title: Counting absolute numbers of molecules using unique molecular identifiers.
abstract: Counting individual RNA or DNA molecules is difficult because they are hard to copy quantitatively for detection. To overcome this limitation, we applied unique molecular identifiers (UMIs), which make each molecule in a population distinct, to genome-scale human karyotyping and mRNA sequencing in Drosophila melanogaster. Use of this method can improve accuracy of almost any next-generation sequencing method, including chromatin immunoprecipitation-sequencing, genome assembly, diagnostics and manufacturing-process control and monitoring.
authors.affiliation: Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Helsinki, Finland.
authors.forename: Teemu
authors.initials: T
authors.lastname: Kivioja
authors.forename: Anna
authors.initials: A
authors.lastname: Vähärautio
authors.forename: Kasper
authors.initials: K
authors.lastname: Karlsson
authors.forename: Martin
authors.initials: M
authors.lastname: Bonke
authors.forename: Martin
authors.initials: M
authors.lastname: Enge
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
authors.forename: Jussi
authors.initials: J
authors.lastname: Taipale
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods; D004314:Down Syndrome / Q000235:genetics; D004331:Drosophila melanogaster; D005260:Female; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D006801:Humans; D007621:Karyotyping / Q000379:methods*; D008297:Male; D012333:RNA, Messenger / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Exp Cell Res. 2010 May 1;316(8):1339-43
references.pmid: 20211618
references.citation: Proc Natl Acad Sci U S A. 2011 May 31;108(22):9026-31
references.pmid: 21562209
references.citation: Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9530-5
references.pmid: 21586637
references.citation: Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9236-41
references.pmid: 10430926
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16266-71
references.pmid: 18838674
references.citation: Nat Biotechnol. 2009 Jul;27(7):652-8
references.pmid: 19581875
references.citation: Nat Methods. 2008 Jul;5(7):613-9
references.pmid: 18516046
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20458-63
references.pmid: 19073917
references.citation: Biotechniques. 2001 Apr;30(4):892-7
references.pmid: 11314272
references.citation: Nat Methods. 2010 Aug;7(8):619-21
references.pmid: 20639869
references.citation: Nucleic Acids Res. 2003 Aug 15;31(16):e99
references.pmid: 12907751
references.citation: Nat Methods. 2010 Sep;7(9):709-15
references.pmid: 20711195
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Nature. 2009 Oct 8;461(7265):814-8
references.pmid: 19776739
references.citation: Nucleic Acids Res. 2011 Jul;39(12):e81
references.pmid: 21490082
references.citation: PLoS Biol. 2010 Oct 26;8(10):e1000530
references.pmid: 21048981
references.citation: Nat Struct Mol Biol. 2010 Jul;17(7):909-15
references.pmid: 20601959
references.citation: J Theor Biol. 2003 Apr 21;221(4):615-24
references.pmid: 12713944