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short tandem repeats

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https://www.readbyqxmd.com/read/28792614/mutation-rates-in-21-autosomal-short-tandem-repeat-loci-in-a-population-from-goi%C3%A3-s-brazil
#1
Thaís Cidália Vieira, Marc Alexandre Duarte Gigonzac, Ricardo Goulart Rodovalho, Luana Morais Cavalcanti, Lysa Bernardes Minasi, Flávia Melo Rodrigues, Aparecido Divino da Cruz
The appearance of new mutations in polymorphic markers plays a central role in a range of genetic applications, including dating phylogenetic events, informing disease studies, and evaluating forensic evidence. The present study estimated the mutation rates of 21 autosomal short tandem repeat (STR) loci in a population from Central Brazil. We studied 15,046 paternity cases from Goiás, Brazil from August 2012 to February 2015. We identified 262 mutations in the 21 loci. The loci that presented more mutations were FGA and D18S51, with a total of 46 and 28 mutations, respectively...
August 9, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28777843/-genetic-and-prenatal-diagnosis-for-a-haemophilia-a-family-with-two-novel-mutations-of-f8-gene
#2
Tao Li, Qiaofang Hou, Hongyan Liu, Hai Xiao, Bo Zhang, Shiling Liu, Yanli Yang, Chaoyang Zhang, Xuebing Ding, Shixiu Liao
OBJECTIVE: To conduct genetic diagnosis for a family affected with hamophilia A. METHODS: Potential mutations of the F8 gene were analyzed with PCR and Sanger sequencing. Carriers of the mutation were identified through linkage analysis using short tandem repeat (STR) markers. Suspected mutations were verified among 100 healthy controls to rule out genetic polymorphism. Prenatal diagnosis was provided based on the above results. RESULTS: Sequencing analysis has identified two mutations, c...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28771684/high-y-chromosomal-differentiation-among-ethnic-groups-of-dir-and-swat-districts-pakistan
#3
Inam Ullah, Jill K Olofsson, Ashot Margaryan, Melissa Ilardo, Habib Ahmad, Martin Sikora, Anders J Hansen, Muhammad Shahid Nadeem, Numan Fazal, Murad Ali, Anders Buchard, Brian E Hemphill, Eske Willerslev, Morten E Allentoft
The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y-chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y-chromosomal short tandem repeats (Y-STRs) and 331 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) were investigated...
August 3, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28755253/as-solid-as-a-rock-comparison-of-ce-and-mps-based-analyses-of-the-petrosal-bone-as-a-source-of-dna-for-forensic-identification-of-challenging-cranial-bones
#4
Galina Kulstein, Thorsten Hadrys, Peter Wiegand
Short tandem repeat (STR) typing from skeletal remains can be a difficult task. Dependent on the environmental conditions of the provenance of the bones, DNA can be degraded and STR typing inhibited. Generally, dense and compact bones are known to preserve DNA better. Several studies already proved that femora and teeth have high DNA typing success rates. Unfortunately, these elements are not present in all cases involving skeletal remains. Processing partial or singular skeletal elements, it is favorable to select bone areas where DNA preservation is comparably higher...
July 28, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28754995/genetic-variation-and-population-structure-of-botswana-populations-as-identified-with-ampflstr-identifiler-short-tandem-repeat-str-loci
#5
Tiroyamodimo Tau, Anthony Wally, Thokozile Patricia Fanie, Goitseone Lorato Ngono, Sununguko Wata Mpoloka, Sean Davison, María Eugenia D'Amato
Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10(-19). CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0...
July 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28750064/modified-human-glucagon-like-peptide-1-glp-1-produced-in-e-coli-has-a-long-acting-therapeutic-effect-in-type-2-diabetic-mice
#6
Fangfang Xu, Kevin Yueju Wang, Nan Wang, Gangqiang Li, Dehu Liu
Glucagon-like peptide 1 (GLP-1) is a very potent insulinotropic hormone secreted into the blood stream after eating. Thus, it has potential to be used in therapeutic treatment of diabetes. The half-life of GLP-1, however, is very short due to its rapid cleavage by dipeptidyl peptidase IV (DPP-IV). This presents a great challenge if it is to be used as a therapeutic drug. GLP-1, like many other small peptides, is commonly produced through chemical synthesis, but is limited by cost and product quantity. In order to overcome these problems, a sequence encoding a six codon-optimized tandem repeats of modified GLP-1 was constructed and expressed in the E...
2017: PloS One
https://www.readbyqxmd.com/read/28748403/evaluation-of-innotyper%C3%A2-21-in-a-sample-of-rio-de-janeiro-population-as-an-alternative-forensic-panel
#7
R S Moura-Neto, I C T Mello, R Silva, A P C Maette, C G Bottino, A Woerner, J King, F Wendt, B Budowle
The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of short tandem repeat (STR) loci in typing forensic biological evidence. This study investigated the efficiency of the InnoTyper® 21 Innul markers in an urban admixed population sample in Rio de Janeiro (n = 40) and one highly compromised sample collected as evidence by the Rio de Janeiro police. No significant departures from Hardy-Weinberg equilibrium were detected after the Bonferroni correction (α' ≈ 0...
