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. 2017 Dec 28;39(3):394–405. doi: 10.1002/humu.23375

Table 3.

Summary of BRCA1/2 genotyping results compared with expected genotypes after initial analysis and on re‐analysis

Process/Variant Analysis P1 P2 P3 P4 P5 P6 P7 P8 P9 P10 Concordance if data passed QC Fails

  • Sample 1

  • BRCA2 c.7007 + 1G > C

 Initial analysis C C C C C F C F C DC 7/8 (88%) 2/10 (2%)
Re‐evaluation C C C C C F C F C C 4 8/8 (100%) 2/10 (2%)

  • Sample 2

  • No pathogenic variant

 Initial analysis C C C C C F C C C C 9/9 (100%) 1/10 (1%)
Re‐evaluation C C C C C F C C C C 9/9 (100%) 1/10 (1%)

  • Sample 3

  • No pathogenic variant

 Initial analysis C C C C C F C C C C 9/9 (100%) 1/10 (1%)
  Re‐evaluation C C C C C F C C C C 9/9 (100%) 1/10 (1%

  • Sample 4

  • BRCA1 c.4675G > A

 Initial analysis C C C* F C F C F C DC 6/7 (71%) 3/10 (30%)
  Re‐evaluation C C C F C F C F C C 4 7/7 (100%) 3/10 (30%)

  • Sample 5

  • BRCA1 c.213‐11T > G

 Initial analysis C C DC C C DC C DC C DC 6/10 (60%) 0/10 (0%)
  Re‐evaluation C C C 1 C C C 1 C C 1 C C 1 10/10 (100%) 0/10 (0%)

  • Sample 6

  • BRCA1 c.1105delG

 Initial analysis C C C C C C C C C DC 9/10 (90%) 0/10 (0%)
  Re‐evaluation C C C C C C C C C C 4 10/10 (100%) 0/10 (0%)

  • Sample 7

  • BRCA1 exon13ins6kb

 Initial analysis DC DC DC DC DC DC F DC DC DC 0/9 (100%) 1/10 (10%)
  Re‐evaluation DC DC DC DC DC DC F DC C DC 1/9 (11%) 1/10 (10%)

  • Sample 8

  • No pathogenic variant

 Initial analysis C C C C F C F C C C 8/8 (100%) 2/10 (2%)
  Re‐evaluation C C C C F C F C C C 8/8 (100%) 2/10 (2%)

  • Sample 9

  • BRCA2 c.7788delAinsGGGT

 Initial analysis C C No DNA supplied F DC F F C C DC 4/6 (67%) 3/9 (33%)
  Re‐evaluation C C F DC 5 F F C C C 4 5/6 (83%) 3/9 (33%)

  • Sample 10

  • No pathogenic variant

 Initial analysis C C No DNA supplied C C C F C C C 8/8 (100%) 1/9 (11%)
  Re‐evaluation C C C C C F C C C 8/8 (100%) 1/9 (11%)

  • Sample 11

  • BRCA2 c.6952C > T– Admix ∼5%

 Initial analysis C C No DNA supplied C C F F DC F DC 4/6 (67%) 3/9 (33%)
  Re‐evaluation C C C C F F C 3 F C 3 6/6 (100%) 3/9 (33%)

  • Sample 12

  • BRCA2 c.10024G > A Admix ∼40%

 Initial analysis C* C C C DC F F DC DC DC 4/8 (50%) 2/10 (20%)
Re‐evaluation C C C C C 2 F F C 2 DC 6 C 7/8 (88%) 2/10 (20%)
Concordance if data passed QC Initial analysis 11/12 (92%) 11/12 (92%) 7/9 (78%) 9/10 (90%) 7/11 (64%) 3/5 (60%) 6/6 (100%) 6/10 (60%) 9/11 (82%) 4/12 (33%) 73/98 (74%)
Re‐evaluation 11/12 (92%) 11/12 (92%) 8/9 (89%) 9/10 (90%) 9/11 (82%) 4/5 (80%) 6/6 (100%) 9/10 (90%) 10/11 (91%) 11/12 (92%) 87/98 (89%)
Fails Both 0/12 (0%) 0/12 (0%) 0/9 (0%) 2/12 (16%) 1/12 (8%) 7/12 (58%) 6/12 (50%) 2/12 (16%) 1/12 (8%) 0/12 (0%) 19/117 (16%)

C, Concordant with expected result; DC, discordant—expected variant not detected; F, failed laboratories QC criteria; *, additional low confidence variant detected. Subcategory reason for initial non‐concordance after re‐analysis: 1, intronic variant >2 bp into the intron not reported; 2, variant reported as benign in database therefore not reported; 3, low‐level variant below acceptance cut‐off for variant detection; 4, incorrect reference sequence used for reporting; 5, no replicate for confirmation; 6, sub‐optimal DNA input (too low); F, failed laboratories QC criteria; *, additional low confidence variant detected; C, concordant; DC, discordant/not present; F, failed laboratories QC criteria; subcategory reason for initial non‐concordance after re‐analysis: 1, intronic variant >2 bp into the intron not reported; 2, variant reported as benign in database therefore not reported; 3, low‐level variant below acceptance cut‐off for variant detection; 4, incorrect reference sequence used for reporting; 5, no replicate for confirmation; 6, sub‐optimal DNA input (too low).