Abstract 925: Whole exome analysis of myelodysplastic syndromes
Authors: Yoshida Kenichi , Sanada Masashi , Nagata Yasunobu , Kawahata Ryoichiro , Kato Motohiro , Matsubara Aiko , Takita Jyunko , Mori Hiraku , Nowak Daniel , Hofmann Wolf-Karsten , Ishikawa Takayuki , Ishiyama Ken , Miyawaki Shuichi , Obara Naoshi , Chiba Shigeru , Ogawa Seishi 
Published: June 2012

Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous groups of myeloid neoplasms characterized by multi-lineage cytopenias of varying degrees and transition to acute myeloid leukemia (AML). At present, no curative therapeutics for MDS has been established except for allogeneic hematopoietic stem-cell transplantation, which is not applicable to the majority of the MDS patients due to their higher ages. Thus, to improve the outcome of MDS, it is essential to develop novel therapeutic agents with both high efficacy and low toxicity, and to this goal, the discovery of the key molecules for MDS pathogenesis is of particular importance. To date, a number of gene mutations have been identified and implicated in the pathogenesis of MDS, including NRAS, TP53, RUNX1, c-CBL, TET2, ASXL1, and more recently, IDH1, IDH2 and EZH2. However, in view of therapeutic targets, our current knowledge of disease causing mutations in MDS is still incomplete.
Recently, next-generation resequencing technologies have been shown to be effective for the identification of disease-related gene and been successfully used to determine the genetic basis of some neoplastic disorders, such as AML and diffuse large B-cell lymphoma. More recently, the resequencing technology targeted for all protein-coding subsequences (i.e., whole exome analysis) has enabled cost-effective comprehensive mutation analysis of coding sequences. In this study, to obtain a complete registry of genetic lesions in MDS and to identify novel therapeutic targets, we performed whole exome analysis for novel mutations using high-throughput resequencing technologies, combined with large-scale screening of mutations in candidate genes using barcode-labeled DNA for a panel of ∼200 MDS samples.
Whole exome analysis was performed for 20 MDS samples, where entire exon sequences were enriched by using SureSelect Human All Exon kit (Agilent Technologies) and were subjected to resequencing analysis using Genome Analizer IIx (Illumina). More than 60% of mapped reads contained exon sequences. &gt; 80% of exons were sequenced at the depth of &gt;20 and average fold-coverage was &gt;50 times. Given that the constitutive genomic DNA was difficult to obtain in MDS patients, paired CD3-positive T cells were used as a normal control. By comparing sequences in tumors and paired T cells, 8 somatic mutations and one insertions-deletion per patient were detected. Novel gene targets were also explored by resequencing barcord-labeled DNAs from 200 MDS specimens, which targeted 80 candidate genes for MDS. A number of mutations were identified, including those in IDH2, ASXL1, TET2, EZH2 and novel target genes such as PHF6, which has been reported to be mutated in T-ALL previously. Our results suggested that target-capture resequencing technology is a powerful method to identify new gene mutations that are implicated in the pathogenesis of MDS.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 925. doi:10.1158/1538-7445.AM2011-925