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Human whole genome sequencing

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https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#1
Diyan Li, Tiandong Che, Binlong Chen, Shilin Tian, Xuming Zhou, Guolong Zhang, Miao Li, Uma Gaur, Yan Li, Majing Luo, Long Zhang, Zhongxian Xu, Xiaoling Zhao, Huadong Yin, Yan Wang, Long Jin, Qianzi Tang, Huailiang Xu, Mingyao Yang, Rongjia Zhou, Ruiqiang Li, Qing Zhu, Mingzhou Li
Background: Since the domestication of the red jungle fowls ( Gallus gallus ) (dating back to ∼10,000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28430103/genomic-characterization-of-recrudescent-plasmodium-malariae-after-treatment-with-artemether-lumefantrine
#2
Gavin G Rutledge, Ian Marr, G Khai Lin Huang, Sarah Auburn, Jutta Marfurt, Mandy Sanders, Nicholas J White, Matthew Berriman, Chris I Newbold, Nicholas M Anstey, Thomas D Otto, Ric N Price
Plasmodium malariae is the only human malaria parasite species with a 72-hour intraerythrocytic cycle and the ability to persist in the host for life. We present a case of a P. malariae infection with clinical recrudescence after directly observed administration of artemether/lumefantrine. By using whole-genome sequencing, we show that the initial infection was polyclonal and the recrudescent isolate was a single clone present at low density in the initial infection. Haplotypic analysis of the clones in the initial infection revealed that they were all closely related and were presumably recombinant progeny originating from the same infective mosquito bite...
August 15, 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28428825/comprehensive-evaluation-of-genome-wide-5-hydroxymethylcytosine-profiling-approaches-in-human-dna
#3
Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M Gould, Shalima S Nair, Susan J Clark, Clare Stirzaker
BACKGROUND: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28427244/whole-genome-expression-analyses-of-type-2-diabetes-in-human-skin-reveal-altered-immune-function-and-burden-of-infection
#4
Chun Wu, Xiaopan Chen, Jing Shu, Chun-Ting Lee
Skin disorders are among most common complications associated with type 2 diabetes mellitus (T2DM). Although T2DM patients are known to have increased risk of infections and other T2DM-related skin disorders, their molecular mechanisms are largely unknown. This study aims to identify dysregulated genes and gene networks that are associated with T2DM in human skin. We compared the expression profiles of 56,318 transcribed genes on 74 T2DM cases and 148 gender- age-, and race-matched non-diabetes controls from the Genotype-Tissue Expression (GTEx) database...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424085/the-within-host-population-dynamics-of-mycobacterium-tuberculosis-vary-with-treatment-efficacy
#5
Andrej Trauner, Qingyun Liu, Laura E Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sebastien Gagneux, Clifton E Barry, Qian Gao
BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics...
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28422133/gene-set-analysis-shows-association-between-fmrp-targets-and-autism-spectrum-disorder
#6
Arija Jansen, Gwen C Dieleman, August B Smit, Matthijs Verhage, Frank C Verhulst, Tinca J C Polderman, Danielle Posthuma
Autism spectrum disorder (ASD) is a heterogeneous group of disorders characterized by problems with social interaction, communication, and repetitive and restricted behavior. Despite its high heritability and the substantial progress made in elucidating genetic associations, the corresponding biological mechanisms are largely unknown. Our objective is to investigate the contribution of common genetic variation to biological pathways functionally involved in ASD. We conducted gene-set analyses to identify ASD-associated functional biological pathways using the statistical tools MAGMA and INRICH...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28421052/whole-genome-based-amplified-fragment-length-polymorphism-analysis-reveals-genetic-diversity-in-candida-africana
#7
Anuradha Chowdhary, Ferry Hagen, Cheshta Sharma, Abdullah M S Al-Hatmi, Letterio Giuffrè, Domenico Giosa, Shangrong Fan, Hamid Badali, Maria Rosa Felice, Sybren de Hoog, Jacques F Meis, Orazio Romeo
This study aimed at investigating the genetic diversity of a panel of Candida africana strains recovered from vaginal samples in different countries. All fungal strains were heterozygous at the mating-type-like locus and belonged to the genotype A of Candida albicans. Moreover, all examined C. africana strains lack N-acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed a distinctive polymorphism that impair the utilization of this amino sugar in this yeast. Multi-locus sequencing of seven housekeeping genes revealed a substantial genetic homogeneity among the strains, except for the CaMPIb, SYA1 and VPS13 loci which contributed significantly to the classification of our set of C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28420607/the-research-progress-of-farm-animal-genomics-based-on-sequencing-technologies
#8
Liang Suyun, Zhou Zhengkui, Hou Shuisheng
Various farm animal breeds have been domesticated and bred for thousands years, and they provide adequate animal-derived proteins to meet the human nutrition requirement. Although quantitative genetics was applied in animal breeding, which launched a technological revolution in the past century, a number of complex traits remain difficult to be selected based on pedigree derived breeding, due to complicated animal genetics and development mechanisms. Farm animal's genetic potential hasn't yet to be fully exploited...
