Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing: A Solution for Transferring Integrated Pangenomic Studies into Routine Practice?

Simon Garinet; Mario Néou; Bruno de La Villéon; Simon Faillot; Julien Sakat; Juliana P Da Fonseca; Anne Jouinot; Christophe Le Tourneau; Maud Kamal; Windy Luscap-Rondof; Valentina Boeva; Sebastien Gaujoux; Michel Vidaud; Eric Pasmant; Franck Letourneur; Jérôme Bertherat; Guillaume Assié

doi:10.1016/j.jmoldx.2017.06.005

Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing: A Solution for Transferring Integrated Pangenomic Studies into Routine Practice?

J Mol Diagn. 2017 Sep;19(5):776-787. doi: 10.1016/j.jmoldx.2017.06.005.

Authors

Simon Garinet¹, Mario Néou¹, Bruno de La Villéon¹, Simon Faillot¹, Julien Sakat², Juliana P Da Fonseca¹, Anne Jouinot¹, Christophe Le Tourneau³, Maud Kamal³, Windy Luscap-Rondof⁴, Valentina Boeva¹, Sebastien Gaujoux², Michel Vidaud⁵, Eric Pasmant⁵, Franck Letourneur¹, Jérôme Bertherat⁶, Guillaume Assié⁷

Affiliations

¹ Institut Cochin, INSERMU1016, Centre National de la Recherche Scientifique UMR_8104, Paris, France.
² Institut Cochin, INSERMU1016, Centre National de la Recherche Scientifique UMR_8104, Paris, France; Department of Digestive and Endocrine Surgery, Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris.
³ Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France.
⁴ Institut Curie, Paris Sciences et Lettres Research University, Mines Paris Tech, INSERM, U900, F-75005, Paris, France.
⁵ Department of Molecular Genetics, Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris; University of Pharmaceutic and Biologic Sciences, INSERM UMR_S745 and EA7331, Paris Descartes University, Sorbonne Paris Cité, Paris, France.
⁶ Institut Cochin, INSERMU1016, Centre National de la Recherche Scientifique UMR_8104, Paris, France; Department of Endocrinology, Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris.
⁷ Institut Cochin, INSERMU1016, Centre National de la Recherche Scientifique UMR_8104, Paris, France; Department of Endocrinology, Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris. Electronic address: [email protected].

PMID: 28826610
DOI: 10.1016/j.jmoldx.2017.06.005

Abstract

Pangenomic studies identified distinct molecular classes for many cancers, with major clinical applications. However, routine use requires cost-effective assays. We assessed whether targeted next-generation sequencing (NGS) could call chromosomal alterations and DNA methylation status. A training set of 77 tumors and a validation set of 449 (43 tumor types) were analyzed by targeted NGS and single-nucleotide polymorphism (SNP) arrays. Thirty-two tumors were analyzed by NGS after bisulfite conversion, and compared to methylation array or methylation-specific multiplex ligation-dependent probe amplification. Considering allelic ratios, correlation was strong between targeted NGS and SNP arrays (r = 0.88). In contrast, considering DNA copy number, for variations of one DNA copy, correlation was weaker between read counts and SNP array (r = 0.49). Thus, we generated TARGOMICs, optimized for detecting chromosome alterations by combining allelic ratios and read counts generated by targeted NGS. Sensitivity for calling normal, lost, and gained chromosomes was 89%, 72%, and 31%, respectively. Specificity was 81%, 93%, and 98%, respectively. These results were confirmed in the validation set. Finally, TARGOMICs could efficiently align and compute proportions of methylated cytosines from bisulfite-converted DNA from targeted NGS. In conclusion, beyond calling mutations, targeted NGS efficiently calls chromosome alterations and methylation status in tumors. A single run and minor design/protocol adaptations are sufficient. Optimizing targeted NGS should expand translation of genomics to clinical routine.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Biomarkers, Tumor*
Chromosome Aberrations*
Computational Biology / methods
CpG Islands
DNA Copy Number Variations
DNA Methylation*
Diagnostic Tests, Routine / methods
Gene Frequency
Genomics / methods
Genotype
High-Throughput Nucleotide Sequencing* / methods
Humans
Mutation*
Neoplasms / diagnosis*
Neoplasms / genetics*
Polymorphism, Single Nucleotide
Sequence Analysis, DNA

Substances

Biomarkers, Tumor