Francisco M. De La Vega

Analysis of a deeply-phenotyped familial hypercholesterolemia cohort from Mexico shows a role for both rare and common alleles across known dyslipidemia genes and reveals structural variation in a novel locus.

The paper analyzes a Mexican FH cohort to show rare and common alleles in FH genes and a novel locus contribute to disease risk, with replication in UK Biobank.

Benchmarking of Germline Copy Number Variant Callers from Whole Genome Sequencing Data for Clinical Applications

This study benchmarks CNV callers for WGS clinical applications, finding DRAGEN v4.2 offers the best balance of sensitivity and precision for detecting deletions and some duplications.

A Deep-learning based RNA-seq Germline Variant Caller

This paper develops a deep-learning based RNA-seq germline variant caller that outperforms existing tools like Platypus and GATK.

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

GEM, an AI-based tool, ranks causal genes highly for rare genetic diseases, improving diagnostic efficiency and reducing manual effort.

Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials

The paper develops a reproducible pipeline to integrate sequencing datasets for high-confidence SNP, indel, and reference calls in five human genomes, showing improved variant detection compared to prior methods.

Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes

The paper develops standardized tools and best practices for benchmarking germline small variant calls in human genomes using truth sets and performance metrics.

A Robust Targeted Sequencing Approach For Low Input And Variable Quality DNA From Clinical Samples

This paper introduces a targeted sequencing method for low-quality DNA that reduces PCR bias and improves variant detection in clinical samples.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

The paper designs a genotyping array (ADPC) for African-specific genetic variation using whole genome sequences from the CAAPA consortium, improving GWAS for African ancestry populations.

Genome-wide association study of asthma in individuals of African ancestry reveals novel asthma susceptibility loci

This study identifies novel asthma susceptibility loci in individuals of African ancestry through genome-wide association analysis and admixture mapping.

Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines

The paper develops a novel algorithm to accurately compare variant call files by addressing representation discrepancies in VCF data, enabling reliable performance benchmarking of variant calling pipelines.