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Options for Formalin-Fixed, Paraffin-Embedded (FFPE)-derived DNA
CIDR offers genotyping services for specimens that have been formalin-fixed, paraffin-embedded (FFPE). The FFPE process for specimen retention leads to nucleic acid degradation. Illumina has introduced a QC protocol (based on QPCR), restoration protocol and an optimized Infinium HD Assay to maximize genotyping results. The assay is currently optimized to be used in conjunction with the Illumina Human OmniExpress array for GWA studies and the Illumina 450K Infinium Methylation array.
CIDR has experience using the restoration protocol on both highly degraded blood-derived genomic DNA and DNA extracted from serum with very good success. Please inquire with any questions.
In general >80% of samples passing QC achieve call rates over 90%.
Information regarding GWAS Studies can be found on the Genome Wide Association page.
Array * |
SNPs |
Samples |
Non- |
Comments |
>693,000 |
12 |
0 |
Excellent coverage of common SNPs in Caucasian and Asian populations. 60% overlap in rs numbers with previous Illumina arrays; provides coverage of 97% of cancer genes identified by the Sanger Cancer Genome Project. |
|
>450,000 |
12 |
0 |
99% coverage of RefSeq genes and 96% CpG islands |
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Research Technologist, Amanda Welk, pipettes samples.
See our Services page for a full description of what is included for all study types
See our Sample Requirements page for detailed specifications for each product