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short tandem repeats

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https://www.readbyqxmd.com/read/28942264/polymorphism-of-15-short-tandem-repeat-loci-in-hui-population-of-ningxia-tongxin-district
#1
Xiuzi Ma, Runguang Sun, Changchun Hao
OBJECTIVE: To investigate the polymorphism of 15 STR loci in Hui population from Ningxia Tongxin district. METHODS: Identifiler Plus kit used to detect the allelic frequencies of 15 STR loci in 598 unrelated Tongxin Hui individuals, and the population genetics parameters were calculated by using statistic software. RESULTS: The results demonstrated that all loci were found to be no deviation from Hardy-Weinberg equilibrium (P > 0.05), Heterozygosity (H) ranged from 0...
August 24, 2017: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/28940260/authentication-of-m14-melanoma-cell-line-proves-misidentification-of-mda-mb-435-breast-cancer-cell-line
#2
Christopher Korch, Erin M Hall, Wilhelm G Dirks, Margaret Ewing, Mark Faries, Marileila Varella-Garcia, Steven Robinson, Douglas Storts, Jacqueline A Turner, Ying Wang, Edward C Burnett, Lyn Healy, Douglas Kniss, Richard M Neve, Raymond W Nims, Yvonne A Reid, William A Robinson, Amanda Capes-Davis
A variety of analytical approaches have indicated that melanoma cell line UCLA-SO-M14 (M14) and breast carcinoma cell line MDA-MB-435 originate from a common donor. This indicates that at some point in the past, one of these cell lines became misidentified, meaning that it ceased to correspond to the reported donor and instead became falsely identified (through cross-contamination or other means) as a cell line from a different donor. Initial studies concluded that MDA-MB-435 was the misidentified cell line and M14 was the authentic cell line, although contradictory evidence has been published, resulting in further confusion...
September 22, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28938154/massively-parallel-sequencing-of-forensic-strs-and-snps-using-the-illumina-%C3%A2-forenseq%C3%A2-dna-signature-prep-kit-on-the-miseq-fgx%C3%A2-forensic-genomics-system
#3
Fei Guo, Jiao Yu, Lu Zhang, Jun Li
The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples)...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28938133/genetic-polymorphisms-for-19-x-str-loci-of-sichuan-han-ethnicity-and-its-comparison-with-chinese-populations
#4
Guanglin He, Ye Li, Xing Zou, Mengge Wang, Pengyu Chen, Miao Liao, Jin Wu
X-chromosomal short tandem repeats (X-STRs) can be serviced as a complementary tool in forensic deficiency cases and other complicated kinship identification. To investigate the genetic variation of the western Chinese Han population, genetic polymorphisms of 19 X-STR loci (DXS8378, DXS7423, DXS10148, DXS10159, DXS10134, DXS7424, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103, DXS10101, HPRTB, DXS6809, DXS10075, DXS10074 and DXS10135) included in the AGCU X19 PCR amplification kit were obtained from 201 Chinese Han individuals (108 females and 93 males) residing in Sichuan province, western China...
September 15, 2017: Legal Medicine
https://www.readbyqxmd.com/read/28930976/detection-of-residual-donor-erythroid-progenitor-cells-after-hematopoietic-stem-cell-transplantation-for-patients-with-hemoglobinopathies
#5
Roman Crazzolara, Gabriele Kropshofer, Michael Steurer, Sieghart Sopper, Wolfgang Schwinger
The presence of incomplete chimerism is noted in a large proportion of patients following bone marrow transplant for thalassemia major or sickle cell disease. This observation has tremendous implications, as subsequent therapeutic immunomodulation strategies can improve clinical outcome. Conventionally, polymerase chain reaction-based analysis of short tandem repeats is used to identify chimerism in donor-derived blood cells. However, this method is restricted to nucleated cells and cannot distinguish between dissociated single-cell lineages...
September 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28921603/trace-dna-sampling-success-from-evidence-items-commonly-encountered-in-forensic-casework
#6
Renata Dziak, Amy Peneder, Alicia Buetter, Cecilia Hageman
Trace DNA analysis is a significant part of a forensic laboratory's workload. Knowing optimal sampling strategies and item success rates for particular item types can assist in evidence selection and examination processes and shorten turnaround times. In this study, forensic short tandem repeat (STR) casework results were reviewed to determine how often STR profiles suitable for comparison were obtained from "handler" and "wearer" areas of 764 items commonly submitted for examination. One hundred and fifty-five (155) items obtained from volunteers were also sampled...
