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https://www.readbyqxmd.com/read/28723952/evidence-for-prehistoric-origins-of-the-g2019s-mutation-in-the-north-african-berber-population
#1
Rafiqua Ben El Haj, Ayyoub Salmi, Wafa Regragui, Ahmed Moussa, Naima Bouslam, Houyam Tibar, Ali Benomar, Mohamed Yahyaoui, Ahmed Bouhouche
The most common cause of the monogenic form of Parkinson's disease known so far is the G2019S mutation of the leucine-rich repeat kinase 2 (LRRK2) gene. Its frequency varies greatly among ethnic groups and geographic regions ranging from less than 0.1% in Asia to 40% in North Africa. This mutation has three distinct haplotypes; haplotype 1 being the oldest and most common. Recent studies have dated haplotype 1 of the G2019S mutation to about 4000 years ago, but it remains controversial whether the mutation has a Near-Eastern or Moroccan-Berber ancestral origin...
2017: PloS One
https://www.readbyqxmd.com/read/28722587/lack-of-geospatial-population-structure-yet-significant-linkage-disequilibrium-in-the-reservoir-of-plasmodium-falciparum-in-bongo-district-ghana
#2
Shazia Ruybal-Pesántez, Kathryn E Tiedje, Mary M Rorick, Lucas Amenga-Etego, Anita Ghansah, Abraham Oduro, Kwadwo A Koram, Karen P Day
Malaria control in West Africa is impeded by the large reservoir of chronic asymptomatic Plasmodium falciparum infections in the human population. This study aimed to assess the extent of diversity in the P. falciparum reservoir in Bongo District (BD), Ghana, at the end of the dry season, the lowest point in malaria transmission over the course of the year. Analysis of the variation in 12 microsatellite loci was completed for 200 P. falciparum isolates collected from a cross-sectional survey of residents of all ages from two catchment areas in BD...
July 3, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28720156/fmr1-cgg-repeat-expansion-mutation-detection-and-linked-haplotype-analysis-for-reliable-and-accurate-preimplantation-genetic-diagnosis-of-fragile-x-syndrome
#3
Indhu-Shree Rajan-Babu, Mulias Lian, Felicia S H Cheah, Min Chen, Arnold S C Tan, Ethiraj B Prasath, Seong Feei Loh, Samuel S Chong
Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification...
July 19, 2017: Expert Reviews in Molecular Medicine
https://www.readbyqxmd.com/read/28720120/interrogating-the-unsequenceable-genomic-trinucleotide-repeat-disorders-by-long-read-sequencing
#4
Qian Liu, Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang
Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28717152/effects-of-population-bottleneck-and-balancing-selection-on-the-chinese-alligator-are-revealed-by-locus-specific-characterization-of-mhc-genes
#5
Teng Zhai, Hai-Qiong Yang, Rui-Can Zhang, Li-Ming Fang, Guo-Heng Zhong, Sheng-Guo Fang
Chinese alligator (Alligator sinensis) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717144/radseq-provides-evidence-for-parallel-ecotypic-divergence-in-the-autotetraploid-cochlearia-officinalis-in-northern-norway
#6
Marie K Brandrud, Ovidiu Paun, Maria T Lorenzo, Inger Nordal, Anne K Brysting
Speciation encompasses a continuum over time from freely interbreeding populations to reproductively isolated species. Along this process, ecotypes - the result of local adaptation - may be on the road to new species. We investigated whether three autotetraploid Cochlearia officinalis ecotypes, adapted to different habitats (beach, estuary, spring), are genetically differentiated and result from parallel ecotypic divergence in two distinct geographical regions. We obtained genetic data from thousands of single nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequencing (RADseq) and from six microsatellite markers for 12 populations to assess genetic divergence at ecotypic, geographic and population level...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28715588/caucasian-families-exhibit-significant-linkage-of-myopia-to-chromosome-11p
#7
Anthony M Musolf, Claire L Simpson, Bilal A Moiz, Kyle A Long, Laura Portas, Federico Murgia, Elise B Ciner, Dwight Stambolian, Joan E Bailey-Wilson
Purpose: Myopia is a common visual disorder caused by eye overgrowth, resulting in blurry vision. It affects one in four Americans, and its prevalence is increasing. The genetic mechanisms that underpin myopia are not completely understood. Here, we use genotype data and linkage analyses to identify high-risk genetic loci that are significantly linked to myopia. Methods: Individuals from 56 Caucasian families with a history of myopia were genotyped on an exome-based array, and the single nucleotide polymorphism (SNP) data were merged with microsatellite genotype data...
July 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28713651/amphibian-population-genetics-in-agricultural-landscapes-does-viniculture-drive-the-population-structuring-of-the-european-common-frog-rana-temporaria
#8
Patrick P Lenhardt, Carsten A Brühl, Christoph Leeb, Kathrin Theissinger
Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity) on the genetic population structure of amphibians in agricultural landscapes...
