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short tandem repeats

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https://www.readbyqxmd.com/read/28230980/chitosan-modified-filter-paper-for-nucleic-acid-extraction-and-in-situ-pcr-on-a-thermoplastic-microchip
#1
Wupeng Gan, Yin Gu, Junping Han, Caixia Li, Jing Sun, Peng Liu
Plastic microfluidic devices with embedded chitosan-modified Fusion 5 filter paper (unmodified one purchased from GE Healthcare) have been successfully developed for DNA extraction and concentration, utilizing two different mechanisms for DNA capture: the physical entanglement of long-chain DNA molecules with the fiber matrix of the filter paper and the electrostatic adsorption of DNA to the chitosan-modified filter fibers. This new method not only provided a high DNA extraction efficiency at a pH of 5 by synergistically combining these two capture mechanisms together, but also resisted the elution of DNA from filters at a pH >8 due to the entanglement of DNA with fibers...
February 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28214997/the-human-rit2-core-promoter-short-tandem-repeat-predominant-allele-is-species-specific-in-length-a-selective-advantage-for-human-evolution
#2
Babak Emamalizadeh, Abofazl Movafagh, Hossein Darvish, Somayeh Kazeminasab, Monavvar Andarva, Pegah Namdar-Aligoodarzi, Mina Ohadi
Evolutionary analyses of the critical core promoter interval support a selective advantage for expanding the length of certain short tandem repeats (STRs) in humans. We recently reported genome-wide data on human core promoter STRs that are "exceptionally long" (≥6-repeats). Near the top of the list, the neuron-specific gene, RIT2, contains one of the longest GA-STRs at 11-repeats. In the present study, we analyzed the evolutionary implications of this STR across species. We also studied this STR in a sample of 2,143 Iranian human subjects that encompassed a number of neuropsychiatric disorders and controls...
February 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28213869/persistence-of-touch-dna-on-burglary-related-tools
#3
Céline M Pfeifer, Peter Wiegand
Experts are increasingly concerned by issues regarding the activity level of DNA stains. A case from our burglary-related casework pointed out the need for experiments regarding the persistence of DNA when more than one person touched a tool handle. We performed short tandem repeat (STR) analyses for three groups of tools: (1) personal and mock owned tools; (2) tools, which were first "owned" by a first user and then handled in a burglary action by a second user; and (3) tools, which were first owned by a first user and then handled in a moderate action...
February 6, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28213161/a-genomic-view-of-short-tandem-repeats
#4
REVIEW
Melissa Gymrek
Short tandem repeats (STRs) are some of the fastest mutating loci in the genome. Tools for accurately profiling STRs from high-throughput sequencing data have enabled genome-wide interrogation of more than a million STRs across hundreds of individuals. These catalogs have revealed that STRs are highly multiallelic and may contribute more de novo mutations than any other variant class. Recent studies have leveraged these catalogs to show that STRs play a widespread role in regulating gene expression and other molecular phenotypes...
February 14, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28211539/genetic-analysis-of-19-x-chromosome-str-loci-for-forensic-purposes-in-four-chinese-ethnic-groups
#5
Xingyi Yang, Xiaofang Zhang, Junyong Zhu, Linli Chen, Changhui Liu, Xingling Feng, Ling Chen, Huijun Wang, Chao Liu
A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210813/a-comprehensive-y-str-portrait-of-yousafzai-s-population
#6
Sadia Tabassum, Muhammad Ilyas, Inam Ullah, Muhammad Israr, Habib Ahmad
In the current study, 17 Y-Chromosomal short tandem repeats (Y-STRs) included in theAmpFlSTR Y-Filer amplification kit (Applied Biosystems, Foster City, USA) were investigated in 146 unrelated Yousafzai males residing in the Khyber Pakhtunkhwa Province of Pakistan. A total of 94 (89.52%) unique haplotypes were observed. Discrimination capacity was 71.92%. Haplotype diversity ranged from 0.354 (DYS456) to 0.663 (DYS458). Both Rst pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Yousafzais is significantly different from neighbouring populations...
February 16, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28193505/statistical-modelling-of-ion-pgm-hid-str-10-plex-mps-data
#7
Søren B Vilsen, Torben Tvedebrink, Helle Smidt Mogensen, Niels Morling
We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences...
