Juan Miguel Mosquera

EXaCT-2: An augmented and customizable oncology-focused whole exome sequencing platform

EXaCT-2 is a whole exome sequencing platform that detects various cancer-related genomic features with high accuracy and sensitivity, outperforming standard assays in detecting sub-clonal mutations and molecular metrics.

Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules

This paper introduces ppmSeq, a sequencing technology that improves accuracy and efficiency in detecting SNVs by sequencing both DNA strands, showing superior performance in clinical applications like ctDNA detection.

Genomic alterations in the YAP/TAZ pathway are associated with stem cell-like castration-resistant prostate cancer

The paper identifies genomic alterations in the YAP/TAZ pathway associated with stem cell-like castration-resistant prostate cancer using transcriptomic and whole-genome sequencing data.

Pan-Cancer PDOs Preserve Tumor Heterogeneity and Uncover Therapeutic Vulnerabilities

This study develops a pan-cancer PDO platform to preserve tumor heterogeneity and identify therapeutic vulnerabilities, finding that 58% of PDOs respond to Talazoparib and combination screens reveal resistance-overcoming drugs.

Whole Genome Landscape Analysis of Homologous Recombination Deficiency in a Pan-Cancer Cohort

The paper analyzes whole-genome sequencing data from a pan-cancer cohort to define HRD, showing it extends beyond BRCA1/2 mutations and highlights the benefits of WGS over commercial assays for HRD detection.

The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution

This study examines how mutagenesis and extrachromosomal DNA contribute to urothelial cancer evolution, revealing clonal APOBEC3 mutations and chemotherapy-induced mutational bursts within ecDNA.

Unsupervised discovery of tissue architecture in multiplexed imaging

This paper introduces UTAG, a method to automatically identify tissue structures in multiplexed imaging data, showing it can detect higher-order tissue organization and relate it to disease states.

Weakly-Supervised Tumor Purity Prediction FromFrozen H&E Stained Slides

This paper introduces a weakly-supervised method to predict tumor purity from H&E stained slides, achieving high accuracy and enabling clinical applications.

Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Pore-C reads multi-way chromatin contacts directly off unamplified Nanopore long reads, recovering Hi-C-scale features while also resolving rearranged cancer alleles and supporting de novo assembly.

Integrative genomic, transcriptomic, and epigenomic analyses of benign prostatic hyperplasia reveal new options for therapy

This study identifies molecular subgroups of BPH and suggests mTOR inhibitors as a potential therapy for specific subtypes.

Discovery and reporting of clinically-relevant germline variants in advanced cancer patients assessed using whole-exome sequencing

This study reports that 17% of advanced cancer patients have clinically relevant germline variants, with higher rates of cancer-associated variants compared to control cohorts.