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short tandem repeats

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https://www.readbyqxmd.com/read/28107433/investigation-of-cross-contamination-and-misidentification-of-278-widely-used-tumor-cell-lines
#1
Yaqing Huang, Yuehong Liu, Congyi Zheng, Chao Shen
In recent years, biological research involving human cell lines has been rapidly developing in China. However, some of the cell lines are not authenticated before use. Therefore, misidentified and/or cross-contaminated cell lines are unfortunately commonplace. In this study, we present a comprehensive investigation of cross-contamination and misidentification for a panel of 278 cell lines from 28 institutes in China by using short tandem repeat profiling method. By comparing the DNA profiles with the cell bank databases of ATCC and DSMZ, a total of 46...
2017: PloS One
https://www.readbyqxmd.com/read/28105353/isolated-extramedullary-cutaneous-relapse-despite-concomitant-severe-graft-vs-host-disease-and-tissue-chimerism-analysis-in-a-patient-with-acute-lymphoblastic-leukemia-after-allogeneic-hematopoietic-stem-cell-transplantation-a-case-report
#2
Bulent Kantarcioglu, Huseyin Saffet Bekoz, Yeliz Duvarci Ogret, Asli Cakir, Demet Kivanc, Fatma Savran Oguz, Deniz Sargin
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potentially curative treatment option for patients with acute lymphoblastic leukemia (ALL). The curative potential of allo-HSCT for ALL is, in part, due to the graft-vs.-leukemia (GVL) effect, in addition to the intensive conditioning chemo-radiotherapy. However, relapse remains the major cause of treatment failure following allo-HSCT for ALL. In the allo-HSCT setting, testing for genetic markers of hematopoietic chimerism has become a part of the routine diagnostic program...
December 2016: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28104618/hysa-a-hybrid-structural-variant-assembly-approach-using-next-generation-and-single-molecule-sequencing-technologies
#3
Xian Fan, Mark Chaisson, Luay Nakhleh, Ken Chen
Achieving complete, accurate and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a hybrid structural variant assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variations in human genomes...
January 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28104015/-establishment-and-characterization-of-a-laryngeal-squamous-cell-carcinoma-cell-line
#4
R Wang, X C Bian, Y Q Liu, J G Fang, H Wang, H G Liu, M Lian, H Z Ma, L Feng, H Z Wang
Objective: To establish a laryngeal squamous cell carcinoma (LSCC) cell line through primary cell culture and observe its biological characteristics. Methods: Tissue block culture method was used for primary cell culture. After LSCC cells passed 25 times in vitro, the morphology of cells was observed, keratin was stained histochemically, cell cycle was tested by PI-FACS, and the specie of cells was detected by PCR and short tandem repeat(STR) typing. Results: This newly established LSCC cell line was named as TR-LCC-1, most of the cancer cells were polygonal shape, like the cobblestone, loss of contact inhibition and with overlapping growth...
January 7, 2017: Zhonghua Er Bi Yan Hou Tou Jing Wai Ke za Zhi, Chinese Journal of Otorhinolaryngology Head and Neck Surgery
https://www.readbyqxmd.com/read/28102039/a-dispermic-chimerism-detected-in-a-taiwanese-potential-unrelated-hematopoietic-stem-cell-donor
#5
E K L Yang, S G E Marsh, P-Y Chen, C-P Chen, S-P Chen, P Y Lin
Chimerism is defined as the presence of 2 or more than 1 genetically distinct cell populations in an organism. Dispermic chimeras are derived from the fertilization of 1 or 2 matured nuclei by 2 sperms. We here report detection of a healthy and phenotypically normal female with normal ABO red blood cell typing in whom dispermic chimerism was suspected after 3 alleles were identified at multiple human leukocyte antigen (HLA) loci using molecular HLA analysis. Molecular HLA typing showed the donor to have 3 HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 alleles in blood, saliva and nail samples...
February 2017: HLA
https://www.readbyqxmd.com/read/28099121/early-mixed-hematopoietic-chimerism-detection-by-digital-droplet-pcr-in-patients-undergoing-gender-mismatched-hematopoietic-stem-cell-transplantation
#6
Miguel Waterhouse, Dietmar Pfeifer, Marie Follo, Justus Duyster, Henning Schäfer, Hartmut Bertz, Jürgen Finke
BACKGROUND: Clinical decision making after allogeneic stem cell transplantation (HSCT) is partially based on hematopoietic chimerism analysis. Polymerase chain reaction amplification of polymorphic short tandem repeats (STR-PCR) is currently considered the gold standard for chimerism surveillance after transplantation. Nevertheless, this method has shown several limitations. Emerging technologies such as digital PCR (dPCR) has been applied to detect hematopoietic chimerism. Despite previous reports, the clinical usefulness of dPCR is unclear because the studies were performed in limited patient populations with short follow-ups...
