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Genome Biology

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https://www.readbyqxmd.com/read/27908293/autosomal-genetic-control-of-human-gene-expression-does-not-differ-across-the-sexes
#1
Irfahan Kassam, Luke Lloyd-Jones, Alexander Holloway, Kerrin S Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Greg Gibson, Tim D Spector, Tonu Esko, Grant W Montgomery, Joseph E Powell, Jian Yang, Peter M Visscher, Allan F McRae
BACKGROUND: Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, and has largely been explored by examining the contribution of genotype-by-sex interactions to variation in gene expression. RESULTS: In this study, we use data from a mixture of pedigree and unrelated individuals with verified European ancestry to investigate the sex-specific genetic architecture of gene expression measured in whole blood across n=1048 males and n=1005 females by treating gene expression intensities in the sexes as two distinct traits and estimating the genetic correlation (r G) between them...
December 1, 2016: Genome Biology
https://www.readbyqxmd.com/read/27908289/erratum-to-estimating-the-population-abundance-of-tissue-infiltrating-immune-and-stromal-cell-populations-using-gene-expression
#2
Etienne Becht, Nicolas A Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H Fridman, Aurélien de Reyniès
No abstract text is available yet for this article.
December 1, 2016: Genome Biology
https://www.readbyqxmd.com/read/27903283/systematic-analysis-of-chromatin-interactions-at-disease-associated-loci-links-novel-candidate-genes-to-inflammatory-bowel-disease
#3
Claartje A Meddens, Magdalena Harakalova, Noortje A M van den Dungen, Hassan Foroughi Asl, Hemme J Hijma, Edwin P J G Cuppen, Johan L M Björkegren, Folkert W Asselbergs, Edward E S Nieuwenhuis, Michal Mokry
BACKGROUND: Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate genes is predominantly based on genes that localize close to or within identified loci. We have recently shown that 92 of the 163 inflammatory bowel disease (IBD)-loci co-localize with non-coding DNA regulatory elements (DREs). Mutations in DREs can contribute to IBD pathogenesis through dysregulation of gene expression...
November 30, 2016: Genome Biology
https://www.readbyqxmd.com/read/27899157/disorders-of-sex-development-insights-from-targeted-gene-sequencing-of-a-large-international-patient-cohort
#4
Stefanie Eggers, Simon Sadedin, Jocelyn A van den Bergen, Gorjana Robevska, Thomas Ohnesorg, Jacqueline Hewitt, Luke Lambeth, Aurore Bouty, Ingrid M Knarston, Tiong Yang Tan, Fergus Cameron, George Werther, John Hutson, Michele O'Connell, Sonia R Grover, Yves Heloury, Margaret Zacharin, Philip Bergman, Chris Kimber, Justin Brown, Nathalie Webb, Matthew F Hunter, Shubha Srinivasan, Angela Titmuss, Charles F Verge, David Mowat, Grahame Smith, Janine Smith, Lisa Ewans, Carolyn Shalhoub, Patricia Crock, Chris Cowell, Gary M Leong, Makato Ono, Antony R Lafferty, Tony Huynh, Uma Visser, Catherine S Choong, Fiona McKenzie, Nicholas Pachter, Elizabeth M Thompson, Jennifer Couper, Anne Baxendale, Jozef Gecz, Benjamin J Wheeler, Craig Jefferies, Karen MacKenzie, Paul Hofman, Philippa Carter, Richard I King, Csilla Krausz, Conny M A van Ravenswaaij-Arts, Leendert Looijenga, Sten Drop, Stefan Riedl, Martine Cools, Angelika Dawson, Achmad Zulfa Juniarto, Vaman Khadilkar, Anuradha Khadilkar, Vijayalakshmi Bhatia, Vũ Chí Dũng, Irum Atta, Jamal Raza, Nguyen Thi Diem Chi, Tran Kiem Hao, Vincent Harley, Peter Koopman, Garry Warne, Sultana Faradz, Alicia Oshlack, Katie L Ayers, Andrew H Sinclair
BACKGROUND: Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously. RESULTS: We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD)...
