keyword
MENU ▼
Read by QxMD icon Read
search

short tandem repeats

keyword
https://www.readbyqxmd.com/read/28430826/geographic-origin-and-individual-assignment-of-shorea-platyclados-dipterocarpaceae-for-forensic-identification
#1
Chin Hong Ng, Soon Leong Lee, Lee Hong Tnah, Kevin Kit Siong Ng, Chai Ting Lee, Bibian Diway, Eyen Khoo
The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases...
2017: PloS One
https://www.readbyqxmd.com/read/28420341/genetic-sequence-based-prediction-of-long-range-chromatin-interactions-suggests-a-potential-role-of-short-tandem-repeat-sequences-in-genome-organization
#2
Sarvesh Nikumbh, Nico Pfeifer
BACKGROUND: Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions - the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28417259/comparison-between-magnetic-bead-and-qpcr-library-normalisation-methods-for-forensic-mps-genotyping
#3
Bhavik Mehta, Samantha Venables, Paul Roffey
Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample...
April 18, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28414318/initial-sites-of-hepadnavirus-integration-into-host-genome-in-human-hepatocytes-and-in-the-woodchuck-model-of-hepatitis-b-associated-hepatocellular-carcinoma
#4
R Chauhan, N D Churchill, P M Mulrooney-Cousins, T I Michalak
Hepatitis B virus (HBV) and the closely related woodchuck hepatitis virus (WHV) are potent carcinogens that trigger development of primary hepatocellular carcinoma (HCC). The initial sites of hepadnavirus-host genome integration, their diversity and kinetics of formation can be central to virus persistence and the initiation and progression of HCC. To recognize the nature of the very early virus-host interactions, we explored de novo infection of human hepatocyte-like HepaRG cells with authentic HBV and naive woodchucks with WHV...
April 17, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28412872/chinese-xibe-population-genetic-composition-according-to-linkage-groups-of-x-chromosomal-strs-population-genetic-variability-and-interpopulation-comparisons
#5
Hao-Tian Meng, Chun-Mei Shen, Yu-Dang Zhang, Qian Dong, Yu-Xin Guo, Guang Yang, Jiang-Wei Yan, Yao-Shun Liu, Ting Mei, Jian-Feng Shi, Bo-Feng Zhu
BACKGROUND: The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application especially for complex or deficiency cases. SUBJECTS AND METHODS: We obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations...
April 16, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28402514/tarean-a-computational-tool-for-identification-and-characterization-of-satellite-dna-from-unassembled-short-reads
#6
Petr Novák, Laura Ávila Robledillo, Andrea Koblížková, Iva Vrbová, Pavel Neumann, Jirí Macas
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads...
April 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28401988/a-rapid-nuclear-staining-test-using-cationic-dyes-contributes-to-efficient-str-analysis-of-telogen-hair-roots
#7
So-Yeon Lee, Eun-Ju Ha, Seung-Kyun Woo, So-Min Lee, Kyung-Hee Lim, Yong-Bin Eom
Telogen hairs presented in the crime scene are commonly encountered as trace evidence. However, short tandem repeat (STR) profiling of the hairs currently have low and limited use due to poor success rate. To increase the success rate of STR profiling of telogen hairs, we developed a rapid and cost-effective method to estimate the number of nuclei in the hair roots. Five cationic dyes, Methyl green (MG), Harris hematoxylin (HH), Methylene blue (MB), Toluidine blue (TB) and Safranin O (SO) were evaluated in this study...
