Table 1 Overview of the most relevant WES comparison studies between FF and matched FFPE tissue samples

Holley et al. [22]

1 matched FF/FFPE

pancreatic ductal adenocarcinoma

Agilent SureSelect All Exon Plus

Van Allen et al. [23]

11 matched FF/FFPE

lung adenocarcinoma + lung normal tissue

Agilent SureSelect Human All Exon v.2

Hedegaard et al. [24]

19 matched FF/FFPE

colorectal carcinoma + 13 matching normal FF colon samples

Illumina TruSeq Exome Enrichment

Munchel et al. [25]

13 matched FF/FFPE

9 ovarian carcinomas, 2 breast tumor/normal pairs, 2 colon tumor/normal pairs

Illumina TruSeq Exome Enrichment

Astolfi et al. [26]

4 matched FF/FFPE

gastrointestinal stromal tumors + normal samples (peripheral blood)

Illumina Nextera Rapid Capture Exome Enrichment

De Paoli-Iseppi et al. [27]

10 matched FF/FFPE

melanoma

Illumina TruSeq Exome (10 FF)

Illumina Nextera Rapid Capture Expanded Exome (7 FFPE)

Roche NimbleGen SeqCap EZ Exome +UTR (4 FFPE)

Oh et al. [28]

4 matched FF/FFPE

cancer type not defined + matched blood or normal frozen sample

NimbleGen exome 2.1 M array (pair 1 and 4);

Agilent SureSelect All Human exon v.5 (pair 2 and 3).