July 26, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28739746/association-of-intron-microsatellite-instability-and-exon-mutational-profile-of-tp53-in-human-gastric-cancers
#8
Xueyun Huo, Xiaoqin Xiao, Shuangyue Zhang, Deshan Zhou, Zhenwen Chen
BACKGROUND/AIM: Microsatellite instability (MSI) is a hallmark of genomic instability. In gastric cancer (GC), MSI phenotype is an important molecular subgroup that is often closely correlated with elevated mutation rates on the whole genome level. However, on a single gene level, it is still unknown whether the MSI status of a gene is correlated with the mutational profile of the gene itself. MATERIALS AND METHODS: We analyzed intron MSI status and exon mutational profile of TP53 through short tandem repeat (STR) scanning and direct sequencing respectively in gastric cancers and their matched normal tissues...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28730502/establishment-of-11-linked-x-str-loci-within-1-1-mb-to-assist-with-kinship-testing
#9
James Chun-I Lee, Chun-Yen Lin, Li-Chin Tsai, Yu-Jen Yu, Keng-Hsien Liao, Adrian Linacre, Hsing-Mei Hsieh
This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci...
July 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28724489/population-genetic-structure-of-the-cayo-santiago-colony-of-rhesus-macaques-macaca-mulatta
#10
Sreetharan Kanthaswamy, Robert F Oldt, Jillian Ng, Angelina V Ruiz-Lambides, Elizabeth Maldonado, Melween I Martínez, Carlos A Sariol
The rhesus macaque population at Cayo Santiago increases annually and is in urgent need of control. In-depth assessments of the colony's population genetic and pedigree structures provide a starting point for improving the colony's long-term management program. We evaluated the degree of genetic variation and coefficients of inbreeding and kinship of the Cayo Santiago colony by using pedigree and short tandem repeat (STR) data from 4738 rhesus macaques, which represent 7 extant social groups and a group of migrant males...
July 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28724409/hybrid-assembly-with-long-and-short-reads-improves-discovery-of-gene-family-expansions
#11
Jason R Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P Walenz, Junqi Liu, Robert M Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G Maron, Susan R McCouch, W Richard McCombie, Michael C Schatz, Peter Tiffin, Nevin D Young, Kevin A T Silverstein
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28723299/support-for-disease-only-genotypes-and-excess-of-homozygosity-at-the-cyth4-primate-specific-gttt-repeat-in-schizophrenia
#12
Ehteram Khademi, Elham Alehabib, Ehsan Esmaili Shandiz, Azadeh Ahmadifard, Monavvar Andarva, Javad Jamshidi, Simin Rahimi-Aliabadi, Ramin Pouriran, Farhad Ramezani Nejad, Nader Mansoori, Neda Shahmohammadibeni, Shaghyegh Taghavi, Parasto Shokraeian, Haleh Akhavan-Niaki, Coro Paisán-Ruiz, Hossein Darvish, Mina Ohadi
OBJECTIVE: The role of short tandem repeats (STRs) in the control of gene expression among species is being increasingly understood following the identification of several instances in which certain STRs occur identically, or expand differentially, in primates versus nonprimates. These STRs may regulate genes that participate in characteristics that have diverged primates from other species (e.g., brain higher order functions). The CYTH4 gene contains the longest tetranucleotide STR in its core promoter, at 7-repeats, and links to the evolution of human and nonhuman primates...
July 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28721719/imprinted-nanovelcro-microchips-for-isolation-and-characterization-of-circulating-fetal-trophoblasts-toward-noninvasive-prenatal-diagnostics
#13
Shuang Hou, Jie-Fu Chen, Min Song, Yazhen Zhu, Yu Jen Jan, Szu Hao Chen, Tzu-Hua Weng, Dean-An Ling, Shang-Fu Chen, Tracy Ro, An-Jou Liang, Tom Lee, Helen Jin, Man Li, Lian Liu, Yu-Sheng Hsiao, Peilin Chen, Hsiao-Hua Yu, Ming-Song Tsai, Margareta D Pisarska, Angela Chen, Li-Ching Chen, Hsian-Rong Tseng
Circulating fetal nucleated cells (CFNCs) in maternal blood offer an ideal source of fetal genomic DNA for noninvasive prenatal diagnostics (NIPD). We developed a class of nanoVelcro microchips to effectively enrich a subcategory of CFNCs, i.e., circulating trophoblasts (cTBs) from maternal blood, which can then be isolated with single-cell resolution by a laser capture microdissection (LCM) technique for downstream genetic testing. We first established a nanoimprinting fabrication process to prepare the LCM-compatible nanoVelcro substrates...
July 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28717961/determining-the-optimal-forensic-dna-analysis-procedure-following-investigation-of-sample-quality
#14
Ronny Hedell, Johannes Hedman, Petter Mostad
Crime scene traces of various types are routinely sent to forensic laboratories for analysis, generally with the aim of addressing questions about the source of the trace. The laboratory may choose to analyse the samples in different ways depending on the type and quality of the sample, the importance of the case and the cost and performance of the available analysis methods. Theoretically well-founded guidelines for the choice of analysis method are, however, lacking in most situations. In this paper, it is shown how such guidelines can be created using Bayesian decision theory...
