Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Short tandem repeat”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources
PubMed1993

Identification of short tandemly repeated sequences in extrachromosomal circular DNAs from Drosophila melanogaster embryos.

A sequence (scl) belonging to the recently identified dodeca satellite family was found to be a major family of extrachromosomal circular DNA molecules from Drosophila melanogaster embryos. The basic unit consists of the 11-bp repeat 5' ACTGGTCCCGT 3', is 63% G + C rich, and shares some similarity with the Escherichia coli chi sequence. This family accounts for only about 0.06% of the genome but very likely for a higher proportion of the circular DNA molecules. It is organized in the genome into at least five main clusters contained in DNA fragments larger than 20 kb and several minor clusters. These clusters are located in the heterochromatic pericentromeric regions. Two other families of simple repeated sequences, the 1.686 g/cm3 (5' AATAACATAG 3') and the 1.705 g/cm3 (5' AAGAG 3') satellite DNAs, were also found in circular DNAs, while another family, the 1.672 g/cm3 (5' AATAT 3'), was not detected. The representation of the simple repeated sequences in circular molecules is not correlated to their genomic representation. Among the seven families of sequences identified to date in extrachromosomal circular DNAs from embryos, the dodeca satellite, the 240-bp repeat of the rDNA intergenic spacer, and the 1.688 and 1.705 g/cm3 satellite DNAs are the most represented families, while the 5S genes, the histone genes, and the 1.686 g/cm3 satellite DNA are present in a lower amount.

Animals↗
PubMedDate not supplied

Automated selection of short tandem repeat polymorphism markers for whole genome screening for segmental aneusomy.

Current clinical diagnostic techniques for the detection of small duplications and deletions include microscopic cytogenetics with Giemsa banding and FISH. An alternative approach is to use genetic markers, to detect duplications and deletions. The application of this technique to the entire genome as a test for segmental aneusomy requires a method for selecting a panel of markers that could be used and an estimate of the statistical power. We have developed a computer program, DECIDE, that performs these tasks. Given an input map of markers, DECIDE generates a near optimal list of markers and estimates the probability of detecting monosomy or trisomy of varying physical size. We demonstrate the program on a large map of markers obtained from the Southampton and CEPH databases. We conclude that this approach to screening for duplications and deletions is theoretically possible and would have a power comparable to routine Giemsa-banded chromosome analysis.

Automation↗
PubMed2005

Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats.

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.

Alleles↗
PubMed2001

Molecular characterization of chromosome 22 deletions by short tandem repeat polymorphism (STRP) in patients with conotruncal heart defects.

The haploinsufficiency of chromosome 22q11.2 can cause both DiGeorge and velocardiofacial syndromes, both of which are characterized by conotruncal heart defects as well as a wide range of other extracardiac anomalies. Several studies have demonstrated that approximately 10-20% of patients with conotruncal heart defects have a 22q11.2 deletion. In clinical laboratories, the deletion is usually detected by fluorescent in situ hybridization (FISH). We set up a polymerase chain reaction-based non-radioactive method for molecular analysis of the 22q11.2 region in conotruncal cardiac patients with conotruncal defects. Sixty-four children with conotruncal defects and their parents were genotyped by polymerase chain reaction, using fifteen polymorphic markers. We identified nine deletions (confirmed by FISH): eight were "de novo" and one familial, maternally inherited. Six deletions were of paternal and three of maternal origin. There were seven deletions of 3 Mb and the other two were of 1.5 Mb. This method is a cost-effective means of characterizing the 22q11.2 region and it can be applied for a rapid screening of 22q11.2 deletion in patients at risk. In agreement with previously published data, we found no correlation between the sizes and the parental origin of deletions and cardiac or extra-cardiac phenotypes.

Adolescent↗