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short tandem repeats

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https://www.readbyqxmd.com/read/28521734/higher-order-organisation-of-extremely-amplified-potentially-functional-and-massively-methylated-5s-rdna-in-european-pikes-esox-sp
#1
Radka Symonová, Konrad Ocalewicz, Lech Kirtiklis, Giovanni Battista Delmastro, Šárka Pelikánová, Sonia Garcia, Aleš Kovařík
BACKGROUND: Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogeneity and copy number estimation was carried out using Illumina reads. The higher-order structure of rDNA arrays was investigated by the analysis of long PacBio reads...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28516222/population-data-of-17-y-strs-yfiler-from-punjabis-and-kashmiris-of-pakistan
#2
Atif Adnan, Allah Rakha, Anum Noor, Mannis van Oven, Arwin Ralf, Manfred Kayser
Pakistan harbors 16 major ethnic groups including Punjabis (56% of total population) and Kashmiri (6% of total population). Here, we report data of 17 Y-chromosomal short tandem repeats (Y-STRs) genotyped with the AmpFlSTR Y-filer™ PCR Amplification kit in 94 Punjabis and 101 Kashmiris. The estimated haplotype diversity was higher in Punjabis (0.996) than that in Kashmiris (0.983). Furthermore, we performed population genetic analyses by including data from six other Pakistani groups. The presented haplotype data were recently included in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage...
May 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28513665/a-fully-integrated-microchip-system-for-automated-forensic-short-tandem-repeat-analysis
#3
Junping Han, Wupeng Gan, Bin Zhuang, Jing Sun, Lei Zhao, Jian Ye, Yao Liu, Cai-Xia Li, Peng Liu
We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection...
May 17, 2017: Analyst
https://www.readbyqxmd.com/read/28507140/linkage-disequilibrium-matches-forensic-genetic-records-to-disjoint-genomic-marker-sets
#4
Michael D Edge, Bridget F B Algee-Hewitt, Trevor J Pemberton, Jun Z Li, Noah A Rosenberg
Combining genotypes across datasets is central in facilitating advances in genetics. Data aggregation efforts often face the challenge of record matching-the identification of dataset entries that represent the same individual. We show that records can be matched across genotype datasets that have no shared markers based on linkage disequilibrium between loci appearing in different datasets. Using two datasets for the same 872 people-one with 642,563 genome-wide SNPs and the other with 13 short tandem repeats (STRs) used in forensic applications-we find that 90-98% of forensic STR records can be connected to corresponding SNP records and vice versa...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28506636/multiple-dna-interactions-contribute-to-the-initiation-of-telomerase-elongation
#5
Ahu Karademir Andersson, Cecilia Gustafsson, Roopesh Krishnankutty, Marita Cohn
Telomerase maintains telomere length and chromosome integrity by adding short tandem repeats of single-stranded DNA to the 3' ends, via reverse transcription of a defined template region of its RNA subunit. To further understand the telomerase elongation mechanism, we studied the primer utilization and extension activity of the telomerase from the budding yeast Naumovozyma castellii (Saccharomyces castellii), which displays a processive nucleotide and repeat addition polymerization. For the efficient initiation of canonical elongation, telomerase required 4nt primer 3' end complementarity to the template RNA...
May 12, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28493834/establishing-a-patient-derived-xenograft-model-of-human-myxoid-and-round-cell-liposarcoma
#6
Yiming Qi, Yu Hu, Hua Yang, Rongyuan Zhuang, Yingyong Hou, Hanxing Tong, Yi Feng, Yuan Huang, Quan Jiang, Qunsheng Ji, Qingyang Gu, Zhixiang Zhang, Xuzhen Tang, Weiqi Lu, Yuhong Zhou
Myxoid and round cell liposarcoma (MRCL) is a common type of soft tissue sarcoma. The lack of patient-derived tumor xenograft models that are highly consistent with human tumors has limited the drug experiments for this disease. Hence, we aimed to develop and validate a patient-derived tumor xenograft model of MRCL. A tumor sample from a patient with MRCL was implanted subcutaneously in an immunodeficient mouse shortly after resection to establish a patient-derived tumor xenograft model. After the tumor grew, it was resected and divided into several pieces for re-implantation and tumor passage...
April 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28490578/investigating-clinical-issues-by-genotyping-of-medically-important-fungi-why-and-how
#7
REVIEW
Alexandre Alanio, Marie Desnos-Ollivier, Dea Garcia-Hermoso, Stéphane Bretagne
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes...
