CI-FISH, GEP, and SNPs Correlate Genomic Categories with Risk Stratification in Children with T-ALL

• Published in: Blood 2012-11, Vol.120 (21), p.2485-2485
• Main Authors: la Starza, Roberta, Lettieri, Antonella, Pierini, Valentina, Matteucci, Caterina, Nofrini, Valeria, Gorello, Paolo, Songia, Simona, Crescenzi, Barbara, te Kronnie, Geertruy, Giordan, Marco, Leszl, Anna, Valsecchi, Maria Grazia, Aversa, Franco, Basso, Giuseppe, Biondi, Andrea, Conter, Valentino, Cazzaniga, Giovanni, Mecucci, Cristina
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood.V120.21.2485.2485

Abstract 2485 T-cell acute lymphoblastic leukemia (T-ALL) is caused by multiple lesions affecting genes involved in cell cycle control, proliferation, survival and differentiation. Type A abnormalities are driving events in the leukemogenic process; they are mutually exclusive genomic rearrangements, mainly translocations, which delineate specific T-ALL subgroups such as the TAL/LMO, TLX1, TLX3, and HOXA (MLL, CALM-AF10, and SET-NUP214). Type B abnormalities, on the other hand, are much greater in number and cooperate with different molecular lesions, as they are widespread in diverse genetic subgroups. They include genomic imbalances, chromosome translocations and mutations. To confront the heterogeneity of T-ALL associated genomic lesions we used CI-FISH, SNP and GEP, explored their utility as potential diagnostic tools in pediatric T-ALL and correlated the genetic lesions at diagnosis with the Minimal Residual Disease (MRD) clinical stratification. We examined 51 children with T-ALL enrolled in Italy into the AIEOP-BFM ALL2000 protocol; MRD was performed by RQ-PCR monitoring of IG and TCR clonal rearrangements at days 33 and 78. Based on tumor load levels at both time points, patients were classified as MRD standard (MRD-SR), intermediate (MRD-IR) or high risk (MRD-HR)(Schrappe M, et al. Blood 2011;118:2077-84). Combined Interphase FISH (CI-FISH) was done using a panel of probes for 42 candidate genes. Cases with TCR-rearrangements were investigated for partners; aneuploidies were confirmed with probes for the centromeric alpha satellite regions. Single Nucleotide Polymorphism (SNP) arrays were done with Whole-Genome Cytogenetic 2.7M array (Affymetrix, Santa Clara, CA, USA) following the manufacturer’s protocol. Data were analyzed by Chromosome Analysis Suite (ChAS) Software (Affymetrix) with hg19 genome built (http://genome.ucsc.edu/) as reference. Copy number (CN) filters were set at ≥ 20 markers and ≥ 30kb size for losses, ≥50kb for gains, and ≥ 2Mb for CNN-LOH. Gene expression profiles (GEP) (Affymetrix HU-133 Plus 2.0 arrays) were obtained following previously described protocols. Data were normalized with Robust Multi-array Avarage algorithm (RMA). Prediction was performed using the method Prediction Analysis of Microarrays (PAM): a threshold for the selection of predictive probe sets was established using cross validation. This procedure was used to predict and compare classification of 34 cases with CI-FISH and 6 samples for which CI-FISH was no