September 15, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28915660/mass-spectrometry-based-assay-for-the-molecular-diagnosis-of-glioma-concomitant-detection-of-chromosome-1p-19q-codeletion-and-idh1-idh2-and-tert-mutation-status
#7
Chiara Pesenti, Leda Paganini, Laura Fontana, Emanuela Veniani, Letterio Runza, Stefano Ferrero, Silvano Bosari, Maura Menghi, Giovanni Marfia, Manuela Caroli, Rosamaria Silipigni, Silvana Guerneri, Silvia Tabano, Monica Miozzo
The World Health Organization recently revised the diagnosis of glioma, to integrate molecular parameters, including IDH mutations and codeletion (loss of heterozygosity; LOH) of chromosome arms 1p/19q, into the definitions of adult glioma histological subtypes. Mutations in the TERT promoter may also be useful for glioma diagnosis and prognosis. The integration of molecular markers into routine diagnosis requires their rapid and reliable assessment. We propose a MassARRAY (MS)-based test that can identify 1p/19q codeletion using quantitative SNP genotyping and, simultaneously, characterize hotspot mutations in the IDH1, IDH2, and TERT genes in tumor DNA...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903344/establishing-a-patient-derived-xenograft-model-of-human-myxoid-and-round-cell-liposarcoma
#8
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...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28901559/single-nucleotide-polymorphisms-for-dna-typing-in-the-domestic-horse
#9
H M Holl, J Vanhnasy, R E Everts, K Hoefs-Martin, D Cook, S A Brooks, M L Carpenter, C D Bustamante, C Lafayette
Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds...
September 13, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28900279/next-generation-sequencing-plus-ngs-with-y-chromosomal-markers-for-forensic-pedigree-searches
#10
Xiaoqin Qian, Jiayi Hou, Zheng Wang, Yi Ye, Min Lang, Tianzhen Gao, Jing Liu, Yiping Hou
There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs)...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28892497/improved-dop-pcr-idop-pcr-a-robust-and-simple-wga-method-for-efficient-amplification-of-low-copy-number-genomic-dna
#11
Konstantin A Blagodatskikh, Vladimir M Kramarov, Ekaterina V Barsova, Alexey V Garkovenko, Dmitriy S Shcherbo, Andrew A Shelenkov, Vera V Ustinova, Maria R Tokarenko, Simon C Baker, Tatiana V Kramarova, Konstantin B Ignatov
Whole-genome amplification (WGA) techniques are used for non-specific amplification of low-copy number DNA, and especially for single-cell genome and transcriptome amplification. There are a number of WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which is a very simple, fast and inexpensive WGA technique. Although DOP-PCR has been regarded as one of the pioneering methods for WGA, it only provides low genome coverage and a high allele dropout rate when compared to more modern techniques...
2017: PloS One
https://www.readbyqxmd.com/read/28892063/interpreting-short-tandem-repeat-variations-in-humans-using-mutational-constraint
#12
Melissa Gymrek, Thomas Willems, David Reich, Yaniv Erlich
Identifying regions of the genome that are depleted of mutations can distinguish potentially deleterious variants. Short tandem repeats (STRs), also known as microsatellites, are among the largest contributors of de novo mutations in humans. However, per-locus studies of STR mutations have been limited to highly ascertained panels of several dozen loci. Here we harnessed bioinformatics tools and a novel analytical framework to estimate mutation parameters for each STR in the human genome by correlating STR genotypes with local sequence heterozygosity...
September 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28888135/strseq-a-catalog-of-sequence-diversity-at-human-identification-short-tandem-repeat-loci
#13
Katherine Butler Gettings, Lisa A Borsuk, David Ballard, Martin Bodner, Bruce Budowle, Laurence Devesse, Jonathan King, Walther Parson, Christopher Phillips, Peter M Vallone
The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence-based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by the ISFG DNA Commission, provides a framework for communication among laboratories. The initial data used to populate the project are the aggregate alleles observed in targeted sequencing studies across four laboratories: National Institute of Standards and Technology (N=1786), Kings College London (N=1043), University of North Texas Health Sciences Center (N=839), and University of Santiago de Compostela (N=944), for a total of 4612 individuals...
September 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28887705/population-data-and-mutation-rates-of-20-autosomal-str-loci-in-a-chinese-han-population-from-yunnan-province-southwest-china
#14
Xiufeng Zhang, Linlin Liu, Runfang Xie, Guiyi Wang, Yuan Shi, Tao Gu, Liping Hu, Shengjie Nie
The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated from 2068 unrelated, healthy individuals from the Chinese Han population of Yunnan Province in southwest China. All of the loci reached Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationships among the Yunnan Han and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0...
