Literature DB >> 22422963

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".

Joseph K Pickrell1, Yoav Gilad, Jonathan K Pritchard.   

Abstract

Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported more than 10,000 mismatches between messenger RNA and DNA sequences from the same individuals, which they attributed to previously unrecognized mechanisms of gene regulation. We found that at least 88% of these sequence mismatches can likely be explained by technical artifacts such as errors in mapping sequencing reads to a reference genome, sequencing errors, and genetic variation.

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Year:  2012        PMID： 22422963      PMCID： PMC5207799          DOI： 10.1126/science.1210484

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   47.728


  9 in total

Review 1.  RNA editing by adenosine deaminases that act on RNA.

Authors:  Brenda L Bass
Journal:  Annu Rev Biochem       Date:  2001-11-09       Impact factor: 23.643

2.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

3.  DARNED: a DAtabase of RNa EDiting in humans.

Authors:  Anmol Kiran; Pavel V Baranov
Journal:  Bioinformatics       Date:  2010-06-14       Impact factor: 6.937

4.  A map of human genome variation from population-scale sequencing.

Authors:  Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  Origins and functional impact of copy number variation in the human genome.

Authors:  Donald F Conrad; Dalila Pinto; Richard Redon; Lars Feuk; Omer Gokcumen; Yujun Zhang; Jan Aerts; T Daniel Andrews; Chris Barnes; Peter Campbell; Tomas Fitzgerald; Min Hu; Chun Hwa Ihm; Kati Kristiansson; Daniel G Macarthur; Jeffrey R Macdonald; Ifejinelo Onyiah; Andy Wing Chun Pang; Sam Robson; Kathy Stirrups; Armand Valsesia; Klaudia Walter; John Wei; Chris Tyler-Smith; Nigel P Carter; Charles Lee; Stephen W Scherer; Matthew E Hurles
Journal:  Nature       Date:  2009-10-07       Impact factor: 49.962

7.  Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Authors:  Yaniv Erlich; Partha P Mitra; Melissa delaBastide; W Richard McCombie; Gregory J Hannon
Journal:  Nat Methods       Date:  2008-07-06       Impact factor: 28.547

8.  Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing.

Authors:  Jin Billy Li; Erez Y Levanon; Jung-Ki Yoon; John Aach; Bin Xie; Emily Leproust; Kun Zhang; Yuan Gao; George M Church
Journal:  Science       Date:  2009-05-29       Impact factor: 47.728

9.  A framework for variation discovery and genotyping using next-generation DNA sequencing data.

Authors:  Mark A DePristo; Eric Banks; Ryan Poplin; Kiran V Garimella; Jared R Maguire; Christopher Hartl; Anthony A Philippakis; Guillermo del Angel; Manuel A Rivas; Matt Hanna; Aaron McKenna; Tim J Fennell; Andrew M Kernytsky; Andrey Y Sivachenko; Kristian Cibulskis; Stacey B Gabriel; David Altshuler; Mark J Daly
Journal:  Nat Genet       Date:  2011-04-10       Impact factor: 38.330
  9 in total
  108 in total

1.  Genetic Architectures of Quantitative Variation in RNA Editing Pathways.

Authors:  Tongjun Gu; Daniel M Gatti; Anuj Srivastava; Elizabeth M Snyder; Narayanan Raghupathy; Petr Simecek; Karen L Svenson; Ivan Dotu; Jeffrey H Chuang; Mark P Keller; Alan D Attie; Robert E Braun; Gary A Churchill
Journal:  Genetics       Date:  2015-11-27       Impact factor: 4.562

2.  RASER: reads aligner for SNPs and editing sites of RNA.

Authors:  Jaegyoon Ahn; Xinshu Xiao
Journal:  Bioinformatics       Date:  2015-08-30       Impact factor: 6.937

3.  RNA Sequencing and Analysis.

Authors:  Kimberly R Kukurba; Stephen B Montgomery
Journal:  Cold Spring Harb Protoc       Date:  2015-04-13

4.  Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.

Authors:  Sandrine Lagarrigue; Lisa Martin; Farhad Hormozdiari; Pierre-François Roux; Calvin Pan; Atila van Nas; Olivier Demeure; Rita Cantor; Anatole Ghazalpour; Eleazar Eskin; Aldons J Lusis
Journal:  Genetics       Date:  2013-09-11       Impact factor: 4.562

5.  Characterization and comparison of human nuclear and cytosolic editomes.

Authors:  Liang Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-01       Impact factor: 11.205

6.  Reliable identification of genomic variants from RNA-seq data.

Authors:  Robert Piskol; Gokul Ramaswami; Jin Billy Li
Journal:  Am J Hum Genet       Date:  2013-09-26       Impact factor: 11.025

7.  New insights from existing sequence data: generating breakthroughs without a pipette.

Authors:  Alex M Plocik; Brenton R Graveley
Journal:  Mol Cell       Date:  2013-02-21       Impact factor: 17.970

Review 8.  The "Observer Effect" in genome-wide surveys of protein-RNA interactions.

Authors:  Kasandra J Riley; Joan A Steitz
Journal:  Mol Cell       Date:  2013-02-21       Impact factor: 17.970

9.  Assessing the validity and reproducibility of genome-scale predictions.

Authors:  Lauren A Sugden; Michael R Tackett; Yiannis A Savva; William A Thompson; Charles E Lawrence
Journal:  Bioinformatics       Date:  2013-09-17       Impact factor: 6.937

10.  Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer.

Authors:  Timothy D O'Brien; Peilin Jia; Junfeng Xia; Uma Saxena; Hailing Jin; Huy Vuong; Pora Kim; Qingguo Wang; Martin J Aryee; Mari Mino-Kenudson; Jeffrey A Engelman; Long P Le; A John Iafrate; Rebecca S Heist; William Pao; Zhongming Zhao
Journal:  Methods       Date:  2015-04-23       Impact factor: 3.608
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