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Human whole genome sequencing

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https://www.readbyqxmd.com/read/28730524/genetic-characterization-of-novel-reassortant-h5n6-subtype-influenza-viruses-isolated-from-cats-in-eastern-china
#1
Xueliang Cao, Fan Yang, Haibo Wu, Lihua Xu
Cats are susceptible to influenza A viruses and therefore may act as transmission vectors within households, posing a potential public health concern. Two novel reassortant H5N6 influenza viruses were isolated from cats in Zhejiang Province, Eastern China, in 2016. Both viruses were characterized by whole-genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis showed that these viruses received their genes from H5N6, H9N2, and H7N9 influenza viruses isolated from China...
July 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28730479/analysis-of-drug-resistance-using-kinome-wide-functional-screens
#2
Katherine R Singleton, Keith T Earley, Lynn E Heasley
The clinical success of tyrosine kinase inhibitors specific for BCR-ABL-, EGFR-, ALK-, and ROS1-driven cancers continues to spur the quest to match specific oncogene-defined tumor types with an appropriate molecularly targeted therapy. Unfortunately, responses to these agents are not durable with intrinsic or acquired resistance limiting benefit. Additionally, efforts to identify the appropriate targets of new drugs have focused on nonfunctional assays such as large-scale sequencing for somatic mutations or analysis of gene copy number...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729271/whole-genome-sequence-of-acinetobacter-pittii-humv-6483-isolated-from-human-urine
#3
Itziar Chapartegui-González, María Lázaro-Díez, Santiago Redondo-Salvo, Laura Alted-Pérez, Javier Gonzalo Ocejo-Vinyals, Jesús Navas, José Ramos-Vivas
Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28728880/genetic-adaptation-to-historical-pathogen-burdens
#4
Johannes W Fedderke, Robert E Klitgaard, Valerio Napolioni
Historical pathogen burdens are examined as possible triggers for genetic adaptation. Evidence of adaptation emerges for the acid phosphatase locus 1 (ACP1), interleukin-6 (IL6), interleukin-10 (IL10 ), human leukocyte antigen (HLA) polymorphisms, along with a measure of heterozygosity over 783 alleles. Results are robust to controlling for the physical and historical environment humans faced, and to endogeneity of the historical pathogen burden measure. The present study represents a proof-of-concept which may pave the way to the analysis of future aggregate measures coming from whole-genome sequencing/genotyping data...
July 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28725045/genomic-epidemiology-of-global-klebsiella-pneumoniae-carbapenemase-kpc-producing-escherichia-coli
#5
N Stoesser, A E Sheppard, G Peirano, L W Anson, L Pankhurst, R Sebra, H T T Phan, A Kasarskis, A J Mathers, T E A Peto, P Bradford, M R Motyl, A S Walker, D W Crook, J D Pitout
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720731/an-in-vitro-chicken-gut-model-demonstrates-transfer-of-a-multidrug-resistance-plasmid-from-salmonella-to-commensal-escherichia-coli
#6
Roderick M Card, Shaun A Cawthraw, Javier Nunez-Garcia, Richard J Ellis, Gemma Kay, Mark J Pallen, Martin J Woodward, Muna F Anjum
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28716113/whole-metagenome-profiles-of-particulates-collected-from-the-international-space-station
#7
Nicholas A Be, Aram Avila-Herrera, Jonathan E Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing, Kasthuri Venkateswaran
BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized...
July 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28715472/a-novel-isoform-of-il-33-revealed-by-screening-for-transposable-element-promoted-genes-in-human-colorectal-cancer
#8
Frances E Lock, Artem Babaian, Ying Zhang, Liane Gagnier, Sabrina Kuah, Antonia Weberling, Mohammad M Karimi, Dixie L Mager
Remnants of ancient transposable elements (TEs) are abundant in mammalian genomes. These sequences contain multiple regulatory motifs and hence are capable of influencing expression of host genes. TEs are known to be released from epigenetic repression and can become transcriptionally active in cancer. Such activation could also lead to lineage-inappropriate activation of oncogenes, as previously described in lymphomas. However, there are few reports of this mechanism occurring in non-blood cancers. Here, we re-analyzed whole transcriptome data from a large cohort of patients with colon cancer, compared to matched normal colon control samples, to detect genes or transcripts ectopically expressed through activation of TE promoters...
