TY - JOUR. T1 - A new dinucleotide repeat polymorphism at the telomere of chromosome 21q reveals a significant difference between male and female rates of recombination. AU - Blouin, J. L.. AU - Christie, D. H.. AU - Gos, A.. AU - Lynn, A.. AU - Morris, M. A.. AU - Ledbetter, D. H.. AU - Chakravarti, A.. AU - Antonarakis, S. E.. PY - 1995. Y1 - 1995. N2 - We have used a half-YAC containing the human chromosome 21 long-arm telomere to clone, map, and characterize a new dinucleotide repeat polymorphism (D21S1575) close to 21qter. This marker is AB - We have used a half-YAC containing the human chromosome 21 long-arm telomere to clone, map, and characterize a new dinucleotide repeat polymorphism (D21S1575) close to 21qter. This marker is UR - http://www.scopus.com/inward/record.url?scp=0029013276&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0029013276&partnerID=8YFLogxK. M3 - Article. C2 - 7668265. AN - SCOPUS:0029013276. VL - 57. SP - 388. EP - 394. JO - American Journal ...

TY - JOUR. T1 - Dinucleotide repeat polymorphism at the hormone sensitive lipase (LIPE) locus. AU - Levitt, R. C.. AU - Jedlicka, A. E.. AU - Nouri, N.. PY - 1992/5/1. Y1 - 1992/5/1. UR - http://www.scopus.com/inward/record.url?scp=0026864835&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0026864835&partnerID=8YFLogxK. U2 - 10.1093/hmg/1.2.139. DO - 10.1093/hmg/1.2.139. M3 - Comment/debate. C2 - 1301154. AN - SCOPUS:0026864835. VL - 1. JO - Human Molecular Genetics. JF - Human Molecular Genetics. SN - 0964-6906. IS - 2. ER - ...

Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of ,350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA ...

Cardinale, J; Paul, G; Sbalzarini, I F (2012). Discrete region competition for unknown numbers of connected regions. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(8):3531-3545.. Scharl, M; Paul, G; Weber, A; Jung, B C; Docherty, M J; Hausmann, M; Rogler, G; Barrett, K E; McCole, D F (2009). Protection of epithelial barrier function by the Crohns disease associated gene protein tyrosine phosphatase n2. Gastroenterology, 137(6):2030-2040.e5.. Hausmann, M; Paul, G; Kellermeier, S; Frey, I; Schölmerich, J; Falk, W; Menzel, K; Fried, M; Herfarth, H; Rogler, G (2008). (GT)n Dinucleotide repeat polymorphism of haem oxygenase-1 promotor region is not associated with inflammatory bowel disease risk or disease course. Clinical and Experimental Immunology, 153(1):81-85.. Hausmann, M; Paul, G; Menzel, K; Brunner-Ploss, R; Falk, W; Schölmerich, J; Herfarth, H; Rogler, G (2008). NAT1 genotypes do not predict response to mesalamine in patients with ...

OBJECTIVES: In this study, we investigated whether polymorphisms of the HIF-1alpha gene may account for the patterns of HIF-1alpha protein expression in non-small cell lung carcinomas (NSCLC) and the expression of HIF-1alpha down-stream proteins. METHODS: Specific HIF-1alpha polymorphisms were assessed in a series of patients with NSCLC: (a) the C to T transition at nucleotide 1744 (position 2028 according to sequence with accession number , which gives rise to Pro/Ser variation at codon 582), (b) the G to A nucleotide substitution at point 1790 (position 2046 according to sequence with accession number , which gives rise to Ala/Thr variation at codon 588), and (c) the dinucleotide GT repeat polymorphism in intron 13. Immunohistochemistry for HIF-1alpha and down-stream proteins (VEGF, LDH-5, GLUT-1) was also performed in tumor material. RESULTS: A strong association of the P582S polymorphism and of GT repeat polymorphism higher than 14/14 with increased HIF-1alpha expression was noted. HIF-1alpha

