Keck School Faculty

John D. Carpten
John D. Carpten
Professor and Chair of Translational Genomics;Director, Institute of Translational Genomics
Department of Translational Genomics
1450 Biggy Street Health Sciences Campus Los Angeles
Dr. Carpten is an internationally recognized expert in genome science, and possesses unique training in multiple disciplines including germline genetics for disease risk and predisposition, somatic cancer genomics, health disparities research, cell biology, functional genomics, and precision medicine.
Dr. Carpten earned his Ph.D. from the Ohio State University in 1994 with a focus on human genetics. He then went on to complete a postdoctoral fellowship at the National Human Genome Research Institute, NIH, Bethesda, in Cancer Genetics, where he was later promoted to the tenure track in 2000. Then in 2003, Dr. Carpten accepted a position to become Division Director, Division of Integrated Cancer Genomics, at the Translational Genomics Research Institute (TGen), Phoenix, AZ. Later, in 2012 he was promoted to the position of Deputy Director of Basic Research for TGen. In 2016 he was recruited by the University of Southern California Keck School of Medicine, to build and chair a new Department and Institute of Translational Genomics.

Dr. Carpten’s primary research program centers around the development and application of cutting edge genomic technologies and bioinformatics analysis in search of germ-line and somatic alterations that are associated with cancer risk and tumor characteristics, respectively. A major focus of Dr. Carpten’s research has been related to prostate cancer genetics. 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.). His group has also discovered a number of single nucleotide polymorphisms, which confer increased risk of developing prostate cancer (Journal of the National Cancer Institute. 2007 Dec 19;99(24):1836-44.). Furthermore, he has played a critical role in prostate cancer cell biology studies (Nat Genet. 2004 Sep;36(9):979-83.), and prostate cancer tumor genome profiling studies (Genome Res. 2011 Jan;21(1):47-55.).

Dr. Carpten has also been an early pioneer in the understanding the role of biology in disparate cancer incidence and mortality rates seem among underrepresented populations. Through his leadership, the African American Hereditary Prostate Cancer Study (AAHPC) Network was conceived.  This study has become a model for genetic linkage studies in underrepresented populations and led to the first genome wide scan for prostate cancer susceptibility genes in African Americans (Prostate. 2007 Jan 1;67(1):22-31.). 

Dr. Carpten’ 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 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. It also received a “Must Read” rating, placing the paper in the top 5% of published work in the area of medicine. He extended this work to include an in depth analysis of the functional and mechanistic effects of this mutation on mammary cell biology (Human Mutation). Furthermore, his laboratory participated in and led several high impact studies in Multiple Myeloma research. This includes the seminal study describing common mutation of NF-kB pathway genes in Multiple Myeloma, which was published in Cancer Cell. Importantly, Multiple Myeloma is yet another form of cancer, which disproportionately affects African Americans. Dr. Carpten’s laboratory led the first study to interrogate the somatic features of Multiple Myeloma tumors derived from African American patients, who have higher incidence rates and worse outcomes compared to European descent Myeloma patients (Blood).

Dr. Carpten has also been involved 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.

Dr. Carpten has received research funding awards from various sources to support his research including NIH, Prostate Cancer Foundation, Susan G. Komen for the Cure, Multiple Myeloma Research Foundation, and a number of pharmaceutical companies. Dr. Carpten has co-authored over 160 publications in scientific journals that include Science, Nature, Nature Genetics, Genome Research, Cancer Research, Molecular Cancer Research, Cancer Cell, and the New England Journal of Medicine.