September 8, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28887402/detection-of-long-repeat-expansions-from-pcr-free-whole-genome-sequence-data
#15
Egor Dolzhenko, Joke J F A van Vugt, Richard J Shaw, Mitchell A Bekritsky, Marka van Blitterswijk, Giuseppe Narzisi, Subramanian S Ajay, Vani Rajan, Bryan Lajoie, Nathan H Johnson, Zoya Kingsbury, Sean J Humphray, Raymond D Schellevis, William J Brands, Matt Baker, Rosa Rademakers, Maarten Kooyman, Gijs H P Tazelaar, Michael A van Es, Russell McLaughlin, William Sproviero, Aleksey Shatunov, Ashley Jones, Ahmad Al Khleifat, Alan Pittman, Sarah Morgan, Orla Hardiman, Ammar Al-Chalabi, Chris Shaw, Bradley Smith, Edmund J Neo, Karren Morrison, Pam Shaw, Catherine Reeves, Lara Winterkorn, Nancy S Wexler, David E Housman, Christopher W Ng, Alina L Li, Ryan J Taft, Leonard H van den Berg, David R Bentley, Jan H Veldink, Michael A Eberle
Identifying large expansions of short tandem repeats (STRs) such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step towards integrating WGS into precision medicine. We have developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length...
September 8, 2017: Genome Research
https://www.readbyqxmd.com/read/28886202/fuchs-endothelial-corneal-dystrophy-and-rna-foci-in-patients-with-myotonic-dystrophy
#16
V Vinod Mootha, Brock Hansen, Ziye Rong, Pradeep P Mammen, Zhengyang Zhou, Chao Xing, Xin Gong
Purpose: The most common cause of Fuchs' endothelial corneal dystrophy (FECD) is an intronic CTG repeat expansion in TCF4. Expanded CUG repeat RNA colocalize with splicing factor, muscleblind-like 1 (MBNL1), in nuclear foci in endothelium as a molecular hallmark. Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by a CTG repeat expansion in the 3'-untranslated region (UTR) of DMPK. In this study, we examine for RNA-MBNL1 foci in endothelial cells of FECD subjects with DM1, test the hypothesis that DM1 patients are at risk for FECD, and determine prevalence of TCF4 and DMPK expansions in a FECD cohort...
September 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28878337/precise-mapping-of-17-deletion-breakpoints-within-the-central-hotspot-deletion-region-introns-50-and-51-of-the-dmd-gene
#17
Gabriella Esposito, Maria Roberta Tremolaterra, Evelina Marsocci, Igor Cm Tandurella, Tiziana Fioretti, Maria Savarese, Antonella Carsana
Exon deletions in the human DMD gene, which encodes the dystrophin protein, are the molecular defect in 50-70% of cases of Duchenne/Becker muscular dystrophies. Deletions are preferentially clustered in the 5' (exons 2-20) and the central (exons 45-53) region of DMD, likely because local DNA structure predisposes to specific breakage or recombination events. Notably, innovative therapeutic strategies may rescue dystrophin function by homology-based specific targeting of sequences within the central DMD hot spot deletion region...
September 7, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28877059/choriocarcinoma-in-women-analysis-of-a-case-series-with-genotyping
#18
Johanna Savage, Emily Adams, Emanuela Veras, Kathleen M Murphy, Brigitte M Ronnett
Choriocarcinoma is an uncommon malignant neoplasm, which can be either gestational or nongestational in origin. Distinction of these subtypes has prognostic and therapeutic implications. Twenty-two tumors were genotyped using polymerase chain reaction amplification of 15 short tandem repeat loci and the amelogenin locus (XY determination). DNA patterns from tumor and maternal tissue, as well as villous tissue from any available prior or concurrent gestation, were compared, to determine gestational versus nongestational nature (containing vs...
September 4, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28876418/a-conventional-pcr-for-differentiating-common-taeniid-species-of-dogs-based-on-in-silico-microsatellite-analysis
#19
Saeedeh Shamsaddini, Mohammad Ali Mohammadi, Seyed Reza Mirbadie, Sima Rostami, Mansoureh Dehghani, Balal Sadeghi, Majid Fasihi Harandi
Canine taeniids are among the major tapeworms with remarkable medical and economic significance. Reliable diagnosis and differentiation of dog taeniids using simple and sensitive tools are of paramount importance for establishing an efficient surveillance system. Microsatellites as abundant unique tandem repeats of short DNA motifs are useful genetic markers for molecular epidemiological studies. The purpose of the present study was to find a primer pair for rapid differentiation of major tapeworms of dogs, Taenia hydatigena, T...
September 4, 2017: Revista do Instituto de Medicina Tropical de São Paulo
https://www.readbyqxmd.com/read/28871330/forensic-features-and-phylogenetic-analyses-of-sichuan-han-population-via-23-autosomal-str-loci-included-in-the-huaxia-platinum-system
#20
Guanglin He, Mengge Wang, Jing Liu, Yiping Hou, Zheng Wang
Short tandem repeats (STRs) are DNA regions with a variable number of repeated units (2-6 bp) and attractive to genetic application like forensic, population genetics, and anthropological studies. The Huaxia Platinum System allows the multiplex amplification of 23 autosomal STR loci and two gender determination loci. In the present study, genetic polymorphisms of these 23 autosomal STR loci were first obtained from 309 Sichuan Han individuals, southwest China. No evidence of deviation from the Hardy-Weinberg equilibrium (HWE) was identified...
September 5, 2017: International Journal of Legal Medicine
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