Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks.

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line (HG008-T) and matched normal cells from duodenal tissue (HG008-N-D) and pancreatic tissue (HG008-N-P). The data come from thirteen whole genome measurement technologies: Illumina paired-end, Element standard and long insert, Ultima UG100, PacBio (HiFi and Onso), Oxford Nanopore (standard and ultra-long), Bionano Optical Mapping, Arima and Phase Genomics Hi-C, G-banded karyotyping, directional genomic hybridization, and BioSkryb Genomics single-cell ResolveDNA. Most tumor data is from a large homogenous batch of non-viable cells after 23 passages of the primary tumor cells, along with some data from different passages to enable an initial understanding of genomic instability. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. In addition, extensive data from two different normal tissues from the same individual can enable understanding of mosaicism. Long reads also contain methylation tags for epigenetic analyses. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.

Cell Therapies for Acute Radiation Syndrome.

The risks of severe ionizing radiation exposure are increasing due to the involvement of nuclear powers in combat operations, the increasing use of nuclear power, and the existence of terrorist threats. Exposure to a whole-body radiation dose above about 0.7 Gy results in H-ARS (hematopoietic acute radiation syndrome), which is characterized by damage to the hematopoietic system; higher doses result in further damage to the gastrointestinal and nervous systems. Only a few medical countermeasures for ARS are currently available and approved for use, although others are in development. Cell therapies (cells or products produced by cells) are complex therapeutics that show promise for the treatment of radiation injury and have been shown to reduce mortality and morbidity in animal models. Since clinical trials for ARS cannot be ethically conducted, animal testing is extremely important. Here, we describe cell therapies that have been tested in animal models. Both cells and cell products appear to promote survival and lessen tissue damage after whole-body irradiation, although the mechanisms are not clear. Because radiation exposure often occurs in conjunction with other traumatic injuries, animal models of combined injury involving radiation and future countermeasure testing for these complex medical problems are also discussed.

Expanding access to evidence-based psychotherapy in VA settings: implementation of the brief cognitive behavioral therapy for depression program.

Introduction: Evidence-based psychotherapies (EBPs) are effective for mental health conditions, but access to these services remains limited and rural Veterans are particularly underserved. Specialized implementation and dissemination programs are needed to improve access to known EBPs. Methods: The current project sought to improve access to a known EBP-brief Cognitive Behavioral Therapy for depression (Brief CBT). Diverse Veterans and those from rural settings were a focus of this work. Aligned with the RE-AIM framework, a multifaceted implementation program was used to train and support VHA providers in their use of Brief CBT in VHA mental health settings, with specific outreach efforts made to providers at VHA Community-Based Outpatient Clinics (CBOCs) where rural Veterans often receive care. Evaluation included all facets of RE-AIM with a particular focus on adoption, effectiveness, and maintenance. Results: During the first two years, over 40 VHA facilities adopted the program across four regional networks. Eighty-three providers were approached, and 54 (65.1%) providers completed the training and are delivering the intervention. A total of 688 Veterans, 174 rural (25.7%), received 2,186 sessions (average of 3.5 sessions per Veteran). Veterans receiving Brief CBT with elevated depression scores who completed three or more sessions were found to have significant symptom reductions of 4.6 points (first to last available evaluations). Discussion: Implementation efforts of Brief CBT resulted in rapid uptake and significant clinical impact on Veterans. Rural outreach efforts, including targeted training for CBOC providers and use of tele-mental health, enhanced availability of EBP services for rural Veterans.

Intravenous Autologous Bone Marrow-derived Mesenchymal Stromal Cells Delay Acute Respiratory Distress Syndrome in Swine.

Rationale: Early post injury mitigation strategies in ARDS are in short supply. Treatments with allogeneic stromal cells are administered after ARDS develops, require specialized expertise and equipment, and to date have shown limited benefit. Objectives: Assess the efficacy of immediate post injury intravenous administration of autologous or allogeneic bone marrow-derived mesenchymal stromal cells (MSCs) for the treatment of acute respiratory distress syndrome (ARDS) due to smoke inhalation and burns. Methods: Yorkshire swine (n = 32, 44.3 ± 0.5 kg) underwent intravenous anesthesia, placement of lines, severe smoke inhalation, and 40% total body surface area flame burns, followed by 72 hours of around-the-clock ICU care. Mechanical ventilation, fluids, pressors, bronchoscopic cast removal, daily lung computed tomography scans, and arterial blood assays were performed. After injury and 24 and 48 hours later, animals were randomized to receive autologous concentrated bone marrow aspirate (n = 10; 3 × 106 white blood cells and a mean of 56.6 × 106 platelets per dose), allogeneic MSCs (n = 10; 6.1 × 106 MSCs per dose) harvested from healthy donor swine, or no treatment in injured control animals (n = 12). Measurements and Main Results: The intravenous administration of MSCs after injury and at 24 and 48 hours delayed the onset of ARDS in swine treated with autologous MSCs (48 ± 10 h) versus control animals (14 ± 2 h) (P = 0.004), reduced ARDS severity at 24 (P < 0.001) and 48 (P = 0.003) hours, and demonstrated visibly diminished consolidation on computed tomography (not significant). Mortality at 72 hours was 1 in 10 (10%) in the autologous group, 5 in 10 (50%) in the allogeneic group, and 6 in 12 (50%) in injured control animals (not significant). Both autologous and allogeneic MSCs suppressed systemic concentrations of TNF-α (tumor necrosis factor-α). Conclusions: The intravenous administration of three doses of freshly processed autologous bone marrow-derived MSCs delays ARDS development and reduces its severity in swine. Bedside retrieval and administration of autologous MSCs in swine is feasible and may be a viable injury mitigation strategy for ARDS.

