Genetics Quality Network EMQN Samples with known genotypes were distributed to the year The second column contains number of participating laboratories followed by the genotype of the sample The ID: 938269
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Appendix A. Data Used to Estimate Analytic Sensitivity and Specificity from external Genetics Quality Network (EMQN). Samples with known genotypes wer
e distributed to the year. The second column contains number of participating laboratories, followed by the genotype of the sample. The number of labor
atories reporting specific genotypes is then Table 2-6. Computations for the EMQN Proficiency Testing Surveys Reported AllelesDistribution Labs
Genotype Correct Incorrect 1999Case 1 13 C140T 24 0 Case 2 14 A5176G 28 0 1 * Case 3 13 C4446T 26 0 79 2 Sensitivity 24+1+28+26/80 *
One laboratory identified the correct mutation, but also reported a second base exchange that was not seen by the 2 reference labs or any of the othe
r participants. fn = false negative fp = false positive (Table 2-6 continued on next page) BRCA and Breast/Ovarian Cancer --Analytic Validity Versi
on 2003-6 213 Table 2-6 (Continued) Reported Alleles Distribution Labs Genotype Correct Incorrect 2000 Case 1 24 185delAG 24 185delAG 48
0 Case 2 24 12 22 1259delG 44 0 1 Wild type 1 1 (fn) 1 Wrong position 1 0 (wm) Case 3 20 A10462G 18 A10462G 36 0 2 Wild type 2
2 (fn) 132 3 Sensitivity 48+44+1+1+36+2/136 fn = false negative, wm = wrong mutation Reported Alleles Distribution Labs Genotype Correct Inc
orrect 2001 Case 1 41 3600del11 39 3600del11 78 0 1 Wild type 1 1 (fn) 1 4600del11 1 1 (wm) Case 2 38 G4603A 34 G4603A 68 0 2
Wild type 2 2 (fn) 2 G4603T 2 2 (wm) Case 3 40 G5075A 38 G5075A 76 0 2 Wild type 2 2 (fn) 230 8 Sensitivity 78+1+1+68+2+2+76+2/238
fn = false negative, wm = wrong mutation (Table 2-6 continued on next page) BRCA and Breast/Ovarian Cancer --Analytic Validity Version 2003-6 214 Ta
ble 2-6 (Continued) Reported Alleles Distribution Labs Genotype Correct Incorrect 2000 Case 1 24 185delAG 24 185delAG 48 0 Case 2 24 1
2 22 1259delG 44 0 1 Wild type 1 1 (fn) 1 Wrong position 1 0 (wm) Case 3 20 A10462G 18 A10462G 36 0 2 Wild type 2 2 (fn) 132 3
Sensitivity 48+44+1+1+36+2/136 fn = false negative, wm = wrong mutation Reported Alleles Distribution Labs Genotype Correct Incorrect 2001 Cas
e 1 41 3600del11 39 3600del11 78 0 1 Wild type 1 1 (fn) 1 4600del11 1 1 (wm) Case 2 38 G4603A 34 G4603A 68 0 2 Wild type 2 2 (
fn) 2 G4603T 2 2 (wm) Case 3 40 G5075A 38 G5075A 76 0 2 Wild type 2 2 (fn) 230 8 Sensitivity 78+1+1+68+2+2+76+2/238 fn = false negati
ve, wm = wrong mutation (Table 2-6 continued on next page) BRCA and Breast/Ovarian Cancer --Analytic Validity Version 2003-6 214 Table 2-6 (Continue
d) Reported Alleles Distribution Labs Genotype Correct Incorrect 2002 Case 1 36 5677insA 34 5677insA 68 0 2 Wild type 2 2 (fn) Case
2 36 �300TG 36 �300TG 72 0 Case 3 36 3875del4 34 3875del4 68 0 2 Wild type 2 2 (fn) 212 4 Sensitivity 68+2+72+68+2/216
fn = false negative BRCA and Breast/Ovarian Cancer --Analytic Validity Version 2003-6 215 (ACMG/CAP). Samples with known genotypes were distributed
to participants in 2001 and 2002. Th th DNA sample distributed as part of the Molecular Genetics Laboratory Survey). The second sample. The number of
laboratories reporting specific genotypes is then provided, along with a tabulation of their ‘correct’ and ‘incorrect’ responses.
The table also contains the data used to Table 2-7. Computations for the ACMG/CAP Proficiency Testing Surveys Reported Alleles Distribution Labs
Genotype Correct Incorrect 2001 MGL 12 normal 12 normal 24 0 MGL 12 normal 12 normal 24 0 MGL 17 6174delT 17 6174 delT 29* 0 77 0
Sensitivity 29/29 Specificity (24 + 24)/(24 + 24) * Five laboratories did not test the second allele when the mutation was identified in the first
allele. (Table 2-7 continued on next page) BRCA and Breast/Ovarian Cancer --Analytic Validity Version 2003-6 216 Table 2-7 (Continued) Distributio
n Labs Genotype 2002 MGL3- 11 normal 11 normal MGL 11 normal 11 normal MGL3- 11 6174delT 11 6174 delT Reported Alleles Correct Incorr
ect 22 0 22 0 22 0 77 0 Sensitivity 22/22 Specificity (22 + 22)/(22 + 22) BRCA and Breast/Ovarian Cancer --Analytic Validity Version 2003-6 2