2017: PloS One
https://www.readbyqxmd.com/read/28713351/a-genome-wide-association-study-to-identify-diagnostic-markers-for-human-pathogenic-campylobacter-jejuni-strains
#9
Cody J Buchanan, Andrew L Webb, Steven K Mutschall, Peter Kruczkiewicz, Dillon O R Barker, Benjamin M Hetman, Victor P J Gannon, D Wade Abbott, James E Thomas, G Douglas Inglis, Eduardo N Taboada
Campylobacter jejuni is a leading human enteric pathogen worldwide and despite an improved understanding of its biology, ecology, and epidemiology, limited tools exist for identifying strains that are likely to cause disease. In the current study, we used subtyping data in a database representing over 24,000 isolates collected through various surveillance projects in Canada to identify 166 representative genomes from prevalent C. jejuni subtypes for whole genome sequencing. The sequence data was used in a genome-wide association study (GWAS) aimed at identifying accessory gene markers associated with clinically related C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28711667/identification-of-three-homologous-latex-clearing-protein-lcp-genes-from-the-genome-of-streptomyces-sp-strain-cfmr-7
#10
Jayaram Nanthini, Su Yean Ong, Kumar Sudesh
Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28711147/future-directions-of-genomics-research-in-rheumatic-diseases
#11
REVIEW
Yukinori Okada, Toshihiro Kishikawa, Saori Sakaue, Jun Hirata
Recent developments in human genome genotyping and sequencing technologies, such as genome-wide association studies and whole-genome sequencing analyses, have successfully identified several risk genes of rheumatic diseases. Fine-mapping studies using the HLA imputation method revealed that classical and non-classical HLA genes contribute to the risk of rheumatic diseases. Integration of human disease genomics with biological, medical, and clinical databases should contribute to the elucidation of disease pathogenicity and novel drug discovery...
August 2017: Rheumatic Diseases Clinics of North America
https://www.readbyqxmd.com/read/28708842/evaluating-whole-genome-sequence-data-from-the-genetic-absence-epilepsy-rat-from-strasbourg-and-its-related-non-epileptic-strain
#12
Pablo M Casillas-Espinosa, Kim L Powell, Mingfu Zhu, C Ryan Campbell, Jessica M Maia, Zhong Ren, Nigel C Jones, Terence J O'Brien, Slavé Petrovski
OBJECTIVE: The Genetic Absence Epilepsy Rats from Strasbourg (GAERS) are an inbreed Wistar rat strain widely used as a model of genetic generalised epilepsy with absence seizures. As in humans, the genetic architecture that results in genetic generalized epilepsy in GAERS is poorly understood. Here we present the strain-specific variants found among the epileptic GAERS and their related Non-Epileptic Control (NEC) strain. The GAERS and NEC represent a powerful opportunity to identify neurobiological factors that are associated with the genetic generalised epilepsy phenotype...
2017: PloS One
https://www.readbyqxmd.com/read/28706735/the-importance-of-copy-number-variation-in-congenital-heart-disease
#13
Gregory Costain, Candice K Silversides, Anne S Bassett
Congenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD...
September 14, 2016: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/28706299/findings-of-a-1303-korean-whole-exome-sequencing-study
#14
Soo Heon Kwak, Jeesoo Chae, Seongmin Choi, Min Jung Kim, Murim Choi, Jong-Hee Chae, Eun-Hae Cho, Tai Ju Hwang, Se Song Jang, Jong-Il Kim, Kyong Soo Park, Yung-Jue Bang
Ethnically specific data on genetic variation are crucial for understanding human biology and for clinical interpretation of variant pathogenicity. We analyzed data obtained by deep sequencing 1303 Korean whole exomes; the data were generated by three independent whole exome sequencing projects (named the KOEX study). The primary focus of this study was to comprehensively analyze the variant statistics, investigate secondary findings that may have clinical actionability, and identify loci that should be cautiously interpreted for pathogenicity...