TY - JOUR. T1 - Glucose induces clonal selection and reversible dinucleotide repeat expansion in mesangial cells isolated from glomerulosclerosis-prone mice. AU - Fornoni, Alessia. AU - Lenz, Oliver. AU - Striker, Liliane J.. AU - Striker, Gary E.. PY - 2003/10/1. Y1 - 2003/10/1. N2 - Clonal selection has been proposed as a pathogenetic mechanism in various chronic diseases, such as scleroderma, hypertension, pulmonary fibrosis, interstitial fibrosis of the kidney, atherosclerosis, and uterine leiomyomatosis. We previously found that mesangial cells from ROP mice prone to develop glomerulosclerosis changed their phenotype in response to high glucose concentrations. Here, we investigate whether clonal selection might contribute to this phenotype change. We found that in ROP mice at least two distinct mesangial cell clones exist. They are characterized by a different length of the d(CA) repeat in the MMP-9 promoter and exhibit a significantly different gene expression profile. Exposure of ROP ...

PV mediated by simple sequences or microsatellites is a common feature of many bacteria, but, in Hi, a conspicuous feature is the predominance of tetranucleotide repeat tracts. In this report, we show that mutation of Hi polI, but not of seven other Hi genes, whose products are involved in MMR or other pathways of DNA repair or recombination, increases PV rates mediated by a tetranucleotide repeat tract. Conversely, loss of MMR activity, but not of polI activity, increased PV rates mediated by a dinucleotide repeat tract. This is the first report of a trans‐acting factor that alters PV rates in Hi, and also demonstrates that this bacterial species has apparently uncoupled the hypermutability of tetranucleotides that mediate PV from some important MMR functions. In the context of the biology of commensal and virulence behaviour of pathogenic bacteria, these findings are of particular interest because it has been proposed that mutations in MMR genes are an important source of adaptive evolution ...

Background: Mismatch repair (MMR)-deficiency analysis is increasingly recommended for all endometrial cancers, as it identifies Lynch syndrome patients, and is emerging as a prognostic classifier to guide adjuvant treatment. The aim of this study was to define the optimal approach for MMR-deficiency testing and to clarify discrepancies between microsatellite instability (MSI) analysis and immunohistochemical (IHC) analysis of MMR protein expression. Patients and methods: Six hundred ninety- six endometrial cancers were analyzed for MSI (pentaplex panel) and MMR protein expression (IHC). Agreement between methodologies was calculated using Cohens Kappa. MLH1 promoter hypermethylation, dinucleotide microsatellite markers and somatic MMR and POLE exonuclease domain (EDM) gene variants (using next-generation/Sanger sequencing) were analyzed in discordant cases. Results: MSI was found in 180 patients. Complete loss of expression of one or more MMR proteins was observed in 196 cases. A PMS2- and MSH6

CS1 (CD319) is a member of the SLAM family of receptors, expressed on NK cells, T cells, B cells, DCs, etc. It induces NK cell cytotoxicity and is up regulated on B cell activation. CS1 is aberrantly up regulated on B cells in multiple myeloma and a therapeutic humanized anti-CS1 mAb HuLuc63 (Elotuzumab) is in Phase III of clinical trials. Recently, a unique population of CS1high B cells, implicated as major producers of pathogenic auto antibodies was detected in high SLE disease activity index (SLEDAI) patients. Regression analysis indicated direct correlation between the percentage of CS1high B cells and SLEDAI. With the available information on the pathogenic outcome of CS1 up-regulation on B cells, it is vital to study the molecular basis of CS1 expression. Here, we discuss the transcriptional regulation of mouse CS1 gene. According to our data, mouse CS1 promoter binds to Blimp1, mainly a trans-repressor and the master regulator of B cell maturation. Interestingly, mCS1 promoter also bears ...

R949C06 TC TT CC TC CC TT GG CC AG TT AA GG AA TT CC TC -- CC TC GC TC AA TC AG AG TC AA AA AA AG TC CC AT AA TT AA TT GG AA TC AG TC TA TA AG -- TG TT -- AA -- TT TT CC AG GG TC GG CC AA -- CC AC AA GG -- AA CC CC AA TC AG AA TC CG TT GG CC TT GG AG GG TT AA CC AA CC TC AG GG TC AG AG AG GC CC AG GG AA TC GG AA AA GG TC AG CC AG CC TC AA CC CC CC GG CC AG CC CC AG AC CC GG TT CC AG CC AA TC TT GG AG GG CC TC TC AA GG CC TC AG AG TT GG TG AG AA TG 111034 920283 920207 Susceptible 1 ...

