keyword
MENU ▼
Read by QxMD icon Read
search

whole genome sequence

keyword
https://www.readbyqxmd.com/read/28550183/somatic-mutation-spectrum-in-monoclonal-gammopathy-of-undetermined-significance-indicates-a-less-complex-genomic-landscape-compared-to-multiple-myeloma
#1
Aneta Mikulasova, Christopher P Wardell, Alexander Murison, Eileen M Boyle, Graham H Jackson, Jan Smetana, Zuzana Kufova, Ludek Pour, Viera Sandecka, Martina Almasi, Pavla Vsianska, Evzen Gregora, Petr Kuglik, Roman Hajek, Faith E Davies, Gareth J Morgan, Brian A Walker
Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about the molecular mechanism of malignant transformation. We have performed whole exome sequencing together with CGH+SNP array analysis in 33 flow-cytometry separated abnormal plasma cell samples from MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level...
May 26, 2017: Haematologica
https://www.readbyqxmd.com/read/28550066/rapid-whole-genome-sequencing-identifies-a-novel-homozygous-npc1-variant-associated-with-niemann-pick-type-c1-disease-in-a-7-week-old-male-with-cholestasis
#2
Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Serge Batalov, David M Dimmock, Rcigm Investigators, Stephen F Kingsmore
Niemann-Pick Type C disease (NPC; OMIM #257220) is an inborn error of intracellular cholesterol trafficking. It is an autosomal recessive disorder caused predominantly by mutations in NPC1. While characterized as a progressive neurological disorder, it can also cause cholestasis and liver dysfunction due to intrahepatocyte lipid accumulation. We report a 7 week old who was admitted with neonatal cholestasis, who was diagnosed with a novel homozygous stop-gain variant in NPC1 by rapid whole genome sequencing (WGS)...
May 26, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28550058/whole-genome-and-core-genome-multilocus-sequence-typing-and-single-nucleotide-polymorphism-analyses-of-listeria-monocytogenes-associated-with-an-outbreak-linked-to-cheese-united-states-2013
#3
Yi Chen, Yan Luo, Heather Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey Parish, Thomas S Hammack, Peter S Evans, Cheryl L Tarr, Marc W Allard, Errol A Strain, Eric W Brown
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28550057/prevalence-and-genomic-characterization-of-escherichia-coli-o157-h7-in-cow-calf-herds-throughout-california
#4
Jay N Worley, Kristopher A Flores, Xun Yang, Jennifer A Chase, Guojie Cao, Shuai Tang, Jianghong Meng, Edward R Atwill
Escherichia coli serotype O157:H7 (E. coli O157:H7) is a zoonotic food- and waterborne bacterial pathogen that has a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, like cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle present food safety challenges on a uniquely large scale...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28549490/whole-genome-analysis-reveals-new-insights-into-macrolide-resistance-in-mycoplasma-pneumoniae
#5
Shao Li Li, Hong Mei Sun, Bao Li Zhu, Fei Liu, Han Qing Zhao
OBJECTIVE: Mutations in 23S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae (M. pneumoniae). However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae. METHODS: The whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina HiSeq2000 platform...
May 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28549128/atad3-gene-cluster-deletions-cause-cerebellar-dysfunction-associated-with-altered-mitochondrial-dna-and-cholesterol-metabolism
#6
Radha Desai, Ann E Frazier, Romina Durigon, Harshil Patel, Aleck W Jones, Ilaria Dalla Rosa, Nicole J Lake, Alison G Compton, Hayley S Mountford, Elena J Tucker, Alice L R Mitchell, Deborah Jackson, Abdul Sesay, Miriam Di Re, Lambert P van den Heuvel, Derek Burke, David Francis, Sebastian Lunke, George McGillivray, Simone Mandelstam, Fanny Mochel, Boris Keren, Claude Jardel, Anne M Turner, P Ian Andrews, Jan Smeitink, Johannes N Spelbrink, Simon J Heales, Masakazu Kohda, Akira Ohtake, Kei Murayama, Yasushi Okazaki, Anne Lombès, Ian J Holt, David R Thorburn, Antonella Spinazzola
Although mitochondrial disorders are clinically heterogeneous, they frequently involve the central nervous system and are among the most common neurogenetic disorders. Identifying the causal genes has benefited enormously from advances in high-throughput sequencing technologies; however, once the defect is known, researchers face the challenge of deciphering the underlying disease mechanism. Here we characterize large biallelic deletions in the region encoding the ATAD3C, ATAD3B and ATAD3A genes. Although high homology complicates genomic analysis of the ATAD3 defects, they can be identified by targeted analysis of standard single nucleotide polymorphism array and whole exome sequencing data...
