Contextual Genomics profiled on Global TV News.
Dr. David Huntsman’s Selected Publications
Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nat Genet. 2014 May;46(5):427-9. doi: 10.1038/ng.2928. Epub 2014 Mar 23.
Use of mutation profiles to refine the classification of endometrial carcinomas. J Pathol. 2012 Sep;228(1):20-30. doi: 10.1002/path.4056
Recurrent Somatic DICER1 Mutations in Nonepithelial Ovarian Cancers. N Engl J Med. 2011 Dec 21. [Epub ahead of print]
Olaparib in patients with recurrent high-grade serous or poorly differentiated ovarian carcinoma or triple-negative breast cancer: a phase 2, multicentre, open-label, non-randomised study. Lancet Oncol. 2011 Sep; 12 (9): 852-61.
Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas J Pathol. 2011 Apr;223(5):567-73. doi: 10.1002/path.2848. Epub 2011 Mar 7
ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas. N Engl J Med. 2010 Sep 8. [Epub ahead of print]
Subtyping of Breast Cancer by Immunohistochemistry to Investigate a Relationship between Subtype and Short and Long Term Survival: A Collaborative Analysis of Data for 10,159 Cases from 12 Studies. PLoS Med. 2010 May 25;7(5):e1000279.
Identification of Sister Chromatids by DNA Template Strand Sequences. Nature. 2010 Jan 7;463(7277):93-7.
Does Massively Parallel DNA Resequencing Signify the End of Histopathology As We Know It? J Pathol. 2010 Jan;220(2):307-15.
Mutation of FOXL2 Gene in Granulosa-Cell Tumors of the Ovary. N Engl J Med. 2009 Jun 25;360(26):2719-29.
Germline CDH1 Deletions in Hereditary Diffuse Gastric Cancer Families. Hum Mol Genet. 2009 May 1;18(9):1545-55.
Ovarian Carcinoma Subtypes are Different Diseases: Implications for Biomarker Studies. PLoS Med. 2008 Dec 2;5(12):e232.
Founder and Recurrent CDH1 Mutations in Families with Hereditary Diffuse Gastric Cancer. Jama. 2007 Jun 6;297(21):2360-72.
A Landscape Effect in Tenosynovial Giant-cell Tumor from Activation of CSF1 Expression by a Translocation in a Minority of Tumor cells. Proc Natl Acad Sci USA. 2006 Jan 17;103(3):690-5
EMSY Links the BRCA2 Pathway to Sporadic Breast and Ovarian Cancer. Cell. 2003 Nov 26;115(5):523-35.
Expression of the ETV6-NTRK3 Gene Fusion as a Primary Event in Human Secretory Breast Carcinoma. Cancer Cell. 2002 Nov;2(5):367-76.
Early Gastric Cancer in Young, Asymptomatic Carriers of Germ-Line E-Cadherin Mutations. N Engl J Med. 2001 Jun 21;344(25):1904-9.
Use of mutation profiles to refine the classification of endometrial carcinomas. J Pathol. 2012 Sep;228(1):20-30. doi: 10.1002/path.4056
Recurrent Somatic DICER1 Mutations in Nonepithelial Ovarian Cancers. N Engl J Med. 2011 Dec 21. [Epub ahead of print]
Olaparib in patients with recurrent high-grade serous or poorly differentiated ovarian carcinoma or triple-negative breast cancer: a phase 2, multicentre, open-label, non-randomised study. Lancet Oncol. 2011 Sep; 12 (9): 852-61.
Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas J Pathol. 2011 Apr;223(5):567-73. doi: 10.1002/path.2848. Epub 2011 Mar 7
ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas. N Engl J Med. 2010 Sep 8. [Epub ahead of print]
Subtyping of Breast Cancer by Immunohistochemistry to Investigate a Relationship between Subtype and Short and Long Term Survival: A Collaborative Analysis of Data for 10,159 Cases from 12 Studies. PLoS Med. 2010 May 25;7(5):e1000279.
Identification of Sister Chromatids by DNA Template Strand Sequences. Nature. 2010 Jan 7;463(7277):93-7.
Does Massively Parallel DNA Resequencing Signify the End of Histopathology As We Know It? J Pathol. 2010 Jan;220(2):307-15.
Mutation of FOXL2 Gene in Granulosa-Cell Tumors of the Ovary. N Engl J Med. 2009 Jun 25;360(26):2719-29.
Germline CDH1 Deletions in Hereditary Diffuse Gastric Cancer Families. Hum Mol Genet. 2009 May 1;18(9):1545-55.
Ovarian Carcinoma Subtypes are Different Diseases: Implications for Biomarker Studies. PLoS Med. 2008 Dec 2;5(12):e232.
Founder and Recurrent CDH1 Mutations in Families with Hereditary Diffuse Gastric Cancer. Jama. 2007 Jun 6;297(21):2360-72.