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

National Institutes of Health: Ooops. Something went wrong., 2016-2016

National Institutes of Health: NIH/NHGRI Jeffrey M. Trent Lectureship, 2016-2016

Susan G. Komen for the Cure: AACR Distinguished Lectureship on the Science of Health Disparities, 2014-2014

Susan G. Komen for the Cure: Ooops. Something went wrong., 2014-2014

Science Spectrum Magazine: Science Trailblazer, 2006-2006

Science Spectrum Magazine: Ooops. Something went wrong., 2006-2006

National Institutes of Health: NHGRI Faculty Mentor Awardee , 2002-2002

National Institutes of Health: Ooops. Something went wrong., 2002-2002

Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer Sci Rep. 2019 Feb 06; 9(1):1482. . View in PubMed

E6201, an intravenous MEK1 inhibitor, achieves an exceptional response in BRAF V600E-mutated metastatic malignant melanoma with brain metastases Invest New Drugs. 2018 Sep 28. . View in PubMed

Exogenous IL-6 induces mRNA splice variant MBD2_v2 to promote stemness in TP53 wild-type, African American PCa cells Mol Oncol. 2018 Jun; 12(7):1138-1152. . View in PubMed

Exogenous IL6 induces mRNA splice variant MBD2_v2 to promote stemness in TP53 wild-type, African American PCa cells Mol Oncol. 2018 May 09. . View in PubMed

Exogenous IL-6 induces mRNA splice variant MBD2_v2 to promote stemness in TP53 wild-type, African American PCa cells Mol Oncol. 2018 06; 12(7):1138-1152. . View in PubMed

Comparative analysis of primary versus relapse/refractory DLBCL identifies shifts in mutation spectrum Oncotarget. 2017 Nov 21; 8(59):99237-99244. . View in PubMed

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases PLoS Genet. 2017 Nov; 13(11):e1007087. . View in PubMed

A method to reduce ancestry related germline false positives in tumor only somatic variant calling BMC Med Genomics. 2017 Oct 19; 10(1):61. . 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

Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium PLoS Genet. 2017 Apr; 13(4):e1006719. . 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 08; 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 05; 41(4):297-308. . View in PubMed

Case report: whole exome sequencing of primary cardiac angiosarcoma highlights potential for targeted therapies BMC Cancer. 2017 01 05; 17(1):17. . View in PubMed

A multicenter, randomized study of decitabine as epigenetic priming with induction chemotherapy in children with AML Clin Epigenetics. 2017; 9:108. . View in PubMed

A method to reduce ancestry related germline false positives in tumor only somatic variant calling BMC Med Genomics. 2017 10 19; 10(1):61. . 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

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

A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci Cancer Epidemiol Biomarkers Prev. 2016 12; 25(12):1609-1618. . 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

Generalizability of established prostate cancer risk variants in men of African ancestry Int J Cancer. 2015 Mar 01; 136(5):1210-7. . View in PubMed

An integrated framework for reporting clinically relevant biomarkers from paired tumor/normal genomic and transcriptomic sequencing data in support of clinical trials in personalized medicine Pac Symp Biocomput. 2015; 56-67. . View in PubMed

8q24 risk alleles and prostate cancer in African-Barbadian men Prostate. 2014 Dec; 74(16):1579-88. . View in PubMed

A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer Nat Genet. 2014 Oct; 46(10):1103-9. . View in PubMed

Detection of an atypical teratoid rhabdoid brain tumor gene deletion in circulating blood using next-generation sequencing J Child Neurol. 2014 Sep; 29(9):NP81-5. . View in PubMed

Association analysis of 9,560 prostate cancer cases from the International Consortium of Prostate Cancer Genetics confirms the role of reported prostate cancer associated SNPs for familial disease Hum Genet. 2014 Mar; 133(3):347-56. . View in PubMed

Extramedullary myeloma whole genome sequencing reveals novel mutations in Cereblon, proteasome subunit G2 and the glucocorticoid receptor in multi drug resistant disease Br J Haematol. 2013 Jun; 161(5):748-51. . View in PubMed

A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry Nat Genet. 2013 Jun; 45(6):690-6. . View in PubMed

Expression and phosphorylation of the AS160_v2 splice variant supports GLUT4 activation and the Warburg effect in multiple myeloma Cancer Metab. 2013 May 29; 1(1):14. . View in PubMed

