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• Human brain development single cell sequencing additional samples

  69 tissue samples from various parts of the developing human embryo brain were dissociated and single cells were collected and processed without bias for mRNA-seq using 10X chromium 3' protocol. Libraries were sequenced on Illumina NovaSeq and reads aligned against the human GRCh38 genome. This is an addition to EGAD00001006049 Human development single cell sequencing, consisting of samples added after the original submission to EGA, but included in final paper.

  Dataset EGAD50000001295

• MissionBio single cell DNA and protein seq for 2 samples

  This dataset contains MissionBio Targeted single-cell DNA and Protein sequencing data from a primary sample and a patient-derived xenograft (PDX) model, which is used to investigate the clonal evolution in the FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001793

• Identifying genetic variants that alter TCR usage in the peripheral repertoire

  The relationship between genetic variation and CD8+ T-cell receptor (TCR) repertoire usage in patients receiving Immune Checkpoint Blockade (ICB) therapy for cancer is unexplored. We have conducted a genome-wide and human leukocyte antigen (HLA)-focused analysis of CD8+ T-cell TCR repertoire to identify genetic determinants of variable gene (V-gene) and CDR3 K-mer usage from samples taken prior to and after ICB (n=250). We identify 11 cis and 10 trans V-gene associations, primarily to the MHC, that meet genome-wide significance. TCR clones containing HLA associated V-genes were less stable across treatment, whilst at the single-cell level, genetically associated clones demonstrate subset enrichment and increased tumor reactivity expression profiles. Notably, patients with HLA-matched TCR clones demonstrate improved overall survival. Our work indicates a complex relationship between genotype and TCR repertoire in the context of ICB treatment, with novel implications for understanding factors relating to therapeutic response and patient outcomes.

  Study EGAS00001008189

• Emory University African American Vaginal, Oral, and Gut Microbiome in Pregnancy Cohort Study

  The Emory University African American Microbiome in Pregnancy Cohort Study prospectively enrolls African American women between 18-40 years of age without chronic medical conditions into a longitudinal follow-up study that involves completing microbiome sampling and data collection at two time points in pregnancy (8-14 weeks gestation and 24-30 weeks gestation). The study is investigating the role of the oral, vaginal, and gut microbiome on preterm birth and other pregnancy outcomes as well as biobehavioral factors that shape the microbiome among this socio-demographically diverse group of women. Microbiome sampling involves the oral, vaginal, and gut sites. Biobehavioral factors that are being explored for their association with microbiome composition at the three body sites include measures of sociodemographic status as well as diet and nutrition, infectious and stress exposures.

  Study phs001865

• Anti-tumor and Immune Stimulatory Activity of Iberdomide in Myeloma, Including Patients with Cereblon Dysregulation

  Study showing Iberdomide treatment leads to immune stimulation and shift to effector T cells in triple-class refractory patients and directly after IMiD therapy. This is the first clinical evidence that Iberdomide can overcome Cereblon defects associated with IMiD resistance in late-line myeloma patients.

  Study EGAS50000000265

• Multi-region RNA sequencing of tumour regions and tumour-adjacent normal lung tissue

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Study EGAS00001006517

• Ensilication as a Cold‑Chain–Free Solution for High‑Fidelity DNA Preservation in tumor samples

  Nucleic acid preservation requires continuous refrigeration at -20 °C to -80 °C, creating infrastructure barriers limiting genomic medicine access globally. While ambient-temperature preservation methods exist, their effects on DNA integrity and sequence fidelity remain incompletely characterized. The project aims to evaluate ensilication as a method for preserving DNA at ambient temperatures and to determine whether it can match or exceed the fidelity of conventional ultra‑low‑temperature storage. It seeks to assess the technology’s ability to maintain diagnostic accuracy, including detection of clinically actionable variants in tumor samples. Another goal is to compare sequencing‑related artifact rates between ensilicated and cryogenically stored DNA to quantify improvements in data quality. Ultimately, the project aims to establish ensilication as a cold‑chain‑independent solution that enables more accessible global genomic testing and biobanking.

  Study EGAS50000001698

• Indonesian Genome Diversity Project

  Indonesia, the world’s fourth largest country by population, comprises an archipelago of about 900 permanently inhabited islands in tropical Asia, and hosts an astonishing array of human diversity that remains largely underrepresented in modern biological surveys. The region is unique for its key role in both the early and recent evolution of Homo outside of Africa. It has one of the first traces of anatomically modern humans in Eurasia, and was the focus of extensive interaction between archaic hominins and humans – both in the likely co-existence of H. floresiensis with modern humans, and in the introgression of Denisovans into the ancestors of its present inhabitants. More recently, Indonesia was a center of the spread of Neolithic culture by Austronesian speakers. Advancing maritime technologies allowed farming populations to treat this region as a springboard to reach oceanic islands as remote as Madagascar, Hawaii, Easter Island and New Zealand. Here we present complete human genomes from healthy individuals from multiple key islands in Indonesia and Papua. The genomes were sequenced to high depth (30x). The purpose of this dataset is to address different questions of human evolution in Island Southeast Asia and beyond, including early settlement of the area by anatomically modern humans, population structure, genetic admixture and adaptation, and contacts with archaic hominins. We employed a sampling strategy to capture a broad range of diversity across the region incorporating an average of 12 samples from each of 14 islands spanning Indonesia and Papua, from Sumatra in the west to New Britain in the east. Genomes from this dataset form part of an ongoing project to describe and understand human evolutionary history in Island Southeast Asia and Eurasia in general.

  Study EGAS00001003054

• Single molecule molecular inversion probe capture developed using the CIViC database

  This study evaluated the use of the Clinical Interpretations of Variants in Cancer database (CIViC) to develop an Open-sourced CIViC Annotation Pipeline (OpenCAP). OpenCAP is a resource that allows users to develop a clinical capture panel that can be linked back to clinical summaries within the CIViC database. This method for capture panel development and variant annotation was tested using 27 cancer samples from 5 tumor subtypes with original exome or genome sequencing. Specifically, using OpenCAP, 111 variants were identified as relevant for the capture panel and 2,027 smMIPs were designed to target these variants. The smMIPs panel design was employed on all samples to validate the capture panel design. When compared to original sequencing, the CIViC smMIPs capture panel demonstrated a 95% sensitivity for variant detection (n = 61 variants). Additionally, the CIViC smMIPs capture panel identified 182 additional clinically relevant variants that had been missed on original sequencing.

  Study phs001890

• Genetic Analysis of Limb Malformation Disorders: Freeman Sheldon Syndrome Exome Sequencing Study (LMD-FSS)

  The overall goal of this project is to investigate the etiology and pathogenesis of malformations (i.e., birth defects) of the limb, concentrating on abnormalities of limb patterning such as limb deficiency/duplications and multiple congenital contractures. The exome sequences of four unrelated individuals were obtained by massively parallel DNA sequencing. The three individuals were affected with Freeman Sheldon syndrome (OMIM: 193700).

  Study phs000204