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https://www.readbyqxmd.com/read/28749108/snp-and-haplotype-analysis-of-vascular-endothelial-growth-factor-vegf-gene-in-lung-cancer-patients-of-kashmir
#1
Niyaz A Naikoo, Dil Afroze, Roohi Rasool, Sonaullah Shah, A G Ahangar, Imtiyaz A Bhat, Iqbal Qasim, Mushtaq A Siddiqi, Zafar A Shah
Vascular endothelial growth factor (VEGF) is a major mediator of angiogenesis involving tumor growth and metastasis. In this large case-control study, we investigated whether functional polymorphisms (+405C>G, +936C>T) in the VEGF gene are associated with the risk of lung cancer. The study investigates the association between variants of VEGF gene and lung cancer. We performed single nucleotide polymorphism (SNP), haplotype and linkage disequilibrium studies on 100 patients and 128 healthy controls with 2 SNPs in the VEGF gene...
July 27, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28748635/copy-number-changes-identified-using-whole-exome-sequencing-in-nonsyndromic-cleft-lip-and-palate-in-a-honduran-population
#2
Yi Cai, Karynne E Patterson, Frederic Reinier, Sarah E Keesecker, Elizabeth Blue, Michael Bamshad, Joseph Haddad
BACKGROUND: The majority of cleft lip with or without cleft palate cases appear as an isolated, nonsyndromic entity (NSCLP). With the advent of next generation sequencing, whole exome sequencing (WES) has been used to identify single nucleotide variants and insertion/deletions which cause or increase the risk of NSCLP. However, to our knowledge, there are no published studies using WES in NSCLP to investigate copy number changes (CNCs), which are a major component of human genetic variation...
July 27, 2017: Birth defects research
https://www.readbyqxmd.com/read/28748134/genomic-characterization-reconfirms-the-taxonomic-status-of-lactobacillus-parakefiri
#3
Yasuhiro Tanizawa, Hisami Kobayashi, Eli Kaminuma, Mitsuo Sakamoto, Moriya Ohkuma, Yasukazu Nakamura, Masanori Arita, Masanori Tohno
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573(T) to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L...
2017: Bioscience of Microbiota, Food and Health
https://www.readbyqxmd.com/read/28747922/identification-of-major-quantitative-trait-loci-for-seed-oil-content-in-soybeans-by-combining-linkage-and-genome-wide-association-mapping
#4
Yongce Cao, Shuguang Li, Zili Wang, Fangguo Chang, Jiejie Kong, Junyi Gai, Tuanjie Zhao
Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747921/unreduced-megagametophyte-production-in-lemon-occurs-via-three-meiotic-mechanisms-predominantly-second-division-restitution
#5
Houssem Rouiss, José Cuenca, Luis Navarro, Patrick Ollitrault, Pablo Aleza
Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, "Eureka Frost" and "Fino", using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747902/in-silico-taxonomic-classification-of-373-genomes-reveals-species-misidentification-and-new-genospecies-within-the-genus-pseudomonas
#6
Phuong N Tran, Michael A Savka, Han Ming Gan
The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28747664/mutations-targeting-the-coagulation-pathway-are-enriched-in-brain-metastases
#7
Cristina Richichi, Lorenzo Fornasari, Giorgio E M Melloni, Paola Brescia, Monica Patanè, Massimiliano Del Bene, Dana A M Mustafa, Johan M Kros, Bianca Pollo, Giancarlo Pruneri, Angela Sciandivasci, Elisabetta Munzone, Francesco DiMeco, Pier Giuseppe Pelicci, Laura Riva, Giuliana Pelicci
Brain metastases (BMs) are the most common malignancy of the central nervous system. Recently it has been demonstrated that plasminogen activator inhibitor serpins promote brain metastatic colonization, suggesting that mutations in serpins or other members of the coagulation cascade can provide critical advantages during BM formation. We performed whole-exome sequencing on matched samples of breast cancer and BMs and found mutations in the coagulation pathway genes in 5 out of 10 BM samples. We then investigated the mutational status of 33 genes belonging to the coagulation cascade in a panel of 29 BMs and we identified 56 Single Nucleotide Variants (SNVs)...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747581/protein-tyrosine-phosphatase-nonreceptor-type-22-ptpn22-gene-single-nucleotide-polymorphisms-and-its-interaction-with-t2dm-on-pulmonary-tuberculosis-in-chinese-uygur-population
#8
Xian-Hua Wang, Ai-Guo Ma, Xiu-Xia Han, Lei Chen, Hui Liang, Aishan-Litifu, Abudumijit-Ablez, Feng Xue
AIMS: To investigate the association of several single nucleotide polymorphisms (SNPs) within Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene and additional gene- gene and gene- type 2 diabetes mellitus (T2DM) interaction with pulmonary tuberculosis (PTB) risk in Chinese Uygur population. METHODS: A total of 722 participants (186 males, 536 females) were selected, including 360 PTB patients and 362 control participants. Generalized multifactor dimensionality reduction (GMDR) was used to screen the best interaction combination among SNPs and T2DM...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28747474/male-female-relatedness-at-specific-snp-linkage-groups-influences-cryptic-female-choice-in-chinook-salmon-oncorhynchus-tshawytscha
#9
Cornelia Geßner, Sheri L Johnson, Paul Fisher, Shannon Clarke, Kim Rutherford, Jane Symonds, Neil J Gemmell
In a range of taxa, the relatedness between mates influences both pre- and post-mating processes of sexual selection. However, relatively little is known about the genetic loci facilitating such a bias, with the exception of the major histocompatibility complex. Here, we performed tightly controlled replicated in vitro fertilization trials to explore the impact of relatedness on two possible mechanisms of cryptic female choice (CFC) in Chinook salmon (Oncorhynchus tshawytscha). We tested (i) whether relatedness of mates, assessed using 682 single nucleotide polymorphisms (SNPs) on 29 SNP-linkage groups (LGs), biases a male's sperm velocity in ovarian fluid (a parameter previously shown to predict male fertilization success), and (ii) whether relatedness of mates governs fertilization success via other mechanisms, probably via sperm-egg interactions...
