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• exome sequence of female patients suffering from Ovarian Meiotic Defects

  Exome sequencing was performed on 15 unrelated female patients suffering from primary infertility due to Ovarian Meiotic Defects (OMD). Each reference number corresponds to one of the tested subject. DNA was extracted from Saliva using Oragene saliva DNA collection kit (DNAgenotek Inc., Ottawa, Canada).Exome capture was performed with the Agilent V5 kit and sequencing was performed on Illumina HiSeq 2000.

  Dataset EGAD00001004035

• Whole genome sequencing of metastatic cutaneous squamous cell carcinoma

  This dataset includes somatic small variant calling files derived from fifteen metastatic samples from cutaneous squamous cell carcinoma matched to normal blood samples. These samples were whole-genome sequenced by HiSeq X Ten and the resulting reads were mapped against the human genome (hg37) using BWA-MEM 0.7.10-r789. Somatic variant calling was then performed using strelka 1 (version 2.0.17).

  Dataset EGAD00001004530

• Highly differentiated, fusion-negative rhabdomyosarcoma.

  Sequencing was performed using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 genes, previously linked to human cancer. Sequencing wa sperformed on an Illumina HiSeq 2500. 14 highly differentiated, fusion-negative rhabdomyosarcoma tumor samples, and 8 non-matched normal skeletal muscle samples weer sequenced. BAM files are available for download.

  Dataset EGAD00001003746

• POT1 splice site mutant analysis

  We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient.

  Dataset EGAD00001000786

• Exome sequencing data from tumor progression cohort

  This dataset, named Stockholm tumor progression cohort, contains exome-sequencing samples of matched primary and metastasis samples from 20 metastatic breast cancer patients. All patients have one or more sequenced normal samples as well. The total number of samples is 125. The dataset has been used, apart from other studies, to explore tumor evolution patterns in metastatic breast cancer at Karolinska Institute Stockholm.

  Dataset EGAD00001003837

• WGS dataset for Unraveling mutagenic processes influencing the tumor mutational patterns of individuals with Constitutional Mismatch Repair Deficiency

  Molecular characterization of 41 tumors from 17 individuals with CMMRD to gain a better understandig of mutational processes driving subsequent tumor development. The molecular characterization includes the investigation of tumor mutational load and mutational signatures.

  Dataset EGAD00001015157

• Molecular Characterization for Nasopharyngeal Carcinoma (NPC)

  Total RNA was isolated from 50 formalin-fixed paraffin-embedded nasopharyngeal cancer (NPC) specimens using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Tumor RNA libraries were prepared with 200ng RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold, and sequenced with >80 million 100 bp paired-end reads.

  Dataset EGAD00001009047

• Whole Exome Sequencing of Oro-Gastrointestinal tract cancers

  54 samples consisting of COAD, ESCC, GA and OSCC

  Dataset EGAD00001008455

• RNA-sequencing of a normal CD34+ cells

  Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.

  Dataset EGAD00001007646

• CGH Array

  DNA samples were extracted from peripheral blood lymphocytes using commercially available kit (Puregene Core Kit A, Qiagen) according to manufacturer's protocol. Agilent SurePrint G3 Human CGH Microarray 180K platform was used for screening of copy number aberrations (CNAs) using array-CGH protocol recommended by manufacturer (Agilent Technologies), data mining and interpretation of array-CGH results was performed in same manner as in our previously published results.

  Dataset EGAD00001007743