Background. The SEL1L gene is located on human chromosome 14q24.3-31 close to D14S67 which has been previously proposed to be a type 1 diabetes mellitus locus (IDDM11). Sel-1 is a negative regulator of the Notch signalling pathway and SEL1L is selectively expressed in adult pancreas and islets of Langerhans. This suggests that SEL1L may be a candidate gene for IDDM11. Methods. We have analysed two newly identified CA-repeat polymorphisms within the genomic sequence of the SEL1L locus for association with type 1 diabetes mellitus (T1DM) in 152 Danish T1DM-affected sib-pair families and in 240 Sardinian families (229 simplex and 11 sib-pair families). Results. No evidence for association of the two SEL1L markers with T1DM was observed in either the Danish or the Sardinian families. We have also used allelic sharing methods to analyse linkage with T1DM in the IDDM11 region using the same markers and the Danish collection of affected sib-pair families. No evidence of linkage was observed (Zmax = ...

Finds sub-sequences or patterns in the sequence and highlights the matching regions. The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. More... ...

Finds sub-sequences or patterns in the sequence and highlights the matching regions. The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. More... ...

TY - JOUR. T1 - Genetic mapping of dinucleotide repeat polymorphisms and von Hippel-Lindau disease on chromosome 3p25-26. AU - Pericak-Vance, M. A.. AU - Nunes, K. J.. AU - Whisenant, E.. AU - Loeb, D. B.. AU - Small, K. W.. AU - Stajich, J. M.. AU - Rimmler, J. B.. AU - Yamaoka, L. H.. AU - Smith, D. I.. AU - Drabkin, H. A.. AU - Vance, J. M.. PY - 1993. Y1 - 1993. N2 - A genetic map of highly polymorphic microsatellite markers spanning the von Hippel-Lindau region (VHL) of 3p25 was constructed using the CEPH reference pedigrees. A greater than 1000:1 odds map of pter-D3S1038-RAF1-D3S651-D3S656-D3S110-D3S1255-cen was found. Genotyping of six multigenerational VHL families showed the region surrounding the D3S1038 marker to be the most likely location for the VHL gene with a peak location score of 10.04 with VHL completely linked to D3S1038. These data provide an initial high resolution genetic map of this region; D3S1038 appears to be a highly polymorphic marker that should prove useful in the ...

Next article in issue: Development of 15 novel dinucleotide microsatellite markers in the Senegalese sole Solea senegalensis Next article in issue: Development of 15 novel dinucleotide microsatellite markers in the Senegalese sole Solea senegalensis ...

Define Microsatellite repeats. Microsatellite repeats synonyms, Microsatellite repeats pronunciation, Microsatellite repeats translation, English dictionary definition of Microsatellite repeats. n. 1. A short sequence of DNA consisting of multiple repetitions of a set of two to nine base pairs, used as a genetic marker when individuals differ in the...

The chromosomal localization of the gene for Thomsen disease, an autosomal dominant form of myotonia congenita, is unknown. Electrophysiologic data in Thomsen disease point to defects in muscle-membrane ion-channel function. A mouse model of myotonia congenita appears to result from transposon inactivation of a muscle chloride-channel gene which maps to a region of mouse chromosome 6. The linkage group containing this gene includes several loci which have human homologues on human chromosome 7q31-35 (synteny), and this is a candidate region for the Thomsen disease locus. Linkage analysis of Thomsen disease to the T-cell-receptor beta (TCRB) locus at 7q35 was carried out in four pedigrees (25 affected and 23 unaffected individuals) by using a PCR-based dinucleotide repeat polymorphism in the TCRB gene. Two-point linkage analysis between Thomsen disease and TCRB showed a maximum cumulative lod score of 3.963 at a recombination fraction of .10 (1-lod support interval .048-.275). We conclude that the

Somatic and germ-line mutations: An understanding of microsatellite mutation patterns is central to their use for the accurate reconstruction of population processes. We have developed and validated an experimental approach to estimate the distribution of mutation sizes for each individual microsatellite locus. These distributions were estimated from somatic mutations observed in the tumor tissue of sporadic patients with colorectal cancer.. It is not known whether such mutations arise from the same events that produce variation in the normal population. Microsatellite instability in some cancer patients may reflect defects in mismatch repair; but, in other patients, it may be a consequence of the higher number of cell divisions that occurs in the tumor compared to the normal tissue. Nevertheless, in the absence of specific mechanistic or genetic information on the source of these mutations, it is still possible to test whether they reflect the mutation process in the general population by using ...

