Biology subjects

Freed, D.

Publications and source records attributed to Freed, D..

10 recordsLinked to original sources

bioRxiv2026

The Genome In A Bottle HG002 assembly-based variant benchmark set enables comprehensive benchmarking of small and structural variants.

High-accuracy, high-resolution benchmark data are fundamental to improving the accuracy and generalizability of sequencing technologies and associated algorithms. Most existing benchmarks for DNA sequencing rely on mapping to a single linear reference, omitting inaccessible and highly repetitive complex genomic regions. Here, we present the Genome in a Bottle (GIAB) Consortium's HG002 v5.0q benchmark set, a more comprehensive variant benchmark derived from a fully phased, highly curated, and accurate diploid assembly of HG002. Our approach leverages recent advances in long-read sequencing and assembly to provide confident small- and structural-variant calls across previously inaccessible regions, including segmental duplications, homopolymers, tandem repeats, and complex immune loci. The v5.0 benchmark significantly expands the callable genome relative to v4.2.1, adding x200 Mbp of sequence and increasing variant detection by 18 % for small variants and 3-fold for structural variants compared to previous benchmarks. The benchmark regions include more variants in repetitive regions, including 1.2 x segmental duplications, 1.8 x tandem repeats, and 2.0 x homopolymers, compared to v4.2.1. Separate and combined small- and structural-variant benchmarks are available for three versions of the human reference genome (GRCh37, GRCh38, and CHM13). We validate the reliability of this benchmark set by comparing multiple sequencing technologies and variant calling pipelines and curating differences. The v5.0q benchmark provides a critical resource for the development and validation of next-generation sequencing technologies and analysis methods.

genomics↗

bioRxiv2025

Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant Calling

BackgroundIntegrating short-read and long-read sequencing technologies has become a promising approach for achieving accurate and comprehensive genomic analysis. While short-read sequencing (Illumina, etc.) offers high base accuracy and cost efficiency, it struggles with structural variation (SV) detection and complex genomic regions. In contrast, long-read sequencing (PacBio HiFi) excels in resolving large SVs and repetitive sequences but is limited by throughput, higher Indel error rates, and sequencing costs. Hybrid approaches may combine these technologies and leverage their complementary strengths and different sources of error to provide higher accuracy, more comprehensive results, and higher throughput by lowering the coverage requirement for the long reads. MethodsThis study benchmarks the DNAscope Hybrid pipeline, a novel integrated alignment and variant calling framework that combines short- and long-read data sequenced from the same sample. We evaluate its performance across multiple human genome reference datasets (HG002-HG004) using the draft Q100 and Genome in a Bottle v4.2.1 benchmarks. The pipelines ability to detect small variants (SNPs/Indels), structural variants (SVs), and copy number variations (CNVs) is assessed using data from the Illumina and Pacbio sequencing systems at varying read depths (5x-30x). Benchmark results are compared to DeepVariant. ResultsThe DNAscope Hybrid pipeline significantly improves SNP and Indel calling accuracy, particularly in complex genomic regions. At lower long-read depths (e.g., 5x-10x), the hybrid approach outperforms standalone short- or long-read pipelines at full sequencing depths (30x-35x). Additionally, the DNAscope Hybrid outperforms leading open-source tools for SV and CNV detection, enhancing variant discovery in challenging genomic regions. The pipeline also demonstrates clinical utility by identifying disease- associated variants. Moreover, DNAscope Hybrid is highly efficient, achieving less than 90 minutes runtimes at single standard instance. ConclusionThe DNAscope Hybrid pipeline is a computationally efficient, highly accurate variant calling framework that leverages the advantages of both short- and long-read sequencing. By improving variant detection in challenging genomic regions and offering a robust solution for clinical and large-scale genomic applications, it holds significant promise for genetic disease diagnostics, population-scale studies, and personalized medicine.

bioinformatics↗

bioRxiv2025

Left ventricular transcriptome and extracellular vesicle-derived miRNAs in porcine donation after circulatory death (DCD) hearts undergoing prolonged working mode ex situ perfusion

Donation after circulatory death (DCD) hearts suffer from warm ischemia-reperfusion injury, which compromises graft quality. We have previously demonstrated that a postconditioning-based cardioprotective treatment (1% Intralipid, 2% (v/v) sevoflurane, 3 nM remifentanil) improved the function and viability of porcine DCD hearts undergoing ex situ heart perfusion (ESHP). However, transcriptional changes in DCD hearts subjected to prolonged working mode ESHP as compared with healthy hearts, and more so transcriptional changes in the presence or absence of cardioprotection, as well as the early reperfusion profile of extracellular vesicle (EV)-derived miRNAs, critical regulators of the transcriptional control, have not been investigated. A total of 5,483 differentially expressed transcripts were identified in left ventricular tissue samples of DCD hearts (N=10) collected after 6 hours of ESHP when compared with healthy hearts not subjected to ESHP (N=8), irrespective of cardioprotection. Downregulation of protein synthesis, metabolic, and DNA repair gene sets was most prominent, while inflammatory and remodeling gene sets were upregulated. Between DCD hearts that were treated with (pDCD_ESHP, N=5) or without (uDCD_ESHP, N=5) cardioprotection, only 43 transcripts were differentially regulated. Specifically, lipid breakdown, beta-oxidation, and DNA repair gene sets were upregulated in pDCD_ESHP, whereas lipid accumulation, inflammation, oxidative stress, and maladaptive remodeling gene sets were upregulated in uDCD_ESHP. Predominantly cardioprotective EV-derived miRNAs were released into the perfusate in pDCD_ESHP, while predominantly cardiac injury-associated miRNAs were released into the perfusate in uDCD_ESHP. Cardioprotection promoted adaptive rather than maladaptive transcriptional changes and enabled the release of potentially beneficial miRNAs.