February 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28192379/compensatory-saccades-are-associated-with-physical-performance-in-older-adults-data-from-the-baltimore-longitudinal-study-of-aging
#8
Yanjun Xie, Eric R Anson, Eleanor M Simonsick, Stephanie A Studenski, Yuri Agrawal
OBJECTIVE: To determine whether compensatory saccade metrics observed in the video head impulse test, specifically saccade amplitude and latency, predict physical performance. STUDY DESIGN: Cross-sectional analysis of the Baltimore Longitudinal Study of Aging, a prospective cohort study. SETTING: National Institute on Aging Intramural Research Program Clinical Research Unit in Baltimore, Maryland. PATIENTS: Community-dwelling older adults...
March 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28192074/practical-informativeness-of-short-tandem-repeat-loci-for-chimerism-analysis-in-hematopoietic-stem-cell-transplantation
#9
Eunhee Han, Myungshin Kim, Yonggoo Kim, Kyungja Han, Jihyang Lim, Dain Kang, Gun Dong Lee, Jung Rok Kim, Jae-Wook Lee, Nack-Gyun Chung, Bin Cho, Ki-Seong Eom, Yoo-Jin Kim, Hee-Je Kim, Seok Lee, Seok-Goo Cho, Chang-Ki Min, Dong-Wook Kim, JongWook Lee, Woo-Sung Min
OBJECTIVE: Short tandem repeat (STR) loci are most frequently used for chimerism analysis after hematopoietic stem cell transplantation (HSCT). The aim of this study was to evaluate the practical informativeness of STR chimerism by integrating theoretical and analytical points. METHODS: Theoretical and practical informativess of 16 STR loci were evaluated from 1249 pairs of recipients and donors who were prepared for HSCT. RESULTS: Theoretical informativeness was influenced by genetic diversity including allele frequency and heterozygosity, and was higher in the unrelated HSCT group (90...
February 10, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28186609/-analysis-of-genetic-polymorphisms-of-15-str-loci-among-ethnic-hans-from-xiamen
#10
Lili Wu, Peng Ran, Xiujuan Zheng, Juanjuan Zhou, Bin Pei, Xiuyu Song
OBJECTIVE: To assess the value of 15 short tandem repeat (STR) loci selected by an AmpFLSTR Identifiler(TM) system for personal identification and paternity testing among ethnic Hans from Xiamen, Fujian. METHODS: For 400 unrelated individuals, allelic frequencies for the 15 STR loci from the AmpFLSTR Identifiler(TM) kit were determined. Population genetics parameters for forensic usage were calculated. RESULTS: No deviation of the observed allele frequency from Hardy-Weinberg equilibrium expectations was found by Chi-square test (P>0...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28172841/systematic-profiling-of-short-tandem-repeats-in-the-cattle-genome
#11
Lingyang Xu, Ryan J Haasl, Jiajie Sun, Yang Zhou, Derek M Bickhart, Junya Li, Jiuzhou Song, Tad S Sonstegard, Curtis P Van Tassell, Harris A Lewin, George E Liu
No abstract text is available yet for this article.
January 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28171796/increased-recovery-of-touch-dna-evidence-using-fta-paper-compared-to-conventional-collection-methods
#12
Irina A Kirgiz, Cassandra Calloway
Tape lifting and FTA paper scraping methods were directly compared to traditional double swabbing for collecting touch DNA from car steering wheels (n = 70 cars). Touch DNA was collected from the left or right side of each steering wheel (randomized) using two sterile cotton swabs, while the other side was sampled using water-soluble tape or FTA paper cards. DNA was extracted and quantified in duplicate using qPCR. Quantifiable amounts of DNA were detected for 100% of the samples (n = 140) collected independent of the method...
January 31, 2017: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/28171784/developmental-validation-of-the-miseq-fgx-forensic-genomics-system-for-targeted-next-generation-sequencing-in-forensic-dna-casework-and-database-laboratories
#13
Anne C Jäger, Michelle L Alvarez, Carey P Davis, Ernesto Guzmán, Yonmee Han, Lisa Way, Paulina Walichiewicz, David Silva, Nguyen Pham, Glorianna Caves, Jocelyne Bruand, Felix Schlesinger, Stephanie J K Pond, Joe Varlaro, Kathryn M Stephens, Cydne L Holt
Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction...
January 27, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28169275/crispr-cas9-targeted-fragmentation-and-selective-sequencing-enable-massively-parallel-microsatellite-analysis
#14
GiWon Shin, Susan M Grimes, HoJoon Lee, Billy T Lau, Li C Xia, Hanlee P Ji
Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, typically in the tens. Here, we demonstrate STR-Seq, a next-generation sequencing technology that analyses over 2,000 STRs in parallel, and provides the accurate genotyping of microsatellites. STR-Seq employs in vitro CRISPR-Cas9-targeted fragmentation to produce specific DNA molecules covering the complete microsatellite sequence...