The complete sequence of a human Y chromosome.

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Semi-automated assembly of high-quality diploid human reference genomes.

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Effectiveness and Optimal Duration of Adjunctive Rifampin Treatment in the Management of Staphylococcus aureus Prosthetic Joint Infections After Debridement, Antibiotics, and Implant Retention.

Background: Rifampin is recommended as adjunctive therapy for patients with a Staphylococcus aureus prosthetic joint infection (PJI) managed with debridement, antibiotics, and implant retention (DAIR), with no solid consensus on the optimal duration of therapy. Our study assessed the effectiveness and optimal duration of rifampin for S aureus PJI using Veterans Health Administration (VHA) data. Methods: We conducted a retrospective cohort study of patients with S aureus PJI managed with DAIR between 2003 and 2019 in VHA hospitals. Patients who died within 14 days after DAIR were excluded. The primary outcome was a time to microbiological recurrence from 15 days up to 2 years after DAIR. Rifampin use was analyzed as a time-varying exposure, and time-dependent hazard ratios (HRs) for recurrence were calculated according to the duration of rifampin treatment. Results: Among 4624 patients, 842 (18.2%) received at least 1 dose of rifampin; 1785 (38.6%) experienced recurrence within 2 years. Rifampin treatment was associated with significantly lower HRs for recurrence during the first 90 days of treatment (HR, 0.60 [95% confidence interval {CI}, .45-.79]) and between days 91 and 180 (HR, 0.16 [95% CI, .04-.66]) but no statistically significant protective effect was observed with longer than 180 days (HR, 0.57 [95% CI, .18-1.81]). The benefit of rifampin was observed for subgroups including knee PJI, methicillin-susceptible or -resistant S aureus infection, and early or late PJI. Conclusions: This study supports current guidelines that recommend adjunctive rifampin use for up to 6 months among patients with S aureus PJI treated with DAIR.

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

A complete reference genome improves analysis of human genetic variation.

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

Comparison of next generation diagnostic systems (NGDS) for the detection of SARS-CoV-2.

INTRODUCTION: The World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a pandemic in March 2020. Initially, supply chain disruptions and increased demand for testing led to shortages of critical laboratory reagents and inadequate testing capacity. Thus, alternative means of biosample collection and testing were essential to overcome these obstacles and reduce viral transmission. This study aimed to 1) compare the sensitivity and specificity of Cepheid GeneXpert® IV and BioFire® FilmArray® 2.0 next generation detection systems to detect SARS-CoV-2, 2) evaluate the performance of both platforms using different biospecimen types, and 3) assess saline as an alternative to viral transport media (VTM) for sample collection. METHODS: A total of 1,080 specimens consisting of nasopharyngeal (NP) swabs in VTM, NP swabs in saline, nasal swabs, oropharyngeal (OP) swabs, and saliva were collected from 216 enrollees. Limit of detection (LoD) assays, NP VTM and NP saline concordance, and saliva testing were performed on the BioFire® FilmArray® 2.0 Respiratory Panel 2.1 and Cepheid GeneXpert® Xpress SARS-CoV-2/Flu/RSV assays. RESULTS: LoD and comparative testing demonstrated increased sensitivity with the Cepheid compared with the BioFire® in detecting SARS-CoV-2 in NP VTM and saline, nasal, and OP swabs. Conversely, saliva testing on the Cepheid showed statistically significant lower sensitivity compared to the BioFire® . Finally, NP swabs in saline showed no significant difference compared with NP swabs in VTM on both platforms. CONCLUSION: The Cepheid and BioFire® NGDS are viable options to address a variety of public health needs providing rapid and reliable, point-of-care testing using a variety of clinical matrices.