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• Phase IB/II Study of Bazedoxifene in Combination with Palbociclib in Patients with Endocrine Resistant Hormone Receptor-Positive Breast Cancer

  In this phase Ib/II clinical trial, the investigators evaluated the efficacy and safety of the combination of palbociclib with bazedoxifene in patients with a metastatic endocrine-resistant hormone receptor-positive, HER2-negative breast cancer. Furthermore, whole exome sequencing of cell-free tumor DNA was done on serial samples from these patients, revealing potential molecular changes associated with mechanisms of resistance.

  Study phs002802

• Pilot Sequencing Study: DNA Hydroxymethylation and Gene Expression in Peripheral Blood Mononuclear Cells in Healthy Human Aging

  This study was a pilot analysis of samples of human peripheral blood mononuclear cell (PBMCs) from 10 young (23-30 years) and 10 older (68-76 years) healthy Caucasian female volunteers. Whole genome sequencing was performed to assess multiple epigenetic mechanisms and gene expression, including 5hmC-capture sequencing and RNA-sequencing, followed by integrative analyses to identify regions and genes associated with age.

  Study phs001916

• Genomic sequencing of Ewing's Sarcoma

  The Ewing sarcoma family of tumors (EFT) is a group of malignant small round blue cell tumors that arise in bone or soft tissue. Ewing sarcoma (ES) is the second most common type of primary bone tumor to affect children and adolescents and accounts for 2.9% of all childhood cancers. This data set reports whole-genome sequencing of 6 primary Ewing's Sarcoma samples and matching germline samples.

  Study phs000768

• Epigenetic Mechanisms of Inflammation and Fatigue in Head and Neck Cancer

  This was a longitudinal observational study to examine the association between fatigue and DNA methylation as well as gene expression among patients with head and neck cancer. Demographic and clinical variables were collected before chemoradiotherapy and/or at follow-up visits as appropriate. Fatigue was assessed and biosamples (for DNA methylation and gene expression) were collected before, immediately after, and at six- and twelve-months post-chemoradiotherapy.

  Study phs002106

• Cellular Origins and Genetic Landscape of Cutaneous GD T Cell Lymphoma

  Cutaneous gamma-delta T cell lymphomas are a rare and aggressive subtype of cutaneous lymphoma. In the present study, we analyzed these cancers by DNA and RNA sequencing in order to illuminate the genetic landscape for this rare disease. We obtained tumor samples from multiple institutions, including Northwestern University (Chicago, IL), University of Chicago (Chicago, IL), University of Virginia (Charlottesville, VA), and Massachusetts General Hospital (Boston, MA).

  Study phs001969

• Genome-Wide Approach to Measure Variant-Based Heritability of Drug Outcome Phenotypes

  Current pharmacogenetic approaches often use a few large-effect alleles to predict drug outcomes. However, many drug outcome phenotypes are determined by complex pathways that may be influenced by common single-nucleotide variants (SNVs) across the genome. We ascertained how much variation in drug response is explained by common SNVs for pharmacokinetic (drug levels) and pharmacodynamic phenotypes (highest creatinine) for 4 drugs: vancomycin, gentamicin, cyclosporine and tacrolimus.

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• Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

  Lymphomas are a prevalent and heterogeneous family of cancers arising in cells of the immune system. Drivers of lymphomagenesis include genomic rearrangements that juxtapose active regulatory elements with specific oncogene targets, as well as mutations affecting specific transcription factors and chromatin regulatory proteins. This study seeks to combine genome-wide genetic and epigenetic datasets to better understand mechanisms of oncogene dysregulation across distinct lymphoma types.

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• Collaborative Association Study of Psoriasis

  The goal of this collaborative study is to combine the resources and expertise of three groups with long-standing studies of psoriasis genetics in order to identify new genetic susceptibility factors for psoriasis, a common inflammatory skin disease that affects over 4 million Americans. Consent groups and participant set General research use (GRU): 1677 (950 cases, 692 controls, 35 others) Autoimmune disease (AD): 1198 (449 cases, 734 controls, 15 others)

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• Dana-Farber Cancer Institute (DFCI) Brown Lab CLL Sequencing Study

  Chronic Lymphocytic Leukemia (CLL) is a hematological malignancy characterized by accumulation of CD5+CD19+ B cells in peripheral lymphoid organs, bone marrow and blood. In this study we analyze matched whole genome sequencing and RNA-seq data from CLL patients to characterize the mutational processes operative throughout tumor evolution. Source of tumor and normal DNA used is patient PBMC or B cells and saliva respectively.

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• Non-Coding Mutations Cause Enhancer Targeting Resulting in Protein Synthesis Dysregulation During B-Cell Lymphoma Progression

  In this study, we performed whole-genome sequencing of longitudinal tumor pairs, representing transformation of follicular lymphoma (FL) to high grade B-cell lymphoma with MYC and BCL2 rearrangements (known as "double hit lymphoma" or DHL), a very aggressive class of non-Hodgkin B cell lymphoma (B-NHL). We identified coding and noncoding genomic alterations acquired during the course of lymphoma progression.

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