TY - JOUR. T1 - Variation in dinucleotide (GT) repeat sequence in the first exon of the STAT6 gene is associated with atopic asthma and differentially regulates the promoter activity in vitro. AU - Gao, P. S.. AU - Heller, N. M.. AU - Walker, W.. AU - Chen, C. H.. AU - Moller, M.. AU - Plunkett, B.. AU - Roberts, M. H.. AU - Schleimer, R. P.. AU - Hopkin, J. M.. AU - Huang, S. K.. PY - 2004/7. Y1 - 2004/7. UR - http://www.scopus.com/inward/record.url?scp=3142693973&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=3142693973&partnerID=8YFLogxK. U2 - 10.1136/jmg.2003.015842. DO - 10.1136/jmg.2003.015842. M3 - Article. C2 - 15235025. AN - SCOPUS:3142693973. VL - 41. SP - 535. EP - 539. JO - Journal of Medical Genetics. JF - Journal of Medical Genetics. SN - 0022-2593. IS - 7. ER - ...

A variety of simple di- (DINUCLEOTIDE REPEATS), tri- (TRINUCLEOTIDE REPEATS), tetra-, and pentanucleotide tandem repeats (usually less than 100 bases long). Tandem repeats ...

Hi bionetters I am doing research on the occurrence and polymorphism of microsatellites in co nifers. I havent found a lot of polymorphisms in GT/CA repeats or CT/GA. Howev er, I have an AT/AT microsatellite that shows a high rate of variability. There are a few problems with it though. 1) I originally isolated it as a CA-repeat that was followed by a stretch of TA s. I amplified it from the genomic DNA and found that all the products I obtain ed are shorter than the original. Then I cloned the PCR amplified fragments and sequenced them. To my surprise, the CA/GT microsatellite was not present. What was left was a stretch of TAs. Am I amplifying a microsatellite family and is the CA/GT + TA member that I cloned only a minority???? I am not so sure since I havent obtained more than 2 alleles from a single tree up to now. 2) When I PCR the plasmids containing the different AT stretches, I obtain two or more distinct bands as a result. Instability of the TA repeat in the plasmid /bacterial host ...

Glucokinase, the major enzyme that phosphorylates glucose upon entry into liver and islet β-cells, has been considered a prime candidate for inherited defects predisposing to NIDDM. Now that the human gene has been isolated, this question has been addressed directly. Polymorphic markers flanking the gene were identified. These markers (microsatellites) are composed of variable numbers of dinucleotide repeats that vary in size, resulting in different alleles. Variably sized alleles can be typed rapidly from genomic DNA of individuals by the PCR. Studies of inheritance of glucokinase genes have revealed significant linkage in families with early-onset NIDDM, or MODY, and mutations have been identified within the coding region of the gene in some families. These studies are extremely encouraging, as they indicate that genes can be identified even in this heterogeneous genetic disorder. This study considers the phenotypes that result from glucokinase defects and the relationship of MODY to NIDDM, ...

The most abundant SSR tracts are the homopolymer repeats poly(dA).poly(dT) and poly(dG).poly(dC). Long (, 9 bp) tracts of both types are found at higher than expected frequencies in the non-coding regions of eukaryote genomes. This is particularly true for poly(dA).poly(dT) tracts in the AT-rich genomes [4]. The biological importance of SSR tracts has been clearly delineated. Homopolymer tracts, for example, can serve as protein binding signals, particularly as upstream promoter elements [5]. Also, long homopolymer tracts are spaced non-randomly in the genome of Dictyostelium discoideum, suggesting a preferential linker DNA location in the repeating nucleosome structure of this AT-rich organism [6]. While this restricted localization may be thermodynamically determined, the suggestion is that these tracts may serve some function determined by their accessibility in the linker DNA region between nucleosomes. The heteropolymer tracts are at least as important biologically. Dinucleotide repeats are ...

