147 Matching Annotations
  1. Mar 2021
    1. WT-PALB2 was associated with robust formation of damage-induced RAD51 foci, whereas the four variants were associated with defective foci formation (Fig. 3d, e).

      AssayResult: 1.5

      AssayResultAssertion: Abnormal

      Approximation: Exact assay result value not reported; value estimated from Figure 3e.

    2. WT-PALB2 was associated with robust formation of damage-induced RAD51 foci, whereas the four variants were associated with defective foci formation (Fig. 3d, e).

      AssayResult: <1

      AssayResultAssertion: Abnormal

      Approximation: Exact assay result value not reported; value estimated from Figure 3e.

    3. WT-PALB2 was associated with robust formation of damage-induced RAD51 foci, whereas the four variants were associated with defective foci formation (Fig. 3d, e).

      AssayResult: 1

      AssayResultAssertion: Abnormal

      Approximation: Exact assay result value not reported; value estimated from Figure 3e.

    4. WT-PALB2 was associated with robust formation of damage-induced RAD51 foci, whereas the four variants were associated with defective foci formation (Fig. 3d, e).

      AssayResult: 3

      AssayResultAssertion: Abnormal

      Approximation: Exact assay result value not reported; value estimated from Figure 3e.

    5. WT-PALB2 was associated with robust formation of damage-induced RAD51 foci, whereas the four variants were associated with defective foci formation (Fig. 3d, e).

      AssayResult: 1

      AssayResultAssertion: Abnormal

      ControlType: Abnormal; empty vector

      Approximation: Exact assay result value not reported; value estimated from Figure 3e.

    6. WT-PALB2 was associated with robust formation of damage-induced RAD51 foci, whereas the four variants were associated with defective foci formation (Fig. 3d, e).

      AssayResult: 27

      AssayResultAssertion: Normal

      StandardDeviation: 14

      ControlType: Normal; wild type PALB2 cDNA

      Approximation: Exact assay result and standard deviation values not reported; values estimated from Figure 3e.

    7. ImmunofluorescenceLive cell imaging and microirradiation studies of HeLa cells transfected with peYFP-C1-PALB2 WT or variant constructs were carried out with a Leica TCS SP5 II confocal microscope. To monitor the recruitment of YFP-PALB2 to laser-induced DNA damage sites, cells were microirradiated in the nucleus for 200 ms using a 405-nm ultraviolet (UV) laser and imaged every 30 seconds for 15 minutes. Fluorescence intensity of YFP-PALB2 at DNA damage sites relative to an unirradiated nuclear area was quantified (Supplemental Materials). Cyclin A–positive HeLa cells treated with siCtrl and siRNA against PALB2 were complemented with wild-type and mutant FLAG-tagged PALB2 expression constructs, exposed to 2 Gy of γ-IR, incubated for 6 hours, and subjected to immunofluorescence for RAD51 foci. HeLa cells were fixed with 4% (w/v) paraformaldehyde for 10 minutes at room temperature, washed with tris-buffered saline (TBS), and fixed again with ice-cold methanol for 5 minutes at −20 °C. Cells were incubated for 1 hour at room temperature with the anti-RAD51 (1:7000, B-bridge International, 70-001) and anticyclin A (1:400, BD Biosciences, 611268), and incubated for 1 hour at room temperature with the Alexa Fluor 568 goat antirabbit (Invitrogen, A-11011) and Alexa Fluor 647 goat antimouse (Invitrogen, A-21235) secondary antibodies. Z-stack images were acquired on a Leica CTR 6000 microscope and the number of RAD51 foci per cyclin A–positive cells expressing the indicated YFP-PALB2 constructs was scored with Volocity software v6.0.1 (Perkin–Elmer Improvision). Results represent the mean (± SD) of three independent trials (n = 50 cells per condition). HEK293T cells transfected with PALB2 expression constructs were also subjected to immunofluorescence for PALB2 using the monoclonal anti-FLAG M2 antibody (Sigma) and the Alexa Fluor 568 goat antimouse (Life Technologies) secondary antibody.

