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Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using
Rajesh R Singh1, Meenakshi Mehrotra1, Hui Chen2
1Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
The Journal of Molecular Diagnostics : JMD
|July 10, 2016
Summary
Molecular inversion probe (MIP) arrays effectively detect gene copy number aberrations (CNAs) in solid tumors using low-quality DNA. This validated method offers sensitive, accurate, and reproducible CNA screening for clinical diagnostics.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Diagnostics
Background:
- Gene copy number aberrations (CNAs) are key drivers of solid tumors.
- Detecting CNAs in formalin-fixed, paraffin-embedded (FFPE) samples is challenging due to DNA quality and quantity limitations.
Purpose of the Study:
- To validate a molecular inversion probe (MIP) array for routine clinical screening of CNAs in solid tumors.
- To assess the utility of MIP arrays for detecting genome-wide CNAs using low-input FFPE DNA.
Main Methods:
- Utilized a MIP array targeting 900 cancer-related genes.
- Tested on 76 solid tumors and 4 cancer cell lines with varying cellularity (20-100%).
- Compared MIP array results with orthogonal techniques like next-generation sequencing and fluorescence in situ hybridization.
Main Results:
- MIP array results showed high concordance with orthogonal methods.
- The array detected CNAs in clinically significant genes (e.g., ERBB2, EGFR, KRAS).
- Demonstrated high sensitivity, accuracy, reproducibility, and FFPE compatibility.
Conclusions:
- The MIP array is a sensitive and accurate clinical platform for routine solid tumor CNA screening.
- It provides valuable information, including loss of heterozygosity, with efficient turnaround times.
- The array is suitable for low-input FFPE DNA, overcoming common diagnostic challenges.