April 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420548/expression-of-long-non-coding-rnas-in-autoimmunity-and-linkage-to-enhancer-function-and-autoimmune-disease-risk-genetic-variants
#9
T M Aune, P S Crooke, A E Patrick, J T Tossberg, N J Olsen, C F Spurlock
Genome-wide association studies have identified numerous genetic variants conferring autoimmune disease risk. Most of these genetic variants lie outside protein-coding genes hampering mechanistic explorations. Numerous mRNAs are also differentially expressed in autoimmune disease but their regulation is also unclear. The majority of the human genome is transcribed yet its biologic significance is incompletely understood. We performed whole genome RNA-sequencing [RNA-seq] to categorize expression of mRNAs, known and novel long non-coding RNAs [lncRNAs] in leukocytes from subjects with autoimmune disease and identified annotated and novel lncRNAs differentially expressed across multiple disorders...
April 15, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28420421/analysis-of-100-000-human-cancer-genomes-reveals-the-landscape-of-tumor-mutational-burden
#10
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S Lieber, Steven Roels, Jared White, Geoffrey A Otto, Jeffrey S Ross, Levi Garraway, Vincent A Miller, Phillip J Stephens, Garrett M Frampton
BACKGROUND: High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immunotherapy than PD-1 or PD-L1 expression, as measured by immunohistochemistry (IHC). The distribution of TMB and the subset of patients with high TMB has not been well characterized in the majority of cancer types. METHODS: In this study, we compare TMB measured by a targeted comprehensive genomic profiling (CGP) assay to TMB measured by exome sequencing and simulate the expected variance in TMB when sequencing less than the whole exome...
April 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28420414/integrated-genomic-analysis-of-mitochondrial-rna-processing-in-human-cancers
#11
Youssef Idaghdour, Alan Hodgkinson
BACKGROUND: The mitochondrial genome is transcribed as continuous polycistrons of RNA containing multiple genes. As a consequence, post-transcriptional events are critical for the regulation of gene expression and therefore all aspects of mitochondrial function. One particularly important process is the m(1)A/m(1)G RNA methylation of the ninth position of different mitochondrial tRNAs, which allows efficient processing of mitochondrial mRNAs and protein translation, and de-regulation of genes involved in these processes has been associated with altered mitochondrial function...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28418932/bmpr1b-mutation-causes-pierre-robin-sequence
#12
Yongjia Yang, Jianying Yuan, Xu Yao, Rong Zhang, Hui Yang, Rui Zhao, Jihong Guo, Ke Jin, Haibo Mei, Yongqi Luo, Liu Zhao, Ming Tu, Yimin Zhu
BACKGROUND: We investigated a large family with Pierre Robin sequence (PRS). AIM OF THE STUDY: This study aims to determine the genetic cause of PRS. RESULTS: The reciprocal translocation t(4;6)(q22;p21) was identified to be segregated with PRS in a three-generation family. Whole-genome sequencing and Sanger sequencing successfully detected breakpoints in the intragenic regions of BMRP1B and GRM4. We hypothesized that PRS in this family was caused by (i) haploinsufficiency for BMPR1B or (ii) a gain of function mechanism mediated by the BMPR1B-GRM4 fusion gene...
April 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28413162/whole-genome-sequence-of-the-metastatic-pc3-and-lncap-human-prostate-cancer-cell-lines
#13
Inge Seim, Penny L Jeffery, Patrick B Thomas, Colleen C Nelson, Lisa K Chopin
The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing and de novo assembly of PC3 (ATCC CRL-1435) and LNCaP (clone FGC; ATCC CRL-1740) at ~70X coverage. A known homozygous mutation in TP53 and homozygous loss of PTEN were robustly identified in the PC3 cell line, whereas the LNCaP cell line exhibited a larger number of putative inactivating somatic point and indel mutations (and in particular loss of stop codon events)...
