Comparing Two Different Platforms for Analyzing Genomic DNA Micro-Array in Mental Retardation.
Aaron Leifer, Qiulu Pan. Montefiore Medical Center, Bronx, NY
Background: Most recently, genomic DNA micro-array technology has revolutionized the field of cytogenetics that previously championed karyotyping and FISH. With expanding probe numbers, micro-array is even more effective at identifying any type of segmental imbalance, of any size, on the entire genome. This study serves as a way to evaluate product performance of two commonly used platforms.
Design: Complete genomes of 40 patient's were first assessed using Agilent 4x44k arrays. Of the 40 patients, 16 were affected individuals with major copy number changes, 16 were affected individuals with no major abnormalities, and 8 were normal, unaffected parents. The same patients were then reexamined by using Illumina Human CytoSNP 12 bead chip array and software.
Results: In the 16 patients with major aberrations, Illumina did not confirm two phenotypically critical duplications that were found by Agilent. In the 16 patients without major aberrations and the 8 normal patients, Illumina and Agilent did not find any significant copy number changes. In addition, Illumina recognized 16 normal CNV regions that were not found previously by Agilent. Furthermore, Illumina alone identified 10 UPD regions in the same data set, 6 from phenotypically affected individuals and 4 from normal individuals, with a maximum size of 8.5 Mb.
Conclusions: The data was analyzed with Agilent and then repeated with Illumina. Of the 16 patients with major aberrations found by Agilent, Illumina missed two significant copy number changes. Additionally, Illumina, with a higher density of probes in the array, found more normal CNVs. As expected, Illumina, which utilizes SNP probes detected UPD regions, which were of unknown clinical significance. However, large UPD regions in our cohort were not identified.
Category: Special Category - Pan-genomic/Pan-proteomic approaches to Cancer
Monday, February 28, 2011 1:00 PM
Poster Session II # 244, Monday Afternoon