July 2017: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/28487173/patrilineal-background-of-the-she-minority-population-from-chaoshan-fenghuang-mountain-an-isolated-mountain-region-in-china
#8
Shuhui Liu, Guangcan Chen, Haihua Huang, Wengting Lin, Guo Dan, Zhao Shukun, Dongping Tian, Min Su
The She ethnic minority population is distributed in southern China. The origin of the She population has been controversial. The purpose of this work was to investigate the genomic diversity of She. The Chaoshan She population living in the Chaoshan Fenghuang mountain is a relatively isolated population. We detected 14 Y chromosome biallelic markers (Y-SNPs) and 6 Y chromosome short tandem repeat (Y-STR) loci in Chaoshan She people. Y-SNP analysis showed the Chaoshan She was closely related to the Chaoshan Hakka, Chaoshanese, Tujia and Gaoshan national minority...
May 6, 2017: Genomics
https://www.readbyqxmd.com/read/28486518/complete-mitochondrial-genomes-of-two-blattid-cockroaches-periplaneta-australasiae-and-neostylopyga-rhombifolia-and-phylogenetic-relationships-within-the-blattaria
#9
Jinnan Ma, Chao Du, Chuang Zhou, Yongmei Sheng, Zhenxin Fan, Bisong Yue, Xiuyue Zhang
Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA)...
2017: PloS One
https://www.readbyqxmd.com/read/28467518/mutation-spectrum-of-star-and-a-founder-effect-of-the-p-q258-in-korean-patients-with-congenital-lipoid-adrenal-hyperplasia
#10
Eungu Kang, Yoon-Myung Kim, Gu-Hwan Kim, Beom Hee Lee, Han-Wook Yoo, Jin-Ho Choi
Congenital lipoid adrenal hyperplasia (CLAH) is the most severe form of congenital adrenal hyperplasia, caused by defects in the steroidogenic acute regulatory protein (STAR). The STAR p.Q258* mutation is the most common mutation in China, Japan, and Korea, suggesting a founder effect. This study aimed to investigate the phenotypic and mutation spectrum of STAR defects and identify a founder effect of the p.Q258* mutation in Korean patients with CLAH. For 45 patients from 42 independent pedigrees, haplotype analysis was performed in 10 unrelated trio families, including patients with the p...
May 2, 2017: Molecular Medicine
https://www.readbyqxmd.com/read/28466124/rapidly-mutating-y-str-analyses-of-compromised-forensic-samples
#11
Rashed Alghafri, Irena Zupanič Pajnič, Tomaž Zupanc, Jože Balažic, Pankaj Shrivastava
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were identified to improve differentiation of unrelated males and also to enable separating closely and distantly related males in human identity testing in forensic and other applications. RM-Yplex assay was developed as a single multiplex that is capable of simultaneously amplifying all currently known RM Y-STRs, and reproducibility and sensitivity testing were performed on reference samples. Additional analyses are necessary to test its suitability for analysing compromised forensic samples...
May 2, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28463912/dna-genotyping-of-nonmolar-donor-egg-pregnancies-with-abnormal-villous-morphology-allele-zygosity-patterns-prevent-misinterpretation-as-complete-hydatidiform-mole
#12
Nancy M Joseph, Caryll Pineda, Joseph T Rabban
DNA genotyping is the gold standard diagnostic test to distinguish hydatidiform moles from nonmolar but morphologically abnormal products of conception (POC). The test is based on comparison of alleles at 15 short tandem repeat loci in the chorionic villi of the POC to those in the maternal decidual tissue. If alleles in the POC are not present in the decidua, then the most concerning interpretation is that the POC has a paternal uniparental genome diagnostic of a complete hydatidiform mole (CHM). However, a nonmolar pregnancy from a donated egg would also appear the same because the maternal genome of the POC would match that of the maternal donor, not that of the decidua of the individual carrying the pregnancy...
April 29, 2017: International Journal of Gynecological Pathology
https://www.readbyqxmd.com/read/28457515/terminal-restriction-fragment-length-polymorphism-profiling-of-bacterial-flora-derived-from-single-human-hair-shafts-can-discriminate-individuals
#13
Eiji Nishi, Kota Watanabe, Yukihiro Tashiro, Kenji Sakai
Human hairs are the trace evidence most commonly encountered at many crime scenes. However, they have not been effectively utilized for actual criminal investigations because of the low accuracy of their morphological inspection, low detection rate of short tandem repeat (STR) typing, and the problem of heteroplasmy in mitochondrial DNA analysis. Here, we examined the possibility of individual discrimination by comparing profiles of bacterial flora on hair. We carried out the profiling of terminal restriction fragment length polymorphisms (T-RFLP) of the amplified bacterial 16S ribosomal RNA (rRNA) gene from hair samples...
