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https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#1
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT...
June 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28636673/evaluation-of-molecular-diagnostic-approaches-for-the-detection-of-braf-p-v600e-mutations-in-papillary-thyroid-cancer-clinical-implications
#2
Artur Kowalik, Aldona Kowalska, Agnieszka Walczyk, Renata Chodurska, Janusz Kopczyński, Magdalena Chrapek, Elżbieta Wypiórkiewicz, Małgorzata Chłopek, Liliana Pięciak, Danuta Gąsior-Perczak, Iwona Pałyga, Krzysztof Gruszczyński, Ewelina Nowak, Stanisław Góźdź
Differentiated papillary thyroid cancer (PTC) is the most common cancer of the endocrine system. PTC has a very good prognosis and a high 5 year survival rate; however, some patients are unresponsive to treatment, and their diagnosis eventually results in death. Recent efforts have focused on searching for prognostic and predictive factors that may enable treatment personalization and monitoring across the course of the disease. The presence of the BRAF mutation is considered to contribute to the risk of poor clinical course, according to American Thyroid Association (ATA) recommendations...
2017: PloS One
https://www.readbyqxmd.com/read/28635949/non-coding-variants-contribute-to-the-clinical-heterogeneity-of-ttr-amyloidosis
#3
Andrea Iorio, Antonella De Lillo, Flavio De Angelis, Marco Di Girolamo, Marco Luigetti, Mario Sabatelli, Luca Pradotto, Alessandro Mauro, Anna Mazzeo, Claudia Stancanelli, Federico Perfetto, Sabrina Frusconi, Filomena My, Dario Manfellotto, Maria Fuciarelli, Renato Polimanti
Coding mutations in TTR gene cause a rare hereditary form of systemic amyloidosis, which has a complex genotype-phenotype correlation. We investigated the role of non-coding variants in regulating TTR gene expression and consequently amyloidosis symptoms. We evaluated the genotype-phenotype correlation considering the clinical information of 129 Italian patients with TTR amyloidosis. Then, we conducted a re-sequencing of TTR gene to investigate how non-coding variants affect TTR expression and, consequently, phenotypic presentation in carriers of amyloidogenic mutations...
June 21, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#4
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635630/development-of-a-high-density-snp-based-linkage-map-and-detection-of-qtl-for-%C3%AE-glucans-protein-content-grain-yield-per-spike-and-heading-time-in-durum-wheat
#5
Ilaria Marcotuli, Agata Gadaleta, Giacomo Mangini, Antonio Massimo Signorile, Silvana Addolorata Zacheo, Antonio Blanco, Rosanna Simeone, Pasqualina Colasuonno
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28635424/genome-wide-linkage-and-haplotype-sharing-analysis-implicates-the-mcdr3-locus-as-a-candidate-region-for-a-developmental-macular-disorder-in-association-with-digit-abnormalities
#6
Valentina Cipriani, Ambreen Kalhoro, Gavin Arno, Raquel S Silva, Nikolas Pontikos, Virginie Puech, Michelle E McClements, David M Hunt, Veronica van Heyningen, Michel Michaelides, Andrew R Webster, Anthony T Moore, Bernard Puech
BACKGROUND: Developmental macular disorders are a heterogeneous group of rare retinal conditions that can cause significant visual impairment from childhood. Among these disorders, autosomal dominant North Carolina macular dystrophy (NCMD) has been mapped to 6q16 (MCDR1) with recent support for a non-coding disease mechanism of PRDM13. A second locus on 5p15-5p13 (MCDR3) has been implicated in a similar phenotype, but the disease-causing mechanism still remains unknown. METHODS: Two families affected by a dominant developmental macular disorder that closely resembles NCMD in association with digit abnormalities were included in the study...
March 2, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28635411/single-nucleotide-polymorphisms-in-the-human-rad21l-gene-may-be-a-genetic-risk-factor-for-japanese-patients-with-azoospermia-caused-by-meiotic-arrest-and-sertoli-cell-only-syndrome
#7
Gaku Minase, Toshinobu Miyamoto, Yasushi Miyagawa, Masashi Iijima, Hiroto Ueda, Yasuaki Saijo, Mikio Namiki, Kazuo Sengoku
Genetic mechanisms are implicated in some cases of male infertility. Recently, it was demonstrated that male mice lacking the gene for RAD21L exhibited azoospermia caused by meiotic arrest. Mouse RAD21L is a functionally relevant meiotic α-kleisin that is essential for male fertility. Therefore, we hypothesized that RAD21L mutations or polymorphisms may be associated with male infertility, especially azoospermia secondary to meiotic arrest. To determine if RAD21L defects are associated with azoospermia in groups of patients with meiotic arrest, we performed direct sequencing of the RAD21L coding regions in 38 Japanese patients with meiotic arrest and in 200 normal controls...