Methods. Family description. The index case, a six-year-old child, was diagnosed to have bilateral ectopia lentis. The family history revealed 27 affected members in four generations of which three were deceased (Figure 1). The detailed ophthalmological examination, which included slit lamp examination, performed on 48 members of the family, revealed 24 members as bilaterally affected (some had a history of lens extraction in childhood) and 24 individuals (including seven spouses) were unaffected. The affected unoperated members had myopia in association with ectopia lentis.. Genotyping and linkage analysis. Informed consent was obtained from each individual studied. This study was approved by the Ethics Review Board of the Guru Nanak Dev University, consistent with the provisions of the Declaration of Helsinki. Blood was drawn and DNA isolated by standard methods. Initially, linkage analysis for candidate gene region at 15q and 5q with dinucleotide repeat microsatellite markers (Genethon ...

Despite the central significance of microsatellite mutations to issues of genomic instability, forensic testing, and population genetic analyses, the rate of origin and spectrum of effects of such mutations are still poorly understood, with many estimates being derived from reporter constructs in yeast cultures (e.g., Henderson and Petes 1992; Strand et al. 1995; Wierdl et al. 1996; Sia et al. 1997). Our long-term series of mutation-accumulation lines of C. elegans and D. pulex provide a useful platform for a more direct evaluation of the properties of microsatellite mutations in two key model organisms.. As in previous studies (Wierdl et al. 1997; Brinkmann et al. 1998; Kayser et al. 2000; Beck et al. 2003; Whittaker et al. 2003; Legendre et al. 2007), we find a strong correlation between allele size (repeat number) and mutation rate in C. elegans (Figure 1). In addition, although the variation of repeat numbers among loci sampled in D. pulex does not permit a formal evaluation of length ...

An experimental procedure using biotin-labelled probes and streptavidin-bound magnetic beads (FIASCO) was used to produce a microsatellite-enriched library for the collembolan Orchesella villosa. PCR primers were successfully constructed for seven loci containing, respectively, five pure, one interrupted, and one compound dinucleotide microsatellite repeats. As a preliminary test of their variability, we investigated 15 individuals from 5 locations inside a dismissed mining area in southern Tuscany. All microsatellite loci showed high levels of polymorphism. The mean number of different alleles at each locus across populations was 10.1 and observed heterozygosity per locus was 0.13-0.86. Only 2 out of the 7 loci appeared to be in Hardy-Weinberg equilibrium. The potential application of these loci to test the effects of environmental contamination on the genetic structure of exposed populations is discussed.. ...

Profound MSI is a hallmark of hereditary nonpolyposis colon carcinoma (HNPCC) and is also found in a proportion of sporadic HNPCC-spectrum tumors, such as endometrial carcinoma.21 The underlying cause of MSI is a defect in mismatch repair, which results in tumorigenesis through an accumulation of somatic mutations in genes important for regulating cell cycle, growth, or apoptosis. A lower level of MSI occurs in tumors that are outside the HNPCC spectrum. Previous studies of endothelial cells microdissected from plexiform lesions of PAH lungs have shown monoclonal expansion in 17 of 22 lesions (77%) from 4 patients and microsatellite mutation rates ranging from 21% for BAX to 50% for BAT26.13,15 This suggested that endothelial cell expansion in plexiform lesions is akin to neoplasia and might result from an accumulation of somatic mutations, either through MSI or other mutational mechanisms. We have now conducted similar analyses in a series of FPAH cases in whom BMPR2 has been fully ...

The design and analysis of association studies for repeat polymorphisms has received scant attention in the literature. We present an analytical power calculation for studies of such polymorphisms, based on a case-parent design and an X-linked polymorphism. Existing tools for estimating statistical power in family-based studies (such as Quanto) presume categorical codings of autosomal loci. We extend the underlying method to handle quantitative codings of repeat polymorphisms, and discuss the advantages of doing so. Sample sizes for a conditional logistic regression analysis of a sex-linked repeat polymorphism in a case-parent design are presented. Empirical power for quantitative and categorical codings of the same polymorphism with the same sample size in otherwise identical studies are then compared via Monte Carlo simulation. The differences in information to be expected from male and female case-parent, case-sibling, and case-population pairs are discussed. In addition, the effects of ...

