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• Single Cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumours

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Dataset EGAD00001002727

• PacBio HiFi sequencing of telobait-captured DNA from 68 patients

  PacBio HiFi sequencing was performed on 68 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files. There are 56 new samples and 12 repeated samples from run 1.

  Dataset EGAD00001009397

• Transcriptome sequencing of FFPE and patient-derived cultures

  Transcriptome sequencing of FFPE and patient-derived cultures from clinical study NCT03860376

  Dataset EGAD50000000246

• RNA-Seq Pair End

  RNA analysis of two patients 11 and 15 with WGS done on Illumina HiSeq2000. For research purpose and authorised user only.

  Dataset EGAD00001003429

• CRISPR screen M14, NCI-H3122

  Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung

  Dataset EGAD00001001389

• SCLC study Peifer et al. - RNAseq dataset

  SCLC - RNA sequencing data Publication Peifer et al., 2012, Nature Genetics

  Dataset EGAD00001001431

• Whole-genome variant calling of individuals from the study of allergic diseases in the Canary Islands

  Research study of genetic susceptibility and analyses of polygenic risk scores in allergic diseases. This dataset consists of variant data derived from whole-genome sequencing in reference samples from one of the parental populations (i.e., North Africans). The dataset consist of 15 VCF files (and corresponding index files) with a total of 1.58 million variants called using GATK v4 and following the Broad Variant Calling Best Practices, from a set of unrelated individuals sequenced in paired-read mode 2x150 bp using an Illumina HiSeq 4000 sequencer.

  Dataset EGAD50000000429

• Deciphering the mutational landscape and the genome organization of LMS

  Leiomyosarcoma (LMS) are an uncommon group of malignant mesenchymal tumors composed of cells showing distinct smooth muscle differentiation. These tumors occur mainly in adults in any location of the body (soft-tissue, viscera or uterine). Soft-tissue LMS represent 10-15% of all soft-tissue sarcomas. The most frequent locations are the limbs followed by the retroperitoneum and uterine.

  Study EGAS00001001262

• RRBS MDACC Lung PreCancer

  To study the evolution of DNA methylation at genome level and methylation intra-tumor heterogeneity (ITH) during early lung carcinogenesis, we performed multiregional reduced representation bisulfite sequencing (RRBS) of 62 resected lung nodules from 39 patients including atypical adenomatous hyperplasia (AAH, n=14), adenocarcinoma in situ (AIS, n=15), minimally invasive adenocarcinoma (MIA, n=22), and invasive adenocarcinoma (ADC, n=11).

  Study EGAS00001004610

• The molecular landscape of homologous recombination deficient, end-stage, high grade serous ovarian cancer

  High grade serous ovarian cancer (HGSC) is frequently characterized by homologous recombination (HR) DNA repair deficiency, and while most such tumors are sensitive to initial treatment, acquired resistance is common. We undertook a multi-omics approach to interrogating mechanisms of resistance, using multiple autopsy samples collected from 15 women with HR-deficient HGSC.

  Study EGAS00001006789

• Biesecker Lab (NHGRI) Whole Genome Medical Sequencing for Gene Discovery

  We aim to use whole-genome medical sequencing (WGMS) to discover causative molecular lesions for a set of rare, severe phenotypes hypothesized to be caused by either somatic mutations, germline de nova heterozygous mutations, germline inherited recessive, or germline inherited dominant mutations in currently unknown or uncharacterized genes. The goal of this research is threefold: to identify causative sequence variants for disorders whose molecular etiology was previously unknown, to apply this insight to both the rare disorders under study and more common phenotypes, and to enhance the study of mutation on a genome-wide level.

  Study phs001348

• Japanese Reference Genome JG1

  The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using >100�� Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the major allele for a Japanese population.

  Study JGAS000259

• 86 paired-end MiSeq 16S rRNA sequencing samples

  We compared bacterial communities in breast milk from teen (≤19 yr, n = 26) vs. adult (>19 yr, n = 56) mothers, normal weight (BMI 18.5-24.9, n = 63) vs. overweight (BMI ≥ 25, n = 19) mothers, primiparous (parity = 1, n = 41) vs. multiparous (parity > 1, n = 44), early (5-46d postpartum, n = 39) vs. established lactation (4-6 mo postpartum, n = 45), breastfeeding (EBF: PBF, n = 72) vs. mixed feeding (n = 11) and mothers with (Na/K ratio < 0.6, n = 75) and without SCM (Na/K ration ≥ 0.6, n = 10).

