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https://www.readbyqxmd.com/read/28641396/geneticization-in-mim-omim%C3%A2-exploring-historic-and-epistemic-drivers-of-contemporary-understandings-of-genetic-disease
#1
Rachel A Ankeny
Prior to the genomic sequencing era, the bible for those working in clinical genetics was McKusick's Mendelian Inheritance in Man (MIM), which appeared in multiple editions between the 1960s and the late 1990s. This catalogue was organized according to general patterns of inheritance and focused on phenotypes. Beginning in the mid-1980s, it was replaced by Online Mendelian Inheritance in Man (OMIM®), a continuously updated catalogue documenting molecular relationships between genetic variation and phenotypic expression...
June 21, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28641312/impact-of-novel-mir-145-3p-regulatory-networks-on-survival-in-patients-with-castration-resistant-prostate-cancer
#2
Yusuke Goto, Akira Kurozumi, Takayuki Arai, Nijiro Nohata, Satoko Kojima, Atsushi Okato, Mayuko Kato, Kazuto Yamazaki, Yasuo Ishida, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
BACKGROUND: Despite recent advancements, metastatic castration-resistant prostate cancer (CRPC) is not considered curative. Novel approaches for identification of therapeutic targets of CRPC are needed. METHODS: Next-generation sequencing revealed 945-1248 miRNAs from each lethal mCRPC sample. We constructed miRNA expression signatures of CRPC by comparing the expression of miRNAs between CRPC and normal prostate tissue or hormone-sensitive prostate cancer (HSPC)...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28641145/lack-of-association-between-deletion-polymorphism-of-bim-gene-and-in-vitro-drug-sensitivity-in-b-cell-precursor-acute-lymphoblastic-leukemia
#3
Meixian Huang, Kunio Miyake, Keiko Kagami, Masako Abe, Tamao Shinohara, Atsushi Watanabe, Shinpei Somazu, Hiroko Oshiro, Kumiko Goi, Hiroaki Goto, Masayoshi Minegishi, Shotaro Iwamoto, Nobutaka Kiyokawa, Kanji Sugita, Takeshi Inukai
A deletion polymorphism in the BIM gene was identified as an intrinsic mechanism for resistance to tyrosine kinase inhibitor in chronic myeloid leukemia patients in East Asia. BIM is also involved in the responses to glucocorticoid and chemotherapy in acute lymphoblastic leukemia (ALL), suggesting a possible association between deletion polymorphism of BIM and the chemosensitivity of ALL. Thus, we analyzed 72 B-cell precursor (BCP)-ALL cell lines established from Japanese patients. Indeed, higher BIM gene expression was associated with good in vitro sensitivities to glucocorticoid and chemotherapeutic agents used in induction therapy...
June 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28640983/multiplexed-crispr-cas9-mediated-metabolic-engineering-of-%C3%AE-aminobutyric-acid-levels-in-solanum-lycopersicum
#4
Rui Li, Ran Li, Xindi Li, Daqi Fu, Benzhong Zhu, Huiqin Tian, Yunbo Luo, Hongliang Zhu
In recent years, the type II CRISPR system has become a widely used and robust technique to implement site-directed mutagenesis in a variety of species including model and crop plants. However, few studies manipulated metabolic pathways in plants using the CRISPR system. Here, we introduced the pYLCRISPR/Cas9 system with one or two single-site guide RNAs to target the tomato phytoene desaturase gene. An obvious albino phenotype was observed in T0 regenerated plants, and more than 61% of the desired target sites were edited...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28640915/physiological-and-genomic-features-of-a-novel-violacein-producing-bacterium-isolated-from-surface-seawater
#5
Yue-Hong Wu, Hong Cheng, Lin Xu, Xiong-Bin Jin, Chun-Sheng Wang, Xue-Wei Xu
Strains JW1T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483T (98.2%), P. shioyasakiensis SE3T (97.8%), P. arabiensis JCM 17292T (97.3%), and P. gelatinilytica NH153T (97...
2017: PloS One
https://www.readbyqxmd.com/read/28640911/evolution-of-microrna-in-primates
#6
Jennifer C McCreight, Sean E Schneider, Damien B Wilburn, Willie J Swanson
MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely uncharacterized. A particular miRNA can have one to thousands of messenger RNA targets, establishing the potential for a small change in sequence or overall miRNA structure to have profound phenotypic effects. However, the majority of non-human primate miRNA is predicted solely by homology to the human genome and lacks experimental validation. In the present study, we sequenced thirteen species representing a wide range of the primate phylogeny...
2017: PloS One
https://www.readbyqxmd.com/read/28640891/baculoviral-delivery-of-crispr-cas9-facilitates-efficient-genome-editing-in-human-cells
#7
Sanne Hindriksen, Arne J Bramer, My Anh Truong, Martijn J M Vromans, Jasmin B Post, Ingrid Verlaan-Klink, Hugo J Snippert, Susanne M A Lens, Michael A Hadders
The CRISPR/Cas9 system is a highly effective tool for genome editing. Key to robust genome editing is the efficient delivery of the CRISPR/Cas9 machinery. Viral delivery systems are efficient vehicles for the transduction of foreign genes but commonly used viral vectors suffer from a limited capacity in the genetic information they can carry. Baculovirus however is capable of carrying large exogenous DNA fragments. Here we investigate the use of baculoviral vectors as a delivery vehicle for CRISPR/Cas9 based genome-editing tools...