November 29, 2016: Genome Biology
https://www.readbyqxmd.com/read/27899139/fruitful-analysis-of-sex-chromosomes-reveals-x-treme-genetic-diversity
#5
Angela M Taravella, Melissa A Wilson Sayres
A new study on sex chromosome evolution in papaya helps to illuminate sex chromosome biology, including deviations from expected trajectories.Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1095-9.
November 29, 2016: Genome Biology
https://www.readbyqxmd.com/read/27899133/adaptively-introgressed-neandertal-haplotype-at-the-oas-locus-functionally-impacts-innate-immune-responses-in-humans
#6
Aaron J Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Carolina Alfieri, Jerome E Tanner, Philipp W Messer, Luis B Barreiro
BACKGROUND: The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. RESULTS: Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus...
November 29, 2016: Genome Biology
https://www.readbyqxmd.com/read/27894357/new-insights-into-the-generation-and-role-of-de-novo-mutations-in-health-and-disease
#7
REVIEW
Rocio Acuna-Hidalgo, Joris A Veltman, Alexander Hoischen
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases...
November 28, 2016: Genome Biology
https://www.readbyqxmd.com/read/27894351/characterizing-the-morbid-genome-of-ciliopathies
#8
Ranad Shaheen, Katarzyna Szymanska, Basudha Basu, Nisha Patel, Nour Ewida, Eissa Faqeih, Amal Al Hashem, Nada Derar, Hadeel Alsharif, Mohammed A Aldahmesh, Anas M Alazami, Mais Hashem, Niema Ibrahim, Firdous M Abdulwahab, Rawda Sonbul, Hisham Alkuraya, Maha Alnemer, Saeed Al Tala, Muneera Al-Husain, Heba Morsy, Mohammed Zain Seidahmed, Neama Meriki, Mohammed Al-Owain, Saad AlShahwan, Brahim Tabarki, Mustafa A Salih, Tariq Faquih, Mohamed El-Kalioby, Marius Ueffing, Karsten Boldt, Clare V Logan, David A Parry, Nada Al Tassan, Dorota Monies, Andre Megarbane, Mohamed Abouelhoda, Anason Halees, Colin A Johnson, Fowzan S Alkuraya
BACKGROUND: Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete. RESULTS: We applied genomic approaches on a large patient cohort of 371 affected individuals from 265 families, with phenotypes that span the entire ciliopathy spectrum...
November 28, 2016: Genome Biology
https://www.readbyqxmd.com/read/27890017/extremely-low-nucleotide-diversity-in-the-x-linked-region-of-papaya-caused-by-a-strong-selective-sweep
#9
Robert VanBuren, Ching Man Wai, Jisen Zhang, Jennifer Han, Jie Arro, Zhicong Lin, Zhenyang Liao, Qingyi Yu, Ming-Li Wang, Francis Zee, Richard C Moore, Deborah Charlesworth, Ray Ming
BACKGROUND: The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region. RESULTS: Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity π syn = 0.00017, tenfold lower than the autosomal region (π syn = 0...
November 28, 2016: Genome Biology
https://www.readbyqxmd.com/read/27887642/rapid-scoring-of-genes-in-microbial-pan-genome-wide-association-studies-with-scoary
#10
Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS...
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27887640/functional-and-regulatory-profiling-of-energy-metabolism-in-fission-yeast
#11
Michal Malecki, Danny A Bitton, Maria Rodríguez-López, Charalampos Rallis, Noelia Garcia Calavia, Graeme C Smith, Jürg Bähler
BACKGROUND: The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration. RESULTS: We screened deletion libraries of fission yeast to identify over 200 genes required for respiratory growth...