June 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28548214/the-performance-of-malbac-and-mda-methods-in-the-identification-of-concurrent-mutations-and-aneuploidy-screening-to-diagnose-beta-thalassaemia-disorders-at-the-single-and-multiple-cell-levels
#7
WeiQiang Liu, HuiMin Zhang, Dan Hu, SiJia Lu, XiaoFang Sun
AIM: To select an optimal whole-genome amplification (WGA) method to improve the efficiency of the preimplantation genetic diagnosis and screening (PGD/PGS) of beta-thalassaemia disorders. METHODS: Fifty-seven fibroblast samples with defined beta-thalassaemia variations and forty-eight single-blastomere samples were amplified from single-, two-, and five-cell samples by multiple annealing and looping-based amplification cycles (MALBAC) and the multiple displacement amplification (MDA) method...
May 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28548177/specific-dna-sequences-allosterically-enhance-protein-protein-interaction-in-a-transcription-factor-through-modulation-of-protein-dynamics-implications-for-specificity-of-gene-regulation
#8
Abhishek Mazumder, Subrata Batabyal, Manas Mondal, Tanumoy Mondol, Susobhan Choudhury, Raka Ghosh, Tanaya Chatterjee, Dhananjay Bhattacharyya, Samir Kumar Pal, Siddhartha Roy
Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface...
May 26, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28548113/erratum-the-first-complete-genome-sequences-of-the-aci-lineage-the-most-abundant-freshwater-actinobacteria-obtained-by-whole-genome-amplification-of-dilution-to-extinction-cultures
#9
Ilnam Kang, Suhyun Kim, Md Rashedul Islam, Jang-Cheon Cho
This corrects the article DOI: 10.1038/srep42252.
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#10
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28548082/whole-genome-sequencing-and-imputation-in-isolated-populations-identify-genetic-associations-with-medically-relevant-complex-traits
#11
Lorraine Southam, Arthur Gilly, Dániel Süveges, Aliki-Eleni Farmaki, Jeremy Schwartzentruber, Ioanna Tachmazidou, Angela Matchan, Nigel W Rayner, Emmanouil Tsafantakis, Maria Karaleftheri, Yali Xue, George Dedoussis, Eleftheria Zeggini
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28546995/the-cost-and-cost-trajectory-of-whole-genome-analysis-guiding-treatment-of-patients-with-advanced-cancers
#12
Deirdre Weymann, Janessa Laskin, Robyn Roscoe, Kasmintan A Schrader, Stephen Chia, Stephen Yip, Winson Y Cheung, Karen A Gelmon, Aly Karsan, Daniel J Renouf, Marco Marra, Dean A Regier
BACKGROUND: Limited data exist on the real-world costs of applying whole-genome analysis (WGA) in a clinical setting. We estimated the costs of applying WGA to guide treatments for patients with advanced cancers and characterized how costs evolve over time. METHODS: The setting is the British Columbia Cancer Agency Personalized OncoGenomics (POG) program in British Columbia, Canada. Cost data were obtained for patients who enrolled in the program from 2012 to 2015...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546496/genome-sequence-of-brevibacillus-laterosporus-uniss-18-a-pathogen-of-mosquitoes-and-flies
#13
Salvatore Camiolo, Andrea Porceddu, Luca Ruiu
The entomopathogenic properties of Brevibacillus laterosporus UNISS 18 against insects are well documented. Here, we report the whole-genome sequence of this strain, which revealed the presence of several insecticide action-related genes. The deriving genetic information will help to elucidate the mechanisms underlying strain specificity and virulence against diverse target pests.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546493/whole-genome-sequence-of-the-bacteriophage-sensitive-strain-campylobacter-jejuni-nctc12662
#14
Yilmaz Emre Gencay, Martine C H Sørensen, Lone Brøndsted