January 18, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28070706/analysis-of-12-x-str-loci-in-the-population-of-south-croatia
#7
Gordan Mršić, Petar Ozretić, Josip Crnjac, Siniša Merkaš, Ivana Račić, Sara Rožić, Viktorija Sukser, Maja Popović, Marina Korolija
The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator(®) Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org...
January 9, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28058572/population-genetic-analyses-and-evaluation-of-22-autosomal-strs-in-indian-populations
#8
Mugdha Singh, Madhusudan R Nandineni
The allele frequencies and forensically relevant parameters for the 22 autosomal short tandem repeats (STRs) present in PowerPlex® Fusion (Promega, Madison, WI) were determined for 357 unrelated individuals from 11 states across India. The combined power of discrimination and probability of exclusion were 0.99999999999999999999999999875 and 0.999999997200846, respectively. The panel was found to be informative for Indian populations and generated a total of 275 alleles. Further, analyses with these loci did not show any noticeable clustering among the Indian populations...
January 6, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28057510/investigation-of-extended-y-chromosome-str-haplotypes-in-sardinia
#9
D Lacerenza, S Aneli, C Di Gaetano, R Critelli, A Piazza, G Matullo, C Culigioni, R Robledo, C Robino, C Calò
Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n=40; Central Sardinia, n=56; Southern Sardinia, n=91) and three isolates (Desulo, n=34; Benetutti, n=45, Carloforte, n=42). The tested Y-STRs consisted of Yfiler(®) Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler(®) Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626)...
December 28, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28055236/characterization-of-vntrs-within-the-entire-region-of-slc6a3-and-its-association-with-hypertension
#10
Won-Tae Kim, Se-Ra Lee, Yun-Gil Roh, Seung Il Kim, Yung Hyun Choi, Mi-Hye Mun, Mi-So Jeong, Sang Seok Koh, Sun-Hee Leem
The dopamine transporter SLC6A3 (DAT1) mediates uptake of dopamine into presynaptic terminals. In addition, in previous reports, hypertensive rats were associated with DAT gene, but the genetic association with SLC6A3 and hypertension is still unknown. We examined the distribution of variable number of tandem repeats (VNTRs) and conducted polymorphic analysis of the entire region of SLC6A3. Ten VNTR regions (MS1-10) were revealed throughout the intronic and UTRs; seven VNTR regions were newly isolated and three VNTRs were previously reported...
January 5, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28052650/patient-derived-xenograft-models-of-epithelial-ovarian-cancer-for-preclinical-studies
#11
Eun Jin Heo, Young Jae Cho, William Chi Cho, Ji Eun Hong, Hye-Kyung Jeon, Doo-Yi Oh, Yoon-La Choi, Sang Yong Song, Jung-Joo Choi, Duk-Soo Bae, Yoo-Young Lee, Chel Hun Choi, Tae-Joong Kim, Woong-Yang Park, Byoung-Gie Kim, Jeong-Won Lee
Purpose: Patient-derived tumor xenografts (PDXs) can provide more reliable information about tumor biology than cell line models. We developed PDXs for epithelial ovarian cancer (EOC) that have histopathologic and genetic similarities to the primary patient tissues and evaluated their potential for use as a platform for translational EOC research. Materials and Methods: We successfully established PDXs by subrenal capsule implantation of primary EOC tissues into female BALB/C-nude mice...
January 4, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28052096/sex-determination-from-fragmented-and-degenerated-dna-by-amplified-product-length-polymorphism-bidirectional-snp-analysis-of-amelogenin-and-sry-genes
#12
Kotoka Masuyama, Hideki Shojo, Hiroaki Nakanishi, Shota Inokuchi, Noboru Adachi
Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination...
2017: PloS One
https://www.readbyqxmd.com/read/28043616/whole-genome-sequencing-as-the-ultimate-tool-to-diagnose-tuberculosis
#13
Dick van Soolingen, Rana Jajou, Arnout Mulder, Han de Neeling
In the past two decades, DNA techniques have been increasingly used in the laboratory diagnosis of tuberculosis (TB). The (sub) species of the Mycobacterium tuberculosis complex are usually identified using reverse line blot techniques. The resistance is predicted by the detection of mutations in genes associated with resistance. Nevertheless, all cases are still subjected to cumbersome phenotypic resistance testing. The production of a strain-characteristic DNA fingerprint, to investigate the epidemiology of TB, is done by the 24-locus variable number tandem repeat (VNTR) typing...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28042088/three-loci-allele-combinations-based-on-liver-stomach-cancers-hematencephalon-copd-and-normal-population-a-preliminary-study
#14
Gai Li-Ping, Liu Hui, Cui Jing-Hui, Yu Weijian, Ding Xiao-Dong
The purpose of this study was to examine the specific three loci allele combinations connected with the liver cancers, stomach cancers, hematencephalon and patients with chronic obstructive pulmonary disease (COPD). That is to explore the feasibility of the research methods. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. At the same time we still analyses the statistical results of three loci allele combinations by difference value method and ratio method...