CUL3 and NRF2 mutations confer an NRF2 activation phenotype in a sporadic form of papillary renal cell carcinoma Cancer Res. 2013 Apr 01; 73(7):2044-51. . View in PubMed

A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges PLoS One. 2013; 8(10):e76438. . View in PubMed

Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities Mol Cancer Ther. 2013 Jan; 12(1):104-16. . View in PubMed

Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing Sci Transl Med. 2012 Nov 28; 4(162):162ra154. . View in PubMed

Clonal competition with alternating dominance in multiple myeloma Blood. 2012 Aug 02; 120(5):1067-76. . View in PubMed

Differential effects of AKT1(pE17K) expression on human mammary luminal epithelial and myoepithelial cells. Hum Mutat. 2012 Aug; 33(8):1216-27. . View in PubMed

Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families BMC Med Genet. 2012 Jun 19; 13:46. . View in PubMed

Association of prostate cancer risk with SNPs in regions containing androgen receptor binding sites captured by ChIP-On-chip analyses Prostate. 2012 Mar; 72(4):376-85. . View in PubMed

Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG Prostate. 2012 Mar; 72(4):410-26. . View in PubMed

Germline mutations in HOXB13 and prostate-cancer risk N Engl J Med. 2012 Jan 12; 366(2):141-9. . View in PubMed

Deep clonal profiling of formalin fixed paraffin embedded clinical samples PLoS One. 2012; 7(11):e50586. . View in PubMed

Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing PLoS One. 2012; 7(10):e43192. . View in PubMed

Cancer of the ampulla of Vater: analysis of the whole genome sequence exposes a potential therapeutic vulnerability Genome Med. 2012; 4(7):56. . View in PubMed

DNA methylation in multiple myeloma is weakly associated with gene transcription PLoS One. 2012; 7(12):e52626. . View in PubMed

Advancing a clinically relevant perspective of the clonal nature of cancer Proc Natl Acad Sci U S A. 2011 Jul 19; 108(29):12054-9. . View in PubMed

Genome-wide copy-number variation analysis identifies common genetic variants at 20p13 associated with aggressiveness of prostate cancer Carcinogenesis. 2011 Jul; 32(7):1057-62. . View in PubMed

Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21 Nat Genet. 2011 Jun; 43(6):570-3. . View in PubMed

EphB2 SNPs and sporadic prostate cancer risk in African American men PLoS One. 2011; 6(5):e19494. . View in PubMed

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors Genome Res. 2011 Jan; 21(1):47-55. . View in PubMed

Contribution of HPC1 (RNASEL) and HPCX variants to prostate cancer in a founder population Prostate. 2010 Nov 01; 70(15):1716-27. . View in PubMed

DNA methylation analysis determines the high frequency of genic hypomethylation and low frequency of hypermethylation events in plasma cell tumors Cancer Res. 2010 Sep 01; 70(17):6934-44. . View in PubMed

Genome-wide linkage analysis of 1,233 prostate cancer pedigrees from the International Consortium for Prostate Cancer Genetics using novel sumLINK and sumLOD analyses Prostate. 2010 May 15; 70(7):735-44. . View in PubMed

Correlation between array-comparative genomic hybridization-defined genomic gains and losses and survival: identification of 1p31-32 deletion as a prognostic factor in myeloma Leukemia. 2010 Apr; 24(4):833-42. . View in PubMed

A novel prostate cancer susceptibility locus at 19q13 Cancer Res. 2009 Apr 01; 69(7):2720-3. . View in PubMed

Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk Hum Mol Genet. 2009 Apr 01; 18(7):1368-75. . View in PubMed

Association of a germ-line copy number variation at 2p243 and risk for aggressive prostate cancer. Cancer Res. 2009 Mar 15; 69(6):2176-9. . View in PubMed

Association of reported prostate cancer risk alleles with PSA levels among men without a diagnosis of prostate cancer Prostate. 2009 Mar 01; 69(4):419-27. . View in PubMed