      AssayGeneralClass: BAO:0000450 fluorescence microscopy

      AssayMaterialUsed: CLO:0003684 HeLa cell

      AssayDescription: HeLa cells were treated with PALB2 siRNA and transfected with peYFP-PALB2 expressing PALB2 variants (or empty vector), followed by exposure to 2 Gy of γ-IR. Six hours after irradiation, cells were subjected to immunofluorescence for RAD51 foci (where foci formation serves as marker of normal DNA damage repair function).

      AssayReadOutDescription: The number of RAD51 foci per cyclin A-positive cells expressing the indicated YFP-PALB2 constructs.

      AssayRange: foci/cell

      AssayNormalRange: Not reported

      AssayAbnormalRange: Not reported

      AssayIndeterminateRange: Not reported

      ValidationControlPathogenic: 0

      ValidationControlBenign: 0

      Replication: Three independent experiments with 50 cells per condition

      StatisticalAnalysisDescription: Kruskal–Wallis test with Dunn's multiple comparison post-test

    8. Results for individual PALB2 variants were normalized relative to WT-PALB2 and the p.Tyr551ter (p.Y551X) truncating variant on a 1:5 scale with the fold change in GFP-positive cells for WT set at 5.0 and fold change GFP-positive cells for p.Y551X set at 1.0. The p.L24S (c.71T>C), p.L35P (c.104T>C), p.I944N (c.2831T>A), and p.L1070P (c.3209T>C) variants and all protein-truncating frame-shift and deletion variants tested were deficient in HDR activity, with normalized fold change <2.0 (approximately 40% activity) (Fig. 1a).

      AssayResult: 5.3

      AssayResultAssertion: Normal

      StandardErrorMean: 0.46

    1. RAD51 foci assayHeLa cells were seeded on glass coverslips in 6-well plates at 225 000 cells per well. Knockdown of PALB2 was performed 18 h later with 50 nM PALB2 siRNA using Lipofectamine RNAiMAX (Invitrogen). After 5 h, cells were subjected to double thymidine block. Briefly, cells were treated with 2 mM thymidine for 18 h and release into fresh media for 9 h. Complementation using 800 ng of the peYFP-C1 empty vector or the indicated siRNA-resistant YFP-PALB2 construct was carried out with Lipofectamine 2000 during that release time. Then, cells were treated with 2 mM thymidine for 17 h and protected from light from this point on. After 2 h of release from the second block, cells were irradiated with 2 Gy and processed for immunofluorescence 4 h post-irradiation. Unless otherwise stated, all immunofluorescence dilutions were prepared in PBS and incubations performed at room temperature with intervening washes in PBS. Cell fixation was carried out by incubation with 4% paraformaldehyde for 10 min followed by 100% ice-cold methanol for 5 min at −20°C. This was succeeded by permeabilization in 0.2% Triton X-100 for 5 min and a quenching step using 0.1% sodium borohydride for 5 min. After blocking for 1 h in a solution containing 10% goat serum and 1% BSA, cells were incubated for 1 h with primary antibodies anti-RAD51 (1 :7000, B-bridge International, #70–001) and anti-cyclin A (1:400, BD Biosciences, #611268) diluted in 1% BSA. Secondary antibodies Alexa Fluor 568 goat anti-rabbit (Invitrogen, #A-11011) and Alexa Fluor 647 goat anti-mouse (Invitrogen, #A-21235) were diluted 1:1000 in 1% BSA and applied for 1 h. Nuclei were stained for 10 min with 1 μg/ml 4,6-diamidino-2-phenylindole (DAPI) prior to mounting onto slides with 90% glycerol containing 1 mg/ml paraphenylenediamine anti-fade reagent. Z-stack images were acquired on a Leica CTR 6000 microscope using a 63× oil immersion objective, then deconvolved and analyzed for RAD51 foci formation with Volocity software v6.0.1 (Perkin-Elmer Improvision). The number of RAD51 foci per cyclin A-positive cells expressing the indicated YFP-PALB2 constructs was scored using automatic spot counting by Volocity software and validated manually. Data from three independent trials (total n = 225 cells per condition) were analyzed for outliers using the ROUT method (Q = 1.0%) in GraphPad Prism v6.0 and the remaining were reported in a scatter dot plot. Intensity values, also provided by Volocity, of 500 RAD51 foci from a representative trial were normalized to the WT mean and reported in a scatter dot plot. Horizontal lines on the plots designate the mean values.