April 12, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28401080/comparison-of-the-frequency-of-y-short-tandem-repeats-markers-between-sadat-and-non-sadat-populations-in-isfahan-province-of-iran
#8
Reihaneh Seyedebrahimi, Ebrahim Esfandiari, Bahman Rashidi, Rasoul Salehi, Ali Gholami Dahghi, Shahriar Dabiri, Majid Kheirollahi
BACKGROUND: Y chromosome is one of the two sex chromosomes and is male specific. Due to limited genetic exchange, the main part of that is passed virtually unchanged from one generation to next generation. The short tandem repeats (STRs) are almost constant on chromosomes that make them as an appropriate factor for use in population genetic studies. In this study, we used the STRs of Y chromosome markers in Sadat families and comparison with other families was investigated. MATERIALS AND METHODS: In this study, sampling was done from fifty unrelated males of Sadat families and fifty unrelated males of non-Sadat families...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28401070/simple-and-easy-to-perform-preimplantation-genetic-diagnosis-for-%C3%AE-thalassemia-major-using-combination-of-conventional-and-fluorescent-polymerase-chain-reaction
#9
Rasoul Salehi, Sharifeh Khosravi, Mansour Salehi, Majid Kheirollahi, Hossein Khanahmad
BACKGROUND: Thalassemias are the most common monogenic disorders in many countries throughout the world. The best practice to control the prevalence of the disease is prenatal diagnosis (PND) services. Extensive practicing of PND proved effective in reducing new cases but on the other side of this success high abortion rate is hided, which ethically unfair and for many couples, especially with a previous experience of a therapeutic abortion, or moral concerns, is not a suitable choice...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28399438/internal-validation-of-the-dnascan-ande%C3%A2-rapid-dna-analysis%C3%A2-platform-and-its-associated-powerplex-%C3%A2-16-high-content-dna-biochip-cassette-for-use-as-an-expert-system-with-reference-buccal-swabs
#10
Lilliana I Moreno, Alice L Brown, Thomas F Callaghan
Rapid DNA platforms are fully integrated systems capable of producing and analyzing short tandem repeat (STR) profiles from reference sample buccal swabs in less than two hours. The technology requires minimal user interaction and experience making it possible for high quality profiles to be generated outside an accredited laboratory. The automated production of point of collection reference STR profiles could eliminate the time delay for shipment and analysis of arrestee samples at centralized laboratories...
March 31, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28397234/-analysis-of-genetic-polymorphisms-and-mutations-of-20-frequently-used-str-loci-among-ethnic-hans-from-henan
#11
Hongdan Wang, Bing Kang, Yue Gao, Xiaodong Huo, Tao Li, Qiannan Guo, Bofeng Zhu, Shixiu Liao
OBJECTIVE: To study the genetic polymorphisms and mutations of 20 frequently used autosomal microsatellites among ethnic Hans from Henan. METHODS: Peripheral blood samples of 2604 individuals were collected. DNA was amplified and genotyped using a PowerPlex(TM) 21 system. The frequencies, forensic parameters and mutation rates of the 20 short tandem repeat (STR) loci were analyzed. RESULTS: A total of 323 alleles were found in this population and the allelic frequencies have ranged from 0...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28387876/development-of-a-polymorphic-short-tandem-repeat-locus-multiplex-system-for-efficient-human-identification
#12
R G Rodovalho, E L Rodrigues, G S Santos, L M Cavalcanti, P R Lima, A G Rodovalho, R G Vital, M A D Gigonzac, A D da Cruz
This study aimed to develop a short tandem repeat (STR) multiplex system, made up of 22 highly informative STR loci, for application in forensic genetics. The system comprised 21 polymorphic autosomal loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX, FGA, D2S441, D17S1301, D19S433, D18S853, D20S482, and D14S1434) and the amelogenin gene locus. Strategies were developed to overcome the challenges involved in creating a multiplex system. Based on the literature and available databases, the STR loci were selected with the aim to obtain discriminatory markers, and followed specific criteria for this purpose...
April 5, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28370326/probabilistic-peak-detection-in-ce-lif-for-str-dna-typing
#13
Michael Woldegebriel, Arian van Asten, Ate Kloosterman, Gabriel Vivó-Truyols
In this work we present a novel probabilistic peak detection algorithm based on a Bayesian framework for forensic DNA analysis. The proposed method aims at an exhaustive use of raw electropherogram (epg) data from a laser induced fluorescence multi-capillary electrophoresis (CE-LIF) system. As the raw-data is informative up to a single data point, the conventional threshold-based approaches discard relevant forensic information early in the data analysis pipeline. Our proposed method assigns a posterior probability reflecting the data point's relevance with respect to peak detection criteria...
March 31, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28363008/analysis-of-the-19-y-str-and-16-x-str-loci-system-in-the-han-population-of-shandong-province-china
#14
H M Gao, C Wang, S Y Han, S H Sun, D J Xiao, Y S Wang, C T Li, M X Zhang
The sex-linked short tandem repeats (STR), Y-STR and X-STR, are important for autosomal STRs in forensic paternity testing. We evaluated the forensic parameters of 19 Y-STRs and 16 X-STRs in the Han population of Shandong province, China. A Goldeneye 20Y kit (DYS391, DYS389I, DYS390, DYS389II, DYS348, DYS456, Y-GATA-H4, DYS447, DYS19, DYS392, DYS393, DYS388, DYS439, DYS635, DYS448, DYS460, DYS458, DYS437, DYS385 a/b) was used to analyze the forensic parameters of 534 unrelated males. A Goldeneye17X system (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, DXS6810, amelogenin) was used to analyze 97 unrelated males and 214 females...
