Filters








12,802 Hits in 7.5 sec

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Jacob F. Degner, John C. Marioni, Athma A. Pai, Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K. Pritchard
2009 Computer applications in the biosciences : CABIOS  
Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).  ...  Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data.  ...  We are grateful to the other members of the Jonathan Pritchard, Molly Przeworski and Matthew Stephens labs for helpful advice on this project.  ... 
doi:10.1093/bioinformatics/btp579 pmid:19808877 pmcid:PMC2788925 fatcat:zbejuhmfmbfq7l47xl3rtmsnja

Workshop: Inference of allele specific expression levels from RNA-Seq data

Sahar Al Seesi, Ion Mandoiu
2012 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)  
Most current methods for estimating gene/isoform expression levels from high-throughput whole transcriptome sequencing (RNA-Seq) data rely on mapping the reads to a reference genome and/or transcriptome  ...  all reads, including those that map to more than one isoform, incorporating additional sources of disambiguation information such as the distribution of RNA-Seq fragment lengths, and correcting biases  ...  Most current methods for estimating gene/isoform expression levels from high-throughput whole transcriptome sequencing (RNA-Seq) data rely on mapping the reads to a reference genome and/or transcriptome  ... 
doi:10.1109/iccabs.2012.6182666 dblp:conf/iccabs/SeesiM12 fatcat:fx7z46eayzhkfnukqfsdzxtju4

Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Nikolaos I Panousis, Maria Gutierrez-Arcelus, Emmanouil T Dermitzakis, Tuuli Lappalainen
2014 Genome Biology  
In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.  ...  However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias  ...  These observations suggest that transcript structure and split reads in RNA-seq have a relatively minor effect on allelic mapping bias, and that even genome sequence-based estimates of biased loci are  ... 
doi:10.1186/preaccept-2698578171338911 pmid:25239376 pmcid:PMC4212091 fatcat:ncnxefv77fhojamkkxirazdz4q

Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Nikolaos I Panousis, Maria Gutierrez-Arcelus, Emmanouil T Dermitzakis, Tuuli Lappalainen
2014 Genome Biology  
In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.  ...  However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias  ...  These observations suggest that transcript structure and split reads in RNA-seq have a relatively minor effect on allelic mapping bias, and that even genome sequence-based estimates of biased loci are  ... 
doi:10.1186/s13059-014-0467-2 pmid:25239376 pmcid:PMC4212091 fatcat:rahhevsfbvdqpplwbz7jnyr62a

A haplotype-based normalization technique for the analysis and detection of allele specific expression

Alan Hodgkinson, Jean-Christophe Grenier, Elias Gbeha, Philip Awadalla
2016 BMC Bioinformatics  
Conclusions: The correct treatment and analysis of RNA sequencing data is vital to control for mapping biases and detect genuine ASE signals.  ...  The detection of ASE using high throughput technologies relies on aligning short-read sequencing data, a process that has inherent biases, and there is still a need to develop fast and accurate methods  ...  We acknowledge financial support from the Ontario Institute for Cancer Research and the Ontario Ministry of Research, Fonds de la recherche en santé du Québec Availability of data and materials Requests  ... 
doi:10.1186/s12859-016-1238-8 pmid:27618913 pmcid:PMC5020486 fatcat:y5ybp7f57bgwzgvzt2uqptbg2a

AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing

Jesper R. Gådin, Ferdinand M. van't Hooft, Per Eriksson, Lasse Folkersen
2015 BMC Bioinformatics  
One aspect in which RNA sequencing is more valuable than microarray-based methods is the ability to examine the allelic imbalance of the expression of a gene.  ...  Conclusions: The software provides a complete framework to perform allelic imbalance analyses of aligned RNA sequencing data, from detection to visualization, within the robust and versatile management  ...  In RNA sequencing data, it is possible to determine the allele from which a specific read originates when there is at least one heterozygous SNP in the sequence read [1] .  ... 
doi:10.1186/s12859-015-0620-2 pmid:26066318 pmcid:PMC4465016 fatcat:gm5lzujawngcpe6dvwwzg3hbg4

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

Graham A. Heap, Jennie H.M. Yang, Kate Downes, Barry C. Healy, Karen A. Hunt, Nicholas Bockett, Lude Franke, Patrick C. Dubois, Charles A. Mein, Richard J. Dobson, Thomas J. Albert, Matthew J. Rodesch (+4 others)
2009 Human Molecular Genetics  
Allele-specific expression (ASE) quantifies transcription from both haplotypes using individuals heterozygous at tested SNPs.  ...  Finally, we show in CD4 1 T cells from a further individual that high-throughput sequencing of genomic DNA and RNA-seq following enrichment for targeted gene sequences by sequence capture methods offers  ...  , analysis server and GAII sequencer use.  ... 
doi:10.1093/hmg/ddp473 pmid:19825846 pmcid:PMC2792152 fatcat:74wawi5eq5hq3ojn3kc4jemmqm

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation

Tomas Babak, Philip Garrett-Engele, Christopher D Armour, Christopher K Raymond, Mark P Keller, Ronghua Chen, Carol A Rohl, Jason M Johnson, Alan D Attie, Hunter B Fraser, Eric E Schadt
2010 BMC Genomics  
Conclusion: Monitoring ASE by sequencing cDNA from as little as one sample is a practical alternative to expression genetics for mapping cis-acting variation that regulates RNA transcription and processing  ...  Results: Here we demonstrate that genomic regions with allele-specific expression (ASE) detected by sequencing cDNA are highly enriched for cis-acting expression quantitative trait loci (cis-eQTL) identified  ...  Acknowledgements We would like to thank Brian DeVeale and Derek van der Kooy at the University of Toronto for donating all mouse embryos used in this study. Author details  ... 
doi:10.1186/1471-2164-11-473 pmid:20707912 pmcid:PMC3091669 fatcat:o2gsqeb2avdibdxk6hw3zo2sc4

