DOI: 10.1371/journal.pcbi.1004105. Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers

10.1371/journal.pcbi.1004105

Crossref journal-article

Public Library of Science (PLoS)

PLOS Computational Biology (340)

Bibliography

DeBoever, C., Ghia, E. M., Shepard, P. J., Rassenti, L., Barrett, C. L., Jepsen, K., Jamieson, C. H. M., Carson, D., Kipps, T. J., & Frazer, K. A. (2015). Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3â Splice Site Selection in SF3B1-mutated Cancers. PLOS Computational Biology, 11(3), e1004105.

Authors 10

Christopher DeBoever (first)
Emanuela M. Ghia (additional)
Peter J. Shepard (additional)
Laura Rassenti (additional)
Christian L. Barrett (additional)
Kristen Jepsen (additional)
Catriona H. M. Jamieson (additional)
Dennis Carson (additional)
Thomas J. Kipps (additional)
Kelly A. Frazer (additional)

References 43 Referenced 193

{'key': 'ref1', 'article-title': 'Emerging patterns of somatic mutations in cancer', 'author': 'IR Watson', 'year': '2013', 'journal-title': 'Nature reviews Genetics'} / Nature reviews Genetics / Emerging patterns of somatic mutations in cancer by IR Watson (2013)
10.1182/blood-2013-02-427641 / Blood / SF3B1 mutations in chronic lymphocytic leukemia by Y Wan (2013)
10.1038/nature11547 / Nature / Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes by AV Biankin (2012)
10.1038/ng.2674 / Nature genetics / Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 by M Martin (2013)
10.1038/nature10496 / Nature / Frequent pathway mutations of splicing machinery in myelodysplasia by K Yoshida (2011)
10.1056/NEJMoa1103283 / The New England journal of medicine / Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts by E Papaemmanuil (2011)
10.1038/ng.2523 / Nature genetics / Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma by JW Harbour (2013)
10.1038/ng.1032 / Nature genetics / Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia by V Quesada (2012)
10.1038/leu.2013.22 / Leukemia / Subclonal evolution involving SF3B1 mutations in chronic lymphocytic leukemia by M Schwaederle (2013)
10.1056/NEJMoa1109016 / The New England journal of medicine / SF3B1 and other novel cancer genes in chronic lymphocytic leukemia by L Wang (2011)
{'key': 'ref11', 'article-title': 'Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia', 'author': 'PG Ferreira', 'year': '2013', 'journal-title': 'Genome Research'} / Genome Research / Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia by PG Ferreira (2013)
10.1016/j.tig.2012.01.001 / Trends in Genetics / New connections between splicing and human disease by RA Padgett (2012)
10.1093/nar/gkn073 / Nucleic Acids Research / Human branch point consensus sequence is yUnAy by KP Gao (2008)
10.1128/MCB.18.8.4752 / Molecular and Cellular Biology / A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site by O Gozani (1998)
10.1101/gad.12.10.1409 / Genes & development / Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis by C Wang (1998)
10.1128/MCB.13.8.4939 / Molecular and Cellular Biology / Scanning and Competition between Ags Are Involved in 3' Splice-Site Selection in Mammalian Introns by CWJ Smith (1993)
10.1128/MCB.21.5.1509-1514.2001 / Molecular and Cellular Biology / An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing by K Chua (2001)
10.1093/nar/gki811 / Nucleic Acids Res / Biased exon/intron distribution of cryptic and de novo 3' splice sites by J Kralovicova (2005)
10.1101/gr.135350.111 / Genome Research / GENCODE: The reference human genome annotation for The ENCODE Project by J Harrow (2012)