molecular biology↗

bioRxiv2023

Small variant benchmark from a complete assembly of X and Y chromosomes

The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To evaluate variant detection on chromosomes X and Y, we created an 111,725 variant benchmark for the Genome in a Bottle HG002 reference material. We show how complete assemblies can expand benchmarks to difficult regions, but highlight remaining challenges benchmarking complex gene conversions, copy number variable gene arrays, and human satellites.

genomics↗

bioRxiv2023

A novel rotavirus reverse genetics platform supports flexible insertion of exogenous genes and enables rapid development of a high-throughput neutralization assay

Despite the success of rotavirus vaccines, rotaviruses are still one of the leading causes of diarrheal diseases, resulting in significant childhood morbidity and mortality especially in low- and middle-income countries. Reverse genetics system enables the manipulation of the rotavirus genome and opens the possibility of using rotavirus as an expression vector for heterologous proteins such as vaccine antigens and therapeutic payloads. Here, we identified three positions in rotavirus genome, the C terminus of NSP1, NSP3 and NSP5, for reporter gene insertion. By using rotavirus expressing GFP, we developed a high-throughput neutralization assay and revealed the pre-existing immunity against rotavirus in human and other animal species. Our work shows the plasticity of rotavirus genome and establishes a high-throughput assay for interrogating humoral immune responses, benefiting the design of next-generation rotavirus vaccines and the development of rotavirus-based expression platforms.

microbiology↗

bioRxiv2022

Processing UMI Datasets at High Accuracy and Efficiency with the Sentieon ctDNA Analysis Pipeline

Liquid biopsy enables identification of low allele frequency (AF) tumor variants and novel clinical applications such as minimum residual disease (MRD) monitoring. However, challenges remain, primarily due to limited sample volume and low read count of low-AF variants. Because of the low AFs, some clinically significant variants are difficult to distinguish from errors introduced by PCR amplification and sequencing. Unique Molecular Identifiers (UMIs) have been developed to further reduce base error rates and improve the variant calling accuracy, which enables better discrimination between background errors and real somatic variants. While multiple UMI-aware ctDNA analysis pipelines have been published and adopted, their accuracy and runtime efficiency could be improved. In this study, we present the Sentieon ctDNA pipeline, a fast and accurate solution for small somatic variant calling from ctDNA sequencing data. The pipeline consists of four core modules: alignment, consensus generation, variant calling, and variant filtering. We benchmarked the ctDNA pipeline using both simulated and real datasets, and found that the Sentieon ctDNA pipeline is more accurate than alternatives.

bioinformatics↗

bioRxiv2022

Sentieon DNAscope LongRead - A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads

PacBio(R) HiFi sequencing is the first technology to offer economical and highly accurate long-read sequencing, with average read lengths greater than 10kb and average base accuracy of 99.8%1. Here, we present DNAscope LongRead, an accurate and efficient pipeline for germline variant calling from PacBio(R) HiFi reads. DNAscope LongRead is a modification and extension of Sentieons DNAscope tool, a precisionFDA award-winning variant caller. DNAscope LongRead is computationally efficient, calling variants from 30x HiFi samples in under 4 hours on a 16-core machine (120 virtual core-hours) and highly accurate, with precision and recall on the most recent GIAB benchmark dataset exceeding 99.83% for HiFi samples sequenced at 30x coverage, and robust to changes in benchmark dataset and upstream library preparation and sequencing.

bioinformatics↗

bioRxiv2021

Vaccine Hyporesponse Induced By Individual Antibiotic Treatment In Mice And Non-Human Primates Is Diminished Upon Recovery Of The Gut Microbiome

Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the interaction between microbes and the immune system could provide novel therapeutic strategies for improving vaccine response. Currently we do not fully understand the mechanisms and dynamics by which the microbiome influences vaccine response. Using both mouse and non-human primate models, we report that short-term oral treatment with a single antibiotic (vancomycin) results in disruption of the gut microbiome and this correlates with a decrease in systemic levels of antigen-specific IgG upon subsequent parenteral vaccination. We further show that recovery of microbial diversity before vaccination prevents antibiotic-induced vaccine hyporesponse, and that the antigen specific IgG response correlates with the recovery of microbiome diversity. RNA-sequencing analysis of small intestine, spleen, whole blood, and secondary lymphoid organs from antibiotic treated mice revealed a dramatic impact on the immune system, and a muted inflammatory signature is correlated with loss of bacteria from Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. These results suggest that microbially modulated immune pathways may be leveraged to promote vaccine response and will inform future vaccine design and development strategies. ImportanceAntibiotic-induced gut microbiome disruption has been linked to reduced vaccine efficacy. Despite these observations, there remains a knowledge gap in the specific mechanisms by which antibiotics and the gut microbiome influence vaccine efficacy. We aim to contribute to the fields growing mechanistic understanding by presenting a detailed analysis of antibiotic treatment and recovery as it relates to vaccine response and the microbiome. Using animal models, we show that short-term antibiotic treatment prior to vaccination results in diminished vaccine-specific immune responses, and that these are correlated with specific microbiome signatures. We also demonstrate the converse, in which gut microbiome recovery can result in improved vaccine response. We further reveal that antibiotics can significantly alter multiple relevant immune pathways and this alteration in immune tone may contribute to the vaccine hyporesponse. We expect our findings will enable the continued prosecution of the role of the microbiome in modulating the host immune system.

immunology↗

bioRxiv2020

Specificity and effector functions of non-neutralizing gB-specific monoclonal antibodies isolated from healthy individuals with human cytomegalovirus infection

Human cytomegalovirus (HCMV) is the most common congenital infection, and the leading nongenetic cause of sensorineural hearing loss (SNHL) in newborns globally. A gB subunit vaccine administered with adjuvent MF59 (gB/MF59) is the most efficacious tested to-date, achieving 50% efficacy in preventing infection of HCMV-seronegative mothers. We recently discovered that gB/MF59 vaccination elicited primarily non-neutralizing antibody responses, that HCMV strains acquired by vaccinees more often included strains with gB genotypes that are distinct from the vaccine antigen, and that protection against HCMV acquisition correlated with ability of vaccine-elicited antibodies to bind to membrane associated gB. Thus, we hypothesized that gB-specific non-neutralizing antibody binding breadth and function are dependent on their epitope and genotype specificity as well as their ability to interact with membrane-associated gB. Twenty-four gB-specific monoclonal antibodies (mAbs) isolated from naturally HCMV-infected individuals were mapped for gB domain specificity by binding antibody multiplex assay (BAMA) and for genotype preference binding to membrane-associated gB presented on transfected cells. We defined their non-neutralizing functions including antibody dependent cellular phagocytosis (ADCP) and antibody dependent cellular cytotoxicity (ADCC). The isolated gB-specific non-neutralizing mAbs were primarily specific for Domain II and linear antigenic domain 2 site 2 (AD2). We observed variability in mAb gB genotype binding preference, with increased binding to gB genotypes 2 and 4. Functional studies identified two gB-specific mAbs that facilitate ADCP and have binding specificities of AD2 and Domain II. This investigation provides novel understanding on the impact of gB domain specificity and antigenic variability on gB-specific non-neutralizing antibody responses. ImportanceHCMV is the most common congenital infection worldwide, but development of a successful vaccine remains elusive. gB-specific non-neutralizing mAbs, represent a distinct anti-HCMV Ab subset implicated in the protection against primary infection during numerous phase-II gB/MF59 vaccine trials. By studying non-neutralizing gB-specific mAbs from naturally infected individuals, this study provides novel characterization of binding site specificity, genotypic preference, and effector cell functions mediated by mAbs elicited in natural infection. We found that a panel of twenty-four gB-specific non-neutralizing mAbs bind across multiple regions of the gB protein, traditionally through to be targeted by neutralizing mAbs only, and bind differently to gB depending if the protein is soluble versus embedded in a membrane. This investigation provides novel insight into the gB-specific binding characteristics and effector cell functions mediated by non-neutralizing gB-specific mAbs elicited through natural infection, providing new endpoints for future vaccine development.

immunology↗

bioRxiv2018

TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering

Detection of somatic mutations in tumor samples is important in the clinic, where treatment decisions are increasingly based upon molecular diagnostics. However, accurate detection of these mutations is difficult, due in part to intra-tumor heterogeneity, contamination of the tumor sample with normal tissue and pervasive structural variation. Here, we describe Sentieon TNscope, a haplotype-based somatic variant caller with increased accuracy relative to existing methods. An early engineering version of TNscope was used in our submission to the most recent ICGC-DREAM Somatic Mutation calling challenge. In that challenge, TNscope is the leader in accuracy for SNVs, indels and SVs. To further improve variant calling accuracy, we combined the improvements in the variant caller with machine learning. We benchmarked TNscope using in-silico mixtures of well-characterized Genome in a Bottle (GIAB) samples. TNscope displays higher accuracy than the other benchmarked tools and the accuracy is substantially improved by the machine learning model.

bioinformatics↗