A. Schefler and D. Abramson, Update on retinoblastoma, Retina, 2004.

R. Bagatell, M. Beck-popovic, W. B. London, Y. Zhang, D. J. Andrew et al., Amplification in International Neuroblastoma Staging System Stage 1 and 2 Neuroblastoma: A Report From the International Neuroblastoma Risk Group Database, Journal of Clinical Oncology, vol.27, issue.3, pp.365-370, 2009.
DOI : 10.1200/JCO.2008.17.9184

T. P. Benjamini and . Speed, Summarizing and correcting the GC content bias in high-throughput sequencing, Nucleic Acids Research, vol.40, issue.10, p.2012
DOI : 10.1093/nar/gks001

V. Boeva, A. Zinovyev, K. Bleakley, J. Vert, I. Janoueix-lerosey et al., Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization, Bioinformatics, vol.27, issue.2, pp.268-269, 2011.
DOI : 10.1093/bioinformatics/btq635

H. Carén, H. Kryh, M. Nethander, R. Sjöberg, C. Träger et al., Highrisk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset, Proceedings of the National Academy of Sciences, vol.10, issue.1079, pp.4323-4328, 2010.

A. Cazes, C. Louis-brennetot, P. Mazot, F. Dingli, B. Lombard et al., Characterization of Rearrangements Involving the ALK Gene Reveals a Novel Truncated Form Associated with Tumor Aggressiveness in Neuroblastoma, Cancer Research, vol.73, issue.1, pp.195-204, 2013.
DOI : 10.1158/0008-5472.CAN-12-1242

X. Locke, R. S. Shi, T. J. Fulton, R. K. Ley, L. Wilson et al., Breakdancer: an algorithm for high-resolution mapping of genomic structural variation, Nat Methods, vol.6, issue.9, pp.677-681, 2009.

J. Thomas-derrien, S. M. Estell, D. G. Sola, E. Knowles, R. Raineri et al., Fast Computation and Applications of Genome Mappability, PLoS ONE, vol.39, issue.Suppl 1, p.30377, 2012.
DOI : 10.1371/journal.pone.0030377.t002

[. Melvin, Genome duplication, 2011.

M. De-lima, S. S. Strom, M. Keating, H. Kantarjian, S. Pierce et al., Implications of potential cure in acute myelogenous leukemia: development of subsequent cancer and return to work, Blood, issue.12, pp.904719-4724, 1997.

A. Tubio, M. Martnez-fundichely, M. Cceres, S. Gut, X. Ossowski et al., Pesv-fisher: identification of somatic and non-somatic structural variants using next generation sequencing data, PLoS One, vol.8, issue.5, p.63377, 2013.

V. Josep, A. Forment, S. P. Kaidi, and . Jackson, Chromothripsis and cancer: causes and consequences of chromosome shattering, Nat Rev Cancer, vol.12, issue.10, pp.663-670, 2012.

. Li, Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence, Gene, vol.259, issue.1 2, pp.81-88, 2000.

[. Hormozdiari, C. Alkan, E. E. Eichler, and . Sahinalp, Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

[. Hatem, D. Bozda, A. E. Toland, and M. V. , Benchmarking short sequence mapping tools, BMC Bioinformatics, vol.14, issue.1, p.184, 2013.
DOI : 10.1186/1471-2164-13-74

I. Hhd-+-10-]-fereydoun-hormozdiari, P. Hajirasouliha, F. Dao, D. Hach, C. Yorukoglu et al., Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery, Bioinformatics, vol.26, issue.12, pp.350-357, 2010.
DOI : 10.1093/bioinformatics/btq216

R. E. Handsaker, J. M. Korn, J. Nemesh, and S. A. Mccarroll, Discovery and genotyping of genome structural polymorphism by sequencing on a population scale, Nature Genetics, vol.467, issue.3, pp.269-276, 2011.
DOI : 10.1101/gr.078212.108

C. [. Harchaoui and . Lvy-leduc, Catching change-points with lasso, Adv. Neural Inform . Process. Syst, vol.20, p.617624, 2008.