July 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28717960/population-genetic-analysis-of-the-globalfiler-str-loci-in-3032-individuals-from-the-altay-han-population-of-xinjiang-in-northwest-china
#15
XueBo Li, Liangliang Li, Qingshan Wang, Jianzhong Zhang, Wendong Ge, Rufeng Bai, Xiaojun Yu, Meisen Shi
The genetic polymorphisms of 21 autosomal short tandem repeat (STR) loci included in the GlobalFiler™ PCR Amplification Kit were evaluated in 3032 unrelated individuals Altay Han of Xinjiang, northwest China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. SE33 showed the greatest power of discrimination in Altay Han population, whereas TPOX showed the lowest. The combined discrimination power and probability of excluding paternity of the 21 autosomal STR loci were 0...
July 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28712775/simple-sequence-repeats-showing-length-preference-have-regulatory-functions-in-humans
#16
Jaya Krishnan, Fathima Athar, Tirupaati Swaroopa Rani, Rakesh Kumar Mishra
Simple sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1-6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about their functional relevance. Analysis of genomes across various taxa show that despite the instability associated with longer stretches of repeats, few SSRs with specific longer repeat lengths are enriched in the genomes indicating a positive selection. This conserved feature of length dependent enrichment hints at not only sequence but also length dependent functionality for SSRs...
July 13, 2017: Gene
https://www.readbyqxmd.com/read/28706611/a-novel-variant-in-the-pah-gene-causing-phenylketonuria-in-an-iranian-pedigree
#17
Elaheh Alavinejad, Seyede Zahra Sajedi, Masoumeh Razipour, Mona Entezam, Neda Mohajer, Aria Setoodeh, Saeed Talebi, Mohammad Keramatipour
BACKGROUND: Phenylalanine hydroxylase (PAH) gene is the well-known causative gene for classic Phenylketonuria (PKU) (OMIM#261600) disease, with more than 500 reported mutations. Through this study, a novel mutation in the PAH gene in an Iranian pedigree with phenylketonuria was introduced. METHODS: A consanguineous family with a 10-year old affected girl was referred for genetic analysis. Mutation screening of all exons and exon-intron boundaries was performed by Sanger sequencing, and mini haplotype analysis was carried out by genotyping of Short Tandem Repeat (STR) and Variable Number Tandem Repeat (VNTR) alleles...
July 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28705464/diversity-of-pneumocystis-jirovecii-across-europe-a-multicentre-observational-study
#18
Alexandre Alanio, Maud Gits-Muselli, Nicolas Guigue, Marie Desnos-Ollivier, Enrique J Calderon, David Di Cave, Damien Dupont, Axel Hamprecht, Philippe M Hauser, Jannik Helweg-Larsen, Marta Kicia, Katrien Lagrou, Martina Lengerova, Olga Matos, Willem J G Melchers, Florent Morio, Gilles Nevez, Anne Totet, Lewis P White, Stéphane Bretagne
Pneumocystis jirovecii is an airborne human-specific ascomycetous fungus responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, affecting >500,000 patients per year (www.gaffi.org). The understanding of its epidemiology is limited by the lack of standardised culture. Recent genotyping data suggests a limited genetic diversity of P. jirovecii. The objective of the study was to assess the diversity of P. jirovecii across European hospitals and analyse P. jirovecii diversity in respect to clinical data obtained from the patients...
August 2017: EBioMedicine
https://www.readbyqxmd.com/read/28690679/trichoderma-reesei-complete-genome-sequence-repeat-induced-point-mutation-and-partitioning-of-cazyme-gene-clusters
#19
Wan-Chen Li, Chien-Hao Huang, Chia-Ling Chen, Yu-Chien Chuang, Shu-Yun Tung, Ting-Fang Wang
BACKGROUND: Trichoderma reesei (Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis, and plant-fungal interactions. The genomes of QM6a and its high enzyme-producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute. While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture, and genetic modification or engineering...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28679522/next-generation-sequence-analysis-reveals-methicillin-resistance-transfer-to-a-methicillin-susceptible-staphylococcus-aureus-mssa-strain-that-subsequently-caused-a-methicillin-resistant-staphylococcus-aureus-mrsa-outbreak-a-descriptive-study
#20
Veronica Weterings, Thijs Bosch, Sandra Witteveen, Fabian Landman, Leo Schouls, Jan Kluytmans
Resistance to methicillin in Staphylococcus aureus is primarily caused by the mecA gene, which is carried on a mobile genetic element: the staphylococcal cassette chromosome mec (SCCmec). Horizontal transfer of this element is supposed to play an important factor in the emergence of new clones of methicillin-resistant Staphylococcus aureus (MRSA), but has been rarely observed in real-time.In 2012, an outbreak occurred involving a healthcare worker (HCW) and three patients all carrying a fusidic-acid resistant MRSA strain...
July 5, 2017: Journal of Clinical Microbiology
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