title: Visualizing SNVs to quantify allele-specific expression in single cells.
abstract: We present a FISH-based method for detecting single-nucleotide variants (SNVs) in exons and introns on individual RNA transcripts with high efficiency. We used this method to quantify allelic expression in cell populations and in single cells, and also to distinguish maternal from paternal chromosomes in single cells.
authors.affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA. MCMartin@lbl.gov
authors.forename: Marshall J
authors.initials: MJ
authors.lastname: Levesque
authors.forename: Paul
authors.initials: P
authors.lastname: Ginart
authors.forename: Yichen
authors.initials: Y
authors.lastname: Wei
authors.forename: Arjun
authors.initials: A
authors.lastname: Raj
mesh_terms: D000483:Alleles; D045744:Cell Line, Tumor; D005091:Exons; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007438:Introns; D008297:Male; D008545:Melanoma / Q000235:genetics; D061848:Optical Imaging / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D012313:RNA / Q000032:analysis; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D012313:RNA; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf
references.citation: Science. 1998 Apr 24;280(5363):585-90
references.pmid: 9554849
references.citation: Nat Methods. 2008 Oct;5(10):877-9
references.pmid: 18806792
references.citation: Nat Chem. 2012 Jan 22;4(3):208-14
references.pmid: 22354435
references.citation: Curr Opin Genet Dev. 2012 Apr;22(2):72-8
references.pmid: 22195775
references.citation: PLoS Genet. 2011 Aug;7(8):e1002228
references.pmid: 21852959
references.citation: Science. 2010 Aug 6;329(5992):643-8
references.pmid: 20616232
references.citation: Nat Methods. 2012 Jun 03;9(7):743-8
references.pmid: 22660740
references.citation: Science. 2002 Aug 16;297(5584):1183-6
references.pmid: 12183631
references.citation: Mol Syst Biol. 2011 Aug 02;7:522
references.pmid: 21811232
references.citation: Nucleic Acids Res. 2002 Jan 15;30(2):E5
references.pmid: 11788731
references.citation: Nature. 2010 Oct 28;467(7319):1061-73
references.pmid: 20981092
references.citation: Science. 2011 Apr 22;332(6028):472-4
references.pmid: 21415320
references.citation: Science. 2007 Nov 16;318(5853):1136-40
references.pmid: 18006746
references.citation: Dev Biol. 2006 Apr 15;292(2):519-32
references.pmid: 16469305
references.citation: J Am Chem Soc. 2009 Dec 2;131(47):17303-14
references.pmid: 19894722
references.citation: Cell. 2005 Dec 16;123(6):1025-36
references.pmid: 16360033
references.citation: Methods Enzymol. 2010;472:365-86
references.pmid: 20580972
references.citation: Nat Methods. 2013 Mar;10(3):246-8
references.pmid: 23416756
references.citation: Nat Rev Genet. 2011 Jul 18;12(8):565-75
references.pmid: 21765458
references.citation: PLoS Biol. 2006 Oct;4(10):e309
references.pmid: 17048983
references.citation: Nat Methods. 2010 May;7(5):395-7
references.pmid: 20383134