Table 1

Comparison of tumour DNA sequencing strategies

Targeted panelsWhole exomeWhole genome
Pro
  • High depth of coverage

  • Readily standardisable

  • Rapid interpretation for clinical use

  • Low costs

  • Easy clinical implementation

  • Detection of unknown variants

  • Detection of CNVs

  • Research applications

  • Feasible in clinical routine

  • Low price/performance ratio

  • Comprehensive assessment of cancer genomes

  • Highest resolution of genomic alterations

  • SNVs in enhancer/promoter and ncRNA regions

  • Decreasing costs

  • Subject to future studies

Contra
  • Limited, ‘peephole’ observations

  • Limited value for research

  • Limited assessment of complex aberrations

  • Not fully comprehensive

  • Lower CNV resolution

  • Amplification or exon capture necessary

  • High bioinformatic effort

  • Demanding clinical interpretation

  • Time-consuming workflow

  • Uncertain value for clinical interpretation

  • Most expensive

  • CNV, copy number variant; ncRNA, non-coding RNA; SNV, single nucleotide variant.