AIMS Genetics, 2015, 2(4): 263-280. doi: 10.3934/genet.2015.4.263.

Research article

Export file:


  • RIS(for EndNote,Reference Manager,ProCite)
  • BibTex
  • Text


  • Citation Only
  • Citation and Abstract

Pros and cons of HaloPlex enrichment in cancer predisposition genetic diagnosis

1 Institut Curie, Département de Biopathologie, Paris, France;
2 Institut Curie, Inserm U830, Paris, France;
3 Institut Curie, Paris, France;
4 Inserm U900, Paris, France;
5 Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France;
6 Université Paris Descartes, Sorbonne Paris Cité, Paris, France;
7 Faculté des Sciences pharmaceutiques et biologiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France

Panel sequencing is a practical option in genetic diagnosis. Enrichment and library preparation steps are critical in the diagnostic setting. In order to test the value of HaloPlex technology in diagnosis, we designed a custom oncogenetic panel including 62 genes. The procedure was tested on a training set of 71 controls and then blindly validated on 48 consecutive hereditary breast/ovarian cancer (HBOC) patients tested negative for BRCA1/2 mutation. Libraries were sequenced on HiSeq2500 and data were analysed with our academic bioinformatics pipeline. Point mutations were detected using Varscan2, median size indels were detected using Pindel and large genomic rearrangements (LGR) were detected by DESeq. Proper coverage was obtained. However, highly variable read depth was observed within genes. Excluding pseudogene analysis, all point mutations were detected on the training set. All indels were also detected using Pindel. On the other hand, DESeq allowed LGR detection but with poor specificity, preventing its use in diagnostics. Mutations were detected in 8% of BRCA1/2-negative HBOC cases. HaloPlex technology appears to be an efficient and promising solution for gene panel diagnostics. Data analysis remains a major challenge and geneticists should enhance their bioinformatics knowledge in order to ensure good quality diagnostic results.
  Article Metrics

Keywords HaloPlex; cancer; predisposition; genetic diagnosis; next generation sequencing; gene panel

Citation: Agnès Collet, Julien Tarabeux, Elodie Girard, Catherine Dubois DEnghien, Lisa Golmard, Vivien Deshaies, Alban Lermine, Anthony Laugé, Virginie Moncoutier, Cédrick Lefol, Florence Copigny, Catherine Dehainault, Henrique Tenreiro, Christophe Guy, Khadija Abidallah, Catherine Barbaroux, Etienne Rouleau, Nicolas Servant, Antoine De Pauw, Dominique Stoppa-Lyonnet, Claude Houdayer. Pros and cons of HaloPlex enrichment in cancer predisposition genetic diagnosis. AIMS Genetics, 2015, 2(4): 263-280. doi: 10.3934/genet.2015.4.263


  • 1. Sie AS, Prins JB, van Zelst-Stams WG, et al. (2015) Patient experiences with gene panels based on exome sequencing in clinical diagnostics: high acceptance and low distress. Clin genet 87: 319-326.    
  • 2. Tarabeux J, Zeitouni B, Moncoutier V, et al. (2014) Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model. Eur j hum genet 22: 535-541.    
  • 3. Domchek SM, Bradbury A, Garber JE, et al. (2013) Multiplex genetic testing for cancer susceptibility: out on the high wire without a net? J clin oncol 31: 1267-1270.    
  • 4. Easton DF, Pharoah PDP, Antoniou AC, et al. (2015) Gene-Panel Sequencing and the Prediction of Breast-Cancer Risk. N engl j med 372: 2243-2257.    
  • 5. Audeh MW, Carmichael J, Penson RT, et al. (2010) Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and recurrent ovarian cancer: a proof-of-concept trial. Lancet 376: 245-251.    
  • 6. Guttmacher AE, McGuire AL, Ponder B, et al. (2010) Personalized genomic information: preparing for the future of genetic medicine. Nat rev genet 11: 161-165.
  • 7. Houdayer C, Caux-Moncoutier V, Krieger S, et al. (2012) Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum mutat 33: 1228-1238.    
  • 8. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat meth 9: 357-359.    
  • 9. Li H, Handsaker B, Wysoker A, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.    
  • 10. Koboldt DC, Zhang Q, Larson DE, et al. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome res 22: 568-576.    
  • 11. Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucl acids res 38: e164-e164.    
  • 12. Ye K, Schulz MH, Long Q, et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865-2871.    
  • 13. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome biol 11: R106.    
  • 14. Mertes F, ElSharawy A, Sauer S, et al. (2011) Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief funct genomics 10: 374-386.    
  • 15. Coonrod EM, Durtschi JD, VanSant WC, et al. (2014) Next-generation sequencing of custom amplicons to improve coverage of HaloPlex multigene panels. Biotechniques 57: 204-207.
  • 16. Claes KBM, De Leeneer K (2014) Dealing with pseudogenes in molecular diagnostics in the next-generation sequencing era. Methods mol biol 1167: 303-315.    
  • 17. Gréen A, Gréen H, Rehnberg M, et al. (2015) Assessment of HaloPlex Amplification for Sequence Capture and Massively Parallel Sequencing of Arrhythmogenic Right Ventricular Cardiomyopathy-Associated Genes. J mol diagn 17: 31-42.    
  • 18. Crobach S, Ruano D, van Eijk R, et al. (2015) Target-enriched next-generation sequencing reveals differences between primary and secondary ovarian tumors in formalin-fixed, paraffin-embedded tissue. J mol diagn 17: 193-200.    
  • 19. Goecks J, Nekrutenko A, Taylor J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome biology 11: R86.    
  • 20. Blankenberg D, Kuster GV, Coraor N, et al. (2001) Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. In: Current Protocols in Molecular Biology. John Wiley & Sons, Inc.; 2001. Available from:
  • 21. Giardine B, Riemer C, Hardison RC, et al. (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome res 15: 1451-1455.    
  • 22. O'Rawe J, Jiang T, Sun G, et al. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome med 5: 28.    


This article has been cited by

  • 1. E. Santana dos Santos, S. M. Caputo, L. Castera, M. Gendrot, A. Briaux, M. Breault, S. Krieger, P. K. Rogan, E. J. Mucaki, L. J. Burke, I. Bièche, C. Houdayer, D. Vaur, D. Stoppa-Lyonnet, M. A. Brown, F. Lallemand, E. Rouleau, Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition, Breast Cancer Research and Treatment, 2017, 10.1007/s10549-017-4602-0
  • 2. Amélie Chaussade, Gaël Millot, Constance Wells, Hervé Brisse, Marick Laé, Alexia Savignoni, Laurence Desjardins, Rémi Dendale, François Doz, Isabelle Aerts, Irène Jimenez, Nathalie Cassoux, Dominique Stoppa Lyonnet, Marion Gauthier Villars, Claude Houdayer, Correlation between RB1 germline mutations and second primary malignancies in hereditary retinoblastoma patients treated with external beam radiotherapy, European Journal of Medical Genetics, 2018, 10.1016/j.ejmg.2018.07.017
  • 3. Alvaro Gallego-Martinez, Teresa Requena, Pablo Roman-Naranjo, Jose A. Lopez-Escamez, Excess of Rare Missense Variants in Hearing Loss Genes in Sporadic Meniere Disease, Frontiers in Genetics, 2019, 10, 10.3389/fgene.2019.00076

Reader Comments

your name: *   your email: *  

Copyright Info: 2015, Claude Houdayer, et al., licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (

Download full text in PDF

Export Citation

Copyright © AIMS Press All Rights Reserved