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Background The identification of molecular alterations that trigger Wilms tumor (WT) development is crucial to understanding the tumorigenesis of this malignancy. Currently, it is estimated that WTX and WT1 genomic losses together with CTNNB1 point mutations occur in about 30% of WTs. However, the majority of cases remain without any identified driver mutation. Results from a previous study by our group pointed to APC and PLCG2 as candidate genes altered in WT [1]. Given the advent of modern DNA sequencing technologies, it is now feasible to evaluate large genomic regions spanning complete genes (exons and introns), allowing the description of the mutation patterns occurring in tumor cells. Thus, the aim of this study was to identify point mutations and indels in the complete sequence of APC, CTNNB1, WT1, WTX and PLCG2 genes in order to characterize both the exonic mutational spectrum and the intronic nucleotide substitution pattern. Material and methods The complete genomic regions of the selected genes, spanning a total of 430 kb, were amplified by long-range PCR in 15 WTs and 3 non-neoplasic control samples, giving a total of 60 amplicons per sample (10 kb on average). The resulting amplicons were mixed at equimolar concentrations and, for each sample, the Ion PGM library preparation protocol was performed. The libraries of the 18 barcoded samples were combined in four sequencing pools that were individually submitted to an Ion PGM™ Sequencer run on an Ion 316™ Chip. Point mutation and indels not present in the non-neoplasic controls were selected for capillary sequencing validation. The validated

Background Genome-wide profiling of rare tumors is crucial for improvement of diagnosis, treatment, and, consequently, achieving better outcomes. Desmoplastic small round cell tumor (DSRCT) is a rare type of sarcoma arising from mesenchymal cells of abdominal peritoneum that usually develops in male adolescents and young adults. A specific translocation, t(11;22)(p13;q12), resulting in EWS and WT1 gene fusion is the only recurrent molecular hallmark and no other genetic factor has been associated to this aggressive tumor. Here, we present a comprehensive genomic profiling of one DSRCT affecting a 26-year-old male, who achieved an excellent outcome. Methods We investigated somatic and germline variants through whole-exome sequencing using a family based approach and, by array CGH, we explored the occurrence of genomic imbalances. Additionally, we performed mate-paired whole-genome sequencing for defining the specific breakpoint of the EWS-WT1 translocation, allowing us to develop a personalized tumor marker for monitoring the patient by liquid biopsy. Results We identified genetic variants leading to protein alterations including 12 somatic and 14 germline events (11 germline compound heterozygous mutations and 3 rare homozygous polymorphisms) affecting genes predominantly involved in mesenchymal cell differentiation pathways. Regarding copy number alterations (CNA) few events were detected, mainly restricted to gains in chromosomes 5 and 18 and losses at 11p, 13q, and 22q. The deletions at 11p and 22q indicated the presence of the classic translocation, t(11;22)(p13;q12). In addition, the mapping of the specific genomic breakpoint of the EWS-WT1 gene fusion allowed the design of a personalized biomarker for assessing circulating tumor DNA (ctDNA) in plasma during patient follow-up. This biomarker has been used in four post-treatment blood samples, 3 years after surgery, and no trace of EWS-WT1 gene fusion was detected, in accordance with imaging tests showing no evidence of disease and with the good general health status of the patient. Conclusions Overall, our findings revealed genes with potential to be associated with risk assessment and tumorigenesis of this rare type of sarcoma. Additionally, we established a liquid biopsy approach for monitoring patient follow-up based on genomic information that can be similarly adopted for patients diagnosed with a rare tumor. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0092-0) contains supplementary material, which is available to authorized users.

Background Wilms tumor (WT) has a not completely elucidated pathogenesis. DNA copy number alterations (CNAs) are common in cancer, and often define key pathogenic events. The aim of this work was to investigate CNAs in order to disclose new candidate genes for Wilms tumorigenesis. Results Array-CGH of 50 primary WTs without pre-chemotherapy revealed a few recurrent CNAs not previously reported, such as 7q and 20q gains, and 7p loss. Genomic amplifications were exclusively detected in 3 cases of WTs that later relapsed, which also exhibited an increased frequency of gains affecting a 16.2 Mb 1q21.1-q23.2 region, losses at 11p, 11q distal, and 16q, and WT1 deletions. Conversely, aneuploidies of chromosomes 13 and 19 were found only in WTs without further relapse. The 1q21.1-q23.2 gain associated with WT relapse harbours genes such as CHD1L, CRABP2, GJA8, MEX3A and MLLT11 that were found to be over-expressed in WTs. In addition, down-regulation of genes encompassed by focal deletions highlighted new potential tumor suppressors such as CNKSR1, MAN1C1, PAQR7 (1p36), TWIST1, SOSTDC1 (7p14.1-p12.2), BBOX and FIBIN (11p13), and PLCG2 (16q). Conclusion This study confirmed the presence of CNAs previously related to WT and characterized new CNAs found only in few cases. The later were found in higher frequency in relapsed cases, suggesting that they could be associated with WT progression. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0227-y) contains supplementary material, which is available to authorized users.