Luis G Carvajal-Carmona
· Professor, Auburn Community Cancer Endowed Chair in Basic Science, and Associate Vice Chancellor for the Office of Academic DiversityUniversity of California, Davis · Biochemistry and Molecular Medicine
Active 1952–2025
Selected publications
npj Breast Cancer · 2025-10-29 · 1 citations
articleOpen accessSomatic mutations and copy number alterations in breast tumors are important to determine prognosis, predict treatment response, and identify targets for therapy. We utilized somatic sequencing data of breast tumors from Foundation Medicine Inc. to evaluate the association between genetic ancestry and somatic mutations. We used germline variants to infer genetic ancestry with both principal components analysis and ADMIXTURE. Overall, we identified 91 ancestry-specific somatic differences across 58 unique genes, which included potentially targetable genes such as PIK3CA found in higher frequency in European ancestry, and EGFR found in higher frequency in East Asian ancestry. Pan-cancer analysis of East Asian ancestry and EGFR also found higher frequency in prostate, thyroid, and kidney cancers. African ancestry was associated with increased frequency of copy number alterations overall and decreased frequency of multiple genes on the PI3K-AKT pathway. Future research is warranted to elicit the genetic and environmental conditions that underly these findings.
European Journal of Human Genetics · 2025-03-10 · 8 citations
articleOpen accessSenior authorCorrespondingGenetic studies in Latin America have expanded, but further efforts are needed to understand cancer susceptibility genes beyond BRCA1 and BRCA2, especially by characterizing the prevalence and spectrum of pathogenic or likely pathogenic variants (PVs) in the region. This study aimed to determine the frequency of hereditary cancer syndromes (HCS) in Colombians with solid tumors and to characterize the spectrum of PVs. Using data from the Colombia's largest Institutional Hereditary Cancer Program, we included patients aged ≥18 years with solid tumors who met HCS criteria and were offered genetic testing with a 105-cancer gene panel. We calculated the prevalence of PVs and HCS by cancer type (beyond breast) and gene. For patients with breast cancer, we examined genotype-phenotype correlations with molecular subtypes and stratified positivity rates by different genetic testing criteria. Among 769 patients, we identified 216 PVs in 43 genes in 197 patients (26%). Thirty-three PVs were recurrent. Autosomal HCS was found in 21% (160/769) of patients (159 dominant, one recessive), while 5% (37/769) were heterozygous carriers of PVs in autosomal recessive genes. In 42% (321/769) of the cases, only one or more variants of uncertain significance (VUS) were identified, whereas 33% (251/769) had neither PVs nor VUS detected (negative results). HCS prevalence varied by cancer type (11-26%). The triple-negative subtype and bilateral presentation were strong predictors of inherited breast cancer. Our study reveals a significant presence of PVs among high-risk Colombian patients with solid tumors, underscoring the importance of genetic counseling and testing in the region.
Genetic and Cellular Architecture of Breast Cancer Risk Across Ancestries
medRxiv · 2025-08-24
preprintOpen accessAbstract Background Breast cancer genome-wide association studies (GWAS) have identified more than 200 susceptibility loci, but most studies are dominated by European and East Asian populations. Methods We analyzed breast cancer GWAS summary statistics from African (AFR), East Asian (EAS), European (EUR), and Hispanic/Latina (H/L) samples (159,297 cases and 212,102 controls). We estimated logit-scale SNP-based heritability, polygenicity, and cross-ancestry genetic correlation, partitioned heritability across functional annotations, and integrated GWAS results with the Tabula Sapiens single-cell atlas using scDRS+. Results The logit-scale heritability of breast cancer ranged from ℎ 2 =0.47 (SE = 0.07) in EAS to AFR ℎ 2 =0.61 (SE = 0.10), with no significant differences across ancestries (p=0.63). The estimated number of susceptibility markers in a sparse normal-mixture effects model also varied from 4,446 (SE = 3,100) in EAS to 8,308 (SE = 2,751) in AFR, but differences were not significant across ancestries (p=0.55). Cross-sample genetic correlations varied, with the strongest correlation between EUR and EAS (𝜌 = 0.79, SE = 0.08) and weakest between AFR and H/L (𝜌 = 0.26, SE = 0.24). Regulatory annotations were enriched for breast cancer heritability across samples. Integration with single-cell expression profiles implicated ancestry-shared associations with innate immune, secretory epithelial, and stromal cell types. Conclusion These results indicate substantial cross-ancestry sharing of breast cancer polygenic architecture, highlight a consistent contribution of regulatory variation, and identify convergent cellular contexts that motivate functional follow-up and inform expectations for the transferability and attainable performance of common-variant risk prediction across populations.