Campylobacter jejuni NCTC12662 has been the choice bacteriophage isolation strain due to its susceptibility to C. jejuni bacteriophages. This trait makes it a good candidate for studying bacteriophage-host interactions. We report here the whole-genome sequence of NCTC12662, allowing future elucidation of the molecular mechanisms of phage-host interactions in C. jejuni.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546492/complete-genome-sequence-of-photobacterium-damselae-subsp-piscicida-strain-ot-51443-isolated-from-yellowtail-seriola-quinqueradiata-in-japan
#15
Takashi Aoki, Yuki Teru, Natsuki Morimoto, Tomoya Kono, Masahiro Sakai, Tomokazu Takano, John P Hawke, Yutaka Fukuda, Haruko Takeyama, Jun-Ichi Hikima
Pseudotuberculosis caused by infection of Photobacterium damselae subsp. piscicida has caused serious economic damages to aquaculture farms worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida strain OT-51443, isolated in Japan, was determined and suggests that this genome consists of two chromosomes and five plasmids.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546491/genome-sequence-of-acinetobacter-lactucae-otec-02-isolated-from-hydrocarbon-contaminated-soil
#16
Marco Antonio Rogel-Hernandez, Gabriela Guerrero, Clara Ivette Rincón-Molina, Víctor Manuel Ruiz-Valdiviezo, Crhistian Cisneros-Pérez, José Humberto Castañón-Gonzalez, Aline López-López, Esperanza Martinez-Romero, Reiner Rincón-Rosales
Acinetobacter lactucae OTEC-02 was isolated from hydrocarbon-contaminated soils. Whole-genome sequence analysis was performed to learn more about the strain's ability to degrade different types of recalcitrant toxic monoaromatic hydrocarbons. The genome of this bacterium revealed its genomic properties and versatile metabolic features, as well as a complete prophage.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546490/complete-genome-sequence-of-the-campylobacter-helveticus-type-strain-atcc-51209
#17
William G Miller, Emma Yee, James L Bono
Campylobacter helveticus has been isolated from domestic dogs and cats. Although C. helveticus is closely related to the emerging human pathogen C. upsaliensis, no C. helveticus-associated cases of human illness have been reported. This study describes the whole-genome sequence of the C. helveticus type strain ATCC 51209 (=CCUG 30682(T)).
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546483/finished-whole-genome-sequences-of-two-clostridium-botulinum-type-a-b-isolates
#18
Jessica L Halpin, Karen Hill, Shannon L Johnson, David Carlton Bruce, T Brian Shirey, Janet K Dykes, Carolina Lúquez
Clostridium botulinum secretes a potent neurotoxin that causes devastating effects when ingested, including paralysis and death if not treated. In the United States, some clinically significant strains produce toxin type A while also harboring a silent B gene. These are the first two closed genome sequences published for this subset.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546482/finished-whole-genome-sequence-of-clostridium-argentinense-producing-botulinum-neurotoxin-type-g
#19
Jessica L Halpin, Karen Hill, Shannon L Johnson, David Carlton Bruce, T Brian Shirey, Janet K Dykes, Carolina Lúquez
Here, we present a closed genome sequence for Clostridium argentinense strain 89G, the first strain identified to produce botulinum neurotoxin type G (BoNT/G). Although discovered in 1970, to date, there have been no reference quality sequences publicly available for this species.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546474/draft-genome-sequence-of-rhodococcus-sp-strain-66b
#20
Louise F Thatcher, Cindy A Myers, Cathryn A O'Sullivan, Margaret M Roper
We report here the draft genome sequence and annotation of Rhodococcus sp. strain 66b isolated from the soil of southwest Western Australia. This strain exhibits a range of bioactivities, including plant growth promotion, biosurfactant production, and wax degradation. Whole-genome sequencing was conducted to uncover the underlying mechanisms.
May 25, 2017: Genome Announcements
keyword
keyword
97998
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"