Highly accurate quantification of allelic gene expression for population and disease genetics

Anna Saukkonen, Helena Kilpinen, Alan Hodgkinson
2022 biorxiv/medrxiv  
However, detection of ASE events relies on accurate alignment of RNA sequencing reads, where challenges still remain, particularly for reads containing genetic variants or those that align to many different  ...  of multi-mapping reads.  ...  Introduction Allele-specific expression (ASE) is the imbalanced expression of the two alleles of a gene.  ... 
doi:10.1101/gr.276296.121 pmid:35794008 pmcid:PMC9435737 fatcat:vd7og4g2urcjblley5q2e7tg2y

WASP: allele-specific software for robust molecular quantitative trait locus discovery

Bryce van de Geijn, Graham McVicker, Yoav Gilad, Jonathan K Pritchard
2015 Nature Methods  
To detect differences in molecular phenotypes from sequencing data, it is essential to remove read-mapping biases, which are a major source of false positives.  ...  WASP accounts for numerous biases in allele-specific data and is flexible enough to work with different read mappers and multiple types of sequencing data such as ChIP-seq and RNA-seq data.  ... 
doi:10.1038/nmeth.3582 pmid:26366987 pmcid:PMC4626402 fatcat:q3dupcbuxzbvxchgiy7ff2wuvm

RNA Sequencing and Analysis

Kimberly R. Kukurba, Stephen B. Montgomery
2015 Cold Spring Harbor Protocols  
K.R.K. is supported by the National Defense Science and Engineering Graduate (NDSEG) Fellowship from the U.S. Department of Defense, and S.B.M. is funded by the Edward Mallinckrodt, Jr. Foundation.  ...  and remove their effects from expression data.  ...  To detect differential expression, a variety of statistical methods have been designed specifically for RNA-Seq data.  ... 
doi:10.1101/pdb.top084970 pmid:25870306 pmcid:PMC4863231 fatcat:iqwyhy37jrh5bmrfw4wjukraja

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

Peter A C 't Hoen, Marc R Friedländer, Jonas Almlöf, Michael Sammeth, Irina Pulyakhina, Seyed Yahya Anvar, Jeroen F J Laros, Henk P J Buermans, Olof Karlberg, Mathias Brännvall, Johan T den Dunnen, Gert-Jan B van Ommen (+6 others)
2013 Nature Biotechnology  
We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data. reproducibility of high-throughput mrNA and small rNA sequencing across laboratories  ...  A r t i c l e s RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance.  ...  (i) The proportion of sites where both alleles are observed in mRNAseq reads, out of all the sites where allele-specific expression is measured.  ... 
doi:10.1038/nbt.2702 pmid:24037425 fatcat:6ttkdli5nbhnlgqigtc7dzz5oq

A new strategy to reduce allelic bias in RNA-Seq readmapping

Ravi Vijaya Satya, Nela Zavaljevski, Jaques Reifman
2012 Nucleic Acids Research  
Accurate estimation of expression levels from RNA-Seq data entails precise mapping of the sequence reads to a reference genome.  ...  This bias in read mapping leads to inaccurate estimates of allele-specific expression (ASE).  ...  (9) for making their RNA-Seq data available and Jacob Degner for providing us some of the R scripts for data analysis.  ... 
doi:10.1093/nar/gks425 pmid:22584625 pmcid:PMC3439884 fatcat:zxqdmk4sw5gu5c23q6576ypx54

Global Survey of Genomic Imprinting by Transcriptome Sequencing

Tomas Babak, Brian DeVeale, Christopher Armour, Christopher Raymond, Michele A. Cleary, Derek van der Kooy, Jason M. Johnson, Lee P. Lim
2008 Current Biology  
By distinguishing parent-of-origin bias from strain-specific bias in embryos derived from a reciprocal cross of mice, we constructed a genome-wide map of imprinted transcription.  ...  This study demonstrates the feasibility of using transcriptome sequencing for mapping of imprinted gene expression in physiologically normal animals.  ...  Acknowledgments We thank Susan Runciman and Brenda Takabe for expert advice and Matt Saunders and Barbara Panning for critical reading of the manuscript.  ... 
doi:10.1016/j.cub.2008.09.044 pmid:19026546 fatcat:gtqi3grtejchhjrarvqtgbsmi4

Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross

Byeongyong Ahn, Min-Kyeung Choi, Joori Yum, In-Cheol Cho, Jin-Hoi Kim, Chankyu Park
2019 Asian-Australasian Journal of Animal Sciences  
Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.  ...  We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal  ...  Determination of parental origin of expressed alleles in F 1 individuals from RNA-seq data can be efficiently achieved using bioinformatic analysis tools if parent-specific SNPs are clearly distinguishable  ... 
doi:10.5713/ajas.19.0097 pmid:31208168 pmcid:PMC6819674 fatcat:56x2wvaip5erlg34kdnhuf4snm
« Previous Showing results 1 — 15 out of 12,802 results