10.1101/gr.133744.111 / Genome Research / Detecting differential usage of exons from RNA-seq data by S Anders (2012)
10.1073/pnas.0506580102 / Proceedings of the National Academy of Sciences of the United States of America / Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles by A Subramanian (2005)
10.1101/gr.849004 / Genome Research / WebLogo: A sequence logo generator by GE Crooks (2004)
10.1371/journal.pcbi.1001016 / Plos Computational Biology / Genome-Wide Association between Branch Point Properties and Alternative Splicing by A Corvelo (2010)
10.1038/ncb2651 / Nature Cell Biology / SCFFbxo9 and CK2 direct the cellular response to growth factor withdrawal via Tel2/Tti1 degradation and promote survival in multiple myeloma by V Fernandez-Saiz (2013)
10.1101/gad.1934210 / Genes & development / A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability by KE Hurov (2010)
10.1074/jbc.M110.121699 / The Journal of biological chemistry / Tti1 and Tel2 are critical factors in mammalian target of rapamycin complex assembly by T Kaizuka (2010)
10.1074/jbc.M910346199 / The Journal of biological chemistry / Activation of NF-kappa B by XIAP, the X chromosome-linked inhibitor of apoptosis, in endothelial cells involves TAK1 by R Hofer-Warbinek (2000)
10.1074/jbc.M908622199 / Journal of Biological Chemistry / BMP2-induced apoptosis is mediated by activation of the TAK1-p38 kinase pathway that is negatively regulated by Smad6 by N Kimura (2000)
10.1093/emboj/18.1.179 / The EMBO journal / XIAP, a cellular member of the inhibitor of apoptosis protein family, links the receptors to TAB1-TAK1 in the BMP signaling pathway by K Yamaguchi (1999)
10.1016/j.canlet.2007.02.018 / Cancer letters / Dysadherin: A new, player in cancer progression by JS Nam (2007)
10.1074/jbc.M106127200 / J Biol Chem / MM-1, a c-Myc-binding protein, is a candidate for a tumor suppressor in leukemia/lymphoma and tongue cancer by Y Fujioka (2001)
10.1093/database/bau093 / Database (Oxford) / The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data by C Wilks (2014)
{'key': 'ref33', 'article-title': 'SF3B1 mutations are associated with alternative splicing in uveal melanoma', 'author': 'SJ Furney', 'year': '2013', 'journal-title': 'Cancer discovery'} / Cancer discovery / SF3B1 mutations are associated with alternative splicing in uveal melanoma by SJ Furney (2013)
10.14806/ej.17.1.200 / Cutadapt removes adapter sequences from high-throughput sequencing reads by M Martin (2011)
10.1093/bioinformatics/bts635 / Bioinformatics / STAR: ultrafast universal RNA-seq aligner by A Dobin (2013)
10.1093/bioinformatics/btl048 / Bioinformatics / The UCSC Known Genes by F Hsu (2006)
10.1186/gb-2006-7-s1-s12 / Genome biology / AceView: a comprehensive cDNA-supported gene and transcripts annotation by D Thierry-Mieg (2006)
10.1101/gad.17446611 / Genes & development / Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses by MN Cabili (2011)
10.1093/nar/gkp1020 / Nucleic Acids Research / H-InvDB in 2009: extended database and data mining resources for human genes and transcripts by C Yamasaki (2010)
10.1038/nmeth.1923 / Nature Methods / Fast gapped-read alignment with Bowtie 2 by B Langmead (2012)
10.1038/nmeth.2251 / Nature Methods / Streaming fragment assignment for real-time analysis of sequencing experiments by A Roberts (2013)
10.1093/nar/gkq929 / Nucleic Acids Research / COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer by SA Forbes (2011)
10.1186/gb-2010-11-10-r106 / Genome biology / Differential expression analysis for sequence count data by S Anders (2010)

