Abstract：
BACKGROUND:Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias downstream results. RESULTS:We show that accounting for genetic variation using a modified reference genome or a de novo assembled genome can alter histone H3K4me1 and H3K27ac ChIP-seq peak calls either by creating new personal peaks or by the loss of reference peaks. Using permissive cutoffs, modified reference genomes are found to alter approximately 1% of peak calls while de novo assembled genomes alter up to 5% of peaks. We also show statistically significant differences in the amount of reads observed in regions associated with the new, altered, and unchanged peaks. We report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs), have the highest probability of modifying peak calls. We show that using a graph personalized genome represents a reasonable compromise between modified reference genomes and de novo assembled genomes. We demonstrate that altered peaks have a genomic distribution typical of other peaks. CONCLUSIONS:Analyzing epigenomic datasets with personalized and graph genomes allows the recovery of new peaks enriched for indels and SNVs. These altered peaks are more likely to differ between individuals and, as such, could be relevant in the study of various human phenotypes.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Groza C,Kwan T,Soranzo N,Pastinen T,Bourque Gdoi
10.1186/s13059-020-02038-8subject
Has Abstractpub_date
2020-05-25 00:00:00pages
124issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-020-02038-8journal_volume
21pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract：:A report on the Plant Genomics European Meeting (Plant-GEMS2004), Lyon, France, 22-25 September 2004. ...
journal_title：Genome biology
pub_type：
doi：10.1186/gb-2004-6-1-302
更新日期：2005-01-01 00:00:00
abstract：:A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008. ...
journal_title：Genome biology
pub_type：
doi：10.1186/gb-2008-9-7-316
更新日期：2008-01-01 00:00:00
abstract：:A central goal of biogerontology is to identify robust gene-expression biomarkers of aging. Here we develop a method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. Tested on Caenorhabditis elegans, our algorithm yields better biomar...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2010-11-2-r13
更新日期：2010-01-01 00:00:00
abstract：:A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...
journal_title：Genome biology
pub_type： 信件
doi：10.1186/s13059-015-0585-5
更新日期：2015-01-31 00:00:00
abstract：BACKGROUND:Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consistin...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2004-5-3-r17
更新日期：2004-01-01 00:00:00
abstract：BACKGROUND:DNA damage leads to cellular responses that include the increased expression of DNA repair genes, repression of DNA replication and alterations in cellular metabolism. Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. RESUL...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-10-r220
更新日期：2007-01-01 00:00:00
abstract：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 lo...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-017-1278-z
更新日期：2017-08-07 00:00:00
abstract：:The functional annotation of proteins identified in genome sequencing projects is based on similarities to homologs in the databases. As a result of the possible strategies for divergent evolution, homologous enzymes frequently do not catalyze the same reaction, and we conclude that assignment of function from sequenc...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2000-1-5-reviews0005
更新日期：2000-01-01 00:00:00
abstract：:Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1610-2
更新日期：2018-12-22 00:00:00
abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2006-7-11-r112
更新日期：2006-01-01 00:00:00
abstract：BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2006-7-9-r85
更新日期：2006-01-01 00:00:00
abstract：:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-7-preprint0005
更新日期：2002-05-29 00:00:00
abstract：BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2005-6-9-r73
更新日期：2005-01-01 00:00:00
abstract：BACKGROUND:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2013-14-12-r148
更新日期：2013-12-31 00:00:00
abstract：BACKGROUND:Alternative pre-mRNA splicing is an important gene regulation mechanism for expanding proteomic diversity in higher eukaryotes. Each splicing regulator can potentially influence a large group of alternative exons. Meanwhile, each alternative exon is controlled by multiple splicing regulators. The rapid accum...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2009-10-1-r3
更新日期：2009-01-01 00:00:00
abstract：BACKGROUND:We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2001-2-1-research0003
更新日期：2001-01-01 00:00:00
abstract：:Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play. ...
journal_title：Genome biology
pub_type： 面试
doi：10.1186/s13059-015-0830-y
更新日期：2015-11-20 00:00:00
abstract：:The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2010-11-3-108
更新日期：2010-01-01 00:00:00
abstract：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-020-01988-3
更新日期：2020-03-17 00:00:00
abstract：BACKGROUND:The H subunit of the purple bacterial photosynthetic reaction center (PRC-H) is important for the assembly of the photosynthetic reaction center and appears to regulate electron transfer during the reduction of the secondary quinone. It contains a distinct cytoplasmic beta-barrel domain whose fold has no clo...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-11-research0061
更新日期：2002-10-14 00:00:00
abstract：BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2009-10-2-r19
更新日期：2009-02-12 00:00:00
abstract：BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2008-9-s2-s12
更新日期：2008-01-01 00:00:00
abstract：BACKGROUND:Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evoluti...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1544-8
更新日期：2018-10-05 00:00:00
abstract：BACKGROUND:Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2012-13-4-r28
更新日期：2012-04-24 00:00:00
abstract：BACKGROUND:Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2008-9-3-r48
更新日期：2008-01-01 00:00:00
abstract：BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-9-research0051
更新日期：2002-08-29 00:00:00
abstract：BACKGROUND:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2014-15-3-r53
更新日期：2014-03-25 00:00:00
abstract：BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/PREACCEPT-1067113631444973
更新日期：2014-01-01 00:00:00
abstract：BACKGROUND:Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2006-7-5-r39
更新日期：2006-01-01 00:00:00
abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...
journal_title：Genome biology
pub_type： 评论,信件
doi：10.1186/s13059-015-0709-y
更新日期：2015-07-11 00:00:00