2017: PloS One
https://www.readbyqxmd.com/read/28640886/epigenomic-diversification-within-the-genus-lupinus
#8
Karolina Susek, Agnieszka Braszewska-Zalewska, Adam J Bewick, Robert Hasterok, Robert J Schmitz, Barbara Naganowska
Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organisation of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment...
2017: PloS One
https://www.readbyqxmd.com/read/28640831/ribosomal-dna-copy-number-loss-and-sequence-variation-in-cancer
#9
Baoshan Xu, Hua Li, John M Perry, Vijay Pratap Singh, Jay Unruh, Zulin Yu, Musinu Zakari, William McDowell, Linheng Li, Jennifer L Gerton
Ribosomal DNA is one of the most variable regions in the human genome with respect to copy number. Despite the importance of rDNA for cellular function, we know virtually nothing about what governs its copy number, stability, and sequence in the mammalian genome due to challenges associated with mapping and analysis. We applied computational and droplet digital PCR approaches to measure rDNA copy number in normal and cancer states in human and mouse genomes. We find that copy number and sequence can change in cancer genomes...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28640830/optimal-sequencing-strategies-for-identifying-disease-associated-singletons
#10
Sara Rashkin, Goo Jun, Sai Chen, Goncalo R Abecasis
With the increasing focus of genetic association on the identification of trait-associated rare variants through sequencing, it is important to identify the most cost-effective sequencing strategies for these studies. Deep sequencing will accurately detect and genotype the most rare variants per individual, but may limit sample size. Low pass sequencing will miss some variants in each individual but has been shown to provide a cost-effective alternative for studies of common variants. Here, we investigate the impact of sequencing depth on studies of rare variants, focusing on singletons-the variants that are sampled in a single individual and are hardest to detect at low sequencing depths...
June 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28640820/whole-genome-analysis-of-selected-human-and-animal-rotaviruses-identified-in-uganda-from-2012-to-2014-reveals-complex-genome-reassortment-events-between-human-bovine-caprine-and-porcine-strains
#11
Josephine Bwogi, Khuzwayo C Jere, Charles Karamagi, Denis K Byarugaba, Prossy Namuwulya, Frederick N Baliraine, Ulrich Desselberger, Miren Iturriza-Gomara
Rotaviruses of species A (RVA) are a common cause of diarrhoea in children and the young of various other mammals and birds worldwide. To investigate possible interspecies transmission of RVAs, whole genomes of 18 human and 6 domestic animal RVA strains identified in Uganda between 2012 and 2014 were sequenced using the Illumina HiSeq platform. The backbone of the human RVA strains had either a Wa- or a DS-1-like genetic constellation. One human strain was a Wa-like mono-reassortant containing a DS-1-like VP2 gene of possible animal origin...
2017: PloS One
https://www.readbyqxmd.com/read/28640747/a-single-amino-acid-change-in-the-non-structural-nv-protein-impacts-the-virulence-phenotype-of-viral-hemorrhagic-septicemia-virus-in-trout
#12
Laury Baillon, Emilie Mérour, Joëlle Cabon, Lénaïg Louboutin, Hélène Quenault, Fabrice Touzain, Thierry Morin, Yannick Blanchard, Stéphane Biacchesi, Michel Brémont
Novirhabdoviruses like the Viral hemorrhagic septicemia virus (VHSV) are rhabdoviruses infecting fish. In the current study, RNA genomes of different VHSV field isolates classified as high, medium or low virulent phenotypes have been sequenced by next-generation sequencing and compared. Various amino acid changes, depending on the VHSV phenotype, have been identified in all the VHSV proteins. As a starting point, we focused our study on the non-virion (NV) non-structural protein in which an arginine residue (R116) is present in all the virulent isolates and replaced by a serine/asparagine residue S/N116 in the attenuated isolates...
June 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28640739/hepatitis-b-virus-core-antigen-mutations-predict-post-operative-prognosis-of-patients-with-primary-hepatocellular-carcinoma
#13
Jian'an Jia, Huiming Li, Hui Wang, Shipeng Chen, Mengmeng Wang, Huijuan Feng, Yuzhen Gao, Yunjiu Wang, Meng Fang, Chunfang Gao
The aim of this study was to explore the relationship between hepatitis B virus (HBV) core antigen (HBc) mutations and the post-operative prognosis of HBV-related hepatocellular carcinoma (HCC). In total, 98 patients suffering from HBV-related HCC and treated with surgery were enrolled, with a 48 month follow-up. The preCore/Core region of the HBV genome from tumour tissue (TT) and paired adjacent non-tumour tissue (ANTT) of these patients was sequenced, and a phylogenetic tree was reconstructed. The correlations between the viral features and evolutionary divergence of preCore/Core amino acid sequences from 67 paired TTs and ANTTs were analysed...
