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• Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

  This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

  Dataset EGAD00001008433

• Genomic Predictors of Response to Immune Checkpoint Therapy

  Immune checkpoint therapies, including monoclonal antibodies to programmed cell death-1 (PD-1) and cytotoxic % lymphocyte associated protein-4 (CTLA-4), yield durable clinical responses across many tumor types, including metastatic melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC). However, predictors of response to these therapies in RCC are still unknown. Genomic characterization of large clinical cohorts of patients treated with anti-CTLA-4 and anti-PD-1 agents in melanoma and NSCLC have suggested that high mutational burden, high neoantigen burden, and high expression of certain genes in pre-treatment tumors may be associated with patient response to these therapies. In this study, we sought to investigate genomic predictors of response to anti-PD1 therapy in metastatic RCC in two independent clinical cohorts using whole exome and whole transcriptome sequencing.

  Study phs001493

• Evolutionary Analysis of Chronic Lymphocytic Leukemia Cells During Relapse After Allogeneic Hematopoietic Stem Cell Transplant

  We investigated the molecular dynamics driving relapse of chronic lymphocytic leukemia (CLL) following allogeneic hematopoietic stem cell transplant (allo-HSCT) through an integrated analysis of whole exome, bulk transcriptome, bulk methylome and single cell transcriptional data from paired leukemic samples representing 19 patients. We found that their clinical kinetics corresponded to distinct genetic and epigenetic evolutionary trajectories and suggest that the selection pressures of the post-transplant, immunologic bottleneck are distinct from those imposed by chemotherapy.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out ribosome profiling (Ribo-seq) and RNA-sequencing on CLL samples and isolated primary B cells from healthy donors. We discovered novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens.

  Study phs001998

• Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

  We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

  Study phs003638

• Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer: DNA Sequencing

  This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. All participants in this study were female. RNA sequencing data from the same patients were published under phs001863. Subject aliases are the same in the two datasets.

  Study phs003801

• Targeted Long-Read Sequencing of the Ewing Sarcoma 6p25.1 Susceptibility Locus

  Ewing Sarcoma (EwS) is rare but the second most common cancer in children, adolescents and young adults. Recent studies suggest germline variation in or around GGAA microsatellites may interact with fusion oncoprotein binding causing changes in binding affinity and potentially impacting enhancer activity on nearby target genes. This study aims to better understand germline variation around EwS susceptibility regions by performing long-range haplotype sequencing of these regions using PacBio sequencing. Our analysis focused on characterizing variation in GGAA microsatellite length as well as germline variants in or around the microsatellite and their association with EwS risk.

  Study phs003159

• Long-read whole-genome sequencing of post-mortem sporadic PD cases and non-PD controls using gut tissue

  This study aims to enable in-depth genomic characterization of Parkinson’s disease (PD) by examining single nucleotide polymorphisms, structural variants, and quantitative trait loci. Long-read whole-genome sequencing was performed using the Oxford Nanopore PromethION platform on colon tissue collected post‑mortem from PD patients and non-PD controls. These data contribute high-resolution insights into genomic variation that may affect PD biology. The project is part of Team Voet’s efforts within the ASAP Collaborative Research Network, which promotes resource sharing and accelerates discovery in Parkinson’s disease research.

  Study EGAS50000001689

• Transcriptional characterization of human innate lymphoid cells (ILCs) and natural killer (NK) cells from fresh umbilical cord blood

  The heterogenicity of cord blood ILCs (ILC1, ILC2, ILC3) and NK cells in humans has so far not been assessed. In this study, we sorted from fresh cord blood the respective cell types from 3 donors and performed single-cell transcriptome analysis. To achieve high resoluation, each sorted population was labelled individually via multiplexing antibodies and subsequent Abseq staining before pooling. To determine single-cell transcriptomes the BD Rhapsody pipeline was performed. This is the first data set to characterize human ILCs and NK cells at such depth.

  Study EGAS50000001204

• Transcriptomic profiling of skin biopsies from psoriasis patients following treatment with Zasocitinib

  The objective of this study is the exploratory analysis and characterization of psoriasis using RNA-seq-based profiling. Specifically, the cutaneous and serum biomarker profiles associated with the molecular, histological and clinical effects of Zasocitinib treatment in patients with moderate-to-severe plaque psoriasis were characterized. To evaluate differences between the transcriptomic profiles of Zasocitinib- and placebo-treated patients, exploratory biomarker endpoints included quantification of skin biomarkers, such as immune cell infiltration and mRNA expression levels in lesional and non-lesional skin, as well as quantification of circulating cytokines and other inflammatory biomarkers.

  Study EGAS50000001548

• 503 genotypes from Inner Asia used in 'Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy' publication

  Inner Asia is particularly interesting to understand human history and evolution, as two groups presenting contrasting cultural traits (notably their language, their social organisation and matrimonial system) cohabit. We sampled 503 individuals from these two groups, belonging to 17 populations from 11 distinct ethnic groups (AltaiKizhi, Kazakh, Khakas, Kyrgyz, Mongolian, Shore, Tajik, Telengit, Tubalar, Turkmen and Uzbek). The samples were then genotyped with 5 different DNA-arrays and, after quality-control, the 253,532 autosomal SNPs present in all the arrays were merged together in the present dataset.

  Study EGAS00001002951