J. Hu, Y. Yuan, J. Shi, B. Lu, Z. Liu et al., pIRS: Profile-based Illumina pair-end reads simulator, Bioinformatics, vol.28, issue.11, pp.281533-1535, 2012.
DOI : 10.1093/bioinformatics/bts187

I. Iakovishina, E. Janoueix-lerosey, M. Barillot, V. Regnier, and . Boeva, SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability, Bioinformatics, vol.32, issue.7, 2015.
DOI : 10.1093/bioinformatics/btv751
URL : https://hal.archives-ouvertes.fr/hal-01217891

Y. Jiang, Y. Wang, and M. Brudno, PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants, Bioinformatics, vol.28, issue.20, pp.282576-2583, 2012.
DOI : 10.1093/bioinformatics/bts484

J. O. Korbel, A. Abyzov, X. J. Mu, N. Carriero, P. Cayting et al., PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data, Genome Biology, vol.10, issue.2
DOI : 10.1186/gb-2009-10-2-r23

R. M. Layer, C. Chiang, A. R. Quinlan, and I. M. Hall, LUMPY: a probabilistic framework for structural variant discovery, Genome Biology, vol.15, issue.6, p.84, 2014.
DOI : 10.1186/gb-2014-15-6-r84

[. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.
DOI : 10.1093/bioinformatics/btp324

A. W. Kevin and . Lee, Ewings family oncoproteins: drunk, disorderly and in search of partners, Cell Research, 2007.

[. Li, J. Ruan, and R. Durbin, Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Research, vol.18, issue.11
DOI : 10.1101/gr.078212.108

R. James and . Lupski, Charcot-marie-tooth polyneuropathy: Duplication, gene dosage, and genetic heterogeneity, Pediatric Research, vol.45, pp.159-165, 1998.

M. Gad, U. Landau, and . Vishkin, Ecient string matching with k mismatches, Theoretical Computer Science, vol.43, pp.239-249, 1986.

S. Moncunill, S. Gonzalez, L. O. Be, I. Andrieux, C. Salaverria et al., Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads, Nature Biotechnology, vol.32, issue.11, pp.321106-1112, 2014.
DOI : 10.1101/gr.092759.109

[. Medvedev, M. Stanciu, and M. Brudno, Computational methods for 106 BIBLIOGRAPHY discovering structural variation with nextgeneration sequencing, Nat Methods, vol.6, issue.11

R. E. Mills, K. Walter, C. Stewart, R. E. Handsaker, K. Chen et al., Mapping copy number variation by population-scale genome sequencing, Korbel, and 1000 Genomes Project, pp.47059-65, 2011.
DOI : 10.1038/nature09708

W. Eugene and . Myers, Ano (nd) di?erence algorithm and its variations, Algorithmica, vol.1, issue.1- 4, pp.251-266, 1986.

M. O. , N. Rivlin, R. Brosh, and V. Rotter, Mutations in the p53 tumor suppressor gene, Genes Cancer, 2011.

. D. Okm-+-92-]-j, K. W. Oliner, P. S. Kinzler, D. L. Meltzer, B. George et al., Amplification of a gene encoding a p53-associated protein in human sarcomas, Nature, issue.6381, pp.35880-83, 1992.

