title: Finding the lost treasures in exome sequencing data.
abstract: Exome sequencing is one of the most cost-efficient sequencing approaches for conducting genome research on coding regions. However, significant portions of the reads obtained in exome sequencing come from outside of the designed target regions. These additional reads are generally ignored, potentially wasting an important source of genomic data. There are three major types of unintentionally sequenced read that can be found in exome sequencing data: reads in introns and intergenic regions, reads in the mitochondrial genome, and reads originating in viral genomes. All of these can be used for reliable data mining, extending the utility of exome sequencing. Large-scale exome sequencing data repositories, such as The Cancer Genome Atlas (TCGA), the 1000 Genomes Project, National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project, and The Sequence Reads Archive, provide researchers with excellent secondary data-mining opportunities to study genomic data beyond the intended target regions.
authors: Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37232, USA.
authors: David C
authors: DC
authors: Samuels
authors: Leng
authors: L
authors: Han
authors: Jiang
authors: J
authors: Li
authors: Sheng
authors: S
authors: Quanghu
authors: Travis A
authors: TA
authors: Clark
authors: Yu
authors: Y
authors: Shyr
authors: Yan
authors: Y
authors: Guo
mesh_terms: D004247:DNA / Q000235:genetics; D030561:Databases, Nucleic Acid; D059472:Exome / Q000235:genetics*; D054629:Genome, Mitochondrial; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: exome capture; mitochondria; mtDNA copy number; unmapped read; virus; virus integration
references: Nat Methods. 2009 Sep;6(9):677-81
references: 19668202
references: Nature. 2012 Sep 6;489(7414):101-8
references: 22955620
references: Genome Biol. 2011 Sep 28;12(9):R95
references: 21955857
references: Genome Res. 2012 Sep;22(9):1760-74
references: 22955987
references: Int J Mol Sci. 2011;12(11):7861-84
references: 22174638
references: Curr Opin Pediatr. 2010 Dec;22(6):711-6
references: 21045694
references: Emerg Infect Dis. 2010 Jun;16(6):918-25
references: 20507741
references: Mitochondrion. 2010 Jan;10(1):62-8
references: 19788937
references: J Virol. 2010 Aug;84(16):8308-15
references: 20519397
references: Hum Mol Genet. 2007 May 15;16(10):1241-52
references: 17403714
references: Science. 2013 Feb 22;339(6122):957-9
references: 23348506
references: BMC Genomics. 2012 May 20;13:194
references: 22607156
references: Bioinformatics. 2009 Jul 15;25(14):1754-60
references: 19451168
references: Nature. 2010 Mar 25;464(7288):610-4
references: 20200521
references: Science. 2010 Jul 2;329(5987):75-8
references: 20595611
references: Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14087-91
references: 22891333
references: Genome Res. 2012 Apr;22(4):593-601
references: 22267523
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Nature. 2010 Oct 28;467(7319):1061-73
references: 20981092
references: Bioinformatics. 2013 Mar 1;29(5):649-51
references: 23314323
references: Annu Rev Pharmacol Toxicol. 2000;40:353-88
references: 10836141
references: Genome Biol. 2012 Sep 26;13(9):R51
references: 22951037
references: Curr Opin Virol. 2011 Oct;1(4):282-8
references: 22003378
references: Biotechniques. 2010 Apr;48(4):287-96
references: 20569205
references: Gastroenterology. 2012 May;142(6):1303-1313.e1
references: 22537437
references: BMC Genomics. 2012 Nov 24;13:666
references: 23176052
references: J Transl Med. 2011 Aug 26;9:144
references: 21871106
references: Ann Hum Genet. 2003 Nov;67(Pt 6):512-24
references: 14641239
references: IUBMB Life. 2007 Jul;59(7):450-7
references: 17654121
references: Nucleic Acids Res. 2011 Mar;39(6):2357-66
references: 21071396
references: Am J Hum Genet. 2003 Sep;73(3):671-6
references: 12870132
references: Nature. 2012 Oct 4;490(7418):61-70
references: 23000897
references: PLoS Pathog. 2009 May;5(5):e1000455
references: 19478873
references: J Bioenerg Biomembr. 1999 Aug;31(4):305-19
references: 10665521
references: J Bioenerg Biomembr. 2012 Dec;44(6):619-22
references: 22892817
references: J Biol Chem. 1974 Dec 25;249(24):7991-5
references: 4473454
references: Clin Microbiol Infect. 2013 Jan;19(1):15-22
references: 23279287
references: J Oncol. 2011;2011:496189
references: 22028711
references: Neuropsychopharmacology. 2011 Mar;36(4):753-62
references: 21150907
references: Mol Biol Evol. 2012 Mar;29(3):915-27
references: 22096215
references: Gut. 2005 Aug;54(8):1162-8
references: 16009689
references: Am J Bioeth. 2003 Summer;3(3):W-IF1
references: 14735880
references: J Gen Virol. 2012 Sep;93(Pt 9):1853-1868
references: 22647373
references: Bioinformatics. 2013 Jan 15;29(2):266-7
references: 23162058
references: Nat Genet. 2011 May;43(5):491-8
references: 21478889
references: J Virol. 2010 Dec;84(23):12100-9
references: 20844040
references: Bioinformatics. 2011 Aug 1;27(15):2027-30
references: 21666269
references: Genes Chromosomes Cancer. 2006 Jul;45(7):629-38
references: 16568452
references: Clin Chim Acta. 2007 Aug;383(1-2):41-50
references: 17532310
references: Nature. 2012 Sep 6;489(7414):57-74
references: 22955616
references: Hum Mutat. 2008 May;29(5):703-8
references: 18320596
references: Nucleic Acids Res. 2012 Oct;40(18):e137
references: 22649055
references: Nat Genet. 2012 May 27;44(7):765-9
references: 22634754
references: Blood. 2007 Aug 1;110(3):1055-63
references: 17409267
references: PLoS One. 2009;4(1):e4219
references: 19156205
references: Genome Biol. 2006;7(7):112
references: 17224040
references: PLoS Genet. 2011 Mar;7(3):e1002028
references: 21455489
references: Bioinformatics. 2013 May 1;29(9):1210-1
references: 23471301
references: Oncogene. 2001 Sep 27;20(43):6233-40
references: 11593432
references: J Biochem Mol Toxicol. 2004;18(4):180-6
references: 15452886
references: Mutat Res. 2012 May 15;744(2):154-60
references: 22387842
references: Mitochondrion. 2004 Sep;4(5-6):755-62
references: 16120430
references: Pharmacogenomics. 2005 Jun;6(4):373-82
references: 16004555
references: Genome Biol. 2011 Sep 28;12(9):R94
references: 21955854
references: PLoS Genet. 2010 Feb 12;6(2):e1000834
references: 20168995
references: Genetics. 1998 Apr;148(4):1667-86
references: 9560386
references: Int J Cancer. 2006 Jun 15;118(12):3030-44
references: 16404738
references: Nat Methods. 2012 May 30;9(6):523-4
references: 22669646
references: Nat Genet. 2010 Jan;42(1):30-5
references: 19915526
references: BMC Genomics. 2010 Apr 16;11:244
references: 20398377
references: Nat Biotechnol. 2011 May;29(5):393-6
references: 21552235
references: Nat Genet. 1999 Oct;23(2):147
references: 10508508
references: N Engl J Med. 2008 Mar 6;358(10):991-8
references: 18256387
references: Nature. 2013 Jan 10;493(7431):216-20
references: 23201682
references: Am J Hum Genet. 2002 Mar;70(3):635-51
references: 11836649