February 21, 2017: Human Fertility: Journal of the British Fertility Society
https://www.readbyqxmd.com/read/28635360/the-association-between-apolipoprotein-a1-c3-a5-gene-cluster-promoter-polymorphisms-and-risk-of-ischemic-stroke-in-the-northern-chinese-han-population
#8
Yanzhe Wang, Fang Liu, Lei Li, Shumin Deng, Zhiyi He
Objective Given its effects on lipid metabolism, the apolipoprotein A1-C3-A5 ( APOA1-C3-A5) gene cluster is thought to play an important role in ischemic stroke pathogenesis. Here, we evaluated whether the APOA1-C3-A5 cluster is associated with ischemic stroke in the northern Chinese Han population. Methods This case-control study analyzed 812 patients with ischemic stroke and 844 healthy controls with regard to four APOA1-C3-A5 cluster promoter single nucleotide polymorphisms (SNPs), rs670, rs2854116, rs2854117, and rs662799, using the SNaPshot Multiplex sequencing assay...
January 1, 2017: Journal of International Medical Research
https://www.readbyqxmd.com/read/28634809/genetic-and-transcriptomic-analyses-of-lignin-and-lodging-related-traits-in-brassica-napus
#9
Lijuan Wei, Hongju Jian, Kun Lu, Nengwen Yin, Jia Wang, Xiujian Duan, Wei Li, Liezhao Liu, Xinfu Xu, Rui Wang, Andrew H Paterson, Jiana Li
Candidate genes associated with lignin and lodging traits were identified by combining phenotypic, genotypic, and gene expression data in B. napus. Brassica napus is one of the world's most important oilseed crops, but its yield can be dramatically reduced by lodging, bending, and falling of its vertical stems. Lignin has been shown to contribute to stem mechanical strength. In this study, we found that the syringyl/guaiacyl (S/G) monolignol ratio exhibits a significant negative correlation with disease and lodging resistance...
June 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28634808/mapping-of-genetic-locus-for-leaf-trichome-in-brassica-oleracea
#10
Jiaqin Mei, Jinhua Wang, Yuehua Li, Shuai Tian, Dayong Wei, Chaoguo Shao, Jun Si, Qing Xiong, Jiana Li, Wei Qian
The genetic locus for leaf trichome was identified via marker-based mapping and SNP microarray assay, and a functional marker was developed to facilitate the breeding for hairiness in Brassica oleracea. Plant trichomes are involved in various functions particularly in protecting plants against some biotic and abiotic damages. In the present study, an F2 segregating population was developed from the cross between a glabrous cultivated B. oleracea (CC, 2n = 18) and a hairy wild relative, B. incana (CC, 2n = 18)...
June 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28634352/differences-in-sequences-between-hbv-relaxed-circular-dna-and-covalently-closed-circular-dna
#11
Magda Rybicka, Anna Woziwodzka, Tomasz Romanowski, Piotr Stalke, Marcin Dręczewski, Krzysztof Piotr Bielawski
The hepatitis B virus (HBV) genome exists in two forms: circular covalently closed DNA (cccDNA) and relaxed circular DNA (RCDNA). Here, we investigated the presence of differences in the sequences of both forms in paired samples of serum and liver tissue. The serum and liver biopsy samples were collected at the same time from 67 chronically infected patients. The genotyping of the RCDNA and cccDNA was performed using mass spectrometry analysis. The HBV mutations located in the HBV pol (P) and the HBV basal core promoter/pre-core (BCP/PC) regions were included...
June 21, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#12
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28633358/phylogeography-of-herbarium-specimens-of-asexually-propagated-paper-mulberry-broussonetia-papyrifera-l-l-h%C3%A3-r-ex-vent-moraceae-reveals-genetic-diversity-across-the-pacific
#13
Claudia Payacan, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, Andrea Seelenfreund
Background and Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28633097/results-of-the-first-international-hiv-1-coreceptor-proficiency-panel-test
#14
Eva Heger, Rolf Kaiser, Elena Knops, Maria Neumann-Fraune, Eugen Schuelter, Alejandro Pironti, Thomas Lengauer, Hauke Walter, Saleta Sierra
BACKGROUND: Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories. OBJECTIVES: We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne. STUDY DESIGN: 12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne...
