The goal of the Yale Center for Genome Analysis (YCGA) is to rapidly and cost-effectively bring state-of the- art genomic technologies within reach of largest possible number of cancer investigators. YCGA occupies 7,000 ft^ of newly constructed, custom-designed laboratory space and is well equipped with several microarray (Affymetrix, lllumina, Sequenom and NimbleGen) and high throughput sequencing (10 lllumina hiiSeqs, one each of PacBio RS, MiSeq and Ion Torrent) platforms. Sequencing operation is supported by 1000 CPU/core cluster and 2 PB data storage. All aspects of sequence data generation, including sample collection, library preparation, sequence data and billing are tracked using WikiLIMS system which is an online, flexible, scalable and password-protected database. YCGA staff from microarray, sequencing and bioinformatics sections will provide an extremely expert and highly dedicated team that will ensure the success of research goals of cancer investigators. The YCGA provides >30 genomic services including: 1) gene expression and whole transcriptome analysis, 2) SNP genotyping and copy number variation, 3) whole-exome and whole-genome sequence analysis, 4) analysis of formalin-fixed paraffin embedded tissue, 5) methylation analysis, 6) miRNA analysis and discovery and 7) chromatin immunoprecipitation to study protein-DNA interactions. Together, the microarray and HT sequencing technologies of YCGA offer comprehensive support to study genetic events in cancer, which has the potential to aid in identification of genetic and biochemical causes of the disease, develop better diagnostic methods, and improve therapeutic outcomes and patient care. Strengths of this application include the extensive expertise, infrastructure, and instrumentation in the YCGA;the experience of PI in overseeing the recent U54-suported Yale Centre for Mendelian Disorder;a strong publication record and the experience of YCGA at providing state-of-the-art microarray, HT sequencing, biostatistical/bioinformatics and other technologies on a service charge basis to several Yale and non-Yale investigators. In addition to providing genomic services, the YCGA staff will consult as needed on experimental design, data interpretation, manuscript preparation, and grant application preparation, and will provide training for primary data analysis to YCC members. During FY 2012, 72 YCC investigators using YCGA Resource services accounted for 49% of the 20,148 provided services.

Public Health Relevance

The Yale Center for Genome Analysis provides cancer investigators a state-of-the-art centralized facility required for carrying out large-scale genomic analyses that would not otherwise be possible in their own laboratories. The genomic data generated at the YCGA is helping cancer scientists to better understand the genetic basis of cancer that will ultimately lead to new approaches for cancer treatment and prevention.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA016359-35
Application #
8755635
Study Section
Subcommittee G - Education (NCI)
Project Start
Project End
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
35
Fiscal Year
2014
Total Cost
$124,875
Indirect Cost
$49,875
Name
Yale University
Department
Type
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
06520
Ols, Michelle L; Cullen, Jaime L; Turqueti-Neves, Adriana et al. (2016) Dendritic Cells Regulate Extrafollicular Autoreactive B Cells via T Cells Expressing Fas and Fas Ligand. Immunity 45:1052-1065
Gale, Molly; Sayegh, Joyce; Cao, Jian et al. (2016) Screen-identified selective inhibitor of lysine demethylase 5A blocks cancer cell growth and drug resistance. Oncotarget 7:39931-39944
Ducker, Gregory S; Chen, Li; Morscher, Raphael J et al. (2016) Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway. Cell Metab 23:1140-53
Adams, Brian D; Wali, Vikram B; Cheng, Christopher J et al. (2016) miR-34a Silences c-SRC to Attenuate Tumor Growth in Triple-Negative Breast Cancer. Cancer Res 76:927-39
Santin, Alessandro D; Bellone, Stefania; Buza, Natalia et al. (2016) Regression of Chemotherapy-Resistant Polymerase ε (POLE) Ultra-Mutated and MSH6 Hyper-Mutated Endometrial Tumors with Nivolumab. Clin Cancer Res 22:5682-5687
de Haydu, Christopher; Black, Jonathan D; Schwab, Carlton L et al. (2016) An update on the current pharmacotherapy for endometrial cancer. Expert Opin Pharmacother 17:489-99
Hollander, Lindsay; Guo, Xiaojia; Velazquez, Heino et al. (2016) Renalase Expression by Melanoma and Tumor-Associated Macrophages Promotes Tumor Growth through a STAT3-Mediated Mechanism. Cancer Res 76:3884-94
Zhao, Siming; Bellone, Stefania; Lopez, Salvatore et al. (2016) Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial-mesenchymal transition. Proc Natl Acad Sci U S A 113:12238-12243
Park, Sin-Aye; Lee, Jong Woo; Herbst, Roy S et al. (2016) GSK-3α Is a Novel Target of CREB and CREB-GSK-3α Signaling Participates in Cell Viability in Lung Cancer. PLoS One 11:e0153075
Stein, Stacey M; James, Edward S; Deng, Yanhong et al. (2016) Final analysis of a phase II study of modified FOLFIRINOX in locally advanced and metastatic pancreatic cancer. Br J Cancer 114:737-43

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