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. Author manuscript; available in PMC: 2020 Aug 1.
Published in final edited form as: J Med Genet. 2020 Mar 9;57(8):509–518. doi: 10.1136/jmedgenet-2019-106368

Table 2.

Categories and performance of functional assays for BRCA1 and BRCA2

Gene Assay Set-up Read-out # of variants assessed [# of known non-pathogenic; pathogenic]a Sensitivity (95%CI)b Specificity (95%CI)b Ref.
BRCA1 Colony size cell-based (yeast) complementation/ perturbation 40 [15; 25] 0.96 (0.80–1.00) 0.93 (0.68–1.00) [58]
BRCA1 Yeast localization cell-based (yeast) complementation/ perturbation 40 [15; 25] 0.84 (0.64–0.95) 0.93 (0.68–1.00) [58]
BRCA1 Transcription activation cell-based (HEK293T) reporter system 204 [25; 10] 1.00 (0.75–1.00) 1.00 (0.83–1.00) [29]
BRCA1 BARD1 binding cell-based (yeast) reporter system 35 n/a n/a [70]
BRCA1 UbcH5a binding cell-based (yeast) reporter system 35 n/a n/a [70]
BRCA1 Uniquitin ligase activity cell-free (in vitro) in vitro enzymatic activity 35 n/a n/a [70]
BRCA1 Protease sensitivity cell-free (in vitro) in vitro binding activity 117 [10; 14] 0.79 (0.49–1.00) 0.80 (0.44–0.98) [56]
BRCA1 Phosphopeptide binding activity cell-free (in vitro) in vitro binding activity 117 [10; 14] 0.86 (0.57–0.98) 1.00 (0.69–1.00) [56]
BRCA1 Phosphopeptide binding specificity cell-free (in vitro) in vitro binding activity 117 [10; 14] 1.00 (0.77–1.00) 0.99 (0.56–1.00) [56]
BRCA1 ES cell survival cell-based (mouse ES cells) complementation/ perturbation 86 [25; 9]c n/a n/a [62]
BRCA1 Cisplatin sensitivity cell-based (mouse ES cells) complementation/ perturbation 86 [25; 9] 1.00 (0.63–1.00) 1.00 (0.83–1.00) [62]
BRCA1 BARD1 binding cell-based (yeast) reporter system 1,287 [3; 19] n/a n/a [71]
BRCA1 Uniquitin ligase activity cell-free (in vitro) in vitro enzymatic activity 1,287 [3; 19] n/a n/a [71]
BRCA1 Haploid cell survival cell-based (HAP1 cells) complementation/ perturbation 3,893 [22; 162]d 0.967 0.982 [10]
BRCA1 Homologous recombination cell-based (RG37-shBRCA1 cells) complementation/ perturbation 78 [6; 7] 1.00 1.00 [72]
BRCA1 Localization cell-based (RG37-shBRCA1 cells) complementation/ perturbation 78 [6; 7] 0.714 1.00 [72]
BRCA1 Protein expression and stability cell-free (in vitro) In vitro solubility and thermostability 78 [6; 7] 0.714 0.83 [72]
BRCA1 Phosphopeptide binding activity Cell-free (in vitro) in vitro binding activity 42 [5; 2] n/a n/a [72]
BRCA1 Homologous recombination Cell-based (HeLa-DR-FRT) complementation / perturbation 1,056 [5; 8] 0.875 1.00 [9]
BRCA1 Homologous recombination Cell-based (HEK293T) complementation / perturbation 35 [23; 5]e 1.00 1.00 [73]
BRCA2 Homologous recombination Cell-based (V-C8 cells) complementation / perturbation 64 [18; 13] 1.00 (0.75–1.00) 1.00 (0.82–1.00) [30]
BRCA2 Homologous recombination Cell-based (V-C8 cells) complementation / perturbation 139 [12; 13] 1.00 (0.75–1.00) 1.00 (0.69–1.00) [74]
BRCA2 Homologous recombination Cell-based (mouse ES cells) complementation/ perturbation 43 [20; 15] 1.00 (0.78–1.00) 1.00 (0.83–1.00) [75]

Only assays in which more than 30 variants were tested are listed.

a

Known pathogenic and non-pathogenic variants used for estimating sensitivity and specificity are those classified using the multifactorial model as IARC Classes 1,2,4 or 5 (Ref.[18]), unless otherwise indicated.

b

As originally published, unless otherwise stated.

c

Used missense variants classified by multifactorial model as IARC Classes 1,2,4 or 5 (Ref.[18]) plus the recently classified G1770V variants as pathogenic.

d

Used ClinVar as a source of known pathogenic and non-pathogenic variants.

e

Used as non-pathogenic variants Align-GVGD grade of C0 and IARC Class 1, and as pathogenic variants Align-GVGD grade of C35-C65 and IARC Class 5).