Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

Area of Science:

• Genomics
• Oncology
• Bioinformatics

Background:

• High-density oligonucleotide microarrays are used for genome-wide single nucleotide polymorphism (SNP) detection and array comparative genomic hybridization (array CGH).
• These technologies are crucial for identifying copy number aberrations in human tumors, particularly bone tumors.

Purpose of the Study:

• To evaluate four commercial high-resolution microarray platforms for mapping DNA copy number aberrations in bone tumors.
• To identify the most suitable technology for analyzing complex karyotypes in bone tumors.

Main Methods:

• Testing DNA from two bone sarcoma cell lines with simple and complex karyotypes on four platforms: Affymetrix, Agilent, Illumina, and Nimblegen.
• Analyzing data using both platform-specific and platform-independent algorithms.
• Measuring DNA copy number at specific chromosomal regions and comparing with cytogenetic data.

Main Results:

• All platforms demonstrated good reproducibility and similar resolution for detecting amplifications and deletions.
• Agilent microarrays exhibited superior linearity and dynamic range.
• Platform-independent analysis yielded accurate copy numbers primarily for Agilent and Affymetrix platforms.

Conclusions:

• Agilent and Affymetrix microarray platforms are recommended for mapping DNA copy numbers in bone tumors due to their robust performance.
• Agilent offers better dynamic range, while Affymetrix provides additional heterozygosity information.
• These platforms are suitable for analyzing heterogeneous bone tumors with complex karyotypes.