Selected Publications


Contextual Genomics’
scientific and medical founders

Drs. Samuel Aparicio, David Huntsman and Sohrab Shah have published several hundred peer reviewed articles on the subject of cancer genomics and diagnosis. Below is a list of selected publications.




Hereditary Diffuse Gastric Cancer Syndrome. CDH1 Mutations and Beyond. JAMA Oncol. 2015;1(1):23-32.

Using Somatic Mutations to Guide Treatment Decisions: Context Matters. JAMA Oncol. 2015;1(3):275-6.

Recurrent DICER1 hotspot mutations in endometrial tumours and their impact on microRNA biogenesis. J Pathol. 2015;237(2):215-25.

Dual loss of the SWI/SNF complex ATPases SMARCA4/BRG1 and SMARCA2/BRM is highly sensitive and specific for small cell carcinoma of the ovary, hypercalcemic type. J Pathol. 2015;238(3):389-400.

The oncogenic roles of DICER1 RNase IIIb domain mutations in ovarian Sertoli-Leydig cell tumors. Neoplasia. 2015;17(8):650-60.

Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality. J Natl Cancer Inst. 2016;108(6).

Rare cancers: a sea of opportunity. Lancet Oncol. 2016;17(2):e52-61.

Molecularly Defined Adult Granulosa Cell Tumor of the Ovary: The Clinical Phenotype. J Natl Cancer Inst. 2016;108(11).

Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research. Sci Rep. 2016;6:34949.

FOXL2 402C>G Mutation Can Be Identified in the Circulating Tumor DNA of Patients with Adult Granulosa Cell Tumors. J Mol Diagn. 2017;19(1):126-136.

The disparate origins of ovarian cancers: pathogenesis and prevention strategies. Nat Rev Cancer. 2017;17(1):65-74.

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nat Genet. 2014;46(5):427-9.

Use of mutation profiles to refine the classification of endometrial carcinomas. J Pathol. 2012;228(1):20-30.

Recurrent Somatic DICER1 Mutations in Nonepithelial Ovarian Cancers. N Engl J Med. 2011;366(3):234-42.

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;2 (9): 852-61.

Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas J Pathol. 2011;223(5):567-73.

ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas. N Engl J Med. 2010;363(16): 1532–1543.

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;7(5):e1000279.

Identification of Sister Chromatids by DNA Template Strand Sequences. Nature. 2010;463(7277):93-7.

Does Massively Parallel DNA Resequencing Signify the End of Histopathology As We Know It? J Pathol. 2010;220(2):307-15.

Mutation of FOXL2 Gene in Granulosa-Cell Tumors of the Ovary. N Engl J Med. 2009;360(26):2719-29.

Germline CDH1 Deletions in Hereditary Diffuse Gastric Cancer Families. Hum Mol Genet. 2009;18(9):1545-55.

Ovarian Carcinoma Subtypes are Different Diseases: Implications for Biomarker Studies. PLoS Med. 2008;5(12):e232.

Founder and Recurrent CDH1 Mutations in Families with Hereditary Diffuse Gastric Cancer. JAMA. 2007;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;103(3):690-5.

EMSY Links the BRCA2 Pathway to Sporadic Breast and Ovarian Cancer. Cell. 2003;115(5):523-35.

Expression of the ETV6-NTRK3 Gene Fusion as a Primary Event in Human Secretory Breast Carcinoma. Cancer Cell. 2002;2(5):367-76.

Early Gastric Cancer in Young, Asymptomatic Carriers of Germ-Line E-Cadherin Mutations. N Engl J Med. 2001;344(25):1904-9.

Scalable whole-genome single-cell library preparation without preamplification. Nat Methods. 2017;14(2):167-173.

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study. PLoS Med. 2016;13(12).

Clonal genotype and population structure inference from single-cell tumor sequencing. Nat Methods. 2016;13(7):573-6.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat Genet. 2016;48(7):758-67.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature. 2015;518(7539):422-6.

PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014;11(4):396-8.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. J Pathol. 2013;231(1):21-34.

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013;122(7):1256-65.

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012;13(12):R124.

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;22(10):1995-2007.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012;486(7403):346-52.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486(7403):395-9.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012;28(7):907-13.

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics. 2012;28(2):167-75.

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011;7(5):e1001138.

ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010;363(16):1532-43.

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature. 2011;471(7338):377-81.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010;26(6):730-6.

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009;461(7265):809-13.

Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med. 2009;360(26):2719-29.

The shaping and functional consequence of the miRNA landscape in breast cancer. Nature. 2013;497, 378–382.

The implications of clonal genome evolution for cancer medicine. N Engl J Med. 2013;368(9):842-851.

The clonal and mutational evolution spectrum of primary triple negative breast cancers. Nature. 2012;486,395–399.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012;486(7403):346-52.

Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood. 2011;117(8):2451-9.

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009;461:809-813.

Loss of MLL5 results in pleiotropic hematopoietic defects, reduced neutrophil immune function and extreme sensitivity to DNA demethylation. Blood. 2009;113(7):1432-43.

Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Res. 2006;16(1):66-77.

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002;297(5585):1301-1310.

Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet. 1997;16(1):79-83.

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc Natl Acad Sci U S A. 1995;92(5):1684-8.

A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1. Nature. 1994;370,567-571.

Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature. 1993;366,265-268.