Genetic variants and family history predict prostate cancer similar to prostate-specific antigen Clin Cancer Res. 2009 Feb 01; 15(3):1105-11. . View in PubMed

Association of HPC2/ELAC2 and RNASEL non-synonymous variants with prostate cancer risk in African American familial and sporadic cases Prostate. 2008 Dec 01; 68(16):1790-7. . View in PubMed

Evidence for two independent prostate cancer risk-associated loci in the HNF1B gene at 17q12 Nat Genet. 2008 Oct; 40(10):1153-5. . View in PubMed

Cumulative effect of five genetic variants on prostate cancer risk in multiple study populations Prostate. 2008 Sep 01; 68(12):1257-62. . View in PubMed

Family-based samples can play an important role in genetic association studies Cancer Epidemiol Biomarkers Prev. 2008 Sep; 17(9):2208-14. . View in PubMed

Association between sequence variants at 17q12 and 17q243 and prostate cancer risk in European and African Americans. Prostate. 2008 May 15; 68(7):691-7. . View in PubMed

Chromosome 8q24 risk variants in hereditary and non-hereditary prostate cancer patients Prostate. 2008 Apr 01; 68(5):489-97. . View in PubMed

Cumulative association of five genetic variants with prostate cancer N Engl J Med. 2008 Feb 28; 358(9):910-9. . View in PubMed

Admixture and population stratification in African Caribbean populations Ann Hum Genet. 2008 Jan; 72(Pt 1):90-8. . View in PubMed

Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus Genome Res. 2007 Dec; 17(12):1717-22. . View in PubMed

Association between two unlinked loci at 8q24 and prostate cancer risk among European Americans J Natl Cancer Inst. 2007 Oct 17; 99(20):1525-33. . View in PubMed

A transforming mutation in the pleckstrin homology domain of AKT1 in cancer Nature. 2007 Jul 26; 448(7152):439-44. . View in PubMed

Compelling evidence for a prostate cancer gene at 22q123 by the International Consortium for Prostate Cancer Genetics. Hum Mol Genet. 2007 Jun 01; 16(11):1271-8. . View in PubMed

Fine-mapping the putative chromosome 17q21-22 prostate cancer susceptibility gene to a 10 cM region based on linkage analysis Hum Genet. 2007 Mar; 121(1):49-55. . View in PubMed

Genome-wide linkage of 77 families from the African American Hereditary Prostate Cancer study (AAHPC) Prostate. 2007 Jan 01; 67(1):22-31. . View in PubMed

A comprehensive association study for genes in inflammation pathway provides support for their roles in prostate cancer risk in the CAPS study Prostate. 2006 Oct 01; 66(14):1556-64. . View in PubMed

A common nonsense mutation in EphB2 is associated with prostate cancer risk in African American men with a positive family history J Med Genet. 2006 Jun; 43(6):507-11. . View in PubMed

Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27 Genome Res. 2005 Nov; 15(11):1477-86. . View in PubMed

A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region Hum Genet. 2005 Aug; 117(4):307-16. . View in PubMed

Evidence for a general cancer susceptibility locus at 3p24 in families with hereditary prostate cancer Cancer Lett. 2005 Mar 10; 219(2):177-82. . View in PubMed

Combined genome-wide scan for prostate cancer susceptibility genes J Natl Cancer Inst. 2004 Aug 18; 96(16):1240-7. . View in PubMed

Germline and de novo mutations in the HRPT2 tumour suppressor gene in familial isolated hyperparathyroidism (FIHP) J Med Genet. 2004 Mar; 41(3):e32. . View in PubMed

Clinical characteristics of African-American men with hereditary prostate cancer: the AAHPC Study Prostate Cancer Prostatic Dis. 2004; 7(2):165-9. . View in PubMed

Familial isolated hyperparathyroidism is rarely caused by germline mutation in HRPT2, the gene for the hyperparathyroidism-jaw tumor syndrome J Clin Endocrinol Metab. 2004 Jan; 89(1):96-102. . View in PubMed