Abstract 1002: BRCA2, ATM, and POT1 genes mutations in Chilean hereditary gastric cancer families
Cancer Research · 2025-04-21
articleSenior authorAbstract The purpose of this study is to describe Chilean families having hereditary Gastric Cancer (GC) presenting pathogenic mutations in BRCA 2 (c.4740_4741dup NP_000050.3:p.Glu1581fs), ATM (c.3381_3384del NP_000042.3:p.Gln1128fs) and Protector of Telomers 1 (POT1, 1087C>T:p.Arg363Ter) genes. Only one hereditary diffuse GC (HDGC) Chilean family with a pathogenic CDH1 mutation has been reported, suggesting a low frequency of pathogenic mutation detection in this population. Whole exome sequencing (WES) was performed using the Agilent SureSelect Human All Exome V7 kit and sequenced in a NovaSeq6000 (Illumina, Inc.) S4 150PE aiming 100x. Alignment and variant calling were performed using Illumina Dragen v3.8. Variant calls were re-calibrated using GATK v4 variant recalibration and annotated with Illumina Nirvana and Annovar. Genotypification of the index patient and their family was performed using KASP-PCR. The index patient having a BRCA2 mutation had metastatic HDGC and his mother had asynchronous breast cancer and GC. The family presenting an ATM gene mutation had three GC-affected subjects, the index patient, and both parents. The index patient of the family having a POT1 mutation presented a CG at 47 yr., and two of her children died of CG at 24 yr. All families show an incomplete penetrance and variable expressivity. We are searching for the second hit in the index patient´s tumor samples. This is the first report of a POT1 gene mutation detected in a hereditary GC. POT1 belongs to the shelterin complex that protects telomeres. This mutation affects the binding to the shelterin complex, and it was previously reported in colorectal cancer. Beca Chile Postdoctorado 74190063, CONICYT-FONDAP 15130011 /ANID-FONDAP APOYO 1523A0008, NIH R01CA223978, R21CA199631, U54CA233306, and P30CA093373. Citation Format: Graciela Adriana Molina Fuentes, Ana Patricia Estrada-Florez, Paul Lott, Osvaldo Torres, Cedric Adelsdorfer, Alejandro H Corvalán, Luis Carvajal-Carmona. BRCA2, ATM, and POT1 genes mutations in Chilean hereditary gastric cancer families [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1002.