March 30, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28362818/vivaxgen-an-open-access-platform-for-comparative-analysis-of-short-tandem-repeat-genotyping-data-in-plasmodium-vivax-populations
#15
Hidayat Trimarsanto, Ernest D Benavente, Rintis Noviyanti, Retno Ayu Setya Utami, Leily Trianty, Zuleima Pava, Sisay Getachew, Jung-Yeon Kim, Youn-Kyoung Goo, Sonam Wangchuck, Yaobao Liu, Qi Gao, Simone Dowd, Qin Cheng, Taane G Clark, Ric N Price, Sarah Auburn
BACKGROUND: The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. RESULTS: The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools...
March 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28362710/detection-of-loss-of-heterozygosity-loh-using-circulating-cell-free-dna-cfdna-by-fluorescence-based-multiplex-pcr-for-identification-of-patients-with-prostate-cancer
#16
S-Maryam Seyedolmohadessin, Mohammad T Akbari, Zahra Nourmohammadi, Abbas Basiri, Gholamreza Pourmand
Several lines of evidence suggest that loss of heterozygosity (LOH) in specific chromosomal regions is a common mechanism for the inactivation of tumor-suppressor genes that are implicated in the pathogenesis of prostate cancer (PCa). Short tandem repeat (STR) sequences are extremely reliable genetic markers for the detection of LOH associated with cancers. Hence, in the current study, we investigated the detection of LOH at 6 STR markers (D8S360, D9S1748, D9S171, D8S137, D6S1631, and THRB) using blood circulating cell-free DNA (cfDNA), which can be used to distinguish PCa from benign prostatic hyperplasia (BPH)...
March 30, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28360231/combination-of-short-read-long-read-and-optical-mapping-assemblies-reveals-large-scale-tandem-repeat-arrays-with-population-genetic-implications
#17
Matthias H Weissensteiner, Andy W C Pang, Ignas Bunikis, Ida Höijer, Olga Vinnere-Petterson, Alexander Suh, Jochen B W Wolf
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow...
March 30, 2017: Genome Research
https://www.readbyqxmd.com/read/28359046/evaluating-130-microhaplotypes-across-a-global-set-of-83-populations
#18
Kenneth K Kidd, William C Speed, Andrew J Pakstis, Daniele S Podini, Robert Lagacé, Joseph Chang, Sharon Wootton, Eva Haigh, Usha Soundararajan
Today the primary DNA markers used in forensics are short tandem repeat (STR) polymorphisms (STRPs), initially selected because they are highly polymorphic. However, the increasingly common need to deal with samples with a mixture of DNA from two or more individuals sometimes is complicated by the inherent stutter involved with PCR amplification, especially in strongly unbalanced mixtures when the minor component coincides with the stutter range of the major component. Also, the STRPs in use provide little evidence of ancestry of a single source sample beyond broad "continental" resolution...
March 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28357668/str-profiling-of-htlv-1-infected-cell-lines
#19
Vittoria Raimondi, Sonia Minuzzo, Vincenzo Ciminale, Donna M D'Agostino
Many investigations of the replication and pathogenesis of human T-cell leukemia virus type 1 (HTLV-1) employ chronically infected cell lines, cell lines stabilized from primary adult T-cell leukemia cells, and noninfected T-cell lines. The validity of data obtained from such studies depends on the unambiguous identification of each cell line, which can be performed by short-tandem-repeat (STR) profiling (DNA fingerprinting). While kit-based profiling represents the standard method for cell line authentication, not all labs have ready access to the required capillary electrophoresis equipment, and the costs of such tests can become substantial, especially if the cell lines are to be tested frequently...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28349239/detecting-past-male-mediated-expansions-using-the-y-chromosome
#20
REVIEW
Chiara Batini, Mark A Jobling
Males and females display biological differences that lead to a higher variance of offspring number in males, and this is frequently exacerbated in human societies by mating practices, and possibly by past socio-cultural circumstances. This implies that the genetic record might contain the imprint of past male-mediated expansions, which can be investigated by analysing the male-specific region of the Y chromosome (MSY). Here, we review studies that have used MSY data to infer such expansions. Sets of short-tandem repeats define haplotypes of very low average frequencies, but in a few cases, high-frequency haplotypes are observed, forming the core of descent clusters...
March 27, 2017: Human Genetics
keyword
keyword
51334
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"