Table 3

Genotype Performance of different passed FFPE and fresh frozen sample sets

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

^ The number of pairs with available data allowing the Mendelian inconsistency calculation

* Fresh frozen

Wang et al. BMC Medical Genomics 2009 2:8   doi:10.1186/1755-8794-2-8