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PGN Services in Molecular Epidemiology

I. Study Design Consultation
Contact Dr. Simin Liu

II. Genotyping Service

I.1. ABI Prism Taqman Allelic Discrimination Assay
Applied Biosystems's (ABI) Taqman® Assay is performed using ABI Prism 7900 HT Sequence Detection System, which allows single-plex SNP interrogation through fluorescence detection in real-time PCR.

I.2. Quality Assurance
For SNPs with existing assays, please contact Lab Manager Yuko ­You:

For new SNP assays, trial primer and assay design will be carried out and a trial genotyping run performed. Depending on those results, we will either proceed with full-scale genotyping or consider alternative genotyping methods as necessary. Quality control procedures include repeat genotyping of at least 5% of DNA samples. Genotype results are provided to the user in electronic format. Extensive bioinformatics support for our Core Facility is in place.

III. DNA Extraction and Sample Handling Service
DNA extraction is performed using QIAmp Blood Kit (Qiagen, Inc.). We have been successful extracting DNA from WBCs, whole blood, blood spots, residual red cell samples and buccal cells. We currently use the Qiagen company protocol which yields high quality DNA in 200ul of buffer ranging from 5-50ng/ul. The concentration and plating or tube storage is included in the cost. We have 3 robots that assist in protocol set up and sample plating.


Yuko You
Lab Manager
Program on Genomics and Nutrition
CHS 1-425A
Department of Epidemiology, UCLA
Los Angeles, CA 95172
Phone: (310) 206-7512
Fax:(310) 206-6039
Email: yuko@ucla.edu 

IV. Clinical Microarray Core (CMC)
With state-of-the-art instruments, the CMC offers a wide range of genomics services and continuously develops new services when needs are identified. Current services include:

* Pre-experiment consultation
* Whole Transcriptome sequencing (RNA-Seq)
* Small RNA sequencing (miRNA-Seq)
* Whole exon sequencing
* Targeted resequencing
* Methylation sequencing (Methy-Seq)
* Chromatin Immunoprecipitation sequencing (ChIP-Seq)
* Large-scale gene expression profiling
* SNP genotyping
* Genome-level copy number variation analysis
* Genome-level methylation and chip-chip analysis
* miRNA profiling
* QRT-PCR confirmation
* RNA/DNA quality evaluation
* Advanced data analysis
* Data analysis software tutorial and consultation
* Assistance with grant applications and publications
* Post experiment support, including developing integrated strategies for following-up microarray experiments
* Educational training

For more information, please visit CMC's website or Applied Biomics.


Xinmin Li, Ph.D
UCLA Clinical Microarray Core
650 Charles Young Drive, CHS 38-123
Los Angeles, CA 90095
Mail Code: 173517
Phone: (310) 825-3664 ♦ Fax: (310) 825-3570
Email: cmc@mednet.ucla.edu