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Peer-Reviewed Publications

Feng X, Pleasance E, Zhao EY, et al. Therapeutic implication of genomic landscape of adult metastatic sarcoma. JCO Precision Oncology. 2019 Jun;3:1-25. doi: 10.1200/PO.18.00325

Williamson LM, Steel M, Grewal JK, et al. Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor. Cold Spring Harb Mol Case Stud. 2019 Jun;5(3): a003814. doi: 10.1101/mcs.a003814

Jones MR, Williamson LM, Topham JT, et al. NRG1 gene fusions are recurrent, clinically actionable gene rearrangements in KRAS wild-type pancreatic ductal adenocarcinoma. Clin Cancer Res. 2019 May. doi: 10.1158/1078-0432.CCR-19-0191. [Epub ahead of print]

Grewal JK, Tessier-Cloutier B, Jones M, et al. Application of a neural network whole transcriptome-based pan-cancer method for diagnosis of primary and metastatic cancers. JAMA Netw Open. 2019 Apr;2(4): e192597. doi: 10.1001/jamanetworkopen.2019.2597

Thibodeau ML, Zhao EY, Reisle C, et al. Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis. Cold Spring Harb Mol Case Stud. 2019 Apr;5(2): a003681. doi: 10.1101/mcs.a003681

Tsang ES, Shen Y, Chooback N, et al. Clinical outcomes after whole-genome sequencing in patients with metastatic non-small-cell lung cancer. Cold Spring Harb Mol Case Stud. 2019 Feb;5(1):a002659. doi: 10.1101/mcs.a002659

Ko JJ, Grewal JK, Ng T, et al. Whole-genome and transcriptome profiling of a metastatic thyroid-like follicular renal cell carcinoma. Cold Spring Harb Mol Case Stud. 2018 Dec;4(6):a003137. doi: 10.1101/mcs.a003137

Wong HL, Zhao EY, Jones MR, et al. Temporal Dynamics of Genomic Alterations in a BRCA1 Germline—Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan. JCO Precis Oncol. 2018 Oct;2:1-8. doi: 10.1200/PO.18.00057

Newton Y, Rassekh RS, Deyell RJ, et al. Comparative RNA-sequencing analysis benefits a pediatric patient with relapsed cancer. JCO Precis Oncol. 2018 Apr;2:1-16. doi: 10.1200/PO.17.00198

Chahal M, Pleasance E, Grewal J, et al. Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision making. Cold Spring Harb Mol Case Stud. 2018 Apr;4(2):a002626. doi: 10.1101/mcs.a002626

Ronsley R, Rassekh SR, Shen Y, et al. Application of genomics to identify therapeutic targets in recurrent pediatric papillary thyroid carcinoma. Cold Spring Harb Mol Case Stud. 2018 Apr;4(2):a002568. doi: 10.1101/mcs.a002568

Owen DR, Wong HL, Bonakdar M, et al. Molecular characterization of ERBB2-amplified colorectal cancer identifies potential mechanisms of resistance to targeted therapies: a report of two instructive cases. Cold Spring Harb Mol Case Stud. 2018 Apr;4(2):a002535. doi: 10.1101/mcs.a002535

Thibodeau ML, Bonakdar M, Zhao E, et al. Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma. NPJ Precis Oncol. 2018 Mar;2(1):8. doi: 10.1038/s41698-018-0050-5

Zhao EY, Shen Y, Pleasance E, et al. Homologous recombination deficiency and platinum-based therapy outcomes in advanced breast cancer. Clin Cancer Res. 2017 Dec;23(24):7521-7530. doi: 10.1158/1078-0432.CCR-17-1941

Jones MR, Lim H, Shen Y, et al. Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer. Ann Oncol. 2017 Dec;28(12):3092-3097. doi: 10.1093/annonc/mdx523

Wong HL, Yang KC, Shen Y, et al. Molecular characterization of metastatic pancreatic neuroendocrine tumours (PNETs) using whole genome and transcriptome sequencing. Cold Spring Harb Mol Case Stud. 2018 Feb;4(1):a002329. doi: 10.1101/mcs.a002329

Grewal JK, Eirew P, Jones M, et al. Detection and genomic characterization of a mammary-like adenocarcinoma. Cold Spring Harb Mol Case Stud. 2017 Nov;3(6):a002170. doi: 10.1101/mcs.a002170.