July 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28747230/full-length-genome-sequence-analysis-of-enzootic-nasal-tumor-virus-isolated-from-goats-in-china
#10
Yapeng He, Qi Zhang, Jing Wang, Man Zhou, Mingzhe Fu, Xingang Xu
BACKGROUND: Enzootic nasal tumor virus (ENTV) is a betaretrovirus of sheep (ENTV-1) and goats (ENTV-2) associated with neoplastic transformation of epithelial cells of the ethmoid turbinate. Confirmation of the role of ENTV in the pathogenesis of enzootic nasal adenocarcinoma (ENA) has yet to be resolved due to the inability to culture the virus. Very little is known about the prevalence of this disease, particularly in China. METHODS: To evaluate the genetic diversity of ENTV-2 from Shaanxi province of China, the complete genome sequence of four isolates from Shaanxi province was determined by RT-PCR...
July 26, 2017: Virology Journal
https://www.readbyqxmd.com/read/28747224/regions-of-common-inter-individual-dna-methylation-differences-in-human-monocytes-genetic-basis-and-potential-function
#11
Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
BACKGROUND: There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. RESULTS: We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before...
July 26, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28746207/integrating-nested-pcr-with-high-throughput-sequencing-to-characterize-mutations-of-hbv-genome-in-low-viral-load-samples
#12
Xianjun Wang, Lihui Xu, Yueming Chen, Anbing Liu, Liqian Wang, Peisong Xu, Yunhui Liu, Lei Li, Fei Meng
Due to the low viral load of hepatitis B virus (HBV) in plasma samples, conventional techniques have limitations to the detection of antiviral resistance mutations. To solve the problem, we developed a fast, highly sensitive, and accurate method to sequence the HBV whole-genome sequencing in plasma samples which had various viral loads from very low to high.Twenty-one plasma samples were collected from patients who were carriers of HBV from the Hangzhou First People's Hospital. Two pairs of conserved, overlapping, nested primers were used to amplify and sequence the whole HBV genome in 8 plasma samples with different viral loads...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28746191/whole-exome-sequencing-unveils-a-frameshift-mutation-in-cngb3-for-cone-dystrophy-a-case-report-of-an-indian-family
#13
Shashank Gupta, Amit Chaurasia, Ekta Pathak, Rajeev Mishra, Vidya Nair Chaudhry, Prashaant Chaudhry, Ashim Mukherjee, Mousumi Mutsuddi
RATIONALE: Genetic elucidation of cone-dominated retinal dystrophies in Indian subcontinent is much needed to identify and catalog underlying genetic defects. In this context, the present study recruited a consanguineous Indian family affected with autosomal recessive cone dystrophy (CD). Considering the huge genetic heterogeneity and recessive inheritance of the disease, we chose to dissect out causal variant in this family by whole exome sequencing (WES). PATIENT CONCERNS: In the recruited family, three of the six siblings had complaints of poor visual acuity, photophobia, and disturbed colour vision since early childhood...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28746172/a-genetic-variant-in-the-catechol-o-methyl-transferase-comt-gene-is-related-to-age-dependent-differences-in-the-therapeutic-effect-of-calcium-channel-blockers
#14
Jiayue Xu, Adrian E Boström, Mohamed Saeed, Raghvendra K Dubey, Gérard Waeber, Peter Vollenweider, Pedro Marques-Vidal, Jessica Mwinyi, Helgi B Schiöth
Hypertension is the leading risk factor for cardiovascular disease and one of the major health concerns worldwide. Genetic factors impact both the risk for hypertension and the therapeutic effect of antihypertensive drugs. Sex- and age-specific variances in the prevalence of hypertension are partly induced by estrogen. We investigated 6 single nucleotide polymorphisms in genes encoding enzymes involved in estrogen metabolism in relation to sex- and age-specific differences in the systolic and diastolic blood pressure (SBP and DBP) outcome under the treatment of diuretics, calcium-channel blockers (CCBs), angiotensin-converting-enzyme inhibitors, and angiotensin-receptor blockers (ARBs)...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28745674/-gene-mutations-in-patients-with-hereditary-cavernous-malformations
#15
O B Belousova, E S Bulygina, D N Okishev, E B Prohorchuk, S V Tsygankova, I N Pronin, L V Shishkina, M V Ryzhova, K G Skryabin, A N Konovalov
AIM: To identify mutations in cerebral cavernous malformation (CCM) genes in patients with hereditary and sporadic CCMs in the Russian population. MATERIAL AND METHODS: Blood samples from 73 randomly selected patients, including 29 MRI-confirmed familial cases, 8 clinically confirmed familial cases and 38 so-called sporadic cases, were examined. A search for large deletions/duplications was performed using multiplex ligation-dependent probe amplification (MPLA)...
