Nicole Zeltser

Sex differences in the cancer proteome

Chenghao Zhu, Nicole Zeltser, Jieun Oh, Constance H. Li et autres

Objectives: Proteins play a central role in cancer biology. They are the most common drug targets and biomarkers. Sex influences the proteome in many diseases ranging from neurological to cardiovascular. In cancer, sex is associated with incidence, progression and therapeutic response, as …

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Sex differences in the cancer proteome

Jieun Oh, Chenghao Zhu, Nicole Zeltser, Constance H. Li et autres

Objectives Proteins play a central role in cancer biology. They are the most common drug targets and biomarkers. Sex influences the proteome in many diseases ranging from neurological to cardiovascular. In cancer, sex is associated with incidence, progression and therapeutic response, as …

Advancing precision health discovery in a genetically diverse health system

Roni Haas, Michael Margolis, Angela Wei, Takafumi N. Yamaguchi et autres

Linking genetic data with electronic health records in hospital biobanks promises to advance precision medicine, but limited ancestral diversity constrains discovery and generalizability. We analyzed 93,936 participants from the UCLA ATLAS Community Health Initiative to inform disease prevalence and genetic risk across …

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Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline

Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi, Nicholas K. Wang et autres

The price, quality, and throughput of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial, and evolutionary aspects of both germline and somatic genomes. To automate analyses of …

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Joint Biochemical and Genetic Prostate Cancer Risk Stratification

Nicole Zeltser, Roni Haas, Christine Ibilibor, Jonathan Gelfond et autres

PURPOSE: Overdiagnosis of prostate cancer (PC) through PSA testing at short intervals remains common. While baseline serum PSA abundance < 1 ng/mL warrants infrequent screening, it is critical to foster advanced diagnostic practices for men with baseline serum PSA ≥ 1 ng/mL, …

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Advancing Precision Health Discovery in a Genetically Diverse Health System

Roni Haas, Michael Margolis, Angela Wei, Takafumi N. Yamaguchi et autres

Summary Linking genetic data with electronic health records in hospital biobanks promises to advance precision medicine, but limited ancestral diversity constrains discovery and generalizability. We analyzed 93,936 participants from the UCLA ATLAS Community Health Initiative to inform disease prevalence and genetic risk …

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The landscape of N6-methyladenosine in localized primary prostate cancer

Xin Xu, Helen He Zhu, Rupert Hugh-White, Julie Livingstone et autres

N6-methyladenosine (m6A), the most abundant internal RNA modification in humans, regulates most aspects of RNA processing. Prostate cancer is characterized by widespread transcriptomic dysregulation; therefore, we characterized the m6A landscape of 162 localized prostate tumors with matched DNA, RNA and protein profiling. …

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ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF

Nicole Zeltser

Simple and transparent parsing of genotype/dosage data from an input Variant Call Format (VCF) file, matching of genotype coordinates to the component Single Nucleotide Polymorphisms (SNPs) of an existing polygenic score (PGS), and application of SNP weights to dosages for the calculation …

Sex Differences in Cancer Functional Genomics: Gene Dependency and Drug Sensitivity

Nicole Zeltser, Chenghao Zhu, Jieun Oh, Constance H. Li et autres

Patient sex influences a wide range of cancer phenotypes, including prevalence, response to therapy and survival endpoints. Molecular sex differences have been identified at all levels of the central dogma. It is hypothesized that these molecular differences may drive the observed clinical …

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ApplyPolygenicScore: An R package for applying polygenic risk score models

Nicole Zeltser, Rachel M. A. Dang, Rupert Hugh-White, Daniel Knight et autres

Purpose: A polygenic score (PGS) predicts an individual's genetic predisposition to a complex trait. A PGS is created by estimating the relative contributions of multiple common variants to the overall trait, creating a polygenic risk model (PGM). The PGM is then applied …

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StableLift: Optimized Germline and Somatic Variant Detection Across Genome Builds

Nicholas K. Wang, Nicholas Wiltsie, Helena Winata, Sorel Fitz‐Gibbon et autres

Reference genomes are foundational to modern genomics. Our growing understanding of genome structure leads to continual improvements in reference genomes and new genome "builds" with incompatible coordinate systems. We quantified the impact of genome build on germline and somatic variant calling by …

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Supplementary Figure 3 from Upgrading of Grade Group 1 Prostate Cancer at Prostatectomy: Germline Risk Factors in a Prospective Cohort

Michael A. Liss, Nicole Zeltser, Yingye Zheng, Camden Lopez et autres

Supplementary Figure 3 displays supplementary information on ancestry calling, genetically adjusted PSA Density, and polygenic risk scoring.