Biology subjects

Metcalf, G. A.

Publications and source records attributed to Metcalf, G. A..

9 recordsLinked to original sources

bioRxiv2026

Genetic and Epigenetic Landscape of Self-Identified Hispanics/Latino in All Of Us

Human genetic studies still underrepresent many populations, limiting discovery and interpretation of medically relevant variation. Extensive admixture in self-identified Hispanic/Latino populations increases the need for representative reference data and ancestry-aware interpretation of medically relevant variation. We used long-read sequencing to analyze genetic variation, ancestry, and DNA methylation in 1,490 self-identified Hispanic/Latino participants from the All of Us Research Program. We identified 10 million novel variants and more than 100 candidate phenotype associations, with fine-mapping prioritizing structural variants over nearby single-nucleotide variants in more than half. We linked 3,329 tandem repeats to DNA methylation, resolved widespread allele-specific methylation, and identified ancestry-linked regulation across paralogous genes. These results reveal previously inaccessible genetic and regulatory variation and show the value of long-read sequencing for diverse populations.

genetics↗

bioRxiv2025

Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA

BackgroundRespiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract infections in infants and poses significant risks to immuno-compromised individuals and the elderly. The COVID-19 pandemic disrupted typical RSV seasonality, leading to unusual patterns of viral circulation and resurgence. However, the impact of these disruptions on RSV evolutionary dynamics remains incompletely understood. This study aimed to investigate the evolutionary dynamics of RSV in Houston, Texas, across pre-pandemic (November 2015 - March 2020), pandemic (April 2021 - June 2023), and post-pandemic periods (July 2023 - December 2024), focusing on genetic diversity, lineage dynamics, and selective pressures. MethodsIn one of the largest comprehensive RSV genomic evolutionary analyses, we analyzed 1,344 RSV-positive respiratory samples collected from children seeking outpatient care or hospitalized with acute respiratory infections between November 2015 to February 2024, which is one of the largest comprehensive RSV genomic evolutionary analyses. We successfully sequenced the whole genomes for 87.5% of the isolates (606 RSV/A and 570 RSV/B). To assess genetic diversity, lineage dynamics, and selective pressures, we conducted phylogenetic analysis, variant calling, and dN/dS ratio calculations. We clustered variant prevalence patterns using k-means and used Shannon entropy to quantify genetic variability. We performed statistical regression analyses to evaluate the accumulation of variants and their impact on gene expression. ResultsRSV circulation in Houston was markedly disrupted during the pandemic, with an absence of cases in 2020-2021 followed by off-season surges from 2021 to 2023. Phylogenetic analysis revealed distinct lineage dynamics, with RSV/A showing remarkable persistence of specific lineages such as A.D.1 and emergence of new lineages including A.D.3. In contrast, RSV/B underwent a dramatic restructuring, dominated by the B.D.E.1 lineage in the pandemic and post-pandemic period. Bayesian molecular clock analysis estimated nucleotide substitution rates of 9.37 x 10-4 (95% HPD: 7.99 x 10-4 - 1.07 x 10-3) substitutions/site/year for RSV/A and 9.79 x 10-4 (95% HPD: 8.96 x 10-4 - 1.06 x 10-3) for RSV/B. The time to the most recent common ancestor (tMRCA) of the dominant RSV/A clade, A.D.1, is dated to approximately 2010 (95% HPD: 2008-2011), while for RSV/B the dominant clade- B.D.E.1 traces back to 2002 (95% HPD: 1997-2007). Despite reduced lineage diversity, RSV/B accumulated non-synonymous variants at nearly twice the rate of RSV/A, notably in the M2-2 gene, reflecting high within-lineage variability. The significant increase in non-synonymous mutations in M2-2 in RSV/B during the pandemic and post-pandemic time phases strongly correlated with increased transcriptional activity. Additionally, antigenic site mutations in the F protein, particularly in RSV/B, were also observed, with implications for immune evasion and effectiveness of the current monoclonal antibody immunoprophylaxis intervention. ConclusionsThe COVID-19 pandemic significantly impacted RSV evolution, leading to reduced genetic diversity during the pandemic and the emergence of novel lineages post-pandemic. RSV/B exhibited more dynamic evolutionary changes, particularly in the M2-2 gene, suggesting potential adaptive advantages. Ongoing genomic surveillance coupled with functional studies is crucial for monitoring variants and assessing the clinical impact of these mutations on transmission, disease severity, fitness, and long-term effectiveness of RSV prevention and treatment strategies.

evolutionary biology↗

bioRxiv2024

K-mer analysis of long-read alignment pileups for structural variant genotyping

Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. We benchmark kanpig against the latest SV benchmarks and show single-sample genotyping concordance of 82.1%, which is higher than existing genotypers averaging 66.3%. We explore kanpigs applicability to multi-sample projects by benchmarking project-level VCFs containing 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), achieving much higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single samples 20x long-reads and can be run on PacBio or ONT long-reads.

bioinformatics↗

bioRxiv2024

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. The Ct values of these samples ranged from 17.0-29.9 for RSV, and from 20.2-34.8 for HuNoV, with some HuNoV having below the detection limit. The mean percentage of post-processing reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries, respectively. Full-length genomes were>99% complete in all RSV positive samples and >96% complete in 47/55 HuNoV positive samples--a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data. Probe-based capture enrichment offers a comprehensive approach for RSV and HuNoV genome sequencing and monitoring emerging variants. IMPORTANCERespiratory syncytial virus (RSV) and human noroviruses (HuNoV) are NIAID category C and category B priority pathogens, respectively, that inflict significant health consequences on children, adults, immunocompromised patients, and the elderly. Due to the high strain diversity of RSV and HuNoV genomes, obtaining complete genomes to monitor viral evolution and pathogenesis is challenging. In this paper, we present the design, optimization, and benchmarking of a comprehensive oligonucleotide target capture method for these pathogens. All 85 RSV samples and 49/55 HuNoV samples were patient-derived with six human intestinal enteroids. The methodology described here results has a higher success rate in obtaining full-length RSV and HuNoV genomes, enhancing the efficiency of studying these viruses and mutations directly from patient-derived samples.

molecular biology↗

bioRxiv2023

Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load

Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.

microbiology↗

bioRxiv2023

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase [~]50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.

genomics↗

bioRxiv2023

Structural variation across 138,134 samples in the TOPMed consortium

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

genomics↗

bioRxiv2022

Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity

For multi-sample structural variant analyses like merging, benchmarking, and annotation, the fundamental operation is to identify when two SVs are the same. Commonly applied approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here we present Truvari - a SV comparison, annotation and analysis toolkit - and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which causes up to a 2.2x inflation of allele frequency relative to Truvari.

bioinformatics↗

bioRxiv2021

Fully resolved assembly of Cryptosporidium parvum

BackgroundCryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. As such, it is important to understand the diversity and genomic makeup of this prevalent parasite to fight established infections and prohibit further transmission. The basis of every genomic study is a high quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. FindingsHere, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on two main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single copy BUSCO genes. ConclusionsThis high quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional and association studies.

genomics↗