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J Mol Diagn. 2017 Sep;19(5):776-787. 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?

Author information

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: guillaume.assie@aphp.fr.

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.

PMID:
28826610
DOI:
10.1016/j.jmoldx.2017.06.005
[Indexed for MEDLINE]

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