Dates

Type	When
Created	10 years, 5 months ago (March 13, 2015, 2:06 p.m.)
Deposited	6 years, 10 months ago (Oct. 19, 2018, 3:13 p.m.)
Indexed	2 days, 18 hours ago (Sept. 3, 2025, 6:41 a.m.)
Issued	10 years, 5 months ago (March 13, 2015)
Published	10 years, 5 months ago (March 13, 2015)
Published Online	10 years, 5 months ago (March 13, 2015)

Funders 0

None

BibTeX

@article{DeBoever_2015, title={Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers}, volume={11}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.1004105}, DOI={10.1371/journal.pcbi.1004105}, number={3}, journal={PLOS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={DeBoever, Christopher and Ghia, Emanuela M. and Shepard, Peter J. and Rassenti, Laura and Barrett, Christian L. and Jepsen, Kristen and Jamieson, Catriona H. M. and Carson, Dennis and Kipps, Thomas J. and Frazer, Kelly A.}, editor={Wang, Edwin}, year={2015}, month=mar, pages={e1004105} }

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      "article-title": "Emerging patterns of somatic mutations in cancer",
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      "DOI": "10.1182/blood-2013-02-427641",
      "article-title": "SF3B1 mutations in chronic lymphocytic leukemia",
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      "author": "Y Wan",
      "year": "2013",
      "journal-title": "Blood"
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      "first-page": "399",
      "DOI": "10.1038/nature11547",
      "article-title": "Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes",
      "volume": "491",
      "author": "AV Biankin",
      "year": "2012",
      "journal-title": "Nature"
    },
    {
      "key": "ref4",
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      "first-page": "933",
      "DOI": "10.1038/ng.2674",
      "article-title": "Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3",
      "volume": "45",
      "author": "M Martin",
      "year": "2013",
      "journal-title": "Nature genetics"
    },
    {
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      "first-page": "64",
      "DOI": "10.1038/nature10496",
      "article-title": "Frequent pathway mutations of splicing machinery in myelodysplasia",
      "volume": "478",
      "author": "K Yoshida",
      "year": "2011",
      "journal-title": "Nature"
    },
    {
      "key": "ref6",
      "doi-asserted-by": "crossref",
      "first-page": "1384",
      "DOI": "10.1056/NEJMoa1103283",
      "article-title": "Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts",
      "volume": "365",
      "author": "E Papaemmanuil",
      "year": "2011",
      "journal-title": "The New England journal of medicine"
    },
    {
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      "doi-asserted-by": "crossref",
      "first-page": "133",
      "DOI": "10.1038/ng.2523",
      "article-title": "Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma",
      "volume": "45",
      "author": "JW Harbour",
      "year": "2013",
      "journal-title": "Nature genetics"
    },
    {
      "key": "ref8",
      "doi-asserted-by": "crossref",
      "first-page": "47",
      "DOI": "10.1038/ng.1032",
      "article-title": "Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia",
      "volume": "44",
      "author": "V Quesada",
      "year": "2012",
      "journal-title": "Nature genetics"
    },
    {
      "key": "ref9",
      "doi-asserted-by": "crossref",
      "first-page": "1214",
      "DOI": "10.1038/leu.2013.22",
      "article-title": "Subclonal evolution involving SF3B1 mutations in chronic lymphocytic leukemia",
      "volume": "27",
      "author": "M Schwaederle",
      "year": "2013",
      "journal-title": "Leukemia"
    },
    {
      "key": "ref10",
      "doi-asserted-by": "crossref",
      "first-page": "2497",
      "DOI": "10.1056/NEJMoa1109016",
      "article-title": "SF3B1 and other novel cancer genes in chronic lymphocytic leukemia",
      "volume": "365",
      "author": "L Wang",
      "year": "2011",
      "journal-title": "The New England journal of medicine"
    },
    {
      "key": "ref11",
      "article-title": "Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia",
      "author": "PG Ferreira",
      "year": "2013",
      "journal-title": "Genome Research"
    },
    {
      "key": "ref12",
      "doi-asserted-by": "crossref",
      "first-page": "147",
      "DOI": "10.1016/j.tig.2012.01.001",
      "article-title": "New connections between splicing and human disease",
      "volume": "28",
      "author": "RA Padgett",
      "year": "2012",
      "journal-title": "Trends in Genetics"
    },
    {
      "key": "ref13",
      "doi-asserted-by": "crossref",
      "first-page": "2257",
      "DOI": "10.1093/nar/gkn073",
      "article-title": "Human branch point consensus sequence is yUnAy",
      "volume": "36",
      "author": "KP Gao",
      "year": "2008",
      "journal-title": "Nucleic Acids Research"
    },
    {
      "key": "ref14",
      "doi-asserted-by": "crossref",
      "first-page": "4752",
      "DOI": "10.1128/MCB.18.8.4752",
      "article-title": "A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site",
