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https://www.readbyqxmd.com/read/29157912/new-paradigm-in-ankyrin-repeats-beyond-protein-protein-interaction-module
#1
REVIEW
Zeyaul Islam, Raghavendra Sashi Krishna Nagampalli, Munazza Tamkeen Fatima, Ghulam Md Ashraf
Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins...
November 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29154002/forensic-evaluation-of-str-typing-reliability-in-lung-cancer
#2
Peng Zhang, Ying Zhu, Yongguo Li, Shisheng Zhu, Ruoxiang Ma, Minzhu Zhao, Jianbo Li
Short tandem repeats (STR) analysis is the gold standard method in the forensics field for personal identification and paternity testing. In cancerous tissues, STR markers are gaining attention, with some studies showing increased instability. Lung cancer, which is one of the most commonmalignancies, has become the most lethal among all cancers. In certain situations, lung cancer tissues may be the only resource available for forensic analysis. Therefore, evaluating the reliability of STR markers in lung cancer tissues is required to avoid false exclusions...
November 11, 2017: Legal Medicine
https://www.readbyqxmd.com/read/29154001/tri-allelic-patterns-of-strs-and-partially-homologous-non-sister-chromatid-crossover-observed-in-a-parentage-test
#3
Huiyong Jiao, He Ren, Yaran Yang, Bin Ni, Haiyan Zhou, Wei Chen, Yunwang Cao, Chuguang Chen, Yanmei Huang, Jiangwei Yan
A maternity testing case is reported, in which the child showed tri-allelic patterns in two short tandem repeat (STR) loci. The genotypes of Penta D of the mother and the child were 9,13 and 9,10,13, respectively. Those of D21S11 were 32.2,35 and 29,35, respectively, but intensity ratio of alleles 29 and 35 of the child was 1:2. These results suggested the copy number variations (CNVs) or trisomy of chromosome 21. By further examination using STR-based chromosome aneuploidy detection kit, three alleles were detected in D21S1411, LFG21 and Penta D, and 2 alleles with intensity ratio of 1:2 were observed in D21S2502, D21S1435, D21S11 and D21S1246...
October 28, 2017: Legal Medicine
https://www.readbyqxmd.com/read/29151122/genetic-polymorphisms-in-18-autosomal-str-loci-in-the-tibetan-population-living-in-tibet-chamdo-southwest-china
#4
Zhenghui Li, Jian Zhang, Hantao Zhang, Ziqing Lin, Jian Ye
Short tandem repeats (STRs) play a vitally important role in forensics. Population data is needed to improve the field. There is currently no large population data-based data set in Chamdo Tibetan. In our study, the allele frequencies and forensic statistical parameters of 18 autosomal STR loci (D5S818, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, VWA, D8S1179, D16S539, PentaE, TPOX, TH01, D19S433, D18S51, FGA, D6S1043, D13S317, and D12S391) included in the DNATyper™19 kit were investigated in 2249 healthy, unrelated Tibetan subjects living in Tibet Chamdo, Southwest China...
November 18, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29150717/genetic-diversity-and-phylogenetic-study-of-the-chinese-gelao-ethnic-minority-via-23-y-str-loci
#5
Pengyu Chen, Yanyan Han, Guanglin He, Haibo Luo, Tianzhen Gao, Feng Song, Dengfu Wan, Jian Yu, Yiping Hou
Haplotype diversity for 23 Y chromosomal short tandem repeat (Y-STR) loci included in the PowerPlex(®) Y23 System was analyzed in the Chinese Gelao minority group of 234 unrelated males living in Daozhen Gelao-Miao Autonomous County in Guizhou Province, southwest China. A total of 216 different haplotypes were detected, of which 199 haplotypes were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9996 and 0.9231, respectively. The gene diversity (GD) ranged from 0.4159 (DYS438) to 0...
November 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29150183/genetic-analysis-of-29-y-str-loci-in-the-chinese-han-population-from-shanghai
#6
Yuxiang Zhou, Chengchen Shao, Liming Li, Yaqi Zhang, Baonian Liu, Qinrui Yang, Qiqun Tang, Shilin Li, Jianhui Xie
The analysis of Y chromosomal short tandem repeats (Y-STRs) provides important information that can be used to forensic investigation and population studies. In this study, typing of 29 Y-STRs included in the PowerPlex(®) Y23 system (PPY23) and Yfiler™ Plus system (Yfiler plus) was performed on 843 unrelated male samples from Han population in Shanghai. Besides null, duplicate, and intermediate alleles reported in previous studies, an allele of 10 at DYS643 with a 2-base deletion in the flanking region was initially observed...
