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Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
Implementation of high resolution single nucleotide polymorphism array analysis as a clinical test for patients with
Margaret J Dougherty1, Donna M Wilmoth, Laura S Tooke
1Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Cancer Genetics
|March 2, 2011
Summary
Single nucleotide polymorphism arrays detect genomic aberrations in pediatric hematologic malignancies, revealing previously unseen genetic changes. These arrays are a valuable addition to standard cytogenetic methods for improved diagnostic accuracy.
Area of Science:
- Genomics
- Oncology
- Molecular Diagnostics
Background:
- Single nucleotide polymorphism (SNP) arrays are established research tools for detecting genomic copy number changes and allelic imbalance in various cancers.
- Their high resolution, genome-wide coverage, minimal DNA needs, and rapid turnaround time make them suitable for clinical applications.
Purpose of the Study:
- To validate the Illumina HumanHap550 BeadChip array for clinical use in pediatric hematologic malignancies.
- To assess the utility of SNP arrays in identifying genetic aberrations not detected by conventional cytogenetic methods.
Main Methods:
- Validation of the Illumina HumanHap550 BeadChip array using 127 pediatric leukemia and lymphoma samples previously characterized by standard cytogenetics and fluorescence in situ hybridization.
- Subsequent clinical testing using the higher-resolution Illumina HumanHap610 BeadChip array on 180 pediatric hematologic malignancy samples.
- Analysis of genomic aberrations, including deletions and copy number neutral loss of heterozygosity.
Main Results:
- The SNP array identified aberrations in 130 out of 180 (72%) clinical samples that were not detected by standard karyotyping.
- Commonly identified deletions involved genes critical to B- or T-cell malignancies, such as CDKN2A/B, PAX5, and IKZF1.
- Copy number neutral loss of heterozygosity was detected in 49 samples, with 75 regions identified above a 5 Mb threshold.
Conclusions:
- Single nucleotide polymorphism arrays are a valuable tool for detecting genomic abnormalities in pediatric hematologic malignancies.
- SNP arrays enhance, but do not replace, standard cytogenetic approaches in the clinical setting.
- The technology offers higher resolution and detects a broader range of genetic alterations compared to traditional methods.
