Carlos D. Bustamante

High Resolution Ancestry Deconvolution for Next Generation Genomic Data

This paper introduces Gnomix, a high-resolution ancestry deconvolution method for next-generation genomic data, achieving higher accuracy and faster performance than existing methods.

Non-Parametric Ancestry Adjustment for Polygenic Scores

This paper introduces non-parametric methods to adjust polygenic scores for ancestry bias, improving accuracy for non-European populations using the UK Biobank.

Mosaic Loss of Y chromosome associates with lung function, emphysema and epigenetic aging

This study investigates the association between mosaic loss of Y chromosome (mLOY) and lung function, emphysema, and epigenetic aging in men across multiple cohorts.

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.

Present-day admixed genomes reveal prehistoric adaptation to cold, maritime diet, and local pathogens in Patagonia

The paper analyzes genome-wide data from Indigenous Patagonians to uncover genetic adaptations to cold, maritime diet, and pathogens, revealing prehistoric selection signals and admixture patterns.

Diverse ancestral representation improves genetic intolerance metrics

This study shows that genetic diversity improves the performance of intolerance metrics in identifying disease-related genes, with multi-ancestry data outperforming European-only datasets.

Polygenic risk score portability for common diseases across genetically diverse populations

This study evaluates polygenic risk score (PRS) performance across four ancestry groups for 14 diseases, finding that ancestry-specific PRS models improve accuracy and identifying cross-trait interactions.

Neural ADMIXTURE: rapid population clustering with autoencoders

Neural ADMIXTURE uses an autoencoder to rapidly cluster large genetic datasets, reducing computation time compared to traditional methods like ADMIXTURE.

Validating and automating learning of cardiometabolic polygenic risk scores from direct-to-consumer genetic and phenotypic data: implications for scaling precision health research.

This study validates and automates polygenic risk score (PRS) development for cardiometabolic diseases using direct-to-consumer genetic and phenotypic data, showing comparable performance to larger clinical datasets.

Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

Archetypal Analysis for Population Genetics

This paper introduces Archetypal Analysis for efficient genetic clustering, showing it outperforms ADMIXTURE in speed and interpretability across human and canid datasets.

Clotting factor genes are associated with preeclampsia in high altitude pregnant women in the Peruvian Andes

This study identifies clotting factor genes PROZ, F7, and F10 on chromosome 13 as associated with preeclampsia in high-altitude Andean families.

ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines

The paper introduces the ClinGen Variant Curation Interface, a platform for applying ACMG/AMP guidelines to classify genetic variants, enabling collaboration and standardization in clinical variant interpretation.

Bayesian model comparison for rare variant association studies

The paper introduces a Bayesian model comparison approach, MRP, for rare variant association studies using summary statistics, demonstrating improved power and discovery of gene-trait associations across multiple phenotypes.

Genome Sequencing Unveils a New Regulatory Landscape of Platelet Reactivity

The paper uses whole genome sequencing to identify genetic loci associated with platelet aggregation, including novel variants in RGS18, SVEP1, and PEAR1.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

This paper develops a high-throughput method to generate host and pathogen genomic data from single nasopharyngeal swabs of COVID-19 patients.

Clinical genetics lacks standard definitions and protocols for the collection and use of diversity measures

The paper highlights the lack of standard definitions and protocols for collecting and using race, ethnicity, and ancestry data in clinical genetics and precision medicine.

XGMix: Local-Ancestry Inference With Stacked XGBoost

XGMix is a gradient boosted tree method for local ancestry inference that is accurate, simple to use, and fast to train on consumer-level hardware.

Development and clinical validation of a targeted RNAseq panel (Fusion-STAMP) for diagnostic and predictive gene fusion detection in solid tumors

The paper develops and validates a targeted RNAseq panel (Fusion-STAMP) for detecting gene fusions in solid tumors, showing high sensitivity and specificity.

Population history and gene divergence in Native Mexicans inferred from 76 human exomes

This study analyzes 76 exomes from five Mexican indigenous populations to infer population history and identify genes under positive selection.

Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities

This study uses ancient DNA to reconstruct the genetic legacies of pre-contact Puerto Rico communities, finding Native American mtDNA haplogroups and shared ancestry with the Bahamas.

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands

The paper analyzes ancient mitogenomes from the Canary Islands to trace the origin and migration patterns of indigenous populations, identifying new lineages and supporting a model of two distinct migrations.

Standardized biogeographic grouping system for annotating populations in pharmacogenetic research

The paper introduces a standardized biogeographic grouping system for pharmacogenetic research to improve consistency in reporting allele frequency variability across populations.

SNAPPY: Single Nucleotide Assignment of Phylogenetic Parameters on the Y chromosome

SNAPPY assigns Y-chromosome haplogroups using genotype data by evaluating haplotypes in a database and considering phylogenetic support and parsimony.

The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits

The paper conducts a GWAS in non-European populations, identifies new genetic loci, and highlights the importance of diverse cohorts for understanding complex traits.

The Clinical Imperative for Inclusivity: Race, Ethnicity, and Ancestry (REA) in Genomics

The paper analyzes REA data collection practices and disparities in gnomAD, highlighting the need for standardized frameworks to improve diversity and variant interpretation in clinical genomics.

Genomic insights into the domestication of the chocolate tree, Theobroma cacao L.

The paper sequenced 200 genomes of Theobroma cacao to show that domestication of the Criollo population occurred around 3,600 years ago, with strong selection on genes related to anthocyanin, theobromine metabolism, and disease resistance, and found a negative correlation between Criollo ancestry and bean yield.

Caring without sharing: Meta-analysis 2.0 for massive genome-wide association studies

This paper introduces a decentralized GWAS workflow that enables meta-analysis without consolidating raw data, improving power for rare alleles and imbalanced case/control proportions across multiple institutions.

Imputation aware tag SNP selection to improve power for multi-ethnic association studies

This paper develops a method to select tag SNPs for multi-ethnic association studies, showing improved imputation power by considering population-specific linkage disequilibrium and demographic impacts.

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

This study applies Y-chromosome capture-enrichment to ancient DNA libraries, showing increased recovery of Y-DNA sequences and enabling haplogroup assignment.