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• The Influence of Gut Microbiota on the Speciation and Toxicity of Mercury During Pregnancy

  There are few studies that have characterized maternal gut microbiota and fetal methylmercury exposure, yet microbes likely modulate this relationship. The primary objective of our pilot study was to determine associations between gut microbial taxa and mercury concentrations in multiple biomarkers (stool, hair, and cord blood). Our secondary objective was to determine the contribution of gut microbial mercury methylation to stool methylmercury.

  Study phs000970

• Canadian prostate cancer samples (CPC-GENE) for PanProstate study

  CPC-GENE has sequenced the genomes of 350 intermediate risk prostate cancers to identify genetic signatures that differ in cancers that responded well to treatment compared with those that did not. CPC-GENE also has sequenced multiple regions of prostate cancer from the same gland to determine if and how the genetic make-up of prostate cancer varies within an individual man’s prostate

  Study EGAS00001003037

• ET_Exome

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Essential Thrombocythemia Myeloproliferative Disease samples and matched normal DNA from the same patients. Samples will be multiplexed in one lane of Illumina HiSeq. Sequencing to a coverage of at least 30x will be performed and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000102

• Mutant_clone_mapping_in_normal_oesohagus_and_skin_2

  We will use targeted exome sequencing to examine normal appearing oesophageal epithelium and skin to determine the mutational burden. DNA will be extracted from epithelia of a defined size and we will overlay positional information from the epithelial pieces to give clone maps over a wide area. This will be done in both oesophageal epithelium and skin

  Study EGAS00001005659

• Targeted sequencing (paired) of HR genes in primary and metastatic patient-derived xenografts (PDXs) of colorectal cancer (CRC)

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we leveraged a comprehensive collection of 69 molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. Genetic analyses revealed that treatment sensitivity was marked by genomic scars indicative of BRCAness, suggesting homologous recombination (HR) deficiency as a key determinant. Accordingly, we surveyed a manually curated panel of 44 genes with a documented role in HR for the potential presence of pathogenic mutations. We did not observe a specific enrichment of HR gene mutations based on response to FOLFIRI. This result, combined with the absence of widespread biallelic inactivation of the analyzed genes and the predominance of mutations categorized as variants of unknown significance, suggests that FOLFIRI sensitivity is not primarily governed by underlying mutations in HR genes responsible for mitigating the genotoxic effects of this therapeutic regimen.

  Study EGAS50000000075

• Determination of cell specific regulatory enhancers in hematopoetic models

  The BLUEPRINT project is a large-scale project investigating epigenetic mechanisms involved in blood formation, in health and disease. The human variation workpackage (WP10, led by NS) of the project seeks to characterize the effect of common sequence variation on the epigenome status of a cell. To do this, the project will use highly purified blood cells to minimise "experimental noise" and therefore enhance the power to discover modest effects. Two peripheral blood cell types, the CD14+CD16- monocyte (an important central orchestrator of adaptive immunity and a bridge between innate and adaptive immunity) and the CD65+CD9- neutrophilic granulocyte (the frontline cell for innate immunity) have been selected for this purpose. The two types of cells will be obtained at high purity from adult blood (AB) of 200 healthy males and females, respectively. Cells will be purified by using already validated and fully operational protocols that are based on density gradient centrifugation of the buffy coat obtained from whole blood, followed by magnetic bead-based purification using monoclonal antibodies against Cluster of Differentiation (CD) lineage-specific cell surface markers. Units of 475 ml of AB will be obtained from consenting volunteers of the Cambridge BioResource (CBR), a panel of 10,000 healthy volunteers local to Cambridge who have already consented to participate in biomedical research and of whom biological samples (DNA, plasma, serum) and lifestyle data have been deposited in a repository and database, respectively. We are requesting funding from the Human Diversity project to sequence the genomes of the 200 CBR volunteers at low pass (6x coverage). Nuclei, DNA and RNA will be recovered from the purified cells and made available for RNA-seq, DNA-seq and ChIP-seq and genomic DNA for entire genome sequencing will be recovered from the DNA repository.

  Dataset EGAD00001002205

• Strabismus, CCDD and other anomalies

  Strabismus is one of the most common ophthalmological diseases affecting our population. It has many detrimental effects for affected individuals, including functional visual loss from amblyopia, secondary psychosocial difficulties, and limited employment opportunities. Strabismus also imposes a significant economical burden on society from the cost of screening programs, surgical correction, and lost productivity. Congenital incomitant strabismus is a broad term that encompasses congenital ocular motility disorders with restricted movement in one or more directions of gaze, and includes various forms of Duane's retraction syndrome, horizontal gaze palsy, congenital fibrosis of extraocular muscles, and Moebius syndrome. Incomitant strabismus together with a group of related disorders such as congenital ptosis and congenital facial palsy have been collectively redefined as congenital cranial dysinnervation disorders (CCDDs). This redefinition stemmed from previous studies in the Engle lab showing that these disorders can be caused by mutations in genes encoding transcription factors critical to ocular cranial motor neuron development and by genes that encode proteins essential to the proper growth and guidance of developing axons. Thus, while these disorders account for only a small percent of strabismus, understanding their genetic etiology has led to our ability to provide genetic testing and counseling, and has provided the first insights into the molecular etiologies of strabismus. While the Engle lab has identified all seven CCDD genes published to date, our cohort still includes >100 familial CCDD pedigrees that are mutation-negative. We continue to utilize co-segregation analysis and whole exome or whole genome sequencing technologies to identify new disease genes in this mutation-negative cohort.

  Study phs000478

• The Genetic and Transcriptomic Evolution of Melanoma

  The overarching goal of the study was to better understand the evolution of melanoma. To do this, we collected archival tissue of melanomas adjacent to their intact, remnant precursor lesions. We also collected archival tissue of primary melanomas and their matching metastases. From the formalin-fixed paraffin-embedded (FFPE) blocks, we microdissected non-neoplastic (normal), precursor, and descendent portions of tissue. Both RNA and DNA were extracted from the microdissected tissues and subjected to next generation sequencing. In summary, we performed matched DNA/RNA sequencing of melanoma/precursor/normal trios, allowing us to trace the genetic and transcriptomic evolution of melanoma.

  Study phs001550

• Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions

  Chromosomal inversions (INV) are particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage sensitive genes in cis. Short-read genome sequencing (srGS) can only resolve ~70% of cytogenetically visible inversions referred to clinical diagnostic laboratories, likely due to breakpoints in repetitive regions. Here we study twelve inversions by srGS (n=3) or long read genome sequencing (lrGS) (n=9)

  Study EGAS50000000436

• STAT5 is a therapeutically targetable vulnerability in cutaneous T-cell lymphoma

  Cutaneous T-cell lymphomas represent a heterogeneous group of lymphoproliferative disorders characterized by the infiltration and expansion of mature malignant T-cells into the skin. The disease encompasses distinct variants such as mycosis fungoides a skin resident variant, in which the malignant cells are restricted to skin lesions, and leukemic variant sézary syndrome characterized by circulating malignant T-cells. Here we integrated shallow whole genome sequencing and whole exome sequencing, on samples from four sézary syndrome patients and two advanced mycosis fungoides patients with blood involvement, to characterize genetic alterations and assess their therapeutic actionability. We identified an elevated copy number of 17q, resulting in increased STAT5 expression and activation, as a key factor in the pathophysiology of the disease.

  Study EGAS00001004719