2017: PeerJ
https://www.readbyqxmd.com/read/28712776/clonal-evolution-in-paired-endometrial-intraepithelial-neoplasia-atypical-hyperplasia-and-endometrioid-adenocarcinoma
#9
Mariano Russo, James Broach, Kathryn Sheldon, Kenneth R Houser, Dajiang J Liu, Joshua Kesterson, Rebecca Phaeton, Carrie Hossler, Nadine Hempel, Maria Baker, Jordan M Newell, Richard Zaino, Joshua I Warrick
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically-defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma...
July 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28712775/simple-sequence-repeats-showing-length-preference-have-regulatory-functions-in-humans
#10
Jaya Krishnan, Fathima Athar, Tirupaati Swaroopa Rani, Rakesh Kumar Mishra
Simple sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1-6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about their functional relevance. Analysis of genomes across various taxa show that despite the instability associated with longer stretches of repeats, few SSRs with specific longer repeat lengths are enriched in the genomes indicating a positive selection. This conserved feature of length dependent enrichment hints at not only sequence but also length dependent functionality for SSRs...
July 13, 2017: Gene
https://www.readbyqxmd.com/read/28709704/epigenetic-silencing-of-mlh1-in-endometrial-cancers-is-associated-with-larger-tumor-volume-increased-rate-of-lymph-node-positivity-and-reduced-recurrence-free-survival
#11
Casey M Cosgrove, David E Cohn, Heather Hampel, Wendy L Frankel, Dan Jones, Joseph P McElroy, Adrian A Suarez, Weiqiang Zhao, Wei Chen, Ritu Salani, Larry J Copeland, David M O'Malley, Jeffrey M Fowler, Ahmet Yilmaz, Alexis S Chassen, Rachel Pearlman, Paul J Goodfellow, Floor J Backes
OBJECTIVES: To determine the relationship between mismatch repair (MMR) classification and clinicopathologic features including tumor volume, and explore outcomes by MMR class in a contemporary cohort. METHODS: Single institution cohort evaluating MMR classification for endometrial cancers (EC). MMR immunohistochemistry (IHC)±microsatellite instability (MSI) testing and reflex MLH1 methylation testing was performed. Tumors with MMR abnormalities by IHC or MSI and MLH1 methylation were classified as epigenetic MMR deficiency while those without MLH1 methylation were classified as probable MMR mutations...
July 11, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28709170/-leptomeningeal-carcinomatosis-as-a-rare-metastatic-spreading-of-braf-mutated-microsatellite-stable-colon%C3%A2-cancer
#12
Aksana Höblinger, Stephanie Weber, Florian Tschirner, Stefan Kröber, Konrad Streetz
Leptomeningeal carcinomatosis is a rare but serious complication of solid tumors such as melanoma, breast and lung cancer, as well as gastrointestinal carcinomas. Its clinical manifestation is highly variable, presenting as radicular pain with or without neurological deficits, as well as with headaches and hallucinatory irritation symptoms. Leptomeningeal carcinomatosis is often misdiagnosed, which delays treatment. Here we report a rare case of a patient with BRAF-mutated microsatellite stable colon carcinoma with lymphatic and skeletal metastases, who developed neurological symptoms one month after the initial diagnosis of malignancy...
July 2017: Zeitschrift Für Gastroenterologie
https://www.readbyqxmd.com/read/28705114/genetic-changes-of-mlh1-and-msh2-genes-could-explain-constant-findings-on-microsatellite-instability-in-intracranial-meningioma
#13
Nives Pećina-Šlaus, Anja Kafka, Anja Bukovac, Tomislav Vladušić, Davor Tomas, Reno Hrašćan
Postreplicative mismatch repair safeguards the stability of our genome. The defects in its functioning will give rise to microsatellite instability. In this study, 50 meningiomas were investigated for microsatellite instability. Two major mismatch repair genes, MLH1 and MSH2, were analyzed using microsatellite markers D1S1611 and BAT26 amplified by polymerase chain reaction and visualized by gel electrophoresis on high-resolution gels. Furthermore, genes DVL3 (D3S1262), AXIN1 (D16S3399), and CDH1 (D16S752) were also investigated for microsatellite instability...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28703879/precarious-maintenance-of-simple-dna-repeats-in-eukaryotes
#14
REVIEW
Alexander J Neil, Jane C Kim, Sergei M Mirkin
In this review, we discuss how two evolutionarily conserved pathways at the interface of DNA replication and repair, template switching and break-induced replication, lead to the deleterious large-scale expansion of trinucleotide DNA repeats that cause numerous hereditary diseases. We highlight that these pathways, which originated in prokaryotes, may be subsequently hijacked to maintain long DNA microsatellites in eukaryotes. We suggest that the negative mutagenic outcomes of these pathways, exemplified by repeat expansion diseases, are likely outweighed by their positive role in maintaining functional repetitive regions of the genome such as telomeres and centromeres...
