A5065526095- Genetic Associations and Epidemiology
- Cancer-related molecular mechanisms research
- BRCA gene mutations in cancer
- Prostate Cancer Treatment and Research
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Genetic factors in colorectal cancer
- Prostate Cancer Diagnosis and Treatment
- Molecular Biology Techniques and Applications
- Multiple and Secondary Primary Cancers
- MicroRNA in disease regulation
- Viral-associated cancers and disorders
- Polyomavirus and related diseases
- Herpesvirus Infections and Treatments
- Artificial Intelligence in Healthcare and Education
- Epigenetics and DNA Methylation
- Nutrition, Genetics, and Disease
- Cancer, Lipids, and Metabolism
- Parkinson's Disease Mechanisms and Treatments
- Biomedical and Engineering Education
- Glutathione Transferases and Polymorphisms
- Fungal and yeast genetics research
- Endoplasmic Reticulum Stress and Disease
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- IL-33, ST2, and ILC Pathways
University of California, San Francisco
2019-2025
23andMe (United States)
2024
University of California San Francisco Medical Center
2021-2022
QB3
2020
University of California, San Diego
2017
Deciphering the shared genetic basis of distinct cancers has potential to elucidate carcinogenic mechanisms and inform broadly applicable risk assessment efforts. Here, we undertake genome-wide association studies (GWAS) comprehensive evaluations heritability pleiotropy across 18 cancer types in two large, population-based cohorts: UK Biobank (408,786 European ancestry individuals; 48,961 cases) Kaiser Permanente Genetic Epidemiology Research on Adult Health Aging cohorts (66,526 16,001...
The majority of polygenic risk scores (PRSs) have been developed and optimized in individuals European ancestry may limited generalizability across other ancestral populations. Understanding aspects PRSs that contribute to this issue determining solutions is complicated by disease-specific genetic architecture knowledge sharing causal variants effect sizes Motivated these challenges, we undertook a simulation study assess the relationship between potential bias Our simulations show magnitude...
Abstract Background Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the mechanisms of immune response to viral infection provides insight into disease etiology therapeutic opportunities. Methods We conducted comprehensive study including genome-wide transcriptome-wide association analyses identify loci associated with immunoglobulin G antibody 28 antigens 16 using serological data from 7924 European ancestry participants UK...
Abstract Genome-wide association study–identified prostate cancer risk variants explain only a relatively small fraction of its familial relative risk, and the genes responsible for many these identified associations remain unknown. To discover novel genetic loci possible causal at previously loci, we performed transcriptome-wide study in 79,194 cases 61,112 controls European ancestry. Using data from Genotype-Tissue Expression Project, established models to predict gene expression across...
Abstract Liquid biopsies have the potential to revolutionize cancer care through non-invasive early detection of tumors. Developing a robust liquid biopsy test requires collecting high-dimensional data from large number blood samples across heterogeneous groups patients. We propose that generative capability variational auto-encoders enables learning and generalizable signature blood-based biomarkers. In this study, we analyze orphan non-coding RNAs (oncRNAs) serum 1050 individuals diagnosed...
Risk factors that contribute to inter-individual differences in the age-of-onset of allergic diseases are poorly understood. The aim this study was identify genetic risk variants associated with age at which symptoms disease first develop, considering information from asthma, hay fever and eczema. Self-reported available for 117,130 genotyped individuals European ancestry UK Biobank study. For each individual, we identified earliest and/or eczema diagnosed performed a genome-wide association...
ABSTRACT Introduction Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the mechanisms of immune response to viral infection provides insight into disease etiology therapeutic opportunities. Methods We conducted comprehensive study including genome-wide transcriptome-wide association analyses identify loci associated with immunoglobulin G antibody 28 antigens 16 using serological data from 7924 European ancestry participants UK...
ABSTRACT The majority of polygenic risk scores (PRS) have been developed and optimized in individuals European ancestry may limited generalizability across other ancestral populations. Understanding aspects PRS that contribute to this issue determining solutions is complicated by disease-specific genetic architecture knowledge sharing causal variants effect sizes Motivated these challenges, we undertook a simulation study assess the relationship between potential bias Our simulations show...
Cell-free RNA (cfRNA) profiling has emerged as a powerful tool for non-invasive disease detection, but its application is limited by data sparsity and complexity, especially in settings with constrained sample availability. We introduce Exai-1, multi-modal, transformer-based generative foundation model that integrates sequence embeddings cfRNA abundance to capture biologically meaningful representations of circulating RNAs. By leveraging both expression modalities, Exai-1 captures latent...