Effects of RNase L mutations associated with prostate cancer on apoptosis induced by 2',5'-oligoadenylates Cancer Res. 2003 Oct 15; 63(20):6795-801. . View in PubMed

Evaluation of DLC1 as a prostate cancer susceptibility gene: mutation screen and association study Mutat Res. 2003 Jul 25; 528(1-2):45-53. . View in PubMed

Germline mutations and sequence variants of the macrophage scavenger receptor 1 gene are associated with prostate cancer risk Nat Genet. 2002 Oct; 32(2):321-5. . View in PubMed

Germline alterations of the RNASEL gene, a candidate HPC1 gene at 1q25, in patients and families with prostate cancer Am J Hum Genet. 2002 May; 70(5):1299-304. . View in PubMed

Germline mutations in the ribonuclease L gene in families showing linkage with HPC1 Nat Genet. 2002 Feb; 30(2):181-4. . View in PubMed

Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile Cancer Res. 2001 Dec 15; 61(24):8624-8. . View in PubMed

African-American heredity prostate cancer study: a model for genetic research J Natl Med Assoc. 2001 Dec; 93(12 Suppl):25S-28S. . View in PubMed

Heterogeneity of genetic alterations in prostate cancer: evidence of the complex nature of the disease Hum Mol Genet. 2001 Oct 01; 10(20):2313-8. . View in PubMed

High-resolution physical and transcript map of human chromosome 2p21 containing the sitosterolaemia locus Eur J Hum Genet. 2001 May; 9(5):364-74. . View in PubMed

Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus Genomics. 2001 Apr 15; 73(2):211-22. . View in PubMed

African-American heredity prostate cancer study: a model for genetic research J Natl Med Assoc. 2001 Apr; 93(4):120-3. . View in PubMed

Evaluation of linkage and association of HPC2/ELAC2 in patients with familial or sporadic prostate cancer Am J Hum Genet. 2001 Apr; 68(4):901-11. . View in PubMed

Fine-mapping, mutation analyses, and structural mapping of cerebrotendinous xanthomatosis in US. pedigrees. J Lipid Res. 2001 Feb; 42(2):159-69. . View in PubMed

A genetic epidemiological study of hereditary prostate cancer (HPC) in Finland: frequent HPCX linkage in families with late-onset disease Clin Cancer Res. 2000 Dec; 6(12):4810-5. . View in PubMed

A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) region Genomics. 2000 Feb 15; 64(1):1-14. . View in PubMed

CACP, encoding a secreted proteoglycan, is mutated in camptodactyly-arthropathy-coxa vara-pericarditis syndrome Nat Genet. 1999 Nov; 23(3):319-22. . View in PubMed

Evidence for a prostate cancer susceptibility locus on the X chromosome Nat Genet. 1998 Oct; 20(2):175-9. . View in PubMed

Early age at diagnosis in families providing evidence of linkage to the hereditary prostate cancer locus (HPC1) on chromosome 1 Cancer Res. 1997 Nov 01; 57(21):4707-9. . View in PubMed

Characteristics of prostate cancer in families potentially linked to the hereditary prostate cancer 1 (HPC1) locus JAMA. 1997 Oct 15; 278(15):1251-5. . View in PubMed

Approach to genotyping errors caused by nontemplated nucleotide addition by Taq DNA polymerase Genome Res. 1995 Oct; 5(3):312-7. . View in PubMed

Association between Ag1-CA alleles and severity of autosomal recessive proximal spinal muscular atrophy Am J Hum Genet. 1994 Dec; 55(6):1218-29. . View in PubMed

A YAC contig of the region containing the spinal muscular atrophy gene (SMA): identification of an unstable region Genomics. 1994 Nov 15; 24(2):351-6. . View in PubMed

A multicopy dinucleotide marker that maps close to the spinal muscular atrophy gene Genomics. 1994 May 15; 21(2):394-402. . View in PubMed

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