November 11, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29149210/development-and-validation-of-open-source-software-for-dna-mixture-interpretation-based-on-a-quantitative-continuous-model
#7
Sho Manabe, Chie Morimoto, Yuya Hamano, Shuntaro Fujimoto, Keiji Tamaki
In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software...
2017: PloS One
https://www.readbyqxmd.com/read/29149052/flanking-variation-influences-rates-of-stutter-in-simple-repeats
#8
August E Woerner, Jonathan L King, Bruce Budowle
It has been posited that the longest uninterrupted stretch (LUS) of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL). While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29144536/isolation-and-whole-genome-sequencing-of-fetal-cells-from-maternal-blood-towards-the-ultimate-non-invasive-prenatal-testing
#9
Fang Chen, Ping Liu, Ying Gu, Zhu Zhu, Amulya Nanisetti, Zhangzhang Lan, Zhiwei Huang, Sophie Jia Liu, Xiongbin Kang, Yuqing Deng, Liqiong Luo, Dan Jiang, Yong Qiu, Jianchang Pan, Jun Xia, Ken Xiong, Chao Liu, Lin Xie, Qianyu Shi, Jing Li, Xiuqing Zhang, Wei Wang, Snezana Drmanac, Hui Jiang, Radoje Drmanac, Xun Xu
OBJECTIVE: To develop a methodology of isolating fetal cells from maternal blood and use deep sequencing demonstrating the promise for more complete and accurate genetic screening compared to other non-invasive prenatal testing (NIPT). METHODS: Here in this study, we developed a double negative selection (DNS) procedure to unbiasedly enrich fetal cells. After validated by short tandem repeat (STR), the isolated CFCs were subjected to deep whole genome sequencing analysis (WGS)...
November 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29143604/fine-organization-of-genomic-regions-tagged-to-the-5s-rdna-locus-of-the-bread-wheat-5b-chromosome
#10
Ekaterina M Sergeeva, Andrey B Shcherban, Irina G Adonina, Michail A Nesterov, Alexey V Beletsky, Andrey L Rakitin, Andrey V Mardanov, Nikolai V Ravin, Elena A Salina
BACKGROUND: The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29141705/phenotypic-and-molecular-genetic-characteristics-of-yersinia-pestis-at-an-emerging-natural-plague-focus-junggar-basin-china
#11
Yujiang Zhang, Tao Luo, Chao Yang, Xihong Yue, Rong Guo, Xinhui Wang, Mingde Buren, Yuqin Song, Ruifu Yang, Hanli Cao, Yujun Cui, Xiang Dai
The 15th natural plague focus in China, the Junggar Basin plague focus, is located near an important communication route connecting China and Central Asia and was discovered after 2005. To characterize the phenotypic and genetic diversity of the Yersinia pestis population in this newly established focus, we collected 25 Y. pestis strains from six counties across Junggar Basin in 2005-2006, and determined their biochemical features and genotypes based on multiple-locus variable number of tandem repeats analysis and clustered regularly interspaced short palindromic repeats analysis...
October 23, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29134366/genetic-characteristics-of-19-strs-in-chinese-uzbek-ethnic-and-its-phylogenetic-relationships-with-other-24-populations
#12
Xiaoye Jin, Wei Cui, Yuanyuan Wei, Yuling Mu, Qian Dong, Chong Chen, Yuxin Guo, Tingting Kong, Bofeng Zhu, Jiangang Chen
Allelic frequencies and genetic polymorphisms of 19 short tandem repeats loci were investigated so as to provide more genetic data for forensic applications in Chinese Uzbek group; besides, we evaluated phylogenetic relationships of Uzbek group with other populations. All loci were observed to conform to Hardy-Weinberg equilibrium after Bonferroni's correction. Two hundred and nine alleles were identified in 212 unrelated healthy Uzbek individuals and their allelic frequencies ranged from 0.0024 to 0.5259. The cumulative discrimination power and cumulative probability of exclusion were 0...