      AssayGeneralClass: BAO:0000450 fluorescence microscopy

      AssayMaterialUsed: CLO:0003684 HeLa cell

      AssayDescription: HeLa cells were treated with PALB2 siRNA and synchronized to G1/S phase by double thymidine block. Cells were then transfected with peYFP-PALB2 expressing PALB2 variants (or empty vector) and irradiated with 2 Gy. Four hours after irradiation, cells were subjected to immunofluorescence for RAD51 foci (where foci formation serves as marker of normal DNA damage repair function).

      AssayReadOutDescription: The number of RAD51 foci per cyclin A-positive cells expressing the indicated YFP-PALB2 constructs was scored and presented as percentage change relative to the wild type mean RAD51 foci number per cell.

      AssayRange: %

      AssayNormalRange: Not reported

      AssayAbnormalRange: Not reported

      AssayIndeterminateRange: Not reported

      ValidationControlPathogenic: 1

      ValidationControlBenign: 3

      Replication: Three independent experiments, each with 225 cells per condition

      StatisticalAnalysisDescription: Kruskal–Wallis test with Dunn's multiple comparison post-test

    2. SUPPLEMENTARY DATA

      AssayResult: 38

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

      Approximation: Exact assay result value not reported; value estimated from Figure 6C.

    3. SUPPLEMENTARY DATA

      AssayResult: -96

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

      ControlType: Abnormal; empty vector

    4. SUPPLEMENTARY DATA

      AssayResult: 0

      AssayResultAssertion: Normal

      ControlType: Normal; wild type PALB2 cDNA

    5. SUPPLEMENTARY DATA

      AssayResult: -34

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    6. SUPPLEMENTARY DATA

      AssayResult: -11

      AssayResultAssertion: Indeterminate

      PValue: Not reported

    7. SUPPLEMENTARY DATA

      AssayResult: -4

      AssayResultAssertion: Indeterminate

      PValue: Not reported

    8. SUPPLEMENTARY DATA

      AssayResult: -14

      AssayResultAssertion: Indeterminate

      PValue: Not reported

    9. SUPPLEMENTARY DATA

      AssayResult: -56

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    10. SUPPLEMENTARY DATA

      AssayResult: -6

      AssayResultAssertion: Normal

      PValue: Not reported

    11. SUPPLEMENTARY DATA

      AssayResult: -25

      AssayResultAssertion: Abnormal

      PValue: < 0.01

    12. SUPPLEMENTARY DATA

      AssayResult: -31

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    13. SUPPLEMENTARY DATA

      AssayResult: -16

      AssayResultAssertion: Normal

      PValue: Not reported

    14. SUPPLEMENTARY DATA

      AssayResult: -10

      AssayResultAssertion: Normal

      PValue: Not reported

    15. SUPPLEMENTARY DATA

      AssayResult: -21

      AssayResultAssertion: Indeterminate

      PValue: < 0.01

    16. SUPPLEMENTARY DATA

      AssayResult: -20

      AssayResultAssertion: Indeterminate

      PValue: < 0.05

    17. SUPPLEMENTARY DATA

      AssayResult: 8

      AssayResultAssertion: Indeterminate

      PValue: Not reported

    18. SUPPLEMENTARY DATA

      AssayResult: -29

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    19. SUPPLEMENTARY DATA

      AssayResult: -98

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    20. SUPPLEMENTARY DATA

      AssayResult: -36

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    21. SUPPLEMENTARY DATA

      AssayResult: 3

      AssayResultAssertion: Indeterminate

      PValue: Not reported

    22. SUPPLEMENTARY DATA

      AssayResult: -32

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    23. SUPPLEMENTARY DATA

      AssayResult: 85.76