The Lancet Oncology · 2025-10-01 · 6 citations
articleOpen accessCancer Epidemiology Biomarkers & Prevention · 2025-09-18
articleSenior authorAbstract Gastric cancer (GC) is a leading cause of health disparities in the country. Recent studies suggest that carriers of germline mutations in cancer predisposition genes, especially in individuals with H. pylori infection, have an increased risk of GC. This study aims to evaluate the prevalence of GC risk factors among subscribers of the Facing Hereditary Cancer Empowerment (FORCE) mailing list who carry germline mutations in cancer predisposition genes. We collected anonymized demographic and biomedical data through an online survey conducted from March to June 2025. The 23-question survey, available in English and Spanish, was self-administered via SurveyMonkey. It included questions on race, nativity, age; GC risk factors (personal and family histories of gastric and other cancers; H. pylori infection; personal history of premalignant gastroesophageal conditions). It also covered use of anti-acid medications or proton pump inhibitors and information on germline genetic variants linked to cancer predisposition. 543 respondents provided detailed complete survey response data. Descriptive association tests between GC risk factors, gastric lesions, H. pylori infection history, and hereditary germline genetic variants were conducted using Pearson’s Chi-square and Fisher’s Exact tests at a significance level of 0.05. All analyses were performed in R. Most participants were female (95%) and largely Non-Hispanic White (91%). We found a significant correlation between gastric lesions and the use of anti-acid medications or proton pump inhibitors, with daily users showing a higher prevalence of gastric lesions (44% vs. 4.2%, p<0.0001). Significant associations were also found between gastric lesions and GC (7.8% vs. 3.1%, p=0.015). Notably, carriers of mutations in Lynch syndrome (LS) genes had a higher likelihood of gastric lesions (21% vs. 15% non-LS mutation gene carriers, p=0.038), while those with mutations in homologous recombination repair (HRR) genes were less likely to have gastric lesions (72% vs. 82% non-HRR gene mutation carriers, p=0.007). A higher prevalence of GC was observed in participants with H. pylori infections (15% vs. 4.8%, p=0.017). Among those diagnosed with GC, a greater proportion also had gastric lesions (73% vs. 50%, p=0.015), along with increased H. pylori infection rates (20% vs. 6.6%, p=0.017). These results suggest a significant association between H. pylori infection and an elevated risk of GC, with infection rates of 15% compared to 4.8% in the non-infected group. The findings imply that H. pylori may play a critical role in GC development, warranting further research to examine underlying mechanisms and potential preventative strategies. Citation Format: Guadalupe Carvajal MSc, C.G. C., Iñigo Verduzco Gallo MIDS, MPA, Nanci Chavarria Villa MPH, Diane Rose, Angelica Rolon MPH, April Vang MSc, Sue Friedman DVM, Luis Carvajal-Carmona Ph.D.. Assessing the prevalence of gastric cancer risk factors among carriers of germline mutations in cancer predisposition genes [abstract]. In: Proceedings of the 18th AACR Conference on the Science of Cancer Health Disparities; 2025 Sep 18-21; Baltimore, MD. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2025;34(9 Suppl):Abstract nr A122.
Cancer Research · 2025-04-21
articleBackground: Cancer disparities among Latinos in the US are a critical public health issue, with this group experiencing inequitable outcomes across the cancer continuum, from screening to end-of-life care. Latinos have higher rates of certain cancers and poorer outcomes compared to other populations, driven by a complex interplay of environmental, genetic, cultural, behavioral, and systemic factors. While earlier research has highlighted some of these disparities, comprehensive analyses of the multilevel factors affecting cancer care among Latinos are still limited. This report aims to identify these factors to help guide the work of current and future researchers who can address Latino cancer outcomes. Methods: The Task Force: Latino Researchers Against Cancer (TFLRAC) held structured meetings in 2023 to share expertise. Participants included specialists in oncology, public health, and behavioral sciences who examined environmental, genetic, cultural, behavioral, and systemic contributors to cancer care disparities among Latinos. The goal was to explore the causes and multilevel drivers of health impacting the Latino cancer experience. Results: Findings show that cancer disparities among Latinos are influenced by multiple factors, including environmental exposures associated with higher pollution levels and occupational hazards, genetic variations affecting cancer risk and prognosis, and cultural and linguistic barriers affecting healthcare decisions. Behavioral factors, such as unhealthy dietary habits, and systemic issues, such as limited access to healthcare, inadequate insurance coverage, and lack of diversity in the healthcare workforce, further contribute to these disparities. Additionally, socioeconomic barriers and restrictive eligibility criteria contribute to the underrepresentation of Latinos in clinical trials, while cultural stigmas, limited support services, and language barriers pose challenges in cancer survivorship. Conclusions: Reducing cancer disparities among Latinos requires a multifaceted approach, including targeted research on environmental and genetic factors, culturally sensitive interventions, and policy reforms to improve healthcare access and workforce diversity. Collaboration among academia, healthcare providers, Latino communities, government, and industry is essential to achieve equitable cancer care for Latinos. Citation Format: Amelie G. Ramirez, Edgar Munoz, Lorna Rodriguez-Rodriguez, Leon Bernal-Mizrachi, Patricia Chalela, Jose Lopez, Paulo S. Pinheiro, Barbara Segarra Vasquez, DHSc, Gregory A. Talavera, Luis G. Carvajal – Carmona, Adolfo Diaz Duque, Cliff Despres, Edward J. Trapido. Unveiling cancer disparities: a task force report on multilevel drivers impacting equitable cancer care among Latinos in the US [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6194.