Chooback N, Shen Y, Jones M, et al. Carcinoma ex pleomorphic adenoma: case report and options for systemic therapy. Curr Oncol. 2017 Jun;24(3):e251-e254. doi: 10.3747/co.24.3588

Chow-White P, Ha D, Laskin J, et al. Knowledge, attitudes, and values among physicians working with clinical genomics: a survey of medical oncologists. Hum Resour Health. 2017 Jun;15(1):42. doi: 10.1186/s12960-017-0218-z

Thibodeau ML, Reisle C, Zhao E, et al. Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma. Cold Spring Harb Mol Case Stud. 2017 Sep;3(5):a001628. doi: 10.1101/mcs.a001628

Weymann D, Laskin J, Roscoe R, et al. The cost and cost-trajectory of whole-genome analysis guiding treatment of patients with advanced cancer. Mol Genet Genomic Med. 2017 Mar;5(3):251-260. doi: 10.1002/mgg3.281

Sheffield BS, Tessier-Cloutier B, Li-Chang H, et al. Personalized oncogenomics in the management of gastrointestinal carcinomas-early experiences from a pilot study. Curr Oncol. 2016 Dec;23(6):e571-e575. doi:10.3747/co.23.3165

Laskin J, Ha D, Chan T, et al. Clinicians identify high need to increase their genomic literacy to applied cancer genomics. Ann Oncol. 2016 Oct;27(suppl_6):1379P. doi: 10.1093/annonc/mdw387.16

Sheffield BS, Fulton R, Kalloger SE, et al. Investigation of PD-L1 biomarker testing methods for PD-1 axis inhibition in non-squamous non-small cell lung cancer. J Histochem Cytochem. 2016 Oct;64(10):587-600. doi: 10.1369/0022155416665338

Alassiri AH, Ali RH, Shen Y, et al. ETV6-NTRK3 is expressed in a subset of ALK-negative inflammatory myofibroblastic tumors. Am J Surg Pathol. 2016 Aug;40(80):1051-61. doi: 10.1097/PAS.0000000000000677

Jones, MR, Schrader KA, Shen Y, et al. Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer. Ann Oncol. 2016 May;27(5):801-806. doi:10.1093/annonc/mdw060

Parker JD, Shen Y, Pleasance E, et al. Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing. Cold Spring Harb Mol Case Stud. 2016 Mar;2(2):a000679. doi: 10.1101/mcs.a000679

Laskin J, Jones S, Aparicio S, et al. Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers. Cold Spring Harb Mol Case Stud. 2015 Oct;1(1):a000570. doi: 10.1101/mcs.a000570

Bose, P, Pleasance ED, Jones M, et al. Integrative genomic analysis of ghost cell odontogenic carcinoma. Oral Oncol. 2015 Sep;51(9):e71-e75. doi:10.1016/j.oraloncology.2015.06.013

Sheffield BS, Tinker AV, Shen Y, et al. Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing. PLoS One. 2015 Mar;10(3):e0119689. doi:10.1371/journal.pone.0119689

Jamshidi F, Pleasance E, Li Y, et al. Diagnostic value of next-generation sequencing in an unusual sphenoid tumor. Oncologist. 2014 Jun;19(6):623-630. doi: 10.1634/theoncologist.2013-0390

Jones SJ, Laskin J, Li YY, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010 Aug;11(8):R82. doi:10.1186/gb-2010-11-8-r82