In this study we examined the LOH of 11 dinucleotide repeat loci on chromosome 10 in 208 meningiomas of all grades. We investigated the incidence and complexity of LOH relative to tumor progression. For all alleles examined, the incidence of LOH was much higher in all grades than that reported previously, with incidence and complexity of LOH increasing with tumor grade. Mapping of the regions of LOH of all of the tumors defined four regions of chromosomal deletion. These deletions coincide with those found in other cancers, supporting the hypothesis that candidate tumor suppressor genes in these regions contribute to meningeal tumorigenesis and progression.. To expand on previous studies, we examined LOH of alleles used in previous meningioma reports (11, 12, 13, 14, 15) , as well as additional loci mapping near known and candidate tumor suppressor genes on 10q. The present data are in good agreement with our reported data (11) that LOH occurs at markers D10S89 and D10S169 and with the 10q LOH ...

TY - JOUR. T1 - Accuracy and sensitivity of DNA pooling with microsatellite repeats using capillary electrophoresis. AU - Breen, G AU - Sham, P AU - Li, T AU - Shaw, D AU - Collier, D A AU - St Clair, D PY - 1999. Y1 - 1999. N2 - DNA pooling is a genetic screening method that combines DNA from many individuals in a single polymerase chain reaction (PCR) reaction to generate a representation of allele frequencies. The substantial saving in effort with DNA pooling over individual genotyping facilitates linkage disequilibrium scanning of the human genome using many thousands of genetic markers, and is applicable to mapping of complex diseases such as schizophrenia. However, the literature to date has not addressed several crucial technical aspects of DNA pooling. These include: DNA quantification; the choice of electrophoresis methods; sensitivity (the minimum reliably detectable difference between poets); and methods of dealing with plus-A stutter. We have examined these points and make ...

TY - JOUR. T1 - Identification of a glutamic acid repeat polymorphism of ALMS1 as a novel genetic risk marker for early-onset myocardial infarction by genome-wide linkage analysis. AU - Ichihara, Sahoko. AU - Yamamoto, Ken. AU - Asano, Hiroyuki. AU - Nakatochi, Masahiro. AU - Sukegawa, Mayo. AU - Ichihara, Gaku. AU - Izawa, Hideo. AU - Hirashiki, Akihiro. AU - Takatsu, Fumimaro. AU - Umeda, Hisashi. AU - Iwase, Mitsunori. AU - Inagaki, Haruo. AU - Hirayama, Haruo. AU - Sone, Takahito. AU - Nishigaki, Kazuhiko. AU - Minatoguchi, Shinya. AU - Cho, Myeong Chan. AU - Jang, Yangsoo. AU - Kim, Hyo Soo. AU - Park, Jeong E.. AU - Tada-Oikawa, Saeko. AU - Kitajima, Hidetoshi. AU - Matsubara, Tatsuaki. AU - Sunagawa, Kenji. AU - Shimokawa, Hiroaki. AU - Kimura, Akinori. AU - Lee, Jong Young. AU - Murohara, Toyoaki. AU - Inoue, Ituro. AU - Yokota, Mitsuhiro. PY - 2013/12/1. Y1 - 2013/12/1. N2 - Background-Myocardial infarction (MI) is a leading cause of death worldwide. Given that a family history is an ...

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Li, Li et al No Association between a Tetranucleotide Repeat Polymorphism of CYP19 and Prostate Cancer. Cancer Epidemiology and Prevention Biomarkers 13.12 (2004): 2280-2281. Web. 16 June. 2021. ...

MSH6, 0.5 ml. An alteration of microsatellite repeats is the result of slippage owing to strand misalignment during DNA replication and is referred to as microsatellite instability (MSI).