Cancer Epidemiology Biomarkers & Prevention · 2025-09-18
articleSenior authorAbstract Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide, with Latinos in the U.S. experiencing higher incidence and poorer survival rates compared to non-Latino whites (NLW). Current molecular characterization efforts, such as The Cancer Genome Atlas (TCGA), lack data on Latino patients, with only 2% of samples from Latino ancestry. To address this gap, the University of California Minority Patient-Derived Xenograft (PDX) Development and Trial Center (UCaMP) and The University of California and the University of Texas Southwestern (UCaTS) Diversity Patient-Derived Xenograft (PDX) Development and Trial Center are developing preclinical models (PDXs and organoids) from diverse populations to identify new drug targets for GC. We have successfully developed 37 preclinical models, reflecting a 44% success rate from 84 GC patients. These models represent diverse backgrounds: 14% Asian, 14% Black or African American, 5% Native Hawaiian or Pacific Islander, 22% NLW, 35% Hispanic or Latino, and 4% Not Reported. Currently, we are characterizing these models genomically and testing their vulnerability to 27 FDA-approved/NCI-CTEP inhibitors. Initial results from 15 models show the highest response to the pan-PI3K inhibitor copanlisib and the anthracycline epirubicin. We have also investigated PARP inhibitors (PARPi), given their success in breast and ovarian tumors. PARPi efficacy in GC ranged across models, with some showing sensitivity, others intermediate response, and some limited response. Next, we evaluated whether PARPi efficacy could be increased when combined with standard chemotherapies in the intermediate- and limited-response GC models. Notably, PARPi Talazoparib demonstrated synergy with epirubicin, as determined by the BLISS model. Ongoing work focuses on understanding this synergy and identifying biomarkers for PARPi response, which could help predict treatment outcomes in GC patients. Our research aims to uncover new drug targets for GC and provide preclinical evidence for their potential efficacy. Citation Format: Leslie Cuellar-Vite, Hongyong Zhang, Nicole B. Halmai, Ana Estrada-Florez, Jasmine Diaz, Paul C. Lott, Dennis J. Montoya, UCaMP Consortium, UCaTS Consortium, Luis G. Carvajal-Carmona. Preclinical evaluation of therapeutics in gastric cancer using diverse patient-derived models [abstract]. In: Proceedings of the 18th AACR Conference on the Science of Cancer Health Disparities; 2025 Sep 18-21; Baltimore, MD. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2025;34(9 Suppl):Abstract nr C052.
Correction: Uncovering multilevel drivers of cancer disparities among Latinos in the United States
Frontiers in Public Health · 2025-10-29
articleOpen accessFrontiers' correction template for authors A correction refers to a change to their article that the author wishes to publish after publication. The publication of this article is subject to Frontiers' editorial approval. Instructions: ● Please read through all the templates before choosing ● Pick the most relevant text template(s) from the following page and delete all others. ● Edit the text as necessary, ensuring that the original incorrect text is included for the record, please see the below. ● Please do not use any extra formatting when editing the templates, and only modify the red text unless absolutely necessary ● Submit to Frontiers following the instructions on this page. When the original text contained incorrect information, to preserve the scientific record, please include that text when editing the below templates. For example: There was a mistake in the Funding statement, an incorrect number was used. The correct number is "2015C03Bd051.". 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2025-02-06
preprintOpen access<p>Supplemental Figure S2 shows performance of PRS panels with addition of 2 or 3 H/L SNPs</p>
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