Copy number, loss of heterozygosity and amplification detection in formalin-fixed paraffin-embedded melanocytic lesions using molecular inversion probes

s 473 GenArray: uncovering novel and recurrent chromosomal alterations with diagnostic and prognostic value in hematological malignancies Annette Leon , Joseph Marino , Kenneth Moreno , Rev Obrera , Swaroop Aradhya , Wendy Chung , Jim Weisberger a GenPath, BioReference Laboratories Inc., Elmwood Park, NJ, USA Traditional cytogenetic techniques such as chromosome analysis and FISH have provided valuable genetic information for the evaluation of hematological malignancies. However, many genomic abnormalities remain undetected due to the limitations intrinsic to these techniques. Recently, the introduction of DNA array-based technologies has enabled the identification of previously undetected copy number changes with an increased resolution and sensitivity and a more precise determination of genomic break points and gene content. We have designed, validated and clinically applied a combined targeted-whole genome custom oligonucleotide microarray for the evaluation of hematological malignancies. The use of this technology not only allowed us to confirm genetic alterations identified by chromosome analysis or FISH, but also enabled the detection of novel genomic imbalances with important diagnostic and prognostic value in myeloid, lymphoid and plasma cell disorders. Several copy number alterations were observed in karyotypically normal patients allowing the discovery of potential tumor suppressor genes or oncogenes important in the pathogenesis of several hematological neoplasms such as myelodysplastic syndrome, multiple myeloma and chronic lymphocytic lymphoma. Our work also emphasizes the importance of incorporating this technology into current algorithms for the diagnosis of cancer. Conflict of Interest: The authors are employees and stockholders in GenPath BioReference Laboratories, Inc. Copy number, loss of heterozygosity and amplification detection in formalin-fixed paraffinembedded melanocytic lesions using molecular inversion probes Leslie R. Rowe , Wells Chandler , Mona Jahromi , Joshua D. Schiffman , Sarah T. South a University of Utah and ARUP Laboratories, Salt Lake City, UT, USA A significant number of melanocytic lesions are called indeterminate for malignancy using standard diagnostic techniques. For these cases, a sensitive and robust molecular method that provides multiple data points predictive of tumorigenicity would be useful. Previous molecular studies have demonstrated characteristic copy number alterations in melanoma. We have used molecular inversion probe (MIP) technology (OncoScan , Affymetrix) to identify and characterize genomic alterations in formalin-fixed, paraffinembedded (FFPE) melanocytic lesions. Sixty-four melanocytic lesions (23 benign nevi, 11 melanocytic lesions of uncertain malignant potential (MLUMP), 27 primary melanoma, 3 metastatic melanoma) were identified for this study. Genomic DNA was isolated from tissue scrolls and processed onto a 330,000 feature MIP microarray. No benign nevi demonstrated copy number alterations associated with melanoma. However, copy number alterations characteristic of melanoma were identified in 24/27 primary (89%) melanoma samples, including gain of 1q, 6p, 7p, 7q and 11q and loss of 6q, 9p, 9q, 10p, 10q, 11q, and 17p. Copy number changes were also identified in 4/11 (36%) MLUMP samples including loss of 1p, 2p, 6q, 7p and chromosomes 3, 9 and 17. Loss of heterozygosity (LOH) was identified in both MLUMP and melanoma samples. Additionally, amplification of CCND1, CKS1B and MYC genes was identified in a subset of the melanoma samples. In summary, we have employed a single molecular platform, using the OncoScan array, to generate information on copy number changes, LOH and amplification in melanocytic lesions. This approach will be useful to classify future melanocytic lesions with unknown malignant potential.