July 14, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28706213/transmission-of-highly-virulent-community-associated-mrsa-st93-and-livestock-associated-mrsa-st398-between-humans-and-pigs-in-australia
#15
S Sahibzada, S Abraham, G W Coombs, S Pang, M Hernández-Jover, D Jordan, J Heller
Pigs have been recognised as a reservoir of livestock associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in Europe, Asia and North America. However, little is known about the presence and distribution of MRSA in the Australian pig population and pig industry. This study describes the presence, distribution and molecular characteristics of the human adapted Australian CA-MRSA ST93 isolated from pigs, people, and the environment within a piggery. Isolates were subjected to antibiotic susceptibility testing, DNA microarray, whole genome sequencing, multi locus sequence typing, virulence and resistance gene characterization and phylogenetic analysis...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705883/assessing-genome-wide-copy-number-variation-in-the-han-chinese-population
#16
Jianqi Lu, Haiyi Lou, Ruiqing Fu, Dongsheng Lu, Feng Zhang, Zhendong Wu, Xi Zhang, Changhua Li, Baijun Fang, Fangfang Pu, Jingning Wei, Qian Wei, Chao Zhang, Xiaoji Wang, Yan Lu, Shi Yan, Yajun Yang, Li Jin, Shuhua Xu
BACKGROUND: Copy number variation (CNV) is a valuable source of genetic diversity in the human genome and a well-recognised cause of various genetic diseases. However, CNVs have been considerably under-represented in population-based studies, particularly the Han Chinese which is the largest ethnic group in the world. OBJECTIVES: To build a representative CNV map for the Han Chinese population. METHODS: We conducted a genome-wide CNV study involving 451 male Han Chinese samples from 11 geographical regions encompassing 28 dialect groups, representing a less-biased panel compared with the currently available data...
July 13, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28702005/insights-into-a-novel-blakpc-2-encoding-incp-6-plasmid-reveal-carbapenem-resistance-circulation-in-several-enterobacteriaceae-species-from-wastewater-and-a-hospital-source-in-spain
#17
Yancheng Yao, Fernando Lazaro-Perona, Linda Falgenhauer, Aránzazu Valverde, Can Imirzalioglu, Lucas Dominguez, Rafael Cantón, Jesús Mingorance, Trinad Chakraborty
Untreated wastewater, particularly from hospitals and other healthcare facilities, is considered to be a reservoir for multidrug-resistant bacteria. However, its role in the spread of antibiotic resistances in the human population remains poorly investigated. We used whole genome sequencing to analyze 25 KPC-2-producing Enterobacteriaceae isolates from sewage water collected during a 3-year period and three clinical Citrobacter freundii isolates from a tertiary hospital in the same collection area in Spain...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28701756/seed-metabolome-analysis-of-a-transgenic-rice-line-expressing-cholera-toxin-b-subunit
#18
Takumi Ogawa, Koji Kashima, Yoshikazu Yuki, Mio Mejima, Shiho Kurokawa, Masaharu Kuroda, Atsushi Okazawa, Hiroshi Kiyono, Daisaku Ohta
Plant-based human vaccines have been actively developed in recent years, and rice (Oryza sativa L.) is one of the best candidate crops for their production and delivery. By expressing a modified cholera toxin B (CTB) subunit, we previously developed MucoRice-CTB, a rice-based vaccine against cholera, which is caused by infection of the intestine with the bacteria Vibrio cholerae. MucoRice-CTB lines have been extensively characterized by whole-genome sequencing and proteome analyses to evaluate the mutation profiles and proteome status, respectively...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701744/massively-parallel-whole-genome-amplification-for-single-cell-sequencing-using-droplet-microfluidics
#19
Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama
Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701400/whole-genome-sequencing-and-variant-analysis-of-hpv16-infections
#20
Pascal van der Weele, Chris J L M Meijer, Audrey J King
Human papillomavirus (HPV) is a strongly conserved DNA virus, of which high-risk types can cause cervical cancer in persistent infections. The most common type found in HPV-attributable cancer is HPV16, which can be subdivided into four lineages (A-D) with different carcinogenic properties. Studies have shown HPV16 sequence diversity in different geographical areas, but only limited information is available regarding HPV16 diversity within a population, especially at the whole genome level. We have analyzed HPV16 major variant diversity, conservation in persistent infections and performed a SNP comparison between persistent and clearing infections...
July 12, 2017: Journal of Virology
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