June 10, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28633070/length-and-repeat-sequence-variation-in-58-strs-and-94-snps-in-two-spanish-populations
#15
Ferran Casals, Roger Anglada, Núria Bonet, Raquel Rasal, Kristiaan J van der Gaag, Jerry Hoogenboom, Neus Solé-Morata, David Comas, Francesc Calafell
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium...
June 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28632339/polymorphisms-of-human-leukocyte-antigen-b-27-on-clinical-phenotype-of-spondyloarthritis-in-chinese
#16
Hai-Jun Ma, Qing-Feng Yin, Yun Liu, Yin Wu, Tie-Chui Zhu, Ming-Hao Guo
BACKGROUND: In recent years, an ever-increasing number of alleles of human leukocyte antigen B*27 (HLA-B*27) have been identified. This study aimed to establish an updated method for HLA-B*27 subtyping, and to investigate the impact of HLA-B*27 polymorphisms on the clinical phenotype of spondyloarthritis (SpA). METHODS: Overall, 184 SpA patients were recruited for analyzing diversity of HLA-B*27 via an updated high-resolution polymerase chain reaction amplification with sequence specific primers (PCR-SSP)...
June 20, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28632119/alkaliphilus-namsaraevii-sp-nov-an-alkaliphilic-iron-and-sulfur-reducing-bacterium-isolated-from-a-steppe-soda-lake
#17
Anastasiya Zakharyuk, Lyudmila Kozyreva, Elena Ariskina, Olga Troshina, Dmitry Kopitsyn, Viktoria Shcherbakova
A novel alkaliphilic spore-forming bacterium was isolated from the benthic sediments of the highly mineralized steppe Lake Khilganta (Transbaikal Region, Russia). Cells of the strain, designated Х-07-2T, were straight to slightly curved rods, Gram-stain-positive and motile. Strain Х-07-2T grew in the pH range from 7.0 to 10.7 (optimum pH 9.6-10.3). Growth was observed at 25-47 °C (optimum 30 °C) and at an NaCl concentration from 5 to 150 g l-1 with an optimum at 40 g l-1. Strain Х-07-2T was a chemo-organoheterotroph able to reduce amorphous ferric hydroxide, Fe(III) citrate and elemental sulfur in the presence of yeast extract as the electron donor...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28631592/blastomonas-quesadae-sp-nov-isolated-from-a-saline-soil-by-dilution-to-extinction-cultivation
#18
David J Castro, Inmaculada Llamas, Victoria Béjar, Fernando Martínez-Checa
We isolated a Gram-stain-negative, aerobic bacterial strain, 912T, from a soil sample taken from Rambla Salada (Murcia), south-eastern Spain, by using the dilution-to-extinction method. Cells of the strain were motile with a polar flagellum, short rod-shaped, catalase- and oxidase-positive and grew at NaCl concentrations within the range 0-5 % (w/v) (optimum 3 %, w/v), at 4-32 °C (optimum 30 °C) and at pH 6-9 (optimum pH 7); bacteriochlorophyll a was produced. Analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Blastomonas in the class Alphaproteobacteria...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28631053/characterization-of-an-orf-virus-isolate-from-an-outbreak-in-heilongjiang-province-china
#19
Yongzhong Yu, Qiang Tan, Wenbo Zhao, Xue Zhang, Jinzhu Ma, Zhijun Wu, Zhanbo Zhu, Yudong Cui
Contagious ecthyma, caused by orf virus (ORFV), is an epitheliotrophic contagious disease with zoonotic implications that mainly affects sheep, goats, wild ruminants, and humans. Recently, a novel ORFV strain, OV/HLJ/04, was successfully isolated from the skin and mucosal lesions of a goat with severe clinical sore mouth symptoms in Heilongjiang province of China. The OV/HLJ/04 isolate was characterized by electron microscopy, serological tests, and experimental reproduction of disease. The purified virions exhibited a typical ovoid shape when observed by electron microscopy...
June 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28629734/immunohistochemical-and-genetic-exploration-of-incompatible-a-blood-group-antigen-expression-in-invasive-micropapillary-breast-carcinoma-a-case-report
#20
S Zouine, Z Orfi, K Kojok, S Benayad, Y Zaid, F Marnissi, N Habti
INTRODUCTION: Invasive Micropapillary Carcinoma (IMPC) of the breast is a relatively rare subtype of invasive ductal carcinoma and represents the most inherently aggressive form. Expression of incompatible blood group A antigen in cancer of type O patients has been reported in several types of cancer, however, the biosynthetic mechanism and the genetic basis remain unclear until today. The aim of the present case report study was to evaluate the expression of incompatible blood group A antigen and to identify the genetic basis of this expression in IMPC of the breast...
June 16, 2017: Current Research in Translational Medicine
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