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Center for Medical Genomics
OVERVIEW
RESEARCH CONTRIBUTION HIGHLIGHTS
The Center for Medical Genomics facilitates cutting-edge
research with state-of-the-art genomic technologies for studying
gene expression and genetics, with the aim of improving health.
• Affymetrix microarray technology
Gene expression on a global scale
Tiling arrays
Genomic SNP arrays (if needed)
• SNP Genotyping, targeted at particular genes or regions
• Epigenetics (genome-wide with tiling arrays or targeted)
• Bioinformatics support for the above
RESOURCES and SERVICES
• Affymetrix microarray technology.
The Center for Medical Genomics is equipped with the latest
instrumentation from Affymetrix, capable of scanning all of their
currently available arrays. Affymetrix GeneChip microarrays can
measure expression of nearly all genes in humans, rats, mice and
most model organisms. We consult on experimental design. We
accept total RNA, and carry out all of the biochemistry, hybridization
and scanning, and return the data to the investigator. We can assist
with data analysis, which is a significant undertaking.
Affymetrix microarray technology
Measurement of global gene expression
• We have carried out the biochemistry for and scanned about 4500 Affymetrix
GeneChips, including human, mouse, rat and many model organisms.
• We have assisted many scientists with analysis of the complex datasets produced.
• These data have been part of many publications and grants in different areas.
Differentiation and development (animals, plants)
Treatment response (hepatitis C, vitamin A deficiency, UV)
Gene expression in different tissues (brain, lymphoblastoid cells)
Rat and mouse models of disease (alcoholism, schizophrenia, bipolar)
Disease susceptibility (Haemophilus ducreyi infection)
• We developed a method of improving the ratio of reproducible data to false
positives by screening out probe sets that are not expressed in a given cell or tissue
McClintick and Edenberg, 2006. BMC Bioinformatics 7: 49
• SNP Genotyping targeted at particular genes or
regions.
The Sequenom MassArray system is an excellent choice for
candidate gene studies in which much of the variation within the
candidate gene can be captured by tagging SNPs and functional
SNPs, and for following up results from genome-wide association
studies (GWAS) or fine-mapping after linkage studies. CMG
recently upgraded to a new iPLEX genotyping assay which allows
multiplexing of SNPs in the range of 20-30 per assay.
• Epigenetics
Targeted Epigenetics: Sequenom EpiTYPER. The CMG is
introducing a new assay for methylated C in specific regions of the
genome. We can make quantitative measurements of multiple
potential methylation sites within targeted regions of 200-400 bp
(smaller regions for FFPE samples).
There are pre-designed assays for imprinting studies and for
studies of selected genes important in cancer.
We can design assays for other genes or regions.
We can run Affymetrix tiling arrays (whole genome or promoters of
known genes) for ChIP-Chip studies to detect which sequences are
bound by a transcription factor, a methylated-DNA binding protein,
or modified histones. This provides a genome-wide assessment of
the epigenetic markings.
• Bioinformatics support for the above
We consult on experimental design for all of the kinds of
experiments we conduct. We are available for consultation and
collaboration on microarray data analysis and for SNP selection
and consultation on LD coverage for genotyping, and for design of
assays and targeting regions for epigenetic studies.
LIST OF SERVICES
Affymetrix microarray technology
Gene expression on a global scale
Tiling arrays
• SNP Genotyping, targeted at particular genes or regions
• Epigenetics (genome-wide with tiling arrays or targeted)
• Bioinformatics support for the above
includes: consultation on experimental design
collaboration on microarray data analysis
SNP selection and consultation on LD coverage
QUALITY CONTROL AND ASSURANCES
We follow carefully tested procedures.
Affymetrix GeneChip data quality is assessed with internal
controls and external validation:
1. We have tested many of the differentially expressed genes by
qRT-PCR and confirmed the vast majority (the expected
fraction, given the calculated False Discovery Rate)
2. For some experiments, we have run replications with results
that are very consistent.
Genotyping: the high quality is demonstrated both by
concordance of duplicates and testing segregation in family
samples.
SNP Genotyping
Targeted at candidate genes or regions
CONTACT INFORMATION
Follow-up of Genome Wide Association Studies or linkage studies
• We have generated about 13 million SNP genotypes to date
• These data have been part of many publications and grants in fields such as:
Alcoholism
Bipolar disorder
Osteoporosis
Hypertension
Director: Howard J. Edenberg, Ph.D. [email protected]
Primary Contacts
Gene Expression studies:
Jeanette McClintick, Ph.D. [email protected]
Howard Edenberg, Ph.D. [email protected]
Genotyping studies:
Xiaoling Xuei, Ph.D. [email protected]
Howard Edenberg, Ph.D. [email protected]
Epigenetics:
Xiaoling Xuei, Ph.D., Howard Edenberg, Ph.D
Ingenuity Pathways Assist:
Jeanette McClintick, Ph.D. [email protected]