      AssayResultAssertion: Indeterminate

      PValue: 0.0445

      Comment: Exact values reported in Table S3.

    1. sensitivity to PARPi treatment using a cellular proliferation assay

      AssayGeneralClass: BAO:0002805 cell proliferation assay

      AssayMaterialUsed: CLO:0037317 mouse embryonic stem cell line

      AssayDescription: Stable expression of wild type and variant PALB2 cDNA constructs in Trp53 and Palb2-null mouse cell line containing DR-GFP reporter; exposure to PARP inhibitor Olaparib for 48 h inhibits end-joining mediated by PARP and sensitizes cells to DNA damage; cell survival is measured by FACS 24 h after Olaparib washout

      AssayReadOutDescription: Relative resistance to PARPi represented as cell survival relative to wild type, which was set to 100%

      AssayRange: %

      AssayNormalRange: PARPi resistance levels comparable to that of cells expressing wild type PALB2; no numeric threshold given

      AssayAbnormalRange: PARPi resistance levels ≤30% of wild type

      AssayIndeterminateRange: Not reported

      ValidationControlPathogenic: 12

      ValidationControlBenign: 9

      Replication: 2 independent experiments

      StatisticalAnalysisDescription: Not reported

    2. Source Data

      AssayResult: 26.03

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 11.42

      Comment: Exact values reported in “Source Data” file.

    3. Source Data

      AssayResult: 24.27

      AssayResultAssertion: Abnormal

      ReplicateCount: Not reported

      StandardErrorMean: Not reported

      Comment: Exact values reported in “Supplementary Data 1” file; result for this variant not reported in “Source Data” file.

    4. Source Data

      AssayResult: 96.22

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 16.7

      Comment: Exact values reported in “Source Data” file. Discrepancy in “Supplementary Data 1” file: nucleotide reported as c.3191A>G.

    5. Source Data

      AssayResult: 15.23

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 6.42

      Comment: Exact values reported in “Source Data” file. Discrepancy in “Source Data” file: protein reported as Q899X.

    6. Source Data

      AssayResult: 52.23

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 6.33

      Comment: Exact values reported in “Source Data” file. Discrepancy in “Source Data” file: protein reported as I1037R.

    7. Source Data

      AssayResult: 74.36

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 1.89

      Comment: Exact values reported in “Source Data” file.

    8. Source Data

      AssayResult: 87.27

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 1.3

      Comment: Exact values reported in “Source Data” file.

    9. Source Data

      AssayResult: 17.29

      AssayResultAssertion: Abnormal

      ReplicateCount: 3

      StandardErrorMean: 6.81

      ControlType: Abnormal; empty vector (set 5)

      Comment: Exact values reported in “Source Data” file.

    10. Source Data

      AssayResult: 7.86

      AssayResultAssertion: Abnormal

      ReplicateCount: 3

      StandardErrorMean: 2.39

      ControlType: Abnormal; empty vector (set 4)

      Comment: Exact values reported in “Source Data” file.

    11. Source Data

      AssayResult: 34.03

      AssayResultAssertion: Abnormal

      ReplicateCount: 3

      StandardErrorMean: 10.86

      ControlType: Abnormal; empty vector (set 3)

      Comment: Exact values reported in “Source Data” file.

    12. Source Data

      AssayResult: 12.78

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 3.65

      ControlType: Abnormal; empty vector (set 2)

      Comment: Exact values reported in “Source Data” file.