June 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28640705/genomic-analysis-of-childhood-brain-tumors-methods-for-genome-wide-discovery-and-precision-medicine-become-mainstream
#14
Stephen C Mack, Paul A Northcott
Recent breakthroughs in next-generation sequencing technology and complementary genomic platforms have transformed our capacity to interrogate the molecular landscapes of human cancers, including childhood brain tumors. Numerous high-throughput genomic studies have been reported for the major histologic brain tumor entities diagnosed in children, including interrogations at the level of the genome, epigenome, and transcriptome, many of which have yielded essential new insights into disease biology. The nature of these discoveries has been largely platform dependent, exemplifying the usefulness of applying different genomic and computational strategies, or integrative approaches, to address specific biologic and/or clinical questions...
June 22, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28640655/usual-interstitial-pneumonia-can-be-detected-in-transbronchial-biopsies-using-machine-learning
#15
Daniel G Pankratz, Yoonha Choi, Urooj Imtiaz, Grażyna M Fedorowicz, Jessica D Anderson, Thomas V Colby, Jeffrey L Myers, David A Lynch, Kevin K Brown, Kevin R Flaherty, Mark P Steele, Steve D Groshong, Ganesh Raghu, Neil M Barth, P Sean Walsh, Jing Huang, Giulia C Kennedy, Fernando J Martinez
RATIONALE: Usual interstitial pneumonia (UIP) is the histopathologic hallmark of idiopathic pulmonary fibrosis. While UIP can be detected by high-resolution computed tomography (HRCT) of the chest, HRCT results are frequently inconclusive, and pathology from transbronchial biopsy (TBB) has poor sensitivity. Surgical lung biopsy (SLB) may be necessary for a definitive diagnosis. OBJECTIVES: To develop a genomic classifier in tissue obtained by TBB that distinguishes UIP from non-UIP, trained against central pathology as the reference standard...
June 22, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28640612/crispr-cas9-based-genome-editing-for-disease-modeling-and-therapy-challenges-and-opportunities-for-nonviral-delivery
#16
Hong-Xia Wang, Mingqiang Li, Ciaran M Lee, Syandan Chakraborty, Hae-Won Kim, Gang Bao, Kam W Leong
Genome editing offers promising solutions to genetic disorders by editing DNA sequences or modulating gene expression. The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) technology can be used to edit single or multiple genes in a wide variety of cell types and organisms in vitro and in vivo. Herein, we review the rapidly developing CRISPR/Cas9-based technologies for disease modeling and gene correction and recent progress toward Cas9/guide RNA (gRNA) delivery based on viral and nonviral vectors...
June 22, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28637346/an-ion-beam-induced-arabidopsis-mutant-with-marked-chromosomal-rearrangement
#17
Ayako N Sakamoto, Vo Thi Thuong Lan, Satoru Fujimoto, Sachihiro Matsunaga, Atsushi Tanaka
Ion beams have been used as an effective tool in mutation breeding for the creation of crops with novel characteristics. Recent analyses have revealed that ion beams induce large chromosomal alterations, in addition to small mutations comprising base changes or frameshifts. In an effort to understand the potential capability of ion beams, we analyzed an Arabidopsis mutant possessing an abnormal genetic trait. The Arabidopsis mutant uvh3-2 is hypersensitive to UVB radiation when photoreactivation is unavailable...
June 15, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/28637339/emergence-of-ceftazidime-avibactam-non-susceptibility-in-an-mdr-klebsiella-pneumoniae-isolate
#18
Anna Both, Henning Büttner, Jiabin Huang, Markus Perbandt, Cristina Belmar Campos, Martin Christner, Florian P Maurer, Stefan Kluge, Christina König, Martin Aepfelbacher, Dominic Wichmann, Holger Rohde
Background: Avibactam is a novel broad-range β-lactamase inhibitor active against Ambler class A (including ESBL and KPC) and some Ambler class C and D (e.g. OXA-48) enzymes. We here report on the emergence of ceftazidime/avibactam resistance in clinical, multiresistant, OXA-48 and CTX-M-14-producing Klebsiella pneumoniae isolate DT12 during ceftazidime/avibactam treatment. Methods and results: Comparative whole-genome sequence analysis identified two SNPs in the CTX-M-14-encoding gene leading to two amino acid changes (P170S and T264I)...
June 16, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#19
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/28637261/further-simulations-and-analyses-demonstrate-open-problems-of-phylostratigraphy
#20
Bryan A Moyers, Jianzhi Zhang
Phylostratigraphy, originally designed for gene age estimation by BLAST-based protein homology searches of sequenced genomes, has been widely used for studying patterns and inferring mechanisms of gene origination and evolution. We previously showed by computer simulation that phylostratigraphy underestimates gene age for a non-negligible fraction of genes and that the underestimation is severer for genes with certain properties such as fast evolution and short protein sequences. Consequently, many previously reported age distributions of gene properties may have been methodological artifacts rather than biological realities...
June 14, 2017: Genome Biology and Evolution
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