Utility of Whole-Genome SNP Microarrays in Renal Tumors: Diagnostic Implications
Selene Koo, Agata Minor, Poluru Reddy, Loren Joseph, Carrie Fitzpatrick, Tatjana Antic, Maria Tretiakova. University of Chicago, Chicago, IL
Background: Conventional cytogenetics has provided a useful adjunct to traditional morphological categorization of renal cell carcinomas (RCC), particularly in histologically ambiguous cases, as the various subtypes have characteristic chromosomal abnormalities. More recently, single nucleotide polymorphism (SNP) microarrays have been shown to complement karyotyping with whole-genome copy number data at high resolution and copy number-neutral loss of heterozygosity (LOH). Few studies have investigated RCC cases with equivocal histology, instead focusing on the common RCC subtypes. In this study, we use SNP microarrays to investigate the genetic profiles of RCCs with conventional and ambiguous morphologies.
Design: Genomic DNA was isolated from twelve fresh frozen RCC specimens and a case of oncocytosis, and processed according to the standard protocol for Affymetrix Genome-Wide Human SNP Array 6.0. Acquired data were analyzed using the Affymetrix Chromosome Analysis Suite.
Results: LOH and copy number analysis data are summarized in the table.
|Tumor type||Chromosomal alterations consistent with published SNP microarray data||Novel chromosomal alterations|
|Clear cell (n=4)||+1q, +2p, +2, -3p, LOH 4q, +5q, +7q, +8q, +12q, LOH 16p, +16p, LOH 16q, +16, LOH 18q||+1p, -4q, -4, -5q, -8p, -9q, +10p, +10q, -13, -14q, +18q, +20, -21q|
|Chromophobe (n=2)||-1, -1p, -2, -6, -10, -13, -17, -20q, -21||-2q, -3, -9|
|Papillary (n=3)||+3, +7, +12, +16, +17, +21||+1q, LOH 3, LOH 8q, -11q, -18, +20, -22, -Y|
|Oncocytosis (n=1)||-1||+7, -Y|
|TFE3 (n=2)||No abnormalities|
|Clear cell papillary (n=1)||No abnormalities|