Department of Translational Genomics Lab Pages, Student Resources, and Web Applications

Faculty

John D. Carpten, Ph.D.

Overview

Dr. Carpten's cancer research program spans many tumor types including, but not limited to, prostate cancer, breast cancer, colon cancer, brain cancer, and multiple myeloma, in addition to several forms of pediatric cancer.  He was a lead author on the first genome wide scan for hereditary prostate cancer genes (Science. 1996 Nov 22;274(5291):1371-4.), and the identification of HOXB13 as the first true hereditary prostate cancer gene (New England Journal of Medicine. 2012 Jan 12;366(2):141-9.).  He also led a landmark study, which culminated in the discovery of the AKT1(E17K) activating mutation in human cancers, published in Nature. This study received an “Exceptional” rating by the Faculty of 1000, placing the paper in the top 1% of published work worldwide in the area of biology in 2007.  He has also helped to pioneer the area of cancer disparities with his leadership in the African American Hereditary Prostate Cancer Study (AAHPC) Network and his work in understanding differences in tumor biology from cancers derived from individuals of different genetic ancestries.

Dr. Carpten has also been involved in the development and application of high throughput genomic methods and technologies throughout his career. Currently, he has a major focus in Precision Medicine, where Next Generation Sequencing is being applied to interrogate the genomes and transcriptomes of tumors in a clinical setting to identify targetable events for select therapeutics (Molecular Cancer Therapeutics. 2013 Jan;12(1):104-16.) (PLoS Genetics. 2014 Feb 13;10(2):e1004135.). Towards these efforts, he coordinated the development of a CLIA-certified laboratory to support clinical genomic testing. This laboratory was later commercialized as Ashion Analytics, LLC.

It is his hope that this work will one day lead to improvements in knowledge based therapeutics toward improvements in outcomes for cancer patients.

Publications

Robotic salvage retroperitoneal and pelvic lymph node dissection for 'node-only' recurrent prostate cancer: technique and initial series. BJU Int. 2017 Sep; 120(3):401-408. View in: PubMed

Enrichment of PI3K-AKT-mTOR Pathway Activation in Hepatic Metastases from Breast Cancer. Clin Cancer Res. 2017 Aug 15; 23(16):4919-4928. View in: PubMed

Comprehensive Genomic Analysis of Metastatic Mucinous Urethral Adenocarcinoma Guides Precision Oncology Treatment: Targetable EGFR Amplification Leading to Successful Treatment With Erlotinib. Clin Genitourin Cancer. 2017 Aug; 15(4):e727-e734. View in: PubMed

gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels. Genet Epidemiol. 2017 May; 41(4):297-308. View in: PubMed

Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. Genome Res. 2017 Apr; 27(4):524-532. View in: PubMed

gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels. Genet Epidemiol. 2017 Feb 16. View in: PubMed

Identifying aggressive prostate cancer foci using a DNA methylation classifier. Genome Biol. 2017 Jan 12; 18(1):3. View in: PubMed

Case report: whole exome sequencing of primary cardiac angiosarcoma highlights potential for targeted therapies. BMC Cancer. 2017 Jan 05; 17(1):17. View in: PubMed

A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy. PLoS One. 2017; 12(6):e0179170. View in: PubMed

Robotic salvage retroperitoneal and pelvic lymph node dissection for 'node-only' recurrent prostate cancer: technique and initial series. BJU Int. 2016 Dec 15. View in: PubMed

Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers. Sci Rep. 2016 Dec; 6(1):25. View in: PubMed

Comprehensive Genomic Analysis of Metastatic Mucinous Urethral Adenocarcinoma Guides Precision Oncology Treatment: Targetable EGFR Amplification Leading to Successful Treatment With Erlotinib. Clin Genitourin Cancer. 2016 Dec 01. View in: PubMed

Molecular Genetic Profiling of Adolescent Glassy Cell Carcinoma of the Cervix Reveals Targetable EGFR Amplification with Potential Therapeutic Implications. J Adolesc Young Adult Oncol. 2016 Sep; 5(3):297-302. View in: PubMed

Post hoc Analysis for Detecting Individual Rare Variant Risk Associations Using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies. Genet Epidemiol. 2016 Sep; 40(6):461-9. View in: PubMed

Prostate Cancer Susceptibility in Men of African Ancestry at 8q24. J Natl Cancer Inst. 2016 Jul; 108(7). View in: PubMed

Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016 May; 17(5):257-71. View in: PubMed

A somatic reference standard for cancer genome sequencing. Sci Rep. 2016 Apr 20; 6:24607. View in: PubMed

Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016 Apr 07; 7:10979. View in: PubMed

Successful Treatment of Genetically Profiled Pediatric Extranodal NK/T-Cell Lymphoma Targeting Oncogenic STAT3 Mutation. Pediatr Blood Cancer. 2016 Apr; 63(4):727-30. View in: PubMed

Molecular Genetic Profiling of Adolescent Glassy Cell Carcinoma of the Cervix Reveals Targetable EGFR Amplification with Potential Therapeutic Implications. J Adolesc Young Adult Oncol. 2016 Mar 14. View in: PubMed

Post hoc Analysis for Detecting Individual Rare Variant Risk Associations Using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies. Genet Epidemiol. 2016 09; 40(6):461-9. View in: PubMed

Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers. Sci Rep. 2016 12 23; 6(1):25. View in: PubMed

Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016; 7:10979. View in: PubMed

A somatic reference standard for cancer genome sequencing. Sci Rep. 2016; 6:24607. View in: PubMed

Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. Hum Mol Genet. 2015 Oct 01; 24(19):5603-18. View in: PubMed

Toward precision medicine in glioblastoma: the promise and the challenges. Neuro Oncol. 2015 Aug; 17(8):1051-63. View in: PubMed

Pilot Trial of Selecting Molecularly Guided Therapy for Patients with Non-V600 BRAF-Mutant Metastatic Melanoma: Experience of the SU2C/MRA Melanoma Dream Team. Mol Cancer Ther. 2015 Aug; 14(8):1962-71. View in: PubMed

Professor and Chair of Translational Genomics
Director, Institute for Translational Genomics
Department of Translational Genomics
Health Sciences Campus
NRT, 1450 Biggy Street, Los Angeles