March 2017: Legal Medicine
https://www.readbyqxmd.com/read/28457419/relevance-of-chimerism-analysis-after-allogeneic-stem-cell-transplantation
#14
I Clemente, A Goncalo, C Faria, M Dias, I Barbosa, C Mendes
Hematopoietic stem cell transplantation is a potentially curative therapy for a range of malignant and non-malignant hematological diseases. Analysis of chimerism following allogeneic stem cell transplantation has been a routine method for the assessment of engraftment and early detection of graft failure. Lineage-specific chimerism monitoring is progressively used to specifically detect chimerism in one or more cell subsets, which may be undetected in assessment of the whole leukocyte population. The chimerism study in different leukocyte subpopulations increases sensitivity and specificity in the monitoring after transplantation, especially the analysis of T lymphocytes...
May 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/28451532/screening-of-myo7a-mutations-in-iranian-patients-with-autosomal-recessive-hearing-loss-from-west-of-iran
#15
Samira Asgharzade, Somayeh Reiisi, Mohammad Amin Tabatabaiefar, Morteza Hashemzadeh Chaleshtori
BACKGROUND: Hearing loss (HL) is the most frequent neurosensory impairment. HL is highly heterogeneous defect. This disorder affects 1 out of 500 newborns. This study aimed to determine the role of DFNB2 locus and frequency of MYO7A gene mutations in a population from west of Iran. METHODS: Thirty families investigated in Shahrekord University of Medical Sciences in 2014, genetic linkage analysis via four short tandem repeat markers linked to MYO7A was performed for two consanguineous families originating from Hamedan (family-13) and Chaharmahal-Bakhtiari (family-32) provinces of Iran, co-segregating autosomal recessive HL and showed no mutation in GJB2 gene in our preliminary investigation...
January 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/28449233/an-evaluation-of-the-international-society-for-animal-genetics-recommended-parentage-and-identification-panel-for-the-domestic-pigeon-columba-livia-domestica
#16
M de Groot, W A van Haeringen
In this study, the International Society for Animal Genetics (ISAG) recommended panel for the identification of the domestic pigeon (Columba livia domestica) is characterized based on commonly used statistical parameters. The marker panel is based on 16 short tandem repeat (STR) loci (PIGN15, PIGN10, PIGN57, PIGN26, CliμD16, CliμD19, PIGN12, CliμD17, CliμT17, PIGN04, CliμD01, CliμD11, CliμD35, CliμT02, CliμT13, CliμT43). The alleles of the 16 loci consist of a mixture of tri-, tetra-, penta- and hexameric repeat patterns...
April 27, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28445836/a-forensic-multiplex-of-nine-novel-pentameric-repeat-strs
#17
M de la Puente, C Phillips, M Fondevila, M Gelabert-Besada, Á Carracedo, M V Lareu
Pentameric-repeat short tandem repeats (STRs), consisting of loci with repeat units of five base-pairs, have the advantage of reduced stutter products compared to their tetrameric-repeat STR counterparts. This characteristic potentially helps the interpretation of mixed DNA profiles when minor component alleles may coincide with stutter peaks from the major components. To develop a simple but informative forensic multiplex with the capability to aid mixture interpretation, we designed an 11-plex assay of nine pentameric STRs new to forensic analysis plus two male- specific markers: DYS391 and the Y-Indel rs2032678 used in GlobalFiler™ (Life Technologies)...
April 15, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28442996/structural-characteristics-of-simple-rna-repeats-associated-with-disease-and-their-deleterious-protein-interactions
#18
REVIEW
Adam Ciesiolka, Magdalena Jazurek, Karolina Drazkowska, Wlodzimierz J Krzyzosiak
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28436466/genome-wide-profiling-of-heritable-and-de-novo-str-variations
#19
Thomas Willems, Dina Zielinski, Jie Yuan, Assaf Gordon, Melissa Gymrek, Yaniv Erlich
Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool...
April 24, 2017: Nature Methods
https://www.readbyqxmd.com/read/28434084/population-data-of-23-autosomal-str-loci-in-the-chinese-han-population-from-guangdong-province-in-southern-china
#20
Luyu Yang, Xiufeng Zhang, Lijuan Zhao, Yanan Sun, Jiajue Li, Renwu Huang, Liping Hu, Shengjie Nie
The genetic polymorphisms of 23 autosomal short tandem repeat (STR) loci included in the HuaxiaTM Platinum kit were evaluated in 1533 unrelated healthy Guangdong Han individuals living in the Guangdong Province in southern China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine the allele frequencies and forensic statistical parameters. The genetic relationship between the Guangdong Han and other Chinese populations was also estimated. The combined discrimination power and the probability of excluding the paternity of 23 STR loci were 0...
April 22, 2017: International Journal of Legal Medicine
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