      "volume": "18",
      "author": "O Gozani",
      "year": "1998",
      "journal-title": "Molecular and Cellular Biology"
    },
    {
      "key": "ref15",
      "doi-asserted-by": "crossref",
      "first-page": "1409",
      "DOI": "10.1101/gad.12.10.1409",
      "article-title": "Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis",
      "volume": "12",
      "author": "C Wang",
      "year": "1998",
      "journal-title": "Genes & development"
    },
    {
      "key": "ref16",
      "doi-asserted-by": "crossref",
      "first-page": "4939",
      "DOI": "10.1128/MCB.13.8.4939",
      "article-title": "Scanning and Competition between Ags Are Involved in 3&apos; Splice-Site Selection in Mammalian Introns",
      "volume": "13",
      "author": "CWJ Smith",
      "year": "1993",
      "journal-title": "Molecular and Cellular Biology"
    },
    {
      "key": "ref17",
      "doi-asserted-by": "crossref",
      "first-page": "1509",
      "DOI": "10.1128/MCB.21.5.1509-1514.2001",
      "article-title": "An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing",
      "volume": "21",
      "author": "K Chua",
      "year": "2001",
      "journal-title": "Molecular and Cellular Biology"
    },
    {
      "key": "ref18",
      "doi-asserted-by": "crossref",
      "first-page": "4882",
      "DOI": "10.1093/nar/gki811",
      "article-title": "Biased exon/intron distribution of cryptic and de novo 3&apos; splice sites",
      "volume": "33",
      "author": "J Kralovicova",
      "year": "2005",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "ref19",
      "doi-asserted-by": "crossref",
      "first-page": "1760",
      "DOI": "10.1101/gr.135350.111",
      "article-title": "GENCODE: The reference human genome annotation for The ENCODE Project",
      "volume": "22",
      "author": "J Harrow",
      "year": "2012",
      "journal-title": "Genome Research"
    },
    {
      "key": "ref20",
      "doi-asserted-by": "crossref",
      "first-page": "2008",
      "DOI": "10.1101/gr.133744.111",
      "article-title": "Detecting differential usage of exons from RNA-seq data",
      "volume": "22",
      "author": "S Anders",
      "year": "2012",
      "journal-title": "Genome Research"
    },
    {
      "key": "ref21",
      "doi-asserted-by": "crossref",
      "first-page": "15545",
      "DOI": "10.1073/pnas.0506580102",
      "article-title": "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles",
      "volume": "102",
      "author": "A Subramanian",
      "year": "2005",
      "journal-title": "Proceedings of the National Academy of Sciences of the United States of America"
    },
    {
      "key": "ref22",
      "doi-asserted-by": "crossref",
      "first-page": "1188",
      "DOI": "10.1101/gr.849004",
      "article-title": "WebLogo: A sequence logo generator",
      "volume": "14",
      "author": "GE Crooks",
      "year": "2004",
      "journal-title": "Genome Research"
    },
    {
      "key": "ref23",
      "doi-asserted-by": "crossref",
      "DOI": "10.1371/journal.pcbi.1001016",
      "article-title": "Genome-Wide Association between Branch Point Properties and Alternative Splicing",
      "volume": "6",
      "author": "A Corvelo",
      "year": "2010",
      "journal-title": "Plos Computational Biology"
    },
    {
      "key": "ref24",
      "doi-asserted-by": "crossref",
      "first-page": "72",
      "DOI": "10.1038/ncb2651",
      "article-title": "SCFFbxo9 and CK2 direct the cellular response to growth factor withdrawal via Tel2/Tti1 degradation and promote survival in multiple myeloma",
      "volume": "15",
      "author": "V Fernandez-Saiz",
      "year": "2013",
      "journal-title": "Nature Cell Biology"
    },
    {
      "key": "ref25",
      "doi-asserted-by": "crossref",
      "first-page": "1939",
      "DOI": "10.1101/gad.1934210",
      "article-title": "A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability",
      "volume": "24",
      "author": "KE Hurov",
      "year": "2010",
      "journal-title": "Genes & development"
    },
    {
      "key": "ref26",
      "doi-asserted-by": "crossref",
      "first-page": "20109",
      "DOI": "10.1074/jbc.M110.121699",
      "article-title": "Tti1 and Tel2 are critical factors in mammalian target of rapamycin complex assembly",
      "volume": "285",
      "author": "T Kaizuka",
      "year": "2010",
      "journal-title": "The Journal of biological chemistry"
    },
    {
      "key": "ref27",
      "doi-asserted-by": "crossref",
      "first-page": "22064",
      "DOI": "10.1074/jbc.M910346199",
      "article-title": "Activation of NF-kappa B by XIAP, the X chromosome-linked inhibitor of apoptosis, in endothelial cells involves TAK1",
      "volume": "275",
      "author": "R Hofer-Warbinek",
      "year": "2000",
      "journal-title": "The Journal of biological chemistry"
    },
    {
      "key": "ref28",
      "doi-asserted-by": "crossref",
      "first-page": "17647",
      "DOI": "10.1074/jbc.M908622199",
      "article-title": "BMP2-induced apoptosis is mediated by activation of the TAK1-p38 kinase pathway that is negatively regulated by Smad6",