July 13, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28700963/application-of-dip-strs-to-sexual-physical-assault-investigations-eight-case-reports
#15
Fabio Oldoni, Vincent Castella, Diana Hall
DIP-STRs are compound markers formed by a deletion/insertion polymorphism linked to a microsatellite. They enable the deconvolution of unbalanced DNA mixtures from two individuals, up to 1000 fold excess of one contributor. In practice, this novel tool allows to test for the presence of a DNA of interest in traces appearing not useful because of the masking effect of the major DNA contributor. Thus far two sets of DIP-STRs have been published: the first set was described as proof-of-principle, while the second set was specifically developed for forensic applications...
July 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28699856/analysis-of-the-origin-of-inherited-chromosomally-integrated-human-herpesvirus-6-in-the-japanese-population
#16
Yoshiki Kawamura, Tamae Ohye, Hiroki Miura, Masaru Ihira, Yuri Kato, Hiroki Kurahashi, Tetsushi Yoshikawa
Integration of the complete human herpesvirus 6 (HHV-6) genome into the telomere of a chromosome has been reported in some individuals (inherited chromosomally integrated HHV-6; iciHHV-6). Since the proportion of iciHHV-6-positive individuals with integration in chromosome 22 is high in Japan, we hypothesized a founder effect. In this study, we sought to elucidate the reason for the high proportion of viral integrations into chromosome 22. We analyzed six cases of iciHHV-6A and two cases of iciHHV-6B, including one iciHHV-6A case with a matched sample from a father and one iciHHV-6B case with a matched sample from a mother...
July 12, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28699276/y-chromosome-and-mtdna-variation-confirms-independent-domestications-and-directional-hybridization-in-south-american-camelids
#17
J C Marín, K Romero, R Rivera, W E Johnson, B A González
Investigations of genetic diversity and domestication in South American camelids (SAC) have relied on autosomal microsatellite and maternally-inherited mitochondrial data. We present the first integrated analysis of domestic and wild SAC combining male and female sex-specific markers (male specific Y-chromosome and female-specific mtDNA sequence variation) to assess: (i) hypotheses about the origin of domestic camelids, (ii) directionality of introgression among domestic and/or wild taxa as evidence of hybridization and (iii) currently recognized subspecies patterns...
July 11, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28699072/expending-role-of-microsatellite-instability-in-diagnosis-and-treatment-of-colorectal-cancers
#18
REVIEW
Liisa Chang, Minna Chang, Hanna M Chang, Fuju Chang
BACKGROUND: Colorectal carcinomas with high-frequency microsatellite instability (MSI-H) account for 15% of all colorectal cancers, including 12% of sporadic cases and 3% of cancers associated with Lynch syndrome (also known as hereditary nonpolyposis colorectal cancer syndrome, HNPCC). Lynch syndrome is an autosomal dominant hereditary cancer syndrome, caused by germline mutations in mismatch repair genes, including MLH1, MSH2, MSH6 and PMS2. METHODS: Published articles from peer-reviewed journals were obtained from PubMed, Google Scholar and Clinicaltrials...
July 11, 2017: Journal of Gastrointestinal Cancer
https://www.readbyqxmd.com/read/28698621/investigating-gene-flow-between-the-blind-cavefish-garra-barreimiae-and-its-conspecific-surface-populations
#19
Sandra Kirchner, Helmut Sattmann, Elisabeth Haring, Lukas Plan, Reginald Victor, Luise Kruckenhauser
Cave-dwelling taxa often share the same phenotypic modifications like absence of eyes and pigmentation. These "troglomorphic characters" are expressed in the populations of Garra barreimiae from the Al Hoota Cave and nearby Hoti Pit in Northern Oman. Surface morphotypes of this cyprinid species are common throughout the distribution area. Very rarely individuals with intermediate phenotypes can be found. In the present study, potential gene flow between cave and surface populations was tested and population structure within five sampling sites was assessed...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698297/disrupted-prenatal-rna-processing-and-myogenesis-in-congenital-myotonic-dystrophy
#20
James D Thomas, Łukasz J Sznajder, Olgert Bardhi, Faaiq N Aslam, Zacharias P Anastasiadis, Marina M Scotti, Ichizo Nishino, Masayuki Nakamori, Eric T Wang, Maurice S Swanson
Myotonic dystrophy type 1 (DM1) is a CTG microsatellite expansion (CTG(exp)) disorder caused by expression of CUG(exp) RNAs. These mutant RNAs alter the activities of RNA processing factors, including MBNL proteins, leading to re-expression of fetal isoforms in adult tissues and DM1 pathology. While this pathogenesis model accounts for adult-onset disease, the molecular basis of congenital DM (CDM) is unknown. Here, we test the hypothesis that disruption of developmentally regulated RNA alternative processing pathways contributes to CDM disease...
June 1, 2017: Genes & Development
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