A Landscape Effect in Tenosynovial Giant-cell Tumor from Activation of CSF1 Expression by a Translocation in a Minority of Tumor cells. Proc Natl Acad Sci USA. 2006 Jan 17;103(3):690-5
EMSY Links the BRCA2 Pathway to Sporadic Breast and Ovarian Cancer. Cell. 2003 Nov 26;115(5):523-35.
Expression of the ETV6-NTRK3 Gene Fusion as a Primary Event in Human Secretory Breast Carcinoma. Cancer Cell. 2002 Nov;2(5):367-76.
Early Gastric Cancer in Young, Asymptomatic Carriers of Germ-Line E-Cadherin Mutations. N Engl J Med. 2001 Jun 21;344(25):1904-9.
Dr. Sohrab Shah’s Selected Publications
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.. J Pathol. 2013 Sep;231(1):21-34. doi: 10.1002/path.4230. PubMed PMID: 23780408; PubMed Central PMCID: PMC3864404.
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PubMed PMID: 23699601; PubMed Central PMCID: PMC3744992.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012 Dec 22;13(12):R124. doi: 10.1186/gb-2012-13-12-r124. PubMed PMID: 23383675; PubMed Central PMCID: PMC4056374.
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res. 2012 Oct;22(10):1995-2007. doi: 10.1101/gr.137570.112. Epub 2012 May 25. PubMed PMID: 22637570; PubMed Central PMCID: PMC3460194.
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983. PubMed PMID: 22522925; PubMed Central PMCID: PMC3440846.
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933. PubMed PMID: 22495314; PubMed Central PMCID: PMC3863681.
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27. PubMed PMID: 22285562; PubMed Central PMCID: PMC3315723.
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics. 2012 Jan 15;28(2):167-75. doi: 10.1093/bioinformatics/btr629. Epub 2011 Nov 13. PubMed PMID: 22084253; PubMed Central PMCID: PMC3259434.
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011 May;7(5):e1001138. doi: 10.1371/journal.pcbi.1001138. Epub 2011 May 19. PubMed PMID: 21625565; PubMed Central PMCID: PMC3098195.
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14;363(16):1532-43. doi: 10.1056/NEJMoa1008433. Epub 2010 Sep 8. PubMed PMID: 20942669; PubMed Central PMCID: PMC2976679.
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature. 2011 Mar 17;471(7338):377-81. doi: 10.1038/nature09754. Epub 2011 Mar 2. PubMed PMID: 21368758; PubMed Central PMCID: PMC3902849.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3. PubMed PMID: 20130035; PubMed Central PMCID: PMC2832826.
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-13. doi: 10.1038/nature08489. PubMed PMID: 19812674.
Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med. 2009 Jun 25;360(26):2719-29. doi: 10.1056/NEJMoa0902542. Epub 2009 Jun 10. PubMed PMID: 19516027.
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PubMed PMID: 23699601; PubMed Central PMCID: PMC3744992.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012 Dec 22;13(12):R124. doi: 10.1186/gb-2012-13-12-r124. PubMed PMID: 23383675; PubMed Central PMCID: PMC4056374.
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res. 2012 Oct;22(10):1995-2007. doi: 10.1101/gr.137570.112. Epub 2012 May 25. PubMed PMID: 22637570; PubMed Central PMCID: PMC3460194.
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983. PubMed PMID: 22522925; PubMed Central PMCID: PMC3440846.
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933. PubMed PMID: 22495314; PubMed Central PMCID: PMC3863681.
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27. PubMed PMID: 22285562; PubMed Central PMCID: PMC3315723.
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics. 2012 Jan 15;28(2):167-75. doi: 10.1093/bioinformatics/btr629. Epub 2011 Nov 13. PubMed PMID: 22084253; PubMed Central PMCID: PMC3259434.
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011 May;7(5):e1001138. doi: 10.1371/journal.pcbi.1001138. Epub 2011 May 19. PubMed PMID: 21625565; PubMed Central PMCID: PMC3098195.
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14;363(16):1532-43. doi: 10.1056/NEJMoa1008433. Epub 2010 Sep 8. PubMed PMID: 20942669; PubMed Central PMCID: PMC2976679.
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature. 2011 Mar 17;471(7338):377-81. doi: 10.1038/nature09754. Epub 2011 Mar 2. PubMed PMID: 21368758; PubMed Central PMCID: PMC3902849.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3. PubMed PMID: 20130035; PubMed Central PMCID: PMC2832826.
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-13. doi: 10.1038/nature08489. PubMed PMID: 19812674.
Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med. 2009 Jun 25;360(26):2719-29. doi: 10.1056/NEJMoa0902542. Epub 2009 Jun 10. PubMed PMID: 19516027.
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