L. Oesper, A. Ritz, S. J. Aerni, R. Drebin, and B. J. Raphael, Reconstructing cancer genomes from paired-end sequencing data, BMC Bioinformatics, vol.13, issue.Suppl 6, p.10, 2012.
DOI : 10.1093/bioinformatics/bth931

[. Ferragina, Opportunistic data structures with applications, Proceedings 41st Annual Symposium on Foundations of Computer Science, 2000.
DOI : 10.1109/SFCS.2000.892127

T. Popova, E. Mani, D. Stoppa-lyonnet, G. Rigaill, E. Barillot et al., Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays, Genome Biology, vol.10, issue.11, pp.10-128, 2009.
DOI : 10.1186/gb-2009-10-11-r128
URL : https://hal.archives-ouvertes.fr/inserm-00663915

E. D. Pleasance, P. J. Stephens, S. O. Meara, D. J. Mcbride, A. Meynert et al., A small-cell lung cancer genome with complex signatures of tobacco exposure, Nature, vol.34, issue.7278, pp.463184-190, 2010.
DOI : 10.1038/nature08629

J. Qi and F. Zhao, inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data, Nucleic Acids Research, vol.39, issue.suppl, pp.567-575, 2011.
DOI : 10.1093/nar/gkr506

[. Md-;-brian, J. Druker, M. Kurzrock, M. Hagop, M. Kantarjian et al., Philadelphia chromosomepositive leukemias: From basic mechanisms to molecular therapeutics, Ann Intern Med, 2003.

T. Rausch, T. Zichner, A. Schlattl, A. M. Sttz, V. Benes et al., DELLY: structural variant discovery by integrated paired-end and split-read analysis, Bioinformatics, vol.28, issue.18, pp.28-333, 2012.
DOI : 10.1093/bioinformatics/bts378

M. Soda, Y. Lim-choi, M. Enomoto, S. Takada, Y. Yamashita et al., Identification of the transforming EML4???ALK fusion gene in non-small-cell lung cancer, Nature, vol.276, issue.7153, pp.561-566, 2007.
DOI : 10.1038/nature05945

M. A. Teague, J. Quail, H. Burton, N. P. Swerdlow, L. A. Carter et al., Massive genomic rearrangement acquired in a single catastrophic event during cancer development, Cell, vol.144, issue.1, pp.27-40, 2011.

G. Boyle, M. Macintyre, R. W. Cmero, R. W. Tothill, M. Johnstone et al., Socrates: identification of genomic rearrangements in tumour genomes by realigning soft clipped reads, Bioinformatics, 2014.

C. D. Mudie, M. Greenman, C. Jia, J. W. Latimer, K. W. Teague et al., Complex landscapes of somatic rearrangement in human breast cancer genomes, Nature, issue.7276, pp.4621005-1010, 2009.

S. S. Sindi, S. Onal, L. C. Peng, H. Wu, and B. J. Raphael, An integrative probabilistic model for identification of structural variation in sequencing data, Genome Biology, vol.13, issue.3, p.22, 2012.
DOI : 10.1093/bioinformatics/btp324

[. Trappe, A. Emde, H. Ehrlich, K. Reinert, and . Gustaf, Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone, Bioinformatics, vol.30, issue.24, pp.3484-3490, 2014.
DOI : 10.1093/bioinformatics/btu431

J. Todd, S. L. Treangen, and . Salzberg, Repetitive dna and next-generation sequencing: computational challenges and solutions Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis, Nat Rev Genet PLoS One, vol.13, issue.1, pp.36-46, 2012.

[. Wong, T. M. Keane, J. Stalker, and D. J. Adams, Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly, Genome Biology, vol.11, issue.12, pp.11-128, 2010.
DOI : 10.1186/gb-2010-11-12-r128

C. G. Wang, J. Mullighan, S. Easton, S. L. Roberts, J. Heatley et al., CREST maps somatic structural variation in cancer genomes with base-pair resolution, Nature Methods, vol.8, issue.8, pp.652-654, 2011.
DOI : 10.1101/gr.078212.108

L. J. Yang, N. Luquette, R. Gehlenborg, P. S. Xi, C. Haseley et al., Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes, Cell, vol.153, issue.4, pp.919-929, 2013.
DOI : 10.1016/j.cell.2013.04.010

Z. Seungtai-yoon, V. Xuan, K. Makarov, J. Ye, and . Sebat, Sensitive and accurate detection of copy