February 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28168818/biochemical-analysis-of-intraplacental-choriocarcinoma-and-fetomaternal-transfusion
#15
Tatsuya Ishiguro, Kazuaki Suda, Takayuki Enomoto
Intraplacental choriocarcinoma is one of the rarest forms of gestational tumors and is believed to be one of the causes of fetomaternal transfusion (FMT). A 35-year-old woman, gravida 2, para 2, with a history of two vaginal deliveries, was incidentally diagnosed as having stage I gestational intraplacental choriocarcinoma with a FIGO/World Health Organization 2000 risk score of 2 after term delivery. This disease caused neonatal anemia but did not metastasize to either the mother or infant. Short tandem repeat analysis with laser microdissection revealed that the tumor had originated from the current pregnancy...
February 6, 2017: Journal of Obstetrics and Gynaecology Research
https://www.readbyqxmd.com/read/28164604/linkage-analysis-based-on-four-microsatellite-markers-to-screen-for-unknown-mutation-in-families-with-wilson-disease
#16
Farzane Arianfar, Majid Fardaei
BACKGROUND: Wilson disease (WD) is a rare autosomal recessive disorder of copper metabolism due to mutations in ATP7B gene on the chromosome 13. Linkage analysis using microsatellite markers is a powerful screening technique to identify mutant chromosomes especially in affected families with unknown mutations. Previous studies in southern Iran have failed to identify mutations in the ATP7B in some clinically diagnosed cases. Hence, the present study was undertaken to provide a screening method for these WD affected families...
August 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28161998/paternal-genetic-structure-in-contemporary-mennonite-communities-from-the-american-midwest
#17
Kristine G Beaty, M J Mosher, Michael H Crawford, Phillip Melton
Over the last 35 years, researchers from the Laboratory of Biological Anthropology at the University of Kansas have been working with Mennonite communities to better understand evolutionary patterns of fission-fusion in relationship to their genetic history and population structure. In this study, short tandem repeat (STR) markers from the nonrecombining region of the Y chromosome (NRY) provided increased resolution of the molecular population structure for these groups. NRY is known to be informative for determining paternal genetic ancestral patterns in recently derived human populations...
April 2016: Human Biology
https://www.readbyqxmd.com/read/28158988/microsatellite-polymorphisms-associated-with-human-behavioural-and-psychological-phenotypes-including-a-gene-environment-interaction
#18
Andrew T M Bagshaw, L John Horwood, David M Fergusson, Neil J Gemmell, Martin A Kennedy
BACKGROUND: The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. METHODS: We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance...
February 3, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28147232/use-of-ubiquitous-highly-heterozygous-copy-number-variants-and-digital-droplet-pcr-to-monitor-chimerism-after-allogeneic-haematopoietic-stem-cell-transplantation
#19
John B Whitlam, Ling Ling, Michael Swain, Tom Harrington, Oksana Mirochnik, Ian Brooks, Sara Cronin, Jackie Challis, Vida Petrovic, Damien L Bruno, Francoise Mechinaud, Rachel Conyers, Howard Slater
Chimerism analysis has an important role in the management of allogeneic haematopoietic stem cell transplantation. It informs response to disease relapse, graft rejection and graft-versus-host disease. We have developed a method for chimerism analysis using ubiquitous copy number variation (CNV), which has the benefit of a "negative background" against which multiple independent informative markers are absolutely quantified using digital droplet PCR. A panel of up to 38 CNV markers with homozygous deletion frequencies of approximately 0...
January 29, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28146572/a-melanoma-lymph-node-metastasis-with-a-donor-patient-hybrid-genome-following-bone-marrow-transplantation-a-second-case-of-leucocyte-tumor-cell-hybridization-in-cancer-metastasis
#20
Greggory S LaBerge, Eric Duvall, Zachary Grasmick, Kay Haedicke, John Pawelek
BACKGROUND: Metastatic disease is the principal cause of mortality in cancer, yet the underlying mechanisms are not fully understood. Macrophage-cancer cell fusion as a cause of metastasis was proposed more than a century ago by German pathologist Prof. Otto Aichel. Since then this theory has been confirmed in numerous animal studies and recently in a patient with metastatic melanoma. METHODS: Here we analyzed tumor DNA from a 51-year-old man who, 8 years following an allogeneic BMT from his brother for treatment of chronic myelogenous leukemia (CML), developed a nodular malignant melanoma on the upper back with spread to an axillary sentinal lymph node...
2017: PloS One
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