Skip to main content

Table 3 Genotype Performance of different passed FFPE and fresh frozen sample sets

From: High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

Institution (type) Median call rate (%) # pairs^ Median rate genotype inconsistencies Range genotype inconsistencies
CHTN (FF) 99.6 12 7.10E-05 2E-5 – 6E-4
CHTN (FFPE) 98.6 11 1.60E-04 2E-5 – 3E-3
CRUK (FFPE) 99.2 14 1.10E-04 2E-5 – 2E-4
Dana Farber (FFPE) 93.9 6 2.80E-03 3E-4 – 8E-3
Leader (FFPE) 98.5 9 2.40E-04 6E-5 – 1E-3
MD Anderson set1 (FFPE) 97.5 6 4.90E-04 6E-5 – 9E-4
MD Anderson set2 (FFPE) 97.8 13 2.70E-04 4E-5 – 2E-2
UCSF (FF) 98.9 10 2.00E-05 2E-5 – 2E-4
UCSF (FFPE) 99.2 7 7.10E-05 2E-5 – 1E-4
All FFPE 98.4 66 2.70E-04 2E-5 – 2E-2
All FF* 99.4 22 4.00E-05 2E-5 – 6E-4
  1. ^ The number of pairs with available data allowing the Mendelian inconsistency calculation
  2. * Fresh frozen