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• Breast_Cancer_Sequential_Sampling_Targeted_Capture

  This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Study EGAS00001000596

• Mutation_burden_in_sun_exposed_eyelid__MSSE_

  Eyelid skin from blepharoplasty surgery will be collected from patients of different ethnic origin (Chinese, Malay, Indian and Caucasion) exposed to tropical sunshine. 2mm2 biopsies will be collected and DNA sequenced using a specific bait capture set and at high depth. The aim is to try and see if different mutations expand in different ethnic populations.

  Study EGAS00001002512

• Bleeding

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who exhibit severe bleeding with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000106

• Whole-genome and transcriptome sequencing of tumor-stage mycosis fungoides

  Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL), a group of malignancies derived from skin-homing malignant T cells. We subjected tumor biopsies from MF patients to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001002860

• Whole genome sequencing of Japanese HCCs

  To determine somatic mutation profiles and substitution signatures in Japanese HCC, we performed whole genome sequencing of 31 HCCs with various epidemiological backgrounds. Somatic mutations and rearrangements were determined as previously reported. The data will be deposited to the ICGC database and is used for further comparative and integrative analyses.

  Study EGAS00001000671

• Partially methylated domains across multiple cell types

  Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them.

  Study EGAS00001003157

• Validation_of_AML_Mutational_Screening

  We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose.

  Study EGAS00001000430

• The genomic landscape of primary cutaneous anaplastic large cell lymphoma (pcALCL)

  Primary cutaneous anaplastic large cell lymphoma (pcALCL) is the second most common variant of cutaneous T-cell lymphoma. We subjected tumor biopsies from patients with pcALCL to whole-genome sequencing, whole-exome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001004429

• Various_Platelet_Disorders

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who have a platelet disorder with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000107

• Dense_fine_mapping_study_identifies_new_susceptibility_loci_for_primary_biliary_cirrhosis

  2,981 primary biliary cirrhosis (PBC) cases were collected by the UK PBC Consortium and genotyped on the Illumina Immunochip where 2,861 passed quality control. These cases were then compared to a UK population control to identify novel PBC risk loci and fine-map association signals. (Liu & Almarri et al., Nat Genet, 2012)

  Study EGAS00001001837