April 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28412522/small-non-coding-rnas-in-adipocyte-biology-and-obesity
#14
REVIEW
Ez-Zoubir Amri, Marcel Scheideler
Obesity has reached epidemic proportions world-wide and constitutes a substantial risk factor for hypertension, type 2 diabetes, cardiovascular diseases and certain cancers. So far, regulation of energy intake by dietary and pharmacological treatments has met limited success. The main interest of current research is focused on understanding the role of different pathways involved in adipose tissue function and modulation of its mass. Whole-genome sequencing studies revealed that the majority of the human genome is transcribed, with thousands of non-protein-coding RNAs (ncRNA), which comprise small and long ncRNAs...
April 12, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28411849/the-molecular-revolution-in-cutaneous-biology-keratin-genes-and-their-associated-disease-diversity-opportunities-and-challenges
#15
REVIEW
Pierre A Coulombe
The abundance of keratin proteins and the filaments they form in surface epithelia has long been appreciated. This said, the remarkable diversity of keratin proteins and the notion that they are encoded by one of the largest gene families in the human genome has come to the fore relatively recently, coinciding with the sequencing of whole genomes. This complexity has generated some practical challenges, notably in terms of nomenclature and tractability. More importantly, however, studies of keratin have seeded the discovery of the genetic basis for a large number of genodermatoses and continue to provide a unique perspective on and insight into epithelial cells and tissues, whether normal or diseased...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411226/the-current-state-of-macrolide-resistance-in-campylobacter-a-review-of-trends-and-impacts-of-resistance-mechanisms
#16
Hannah Bolinger, Sophia Kathariou
Campylobacter spp., especially Campylobacter jejuni and C. coli, are leading bacterial foodborne pathogens worldwide. In the United States, an estimated 0.8 million cases of campylobacteriosis occur annually, mostly involving C. jejuni. Campylobacteriosis is generally self-limiting but in severe cases treatment with antibiotics may be mandated. Increasing incidence of fluoroquinolone resistance in Campylobacter has rendered macrolides like erythromycin and azithromycin the drugs of choice for human campylobacteriosis...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28409126/genomics-and-comparative-genomic-analyses-provide-insight-into-the-taxonomy-and-pathogenic-potential-of-novel-emmonsia-pathogens
#17
Ying Yang, Qiang Ye, Kang Li, Zongwei Li, Xiaochen Bo, Zhen Li, Yingchun Xu, Shengqi Wang, Peng Wang, Huipeng Chen, Junzhi Wang
Over the last 50 years, newly described species of Emmonsia-like fungi have been implicated globally as sources of systemic human mycosis (emmonsiosis). Their ability to convert into yeast-like cells capable of replication and extra-pulmonary dissemination during the course of infection differentiates them from classical Emmonsia species. Immunocompromised patients are at highest risk of emmonsiosis and exhibit high mortality rates. In order to investigate the molecular basis for pathogenicity of the newly described Emmonsia species, genomic sequencing and comparative genomic analyses of Emmonsia sp...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28408976/when-tads-go-bad-chromatin-structure-and-nuclear-organisation-in-human-disease
#18
REVIEW
Vera B Kaiser, Colin A Semple
Chromatin in the interphase nucleus is organised as a hierarchical series of structural domains, including self-interacting domains called topologically associating domains (TADs). This arrangement is thought to bring enhancers into closer physical proximity with their target genes, which often are located hundreds of kilobases away in linear genomic distance. TADs are demarcated by boundary regions bound by architectural proteins, such as CTCF and cohesin, although much remains to be discovered about the structure and function of these domains...
2017: F1000Research
https://www.readbyqxmd.com/read/28408691/whole-genome-sequence-of-staphylococcus-hominis-strain-j31-isolated-from-healthy-human-skin
#19
Rosanna Coates-Brown, Malcolm J Horsburgh
We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus hominis determined using the PacBio long-read sequencing platform. S. hominis is a major commensal of the skin microflora. This genome sequence adds to our understanding of this species and will aid studies of gene traffic between staphylococci.
April 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28408603/single-cell-whole-genome-analyses-by-linear-amplification-via-transposon-insertion-lianti
#20
Chongyi Chen, Dong Xing, Longzhi Tan, Heng Li, Guangyu Zhou, Lei Huang, X Sunney Xie
Single-cell genomics is important for biology and medicine. However, current whole-genome amplification (WGA) methods are limited by low accuracy of copy-number variation (CNV) detection and low amplification fidelity. Here we report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI), which outperforms existing methods, enabling micro-CNV detection with kilobase resolution. This allowed direct observation of stochastic firing of DNA replication origins, which differs from cell to cell...
April 14, 2017: Science
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