YALE CENTER FOR GENOME ANALYSIS SHARED RESOURCE PROJECT SUMMARY/ABSTRACT The Yale Center for Genome Analysis (YCGA) was established in 2010 to provide next-generation sequencing (NGS), single-cell genomics, and microarray support forYCC members. The Center is a full-service facility dedicated to providing RNA expression profiling, DNA genotyping, and next-Gen DNA sequencing and related state-of-the-art technologies. Full microarray and next-generation sequencing services provided by YCGA include: DNA and RNA isolation from tissue and blood; sample preparation ready for microarray and next-Gen sequence (NGS) analysis; providing primary data; full-time YCC-supported staff for downstream bioinformatics data analysis, working collaboratively with YCC investigators and providing methods and other write-ups for grants. Additionally, the staff has obtained equipment and center grants to reduce the cost of sequencing. During the most recent funding period, 211 people have used YCGA Eighty-seven of these users (41%) were YCC members. The majority of this use came from Genomics, Genetics and Epigenetics (GGE). YCGA provides free consultation and training for YCC members. The core is led by Director Shrikant Mane, PhD, Professor of Genetics, whose experience is complemented by the strong expertise of Associate Director Kaya Bilguvar, MD, PhD.
The Specific Aims of YCGA are to provide: (1) Next-generation sequencing services using multiple sequencing platforms, including Illumina, Ion Torrent, and Pacific Biosciences; (2) Microarray services using Affymetrix and Illumina platforms for gene expression, genotyping, and methylation assays; (3) Single cell genomics and structural variation determination using the 10X Genomics platform; (4) Research and development. YCGA continuously carries out biotechnology research to develop improved methodologies and tools, to test the relative merits of new technologies, and to generate preliminary results for NIH grants. (5) Bioinformatics. Dr. Francesc Lopez supports the secondary analysis needs of YCC members. His salary is supported by YCC. (6) Consultation. YCGA makes every effort to develop collaborative relationships with its users, and takes interest in their scientific projects. (7) Education and training. Staff members actively participate in YCC Grand Rounds, departmental seminars, and YSM Dean?s workshops aimed at providing principles and technical details of the various genomic technologies.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
2P30CA016359-39
Application #
9570284
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2018-08-01
Budget End
2019-07-31
Support Year
39
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Yale University
Department
Type
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
Sarma, Elizabeth A; Kawachi, Ichiro; Poole, Elizabeth M et al. (2018) Social integration and survival after diagnosis of colorectal cancer. Cancer 124:833-840
Hartman, Douglas J; Ahmad, Fahad; Ferris, Robert L et al. (2018) Utility of CD8 score by automated quantitative image analysis in head and neck squamous cell carcinoma. Oral Oncol 86:278-287
Chen, Ling; Azuma, Takeshi; Yu, Weiwei et al. (2018) B7-H1 maintains the polyclonal T cell response by protecting dendritic cells from cytotoxic T lymphocyte destruction. Proc Natl Acad Sci U S A 115:3126-3131
Zhang, Jinhua; Song, Kun; Wang, Jun et al. (2018) S100A4 blockage alleviates agonistic anti-CD137 antibody-induced liver pathology without disruption of antitumor immunity. Oncoimmunology 7:e1296996
Kelada, Olivia J; Decker, Roy H; Nath, Sameer K et al. (2018) High Single Doses of Radiation May Induce Elevated Levels of Hypoxia in Early-Stage Non-Small Cell Lung Cancer Tumors. Int J Radiat Oncol Biol Phys 102:174-183
Powles, Ryan L; Redmond, David; Sotiriou, Christos et al. (2018) Association of T-Cell Receptor Repertoire Use With Response to Combined Trastuzumab-Lapatinib Treatment of HER2-Positive Breast Cancer: Secondary Analysis of the NeoALTTO Randomized Clinical Trial. JAMA Oncol 4:e181564
Wang, Shi-Yi; Hsu, Sylvia H; Huang, Siwan et al. (2018) Regional Practice Patterns and Racial/Ethnic Differences in Intensity of End-of-Life Care. Health Serv Res 53:4291-4309
Gettinger, S N; Choi, J; Mani, N et al. (2018) A dormant TIL phenotype defines non-small cell lung carcinomas sensitive to immune checkpoint blockers. Nat Commun 9:3196
Liu, Huafeng; Li, Xin; Hu, Li et al. (2018) A crucial role of the PD-1H coinhibitory receptor in suppressing experimental asthma. Cell Mol Immunol 15:838-845
Altwerger, Gary; Bonazzoli, Elena; Bellone, Stefania et al. (2018) In Vitro and In Vivo Activity of IMGN853, an Antibody-Drug Conjugate Targeting Folate Receptor Alpha Linked to DM4, in Biologically Aggressive Endometrial Cancers. Mol Cancer Ther 17:1003-1011

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