November 14, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29121165/perf-an-exhaustive-algorithm-for-ultra-fast-and-efficient-identification-of-microsatellites-from-large-dna-sequences
#13
Akshay Kumar Avvaru, Divya Tej Sowpati, Rakesh Kumar Mishra
Motivation: Microsatellites or Simple Sequence Repeats (SSRs) are short tandem repeats of DNA motifs present in all genomes. They have long been used for a variety of purposes in the areas of population genetics, genotyping, marker-assisted selection, and forensics. Numerous studies have highlighted their functional roles in genome organization and gene regulation. Though several tools are currently available to identify SSRs from genomic sequences, they have significant limitations. Results: We present a novel algorithm called PERF for extremely fast and comprehensive identification of microsatellites from DNA sequences of any size...
November 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29117225/genomic-comparison-between-staphylococcus-aureus-gn-strains-clinically-isolated-from-a-familial-infection-case-is1272-transposition-through-a-novel-inverted-repeat-replacing-mechanism
#14
Tsai-Wen Wan, Wataru Higuchi, Olga E Khokhlova, Wei-Chun Hung, Yasuhisa Iwao, Masataka Wakayama, Noriyoshi Inomata, Tomomi Takano, Yu-Tzu Lin, Olga V Peryanova, Kenji K Kojima, Alla B Salmina, Lee-Jene Teng, Tatsuo Yamamoto
A bacterial insertion sequence (IS) is a mobile DNA sequence carrying only the transposase gene (tnp) that acts as a mutator to disrupt genes, alter gene expressions, and cause genomic rearrangements. "Canonical" ISs have historically been characterized by their terminal inverted repeats (IRs), which may form a stem-loop structure, and duplications of a short (non-IR) target sequence at both ends, called target site duplications (TSDs). The IS distributions and virulence potentials of Staphylococcus aureus genomes in familial infection cases are unclear...
2017: PloS One
https://www.readbyqxmd.com/read/29100084/profiling-of-short-tandem-repeat-disease-alleles-in-12-632-human-whole-genomes
#15
Haibao Tang, Ewen F Kirkness, Christoph Lippert, William H Biggs, Martin Fabani, Ernesto Guzman, Smriti Ramakrishnan, Victor Lavrenko, Boyko Kakaradov, Claire Hou, Barry Hicks, David Heckerman, Franz J Och, C Thomas Caskey, J Craig Venter, Amalio Telenti
Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci...
November 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29099837/using-long-ssdna-polynucleotides-to-amplify-strs-loci-in-degraded-dna-samples
#16
Martín E Mautner, Agustín Pérez Santángelo, Rodrigo M Corti Bielsa, Andrea Sala, Santiago Ginart, Daniel Corach
Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers...
2017: PloS One
https://www.readbyqxmd.com/read/29091906/a-large-scale-dataset-of-single-and-mixed-source-short-tandem-repeat-profiles-to-inform-human-identification-strategies-provedit
#17
Lauren E Alfonse, Amanda D Garrett, Desmond S Lun, Ken R Duffy, Catherine M Grgicak
DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA...
October 24, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29082507/the-contributions-of-admixture-and-genetic-drift-to-diversity-among-post-contact-populations-in-the-americas
#18
Anthony J Koehl, Jeffrey C Long
OBJECTIVE: We present a model that partitions Nei's minimum genetic distance between admixed populations into components of admixture and genetic drift. We applied this model to 17 admixed populations in the Americas to examine how admixture and drift have contributed to the patterns of genetic diversity. MATERIALS AND METHODS: We analyzed 618 short tandem repeat loci in 949 individuals from 49 population samples. Thirty-two samples serve as proxies for continental ancestors...
October 30, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29075246/crispr-a-useful-genetic-feature-to-follow-vaginal-carriage-of-group-b-streptococcus
#19
Clémence Beauruelle, Adeline Pastuszka, Philippe Horvath, Franck Perrotin, Laurent Mereghetti, Philippe Lanotte
Clustered regularly interspaced short palindromic repeats (CRISPR) and Cas (CRISPR-associated proteins) play a critical role in adaptive immunity against mobile genetic elements, especially phages, through their ability to acquire novel spacer sequences. Polarized spacer acquisition results in spacer polymorphism and temporal organization of CRISPR loci, making them attractive epidemiological markers. Group B Streptococcus (GBS), a genital commensal for 10 to 30% of healthy women and a major neonatal pathogen, possesses a ubiquitous and functional CRISPR1 locus...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29065388/targeted-sequencing-of-clade-specific-markers-from-skin-microbiomes-for-forensic-human-identification
#20
Sarah E Schmedes, August E Woerner, Nicole M M Novroski, Frank R Wendt, Jonathan L King, Kathryn M Stephens, Bruce Budowle
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals...
October 18, 2017: Forensic Science International. Genetics
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