Table 2 Comparison of the correlation for the different gene panels and analysis methods.

From: Analysis of tumor mutational burden: correlation of five large gene panels with whole exome sequencing

Panel

Correlation to exome tumor only

Panel

Correlation to exome tumor paired normal

Illumina 1.3

0.9950

Exome

0.9983

Agilent custom syn

0.9917

Illumina 1.3

0.9970

Illumina 1.3 syn

0.9904

NEO syn

0.9969

Agilent custom

0.9893

Exome syn

0.9968

Qiagen Genomics syn

0.9828

Illumina 1.3 syn

0.9928

Qiagen Genomics

0.9756

Agilent custom syn

0.9904

NEO

0.9582

Agilent custom

0.9867

NEO syn

0.9491

NEO

0.9760

Qiagen Mutect2

0.8877

Qiagen Mutect2 syn

0.9710

Qiagen Mutect2 syn

0.8750

Qiagen Mutect2

0.9687

Thermo non-syn

0.7886

Thermo non-syn

0.9636

  

Qiagen Genomics syn

0.9549

  

Qiagen Genomics

0.9484

avg

0.9439

avg

0.9801

sd

0.0632

sd

0.0167

  1. Exome tumor only analysis for the different gene panels and analysis methods (N = 14) and exome tumor paired normal analysis for the different gene panels and analysis methods (N = 7). Panels: Illumina—TSO500; NEO—NEOplus v2 RUO TMB (NEO New Oncology); Agilent custom—custom panel Agilent SureSelect XT HS, Exome (tumor only)—WES Agilent SureSelect XT HS Human All Exon v6 panel; Qiagen Mutect2—Qiagen TMB v3.0 (Qiagen) analyzed with Mutect2 in-house pipeline; Qiagen Genomics—Qiagen TMB v3.0 (Qiagen) analyzed with Qiagen Genomics Workbench 12.0.2.; Thermo—Oncomine Tumor Mutation Load assay (Thermo Fisher Scientific); syn.–Analysis includes synonymous variants. Panels are ordered by correlation.
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