  Dataset EGAD00001004160

• APOBEC Breast Cancer Whole Genome

  Five tumor-normal human breast cancer cases driven by APOBEC mutagenesis, including normal tissue, primary, and metastatic samples for each patient.

  Dataset EGAD50000001275

• Single cell sequencing of mild and critical COVID19 PBMC

  Single-cell RNA sequencing of 13 ‘mild-moderate’ and 10 ‘critical’ COVID19 PBMC samples

  Dataset EGAD00001006997

• Single Nuclei RNA sequencing batch 1

  This dataset includes the first 9 PTC samples and 6 ATC samples profiled on the same sequencing flowcell.

  Dataset EGAD00001011366

• Somatic genetic basis of Wilms' tumour

  We investigated the somatic genetic basis of Wilms' tumour and found complex phylogenetic relations between tumours

  Dataset EGAD00001005136

• WES data of serially passaged TIC-enriched spheres of colorectal cancer

  WES data of serially passaged TIC-enriched spheres of colorectal cancer (CRC)

  Dataset EGAD00001006266

• Highly complex single-cell mixture of 5 individuals of high cell number

  Mixture of 5 unrelated individuals sequenced by 10x as a scATAC-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile using the De-goulash pipeline. The separation file is submitted as the processed file. The bam are submitted as unprocessed files.

  Dataset EGAD50000000480

• EATL-II STUDY

  Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole exome sequencing of 15 EATL-II tumor-normal tissue pairs. The tumor suppressor gene SETD2 encoding a non-redundant H3K36-specific trimethyltransferase is altered in 14/15 cases (93%), mainly by loss-of-function mutations and/or loss of the corresponding locus (3p21.31). These alterations consistently correlate with defective H3K36 trimethylation. The JAK/STAT pathway comprises recurrent STAT5B (60%), JAK3 (46%) and SH2B3 (20%) mutations, including a STAT5B V712E activating variant. Additionally, frequent mutations in TP53, BRAF and KRAS are observed. Conversely, in EATL-I, no SETD2, STAT5B or JAK3 mutations are found, and H3K36 trimethylation is preserved. This study describes SETD2 inactivation as EATL-II molecular hallmark, supports EATL-I and -II being two distinct entities, and defines potential new targets for therapeutic intervention.

  Study EGAS00001001879

• Whole genome sequencing of intestinal metaplasia

  We generated whole genome sequencing data from 15 pairs of IM and matched normal. The dataset contains cram files from 30 samples.

  Dataset EGAD50000001539

• WGBS data of Atypical teratoid/rhabdoid tumors (ATRT)

  WGBS data of Atypical teratoid/rhabdoid tumors (ATRT)

  Dataset EGAD00001002137

• Chad genetic diversity reveals an African history marked by multiple Holocene Eurasian migrations

  Whole-genome sequencing data from Chad and Lebanon.

  Dataset EGAD00001002742

• Sequencing of pancreatic cancer primary tumors and metastases

  The extent of heterogeneity of driver gene mutations present in naturally occurring metastases is largely unknown, i.e. treatment-naïve metastatic disease. To address this issue, 60x whole genome sequencing of 26 metastases from 4 patients was carried out. We found that the identical driver gene mutations were present in every metastatic lesion of each patient studied. Passenger gene mutations not known or predicted to have functional consequences accounted for all intratumoral heterogeneity. Even with respect to these passenger gene mutations, the genetic similarity among the founding cells of metastases was markedly higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of driver gene mutations among metastases in the same patient has critical, encouraging implications for the success of future targeted therapies in advanced stage disease.

  Study EGAS00001002186

• Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic

  Somatic mutations of RUNX1, which encodes the myeloid and lymphoid transcriptional factor RUNX1, are common in both B- and T- acute lymphoid leukemia (ALL) and are associated with poor prognosis of T-ALL. However, there has been no comprehensive investigation of the pattern or prevalence of RUNX1 germline mutation in both B- and T-ALL. Here we report germline RUNX1 variants in 1.23% of B-ALL and 2.11% of T-ALL, identifying 31 unique variants in 62 B-ALL and 18 unique variants in 26 T-ALL children. The majority of frameshift and nonsense variants affected RUNX1 function in transcriptional regulation, hematopoiesis, and cellular proliferation. We identified JAK3 as the most frequent somatic mutation in T-ALL with RUNX1 variants. These results not only identify RUNX1 as a leukemia predisposition gene but also further underline the importance of germline genetic variants to the development of ALL

  Study EGAS00001005403