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27887629/the-oxford-nanopore-minion-delivery-of-nanopore-sequencing-to-the-genomics-community
#12
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884205/whole-genome-sequence-analysis-of-serum-amino-acid-levels
#13
Bing Yu, Paul S de Vries, Ginger A Metcalf, Zhe Wang, Elena V Feofanova, Xiaoming Liu, Donna Marie Muzny, Lynne E Wagenknecht, Richard A Gibbs, Alanna C Morrison, Eric Boerwinkle
BACKGROUND: Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene-environment interactions. Whole genome sequence analysis of amino acid levels may establish a paradigm for analyzing quantitative risk factors. RESULTS: In a discovery cohort of 1872 African Americans and a replication cohort of 1552 European Americans we sequenced exons and whole genomes and measured serum levels of 70 amino acids...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884178/patterns-of-ribosomal-protein-expression-specify-normal-and-malignant-human-cells
#14
Joao C Guimaraes, Mihaela Zavolan
BACKGROUND: Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some ribosomal proteins (RPs) across tissues and highly specific effects on the translation of individual mRNAs. RESULTS: To determine whether RPs are more generally linked to cell identity, we analyze the heterogeneity of RP expression in a large set of human tissues, primary cells, and tumors...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884173/revisiting-the-morbid-genome-of-mendelian-disorders
#15
Mohamed Abouelhoda, Tariq Faquih, Mohamed El-Kalioby, Fowzan S Alkuraya
BACKGROUND: The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign "disease mutations" are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants. RESULTS: We collated all "disease-related mutations" listed in the Human Gene Mutation Database (HGMD) and ClinVar, including "variants of uncertain significance" (VOUS)...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27863519/tet-dependent-regulation-of-retrotransposable-elements-in-mouse-embryonic-stem-cells
#16
Lorenzo de la Rica, Özgen Deniz, Kevin C L Cheng, Christopher D Todd, Cristina Cruz, Jonathan Houseley, Miguel R Branco
BACKGROUND: Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes. Epigenetic mechanisms controlling TEs have the potential to affect their mobility and to drive the co-adoption of TEs for the benefit of the host. RESULTS: We performed a detailed investigation of the role of TET enzymes in the regulation of TEs in mouse embryonic stem cells (ESCs)...
November 18, 2016: Genome Biology
https://www.readbyqxmd.com/read/27855707/a-novel-codon-based-de-bruijn-graph-algorithm-for-gene-construction-from-unassembled-transcriptomes
#17
Gongxin Peng, Peifeng Ji, Fangqing Zhao
Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions. We present inGAP-CDG, which can construct full-length and non-redundant coding sequences from unassembled transcriptomes by using a codon-based de Bruijn graph to simplify the assembly process and a machine learning-based approach to filter false positives...
November 17, 2016: Genome Biology
https://www.readbyqxmd.com/read/27855702/tumor-immune-microenvironment-characterization-in-clear-cell-renal-cell-carcinoma-identifies-prognostic-and-immunotherapeutically-relevant-messenger-rna-signatures
#18
Yasin Şenbabaoğlu, Ron S Gejman, Andrew G Winer, Ming Liu, Eliezer M Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J Manley, Danny N Khalil, Samuel D Kaffenberger, Yingbei Chen, Ludmila Danilova, Martin H Voss, Jonathan A Coleman, Paul Russo, Victor E Reuter, Timothy A Chan, Emily H Cheng, David A Scheinberg, Ming O Li, Toni K Choueiri, James J Hsieh, Chris Sander, A Ari Hakimi
BACKGROUND: Tumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as the expression of antigen presenting machinery genes, remain poorly characterized. Here, we employ a gene expression-based computational method to profile the infiltration levels of 24 immune cell populations in 19 cancer types. RESULTS: We compare cancer types using an immune infiltration score and a T cell infiltration score and find that clear cell renal cell carcinoma (ccRCC) is among the highest for both scores...
November 17, 2016: Genome Biology
https://www.readbyqxmd.com/read/27855690/the-continuum-of-causality-in-human-genetic-disorders
#19
Nicholas Katsanis
Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare, common, benign, or deleterious based on their population frequencies. The availability of exome and genome data, as well as gene and allele discovery for various conditions, is beginning to challenge classic definitions of genetic causality. Here, I discuss recent advances in our understanding of the overlap between rare and complex diseases and the context-dependent effect of both rare and common alleles that underscores the need for revising the traditional categorizations of genetic traits...
November 17, 2016: Genome Biology
https://www.readbyqxmd.com/read/27846892/choosing-panels-of-genomics-assays-using-submodular-optimization
#20
Kai Wei, Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble
Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a priori which assays to perform is, thus, a critical step in many studies. We present the submodular selection of assays (SSA), a method for choosing a diverse panel of genomic assays that leverages methods from submodular optimization. More generally, this application serves as a model for how submodular optimization can be applied to other discrete problems in biology...
November 15, 2016: Genome Biology
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