcription factors. STAT5A and 5B are two highly related proteins encoded by two distinct genes. Transgenic knockout mice studies have indicated the importance of STAT5 proteins for the regulation of both lactation and growth performance. Moreover, different studies determine the role of STAT5 proteins in the modulation of adipocyte function. In this study, we sequenced one fragment of STAT5B gene from animals of six breeds (Duroc, Iberian, Landrace, Large White, Pie´train and Meishan) to identify genetic variants. A G/A single nucleotide polymorphism in intron 14 creates a polymorphic PstI restriction site and wa…

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y

2014

Significance Eye, hair, and skin pigmentation are highly variable in humans, particularly in western Eurasian populations. This diversity may be explained by population history, the relaxation of selection pressures, or positive selection. To investigate whether positive natural selection is responsible for depigmentation within Europe, we estimated the strength of selection acting on three genes known to have significant effects on human pigmentation. In a direct approach, these estimates were made using ancient DNA from prehistoric Europeans and computer simulations. This allowed us to determine selection coefficients for a precisely bounded period in the deep past. Our results indicate t…

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…

Systematic screening for mutations in the promoter and the coding region of the 5-HT1A gene.

1995

In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains a …

Detection of a novel germline mutation in the von Hippel-Lindau tumour-suppressor gene by fluorescence-labelled base excision sequence scanning (F-BE…

1999

The von Hippel Lindau (VHL) syndrome is an inherited multi-tumour disorder characterised by clinical heterogeneity and high penetrance. The VHL gene has been shown to be a tumour-suppressor gene. A carrier of a germline mutation will be predisposed to a high variety of benign and malign tumours affecting different organ systems. As treatment of VHL malformations in presymptomatic stages will improve significantly the clinical outcome and the patient's quality of life, early and unambiguous detection of a germline mutation is mandatory. Direct sequencing especially of large genes might be laborious and time consuming. Therefore, most laboratories apply single strand conformational polymorphi…

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…

YJL159w does encode Pir2/Hsp150

2001

In this paper we compare the sequence of the gene HSP150/PIR2, independently determined by two different groups, with that present in the yeast database as YJL159w, determined within the Yeast Sequencing Project. Although YJL159w is believed to encode Hsp150/Pir2, there are important differences between the amino acid sequence coded by this ORF and that of HSP150/PIR2. To find out if this divergence is due to strain polymorphism or to a possible sequencing error, we have analysed the diverging zone of this ORF in three strains and have found it entirely consistent with the sequence reported as HSP150/PIR2, concluding that the divergence is probably due to a sequencing error in YJL159w. Copy…