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Genome Biology

Brigitte T Hofmeister, Kevin Lee, Nicholas A Rohr, David W Hall, Robert J Schmitz
BACKGROUND: Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phenotypic diversity beyond changes to nucleotide sequence. Previous research has looked at the rate at which spontaneous epialleles arise but it is currently unknown how they are maintained across generations. RESULTS: We used two Arabidopsis thaliana mutation accumulation (MA) lines and determined that over 99...
August 16, 2017: Genome Biology
Richard J Roberts, Mauricio O Carneiro, Michael C Schatz
No abstract text is available yet for this article.
August 16, 2017: Genome Biology
Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W Hentze, Andreas E Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R Sibley, Kathi Zarnack, Jernej Ule
No abstract text is available yet for this article.
August 15, 2017: Genome Biology
Amin Emad, Junmei Cairns, Krishna R Kalari, Liewei Wang, Saurabh Sinha
BACKGROUND: Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characterization of the mechanism of action of drugs. Furthermore, screening the expression of these genes in the tumor tissue may suggest the best course of chemotherapy or a combination of drugs to overcome drug resistance. RESULTS: We developed a computational method called ProGENI to identify genes most associated with the variation of drug response across different individuals, based on gene expression data...
August 11, 2017: Genome Biology
Ben Langmead
Read alignment is the first step in most sequencing data analyses. Because a read's point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. I describe a framework for predicting mapping qualities that works by simulating a set of tandem reads. These are like the input reads in important ways, but the true point of origin is known...
August 10, 2017: Genome Biology
Pierre J Fabre, Marion Leleu, Benjamin H Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Leonardo Beccari, Denis Duboule
BACKGROUND: The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. RESULTS: To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH...
August 7, 2017: Genome Biology
Alan F Rubin, Hannah Gelman, Nathan Lucas, Sandra M Bajjalieh, Anthony T Papenfuss, Terence P Speed, Douglas M Fowler
Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error estimates for each measurement, capturing both sampling error and consistency between replicates. We apply our model to one novel and five published datasets comprising 243,732 variants and demonstrate its superiority in removing noisy variants and conducting hypothesis testing. Simulations show our model applies to scans based on cell growth or binding and handles common experimental errors...
August 7, 2017: Genome Biology
Koen Van den Berge, Charlotte Soneson, Mark D Robinson, Lieven Clement
RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests and allows post hoc assessment for significant genes. This method provides gene-level FDR control and boosts power for testing interaction effects. In transcript-level analysis, it provides a framework that performs powerful gene-level tests while maintaining biological interpretation at transcript-level resolution...
August 7, 2017: Genome Biology
Nadia M Davidson, Anthony D K Hawkins, Alicia Oshlack
Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. We demonstrate how superTranscripts enable visualisation, variant detection and differential isoform detection in non-model organisms...
August 4, 2017: Genome Biology
Michael R Speicher
A meeting report on the Third European Association for Cancer Research Conference on Cancer Genomics, held at Churchill College, Cambridge, UK, 25-28 June 2017.
August 3, 2017: Genome Biology
Artika P Nath, Scott C Ritchie, Sean G Byars, Liam G Fearnley, Aki S Havulinna, Anni Joensuu, Antti J Kangas, Pasi Soininen, Annika Wennerström, Lili Milani, Andres Metspalu, Satu Männistö, Peter Würtz, Johannes Kettunen, Emma Raitoharju, Mika Kähönen, Markus Juonala, Aarno Palotie, Mika Ala-Korpela, Samuli Ripatti, Terho Lehtimäki, Gad Abraham, Olli Raitakari, Veikko Salomaa, Markus Perola, Michael Inouye
BACKGROUND: Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking. Here, we integrate blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts (total N = 2168), including a subset of individuals with matched multi-omic data at 7-year follow-up. RESULTS: We identify topologically replicable gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity...
August 1, 2017: Genome Biology
Rajiv C McCoy, Joshua M Akey
Using a powerful machine learning approach, a recent study of human genomes has revealed widespread footprints of recent positive selection on standing genetic variation.
August 1, 2017: Genome Biology
Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo, Frank Alber
BACKGROUND: Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments...
July 31, 2017: Genome Biology
Eddie Park, Jiguang Guo, Shihao Shen, Levon Demirdjian, Ying Nian Wu, Lan Lin, Yi Xing
BACKGROUND: A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing. RESULTS: In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis...
July 28, 2017: Genome Biology
Nisha Patel, Arif O Khan, Maher Al-Saif, Walid N Moghrabi, Balsam M AlMaarik, Niema Ibrahim, Firdous Abdulwahab, Mais Hashem, Tarfa Alshidi, Eman Alobeid, Rana A Alomar, Saad Al-Harbi, Mohamed Abouelhoda, Khalid S A Khabar, Fowzan S Alkuraya
BACKGROUND: Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations associated with the multisystem disorder linked to the gene. This remains an incompletely understood phenomenon with proposed mechanisms ranging from allele-specific to stochastic. RESULTS: We report three consanguineous families in which an isolated ocular phenotype is linked to a novel 3' UTR mutation in SLC4A4, a gene known to be mutated in a syndromic form of intellectual disability with renal and ocular involvement...
July 28, 2017: Genome Biology
Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S Rickman, Mark A Rubin, Ekta Khurana
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. Integration of multi-omics data from 521 prostate tumor samples indicated a stronger regulatory impact of structural variants, as they affect more transcription factor hubs in the tissue-specific network. Moreover, crosstalk between transcription factor hub expression modulated by structural variants and methylation levels likely leads to the differential expression of target genes...
July 27, 2017: Genome Biology
Andrew W McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P E de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S Cenk Sahinalp, Sohrab P Shah
Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints...
July 27, 2017: Genome Biology
Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai, Dawei Wang, Yun Huang, Maxime Breban, Nan Qin, Stanislav Dusko Ehrlich
BACKGROUND: The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS: To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals...
July 27, 2017: Genome Biology
Joshua D Welch, Alexander J Hartemink, Jan F Prins
Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type. Using scM&T-seq and sc-GEM data, we confirm that MATCHER accurately predicts true single cell correlations between DNA methylation and gene expression without using known cell correspondences...
July 24, 2017: Genome Biology
Rurika Oka, Johan Zicola, Blaise Weber, Sarah N Anderson, Charlie Hodgman, Jonathan I Gent, Jan-Jaap Wesselink, Nathan M Springer, Huub C J Hoefsloot, Franziska Turck, Maike Stam
BACKGROUND: While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling...
July 21, 2017: Genome Biology
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