2017: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/28743024/a-method-to-evaluate-the-quality-of-clinical-gene-panel-sequencing-data-for-single-nucleotide-variant-detection
#16
Chung Lee, Joon S Bae, Gyu H Ryu, Nayoung K D Kim, Donghyun Park, Jongsuk Chung, Sungkyu Kyung, Je-Gun Joung, Hyun-Tae Shin, Seung-Ho Shin, Younglan Kim, Byung S Kim, Hojun Lee, Kyoung-Mee Kim, Jung-Sun Kim, Woong-Yang Park, Dae-Soon Son
Customized gene-panel tests, based on next-generation sequencing, have demonstrated their usefulness in a plethora of clinical settings. As with other clinical diagnostic techniques, gene-panel sequencing for clinical purposes requires precise quality control (QC) measures to ensure its reliability. Only detected variants are currently recorded in clinical reports; however, identifying whether a nondetected variant is a true or false negative is regarded essential in a clinical setting and, thus, a comprehensive QC measure is in demand...
July 22, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28742912/association-of-genetic-variants-related-to-serum-calcium-levels-with-coronary-artery-disease-and-myocardial-infarction
#17
Susanna C Larsson, Stephen Burgess, Karl Michaëlsson
Importance: Serum calcium has been associated with cardiovascular disease in observational studies and evidence from randomized clinical trials indicates that calcium supplementation, which raises serum calcium levels, may increase the risk of cardiovascular events, particularly myocardial infarction. Objective: To evaluate the potential causal association between genetic variants related to elevated serum calcium levels and risk of coronary artery disease (CAD) and myocardial infarction using mendelian randomization...
July 25, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28742818/first-identification-of-a-recombinant-form-of-hepatitis-c-virus-in-austrian-patients-by-full-genome-next-generation-sequencing
#18
Evelyn Stelzl, Bernhard Haas, Bernd Bauer, Sherry Zhang, Ellen H Fiss, Grantland Hillman, Aaron T Hamilton, Rochak Mehta, Marintha L Heil, Ed G Marins, Brigitte I Santner, Harald H Kessler
Hepatitis C virus (HCV) intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA) was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b...
2017: PloS One
https://www.readbyqxmd.com/read/28741852/polymorphisms-of-mir-146a-mir-149-mir-196a2-and-mir-499-are-associated-with-osteoporotic-vertebral-compression-fractures-in-korean-postmenopausal-women
#19
Tae-Keun Ahn, Jung-Oh Kim, Hemant Kumar, Hyemi Choi, Min-Jae Jo, Seil Sohn, Alexander E Ropper, Nam-Keun Kim, In-Bo Han
Genetic factors have been shown to be a small but significant predictor for osteoporosis and osteoporotic fracture risk. We performed a case-control association study to determine the association between miR-146a, miR-149, miR-196a2 and miR-499 polymorphisms and osteoporotic vertebral compression fracture (OVCF) susceptibility. In total, 286 unrelated postmenopausal Korean women (57 with OVCFs, 55 with non-OVCFs, and 174 healthy controls) were recruited. All subjects underwent dual energy X-ray absorptiometry to determine BMD at the lumbar spine and femoral neck...
July 25, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28740486/evolution-of-acinetobacter-baumannii-in-vivo-international-clone-ii-more-resistance-to-ceftazidime-mutation-in-ptk
#20
Xiaoting Hua, Zhihui Zhou, Qing Yang, Qiucheng Shi, Qingye Xu, Jianfeng Wang, Keren Shi, Feng Zhao, Long Sun, Zhi Ruan, Yan Jiang, Yunsong Yu
Acinetobacter baumannii is an important nosocomial pathogen worldwide. A more comprehensive understanding of the within-host genomic evolution of A. baumannii would provide a molecule basis for improving treatment of A. baumannii infection. To understand the evolutionary mechanism facilitating A. baumannii survived in human body, we here reported the genomic analysis of A. baumannii isolated sampled from Chinese patients. We used whole-genome sequence of A. baumannii isolates from the same patient to determine single-nucleotide variants, insertion sequence mapping, and gene change...
2017: Frontiers in Microbiology
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