Abstract Background: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. Early detection offers best opportunity for effective treatment. Although CRC screening methods exist, there remains a need high performing blood test to both improve adherence and detect early stage disease. We have previously identified developed novel category cancer-associated, small orphan non-coding RNAs (oncRNAs), combined them with generative AI modeling develop liquid...
Abstract Purpose: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide, and early detection significantly improves treatment outcomes, but existing blood-based tests often have limited sensitivity in early-stage disease. We developed a test combining oncRNAs, group small cell-free RNAs (cfRNAs), with generative AI to detect CRC. Experimental Design: leveraged cohort 613 CRC cases controls train model that demonstrated both high clinical performance as well...
Artificial Intelligence (AI) has the power to improve our lives through a wide variety of applications, many which fall into healthcare space; however, lack diversity is contributing limitations in how broadly AI can help people. The UCSF AI4ALL program was established 2019 address this issue by targeting high school students from underrepresented backgrounds AI, giving them chance learn about with focus on biomedicine, and promoting inclusion. In 2020, three-week held entirely online due...
Abstract Background Up to one of every six individuals diagnosed with cancer will be a second primary in their lifetime. Genetic factors contributing the development multiple cancers, beyond known syndromes, have been underexplored. Methods To characterize genetic susceptibility we conducted pan-cancer, whole-exome sequencing study drawn from two large multi-ancestry populations (6429 cases, 165,853 controls). We created groupings cancers: (1) an overall combined set at least cancers across...
Abstract Background: Approximately 1 in 8 women will be impacted by breast cancer their lifetimes. Earlier detection of through screening has improved survival. Liquid biopsies have the potential to complement existing methods enabling earlier and differentiating invasive (IBC) from ductal carcinoma in-situ (DCIS). We previously demonstrated high sensitivity specificity for early IBC using a blood-based liquid biopsy platform analyze novel category cancer-associated small RNAs, termed orphan...
Abstract Background Earlier detection of breast cancer through mammography screening has reduced disease-specific mortality; however, confounding issues such as technical challenges, density, and tumor size can result in false negatives ultimately later stage diagnosis. Next generation liquid biopsy the potential to complement enable earlier for more women. We have previously demonstrated high sensitivity specificity early invasive (IBC) by utilizing a novel category cancer-associated small...
Abstract From extrachromosomal DNA to neo-peptides, the broad reprogramming of cancer genome leads emergence molecules that are specific state. We recently described orphan non-coding RNAs (oncRNAs) as a class cancer-specific small with potential play functional roles in breast progression 1 . Here, we report systematic and comprehensive search identify, annotate, characterize cancer-emergent oncRNAs across 32 tumor types. also leverage large-scale vivo genetic screens xenografted mice...
Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, part due to challenge probing protein structures living cells. Here, we use deep mutational scanning investigate a toxic conformation α-synuclein, dynamic linked Parkinson's disease, responds perturbations proteostasis. In context course for graduate students UCSF Integrative Program Quantitative Biology,...
ABSTRACT Genetic factors that influence etiologic mechanisms shared across cancers could affect the risk of multiple cancer types. We investigated polygenic score (PRS)-specific pleiotropy 17 in two large population-based cohorts. The study population included European ancestry individuals from Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) UK Biobank (48,969 359,802 controls). selected known independent variants published GWAS to construct a PRS for...
3051 Background: Orphan non-coding RNAs (oncRNAs) are a novel category of small (smRNAs) that present in tumors and largely absent healthy tissue. We investigated the utility oncRNAs extracted from serum for early cancer detection across seven types. Methods: collected 2,882 samples individuals with known cancers bladder ( n=152), breast (220), colon rectum (141), kidney (283), lung (281), pancreas (287), stomach (280) as well donors no history (1,238). used 0.5 mL aliquots to generate...
Abstract Deciphering the shared genetic basis of distinct cancers has potential to elucidate carcinogenic mechanisms and inform broadly applicable risk assessment efforts. However, no studies have investigated pan-cancer pleiotropy within single, well-defined populations unselected for phenotype. We undertook novel genome-wide association (GWAS) comprehensive evaluations heritability across 18 cancer types in two large, population-based cohorts: UK Biobank (413,870 European ancestry...
Abstract Background: Orphan non-coding RNAs (oncRNAs) are a novel category of small that present in the tumor tissue and blood people with cancer largely absent without cancer. To examine potential using oncRNAs for early detection via liquid biopsy, we assessed oncRNA content serum from non-small cell lung (NSCLC) developed prediction model NSCLC. Methods: A total 540 samples were obtained Indivumed (Hamburg, Germany) MT Group (Los Angeles, CA) divided into cohort training (150 NSCLC cases,...