LTP2 Results Analysis-Herman-UPittsburgh 2024

Abbreviated Name
LTP2 Results Analysis-Herman-UPittsburgh 2024
Lead Investigator
Herman, James — University of Pittsburgh School of Medicine
Coordinating Investigator
Zheng, Yingye — Fred Hutchinson Cancer Center
Involved Investigators

Abstract

No abstract availalbe.

Aims

Direct, real-time MSP (qMSP). Methylation of individual loci will be performed. We will utilize cancer-specific methylation loci and a control locus (beta actin) for comparison and quantitation, determined by detecting analyte (loci and ACTB) with real-time MSP using molecular beacons. These csDNA methylation markers consisted of parallel amplification/quantification using specific primer and detector pairs for each analyte using the CFX96 Touch Real-Time PCR Detection System | Life . (BioRad Laboratories, Hercules, CA). The methylation promoter sequence detects methylated sequence, while ACTB for normalization uses methylation independent primers. The amplicon is chosen to be ~100 bp for loci and is 103 bp for ACTB. Duplicate or triplicate PCR amplifications are analyzed using iQuant 3.0 software (BioRad), exported as Ct values, and used to calculate methylation quantities. Locus and Primer Selection. Loci will be chosen based upon cancer-specific methylation and absence of methylation in normal tissues, and we will specifically examine normal lung tissues and normal lympohocytes (to exclude blood contamination by lymphocytes). This approach has been successfully used in generating the preliminary data shown above. Our initial evaluation will utilize the already promising loci described in our recent publication, with conditions as described: CDO1, TAC1, HOXA7, and SOX17. If additional loci are required, new assays will be developed based upon the approaches we have published using TCGA data.

Analytic Method

No analytic method available.

Publications

  • No publications available at this time for this protocol.

Biomarkers

  • No biomarkers available at this time for this protocol.

Data Collections

  • No data collections available at this time for this protocol.
Protocol ID
554
Protocol Type
Reference Set
Fields of Research
  • Genomics
Collaborative Group
Lung and Upper Aerodigestive Cancers Research Group
Cancer Types
  • Malignant neoplasm of bronchus and lung

Associated Forms