With an emphasis on reaching historically underrepresented populations, the All of Us Research Program recruits adults aged 18 and above across the United States to share their health data to enable new insights into human health and research on precision medicine. Participants contribute electronic health records (EHR), survey responses, biospecimens, wearable devices (biometrics), and physical measurements....

To construct a fixed time-scaled phylogenetic tree, the investigators combined 828 viral genome sequences obtained from COVID-19 patients at NYU Langone Health between March and May 2020 with 1,899 background sequences that were contributed to the Nextstrain repository. A total of 2,727 SARS-CoV-2 genomic sequences are available in the dataset. The supporting R code included with the dataset will produce...

A Delta-Omicron recombinant of the SARS-CoV-2 virus was sequenced and isolated from an immunosuppressed and unvaccinated male kidney transplant patient who received Sotrovimab for treatment of COVID-19. Further clinical details and medical history of the patient are described in the associated publication. Sotrovimab is a therapeutic monoclonal antibody (mAb) used to treat infections by the BA.1 Omicron...

This dataset was collected to show that there is a decline in cytotoxic T cells and TCR clonality in organ transplant recipients (OTRs) with squamous cell carcinoma (SCC). In this study, 5 SCC tumor samples and 6 transplant-associated SCC (TSCC) tumor samples were analyzed. Among SCC samples, the male to female ratio was 3 to 2 and the mean patient age was 81 years. Among TSCC samples, the male to...

This dataset contains a list of accession numbers of SARS-CoV-2 genomes obtained from 76 patients at NYU Langone Health who were fully vaccinated with the BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) COVID-19 mRNA vaccines but had breakthrough infections between February 1 and April 30, 2021. 37 were male and 39 were female; the median age of patients was 48 years. There...

This dataset was compiled to determine a genome-wide long interspersed element-1 (LINE-1) insertion site mapping method for bulk DNA. This study has shown that transposon insertion profiling by sequencing (TIPseq) is a method that can be used for LINE-1 mapping in single cells. Live GM12878 lymphoblastoid cells were used for this study. The dataset contains sequencing data as well as supplementary...

NHEJ is the dominant double-strand break (DSB) repair pathway. During synapsis, the two DNA ends at a DSB are brought together into physical proximity for DNA repair. Using single-molecule FRET (smFRET), the study showed that both Ku and XRCC4:DNA ligase IV (X4L4) are necessary to achieve a flexible synapsis of blunt DNA ends. The addition of XLF causes a transition to a close synaptic state and the...

The Human Epilepsy Project (HEP) is a multi-institutional series of prospective, observational studies to identify factors that predict disease outcome, progression, and treatment response among participants with epilepsy. HEP, conducted between 2012 and 2020, included 488 participants aged 12 to 60 years old with new onset focal epilepsy recruited in Australia, Canada, and the United States. Participants...

Smoldering multiple myeloma (SMM) is an asymptomatic plasma cell disorder. It is associated with a high-risk of progression to multiple myeloma (MM). For this study, they performed targeted sequencing on 82 patients. The results showed fewer NRAS and FAM46C mutations with SMM, which is consistent with their role as drivers of the transition to MM. They also analyzed the change in clonal structure over...

This dataset was collected to show that direct RNA sequencing using nanopore arrays is an alternative to conventional RNA sequencing approaches, which are complicated by high gene density, overlapping reading frames, and complex splicing patterns. In direct RNA sequencing, individual polyadenylated RNAs are sequenced directly. For this study, direct RNA sequencing was used to profile the herpes simplex...