      "volume": "275",
      "author": "N Kimura",
      "year": "2000",
      "journal-title": "Journal of Biological Chemistry"
    },
    {
      "key": "ref29",
      "doi-asserted-by": "crossref",
      "first-page": "179",
      "DOI": "10.1093/emboj/18.1.179",
      "article-title": "XIAP, a cellular member of the inhibitor of apoptosis protein family, links the receptors to TAB1-TAK1 in the BMP signaling pathway",
      "volume": "18",
      "author": "K Yamaguchi",
      "year": "1999",
      "journal-title": "The EMBO journal"
    },
    {
      "key": "ref30",
      "doi-asserted-by": "crossref",
      "first-page": "161",
      "DOI": "10.1016/j.canlet.2007.02.018",
      "article-title": "Dysadherin: A new, player in cancer progression",
      "volume": "255",
      "author": "JS Nam",
      "year": "2007",
      "journal-title": "Cancer letters"
    },
    {
      "key": "ref31",
      "doi-asserted-by": "crossref",
      "first-page": "45137",
      "DOI": "10.1074/jbc.M106127200",
      "article-title": "MM-1, a c-Myc-binding protein, is a candidate for a tumor suppressor in leukemia/lymphoma and tongue cancer",
      "volume": "276",
      "author": "Y Fujioka",
      "year": "2001",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "ref32",
      "doi-asserted-by": "crossref",
      "DOI": "10.1093/database/bau093",
      "article-title": "The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data",
      "volume": "2014",
      "author": "C Wilks",
      "year": "2014",
      "journal-title": "Database (Oxford)"
    },
    {
      "key": "ref33",
      "article-title": "SF3B1 mutations are associated with alternative splicing in uveal melanoma",
      "author": "SJ Furney",
      "year": "2013",
      "journal-title": "Cancer discovery"
    },
    {
      "key": "ref34",
      "doi-asserted-by": "crossref",
      "DOI": "10.14806/ej.17.1.200",
      "article-title": "Cutadapt removes adapter sequences from high-throughput sequencing reads",
      "author": "M Martin",
      "year": "2011"
    },
    {
      "key": "ref35",
      "doi-asserted-by": "crossref",
      "first-page": "15",
      "DOI": "10.1093/bioinformatics/bts635",
      "article-title": "STAR: ultrafast universal RNA-seq aligner",
      "volume": "29",
      "author": "A Dobin",
      "year": "2013",
      "journal-title": "Bioinformatics"
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      "first-page": "1036",
      "DOI": "10.1093/bioinformatics/btl048",
      "article-title": "The UCSC Known Genes",
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      "author": "F Hsu",
      "year": "2006",
      "journal-title": "Bioinformatics"
    },
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      "DOI": "10.1186/gb-2006-7-s1-s12",
      "article-title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation",
      "volume": "7",
      "author": "D Thierry-Mieg",
      "year": "2006",
      "journal-title": "Genome biology"
    },
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      "first-page": "1915",
      "DOI": "10.1101/gad.17446611",
      "article-title": "Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses",
      "volume": "25",
      "author": "MN Cabili",
      "year": "2011",
      "journal-title": "Genes & development"
    },
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      "key": "ref39",
      "doi-asserted-by": "crossref",
      "first-page": "D626",
      "DOI": "10.1093/nar/gkp1020",
      "article-title": "H-InvDB in 2009: extended database and data mining resources for human genes and transcripts",
      "volume": "38",
      "author": "C Yamasaki",
      "year": "2010",
      "journal-title": "Nucleic Acids Research"
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      "first-page": "357",
      "DOI": "10.1038/nmeth.1923",
      "article-title": "Fast gapped-read alignment with Bowtie 2",
      "volume": "9",
      "author": "B Langmead",
      "year": "2012",
      "journal-title": "Nature Methods"
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    {
      "key": "ref41",
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      "first-page": "71",
      "DOI": "10.1038/nmeth.2251",
      "article-title": "Streaming fragment assignment for real-time analysis of sequencing experiments",
      "volume": "10",
      "author": "A Roberts",
      "year": "2013",
      "journal-title": "Nature Methods"
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      "first-page": "D945",
      "DOI": "10.1093/nar/gkq929",
      "article-title": "COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer",
      "volume": "39",
      "author": "SA Forbes",
      "year": "2011",
      "journal-title": "Nucleic Acids Research"
    },
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      "first-page": "R106",
      "DOI": "10.1186/gb-2010-11-10-r106",
      "article-title": "Differential expression analysis for sequence count data",
      "volume": "11",
      "author": "S Anders",
      "year": "2010",
      "journal-title": "Genome biology"
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