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.

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