HERV GOY PDF - No association was found for HERV-K18 polymorphisms or the CA repeat within the CD48 gene with type 1 diabetes mellitus either in families or by

Fig. 1. Molecular markers commonly used for mapping. SSLP (Bell and Ecker, 1994), SSLP markers exploit the variability of short repetitive sequences for mapping purposes. A primer pair (arrows) is used to amplify a fragment containing a short repetitive element, such as the (AT)-dinucleotide repeat shown in the example. The length of this repeat differs between the two accessions. In the example Columbia (Col) has an (AT)20 repeat whereas Landsbergerecta (Ler) has an (AT)15 repeat. Consequently, the PCR products from Ler and Col DNA also differ in length. In the example, the Col product is 150 bp and the Ler product is 140 bp long. This size difference can be visualized by agarose gel-electrophoresis (GE) with a standard (Std) as comparison. If a plant is heterozygous for the marker (Het), both products are amplified resulting in two bands. Typically the size difference created by short repetitive sequences is small. To facilitate their detection, SSLP primers usually amplify short fragments (80 ...

To facilitate large-scale genetic mapping of the human genome, we have developed chromosome-specific sets of microsatellite marker loci suitable for use with a fluorescence-based automated DNA fragment analyser. We present 254 dinucleotide repeat marker loci (80% from the Genethon genetic linkage map) arranged into 39 sets, covering all 22 autosomes and the X chromosome. The average distance between adjacent markers is 13 centiMorgans, and less than 4% of the genome lies more than 20 cM from the nearest marker. Each set of microsatellites consists of up to nine marker loci, with allele size ranges that do not overlap. We selected marker loci on the basis of their reliability in the polymerase chain reaction, polymorphism content, map position and the accuracy with which alleles can be scored automatically by the Genotyper(TM) program ...

Malignant hyperthermia susceptibility (MHS) is an autosomal dominant disorder of skeletal muscle which manifests as a potentially fatal hypermetabolic crisis triggered by commonly used anaesthetic agents. The demonstration of genetic heterogeneity in MHS prompted the investigation of the roles played by calcium regulatory proteins other than the ryanodine receptor (RYR1), which is known to be linked to MHS in fewer than half of the European MHS families studied to date. Previously, we have excluded the genes encoding the skeletal muscle L-type voltage-dependent calcium channel alpha(1)-, beta(1)- and gamma-subunits as candidates for MHS. In this report, we describe the cloning and partial DNA sequence analysis of the gene encoding the alpha(2)/delta-subunits, CACNL2A, and its localization on the proximal long arm of chromosome 7q. A new dinucleotide repeat marker close to CACNL2A was identified at the D7S849 locus and tested for linkage in six MHS families. D7S849 and flanking genetic markers ...

STAT maps sequencing reads to a taxonomic hierarchy using a two-step strategy based on exact query read matches to precomputed k-mer dictionary databases. In the first pass a small, a coarse reference dictionary database is used to identify organisms matching a read set. In the second pass, organism-specific slices from a fine reference dictionary database are used to compute distribution of reads between identified taxonomy classes (species and higher order taxonomy nodes). When multiple tax nodes are mapped for single spot we use the lowest non-ambiguous mapping. STAT k-mer dictionaries are built using an iterative minhash based approach against reference genomic databases. For every fixed segment length of incoming reference nucleotide sequence, k-mer representing this segment selected based on minimum fvn1 hash function. Several strategies were used to enhance the specificity and accuracy of STAT results. Low complexity k-mers composed of ,50% homo-polymer or dinucleotide repeats (e.g. ...

STAT maps sequencing reads to a taxonomic hierarchy using a two-step strategy based on exact query read matches to precomputed k-mer dictionary databases. In the first pass a small, a coarse reference dictionary database is used to identify organisms matching a read set. In the second pass, organism-specific slices from a fine reference dictionary database are used to compute distribution of reads between identified taxonomy classes (species and higher order taxonomy nodes). When multiple tax nodes are mapped for single spot we use the lowest non-ambiguous mapping. STAT k-mer dictionaries are built using an iterative minhash based approach against reference genomic databases. For every fixed segment length of incoming reference nucleotide sequence, k-mer representing this segment selected based on minimum fvn1 hash function. Several strategies were used to enhance the specificity and accuracy of STAT results. Low complexity k-mers composed of ,50% homo-polymer or dinucleotide repeats (e.g. ...

The Mittelman Lab has published a new manuscript in Nucleic Acids Research, reporting a method for accurately determining microsatellite repeat genotypes in human genomes. Microsatellite repeats are important determinants of human traits and disease, including many cancers. Read paper. ...