December 29, 2016: Gene
https://www.readbyqxmd.com/read/28040139/prenatal-diagnosis-of-paternal-duplication-of-11p15-5%C3%A2-14-3-its-implication-of-beckwith-wiedemann-syndrome
#15
Kuan Ju Chen, Yu Mei Liu, Chien Hong Li, Yao Lung Chang, Shuenn Dyh Chang
OBJECTIVE: To characterize a prenatally detected chromosomal aberration with molecular cytogenetic approaches and explore its relationship with Beckwith-Wiedemann syndrome (BWS). CASE REPORT: A 33-year-old woman, gravida 2, para 0, was referred to our prenatal clinic at 20+ weeks due to an abnormal amniocentesis karyotyping finding, which showed 46,XY,add(11)(q24.2)dn. The mother conceived through in vitro fertilization-intracytoplasmic sperm injection (IVF-ICSI), then embryo transfer...
December 2016: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28032911/alanine-substitutions-in-the-gxxxg-motif-alter-c99-cleavage-by-%C3%AE-secretase-but-not-its-dimerization
#16
Hidekazu Higashide, Seiko Ishihara, Mika Nobuhara, Yasuo Ihara, Satoru Funamoto
The amyloid β (Aβ) protein is a major component of senile plaques, one of the neuropathological hallmarks of Alzheimer's disease (AD). Amyloidogenic processing of amyloid precursor protein (APP) by β- and γ-secretases leads to production of Aβ. APP contains tandem triple repeats of the GXXXG motif in its extracellular juxtamembrane and transmembrane regions. It is reported that the GXXXG motif is related to protein-protein interactions, but it remains controversial whether the GXXXG motif in APP is involved in substrate dimerization and whether dimerization affects γ-secretase-dependent cleavage...
December 29, 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28012541/a-novel-tecta-mutation-causes-arnshl
#17
Samira Asgharzade, Mohammad Amin Tabatabaiefar, Mohammad Hossein Modarressi, Mohammad Hossein Ghahremani, Somayeh Reiisi, Parisa Tahmasebi, Fatemeh Abdollahnejad, Morteza Hashemzadeh Chaleshtori
OBJECTIVE: Autosomal recessive nonsyndromic hearing loss (ARNSHL) is a genetically heterogeneous sensorineural disorder. Alpha-tectorin, which is encoded by the TECTA gene, is a non-collagenous component of the tectorial membrane in the inner ear defect of which leads to moderate to severe hearing loss (HL). METHODS: 25 unrelated Iranian multiplex ARNSHL families, negative for GJB2 mutations, were recruited in this study. Clinical inspections including audiometric and otologic examinations ruled out syndromic forms...
January 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28002593/genetic-variations-of-21-str-markers-on-chromosomes-13-18-21-x-and-y-in-the-south-iranian-population
#18
J Saberzadeh, M R Miri, M B Tabei, M Dianatpour, M Fardaei
Quantitative fluorescent polymerase chain reaction (QF-PCR), in recent years, has been accepted as a rapid, high throughput, and sensitive method for prenatal diagnosis of common chromosomal aneuploidies. Since short tandem repeats (STRs) are the cornerstone of QF-PCR technique, selection of the most polymorphic STR markers is an essential step for a successful QF-PCR assay. The genetic variation parameters of each STR marker differ among different populations. In this study, we investigated the size, frequency, heterozygosity, polymorphism information content, power of discrimination, and other genetic polymorphism data for 21 STR markers on chromosomes 13, 18, 21, X, and Y in 1000 amniotic fluid samples obtained from south Iranian women...
December 19, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28002585/case-report-association-between-an-acan-gene-variable-number-tandem-repeat-polymorphism-and-lumbar-disc-herniation-a-case-control-study
#19
N L L Casa, A J Casa Junior, A V Melo, L S Teodoro, G R Nascimento, A F Sousa, T C Flausino, D Brito, R Bergamini, L B Minasi, A D da Cruz, T C Vieira, M P Curado
We investigated the association between an aggrecan gene (ACAN) polymorphism and lumbar disc herniation (LDH). This was a case-control study with quinquennial age and gender groups. The study comprised 119 men and women aged between 20 and 60 from Goiânia (Brazil). Of these, 39 were allocated to the case group (Ca) and 80 to the control group (Ct). We gathered sociodemographic and clinical data, and peripheral blood samples. DNA was isolated for genotyping the ACAN variable number tandem repeat (VNTR) via conventional polymerase chain reaction (PCR)...
December 19, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27992827/development-of-a-snp-based-panel-for-human-identification-for-indian-populations
#20
Anujit Sarkar, Madhusudan R Nandineni
The widely employed short tandem repeat (STR)-based panels for forensic human identification (HID) have limitations while dealing with challenging forensic samples involving DNA degradation, resulting in dropping-out of higher molecular weight alleles/loci. To address this issue, bialleic markers like single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), which can be scored even when the template DNA is heavily degraded (<100bp), have been suggested as alternative markers for HID testing...
December 5, 2016: Forensic Science International. Genetics
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