Microsatellites or simple sequence repeat (SSR) polymorphisms are used widely in the construction of linkage maps in many species. High levels of polymorph

AUG 2014 ARTICLE LIST || PharmaTutor (August- 2014) ISSN: 2347 - 7881 (Volume 2, Issue 8) Received On: 16/04/2014; Accepted On: 29/05/2014; Published On: 01/08/2014 AUTHORS: Shikha Jain*, Ranjana Joshi, Kirti Jatwa, Avnish Sharma, S.C. Mahajan Department of Pharmaceutics, Mahakal Institite of Pharmaceutical Studies, Behind Air strip, Datana, Dewas Road, Ujjain, M.P.

The rare orchid, Isotria medeoloides (Pursh) Raf., is a threatened species native to the Eastern United States. The species range extends from Maine to Georgia, with many populations including fewer than 25 individuals. The degree of genetic variation among populations could have important implications for conservation strategies. This study evaluated the level of genetic variation within and among I. medeoloides populations through analysis of microsatellite regions, which contain dinucleotide repeats. The lengths of these regions are highly variable and have high mutation rates, making microsatellites a powerful genetic marker. Genetic variation was assessed at two microsatellite loci among 15 populations and three regions (New England, Virginia and Georgia). In this largely self-pollinating species, the inbreeding coefficient was high (Fis =0.964) indicating a high rate of self-fertilization. Populations in New England harbor the most genetic diversity. Southern populations are monomorphic, or

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To date, two forms of microsatellite instability (MSI) have been described in human cancer. MSI typical of hereditary nonpolyposis colon cancer (HNPCC), is due to deficient DNA mismatch repair (MMR) and is defined with mono- and dinucleotide repeat microsatellites. A second variety of instability is best seen at selective tetranucleotide repeats (EMAST; elevated microsatellite alterations at select tetranucleotides). While MSI occurs infrequently in bladder cancers, EMAST is common. Sporadic tumours with the largest proportion showing MSI are those found most frequently in HNPCC kindreds. While bladder cancer is not frequently seen in HNPCC, upper urinary tract tumours (UTTs) are. Having previously found a low frequency of MSI in bladder cancer, we sought to determine the relative levels of MSI and EMAST in transitional cell carcinoma (TCC) of the upper and lower urinary tracts. Microsatellite analysis was performed at 10 mono- and dinucleotide and eight tetranucleotide loci, in 89 bladder and 71 UTT

Background: Accurate individual identification is essential to wildlife crime investigation or associating individuals to source populations in conservation genetics. Current methodology utilized dinucleotide short tandem repeats (STRs) that can be difficult to type accurately and have high mutation rates. Tetranucleotide STRs, like those used in human forensics and population genetics, are more stable and can have a more diverse allele composition due to inherent motif substructure, making them more robust and informative for finer grained individualization. STRs are currently typed by PCR amplification followed by electrophoretic sizing that cannot identify polymorphisms in the repeat motif structure often observed at tetranucleotide loci. Hypothesis: The main objective of this study was to perform a preliminary identification of a suite of new tetranucleotide repeat STR loci, for each of the three primary bear species in North America: the American black bear, the brown (grizzly) bear, and the polar

|.. ۞ These murine CCAs bear histologic and genetic features of human intrahepatic CCA inducible nitric oxide synthase of uvomorulin (prosta-glandin-endo-peroxide synthase 2, NCAM; 116930) to COX-2, (Cyclo-oxygenase-2) and cyclo-oxygenase-2 [?] ۞ expression PTGS2. This mechanism restrained both oxidant stress and platelet G0 phase activation. Mice lacking Cox2 (Ptgs2, allergen-induced by dexamethasone or anti-Ifng (Interferon)…

Ive talked a lot about DNA mutations, transposons and retrotransposons, microsatellite repeat sequences in cancer and autism, and even somatic mosaicism on this blog. But I havent really talked about all these things in relation to my favorite organ system: the brain. Now why, above any other system, would I single out the brain? Aside…

The Geneious Microsatellite Plugin can analyze microsatellite traces from ABI fragment analysis machines. This guide covers how to view...

The 5 and 3 ends of each intron are marked with GU and AG dinucleotide sequences; a short tract of poly-pyrimidines (C or T) also occurs near the 3 end ahead of the AG singal. ...