    13. Source Data

      AssayResult: 10.93

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 0.78

      ControlType: Abnormal; empty vector (set 1)

      Comment: Exact values reported in “Source Data” file.

    14. Source Data

      AssayResult: 100

      AssayResultAssertion: Normal

      ReplicateCount: 38

      StandardErrorMean: 0

      ControlType: Normal; wild type

      Comment: Exact values reported in “Source Data” file.

    15. Source Data

      AssayResult: 102.22

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 8.29

      Comment: Exact values reported in “Source Data” file.

    16. Source Data

      AssayResult: 21.7

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.42

      Comment: Exact values reported in “Source Data” file.

    17. Source Data

      AssayResult: 55.4

      AssayResultAssertion: Not reported

      ReplicateCount: 4

      StandardErrorMean: 13.29

      Comment: Exact values reported in “Source Data” file.

    18. Source Data

      AssayResult: 17.5

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 7.75

      Comment: Exact values reported in “Source Data” file.

    19. Source Data

      AssayResult: 102.7

      AssayResultAssertion: Not reported

      ReplicateCount: 3

      StandardErrorMean: 12.82

      Comment: Exact values reported in “Source Data” file.

    20. Source Data

      AssayResult: 94.47

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 0.99

      Comment: Exact values reported in “Source Data” file.

    21. Source Data

      AssayResult: 13.87

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.32

      Comment: Exact values reported in “Source Data” file.

    22. Source Data

      AssayResult: 93.44

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 2.24

      Comment: Exact values reported in “Source Data” file.

    23. Source Data

      AssayResult: 9.67

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.31

      Comment: Exact values reported in “Source Data” file.

    24. Source Data

      AssayResult: 109.07

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 9.27

      Comment: Exact values reported in “Source Data” file.

    25. Source Data

      AssayResult: 98.64

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 5.5

      Comment: Exact values reported in “Source Data” file.

    26. Source Data

      AssayResult: 102.88

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 20.71

      Comment: Exact values reported in “Source Data” file.

    27. Source Data

      AssayResult: 16.6

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 4.35

      Comment: Exact values reported in “Source Data” file.

    28. Source Data

      AssayResult: 103.21

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 8.98

      Comment: Exact values reported in “Source Data” file.

    29. Source Data

      AssayResult: 108.27

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 16.12

      Comment: Exact values reported in “Source Data” file.

    30. Source Data

      AssayResult: 98.43

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 14.96

      Comment: Exact values reported in “Source Data” file.

    31. Source Data

      AssayResult: 102.57

      AssayResultAssertion: Not reported

      ReplicateCount: 3

      StandardErrorMean: 11.51

      Comment: Exact values reported in “Source Data” file.

    32. Source Data

      AssayResult: 103.83

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 3.67

      Comment: Exact values reported in “Source Data” file.

    33. Source Data

      AssayResult: 87.51

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 4.4

      Comment: Exact values reported in “Source Data” file.

    34. Source Data

      AssayResult: 56.67

      AssayResultAssertion: Not reported

      ReplicateCount: 4

      StandardErrorMean: 12.4

      Comment: Exact values reported in “Source Data” file.

    35. Source Data

      AssayResult: 85.13

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 15.04

      Comment: Exact values reported in “Source Data” file.

    36. Source Data

      AssayResult: 108.56

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 19.59

      Comment: Exact values reported in “Source Data” file.

    37. Source Data

      AssayResult: 10.42

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 0.01

      Comment: Exact values reported in “Source Data” file.

    38. Source Data

      AssayResult: 99.69

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 3.09

      Comment: Exact values reported in “Source Data” file.

    39. Source Data

      AssayResult: 12.35

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.48

      Comment: Exact values reported in “Source Data” file.

    40. Source Data

      AssayResult: 14.79

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 7.81

      Comment: Exact values reported in “Source Data” file.

    41. Source Data

      AssayResult: 84.41

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 1.42

      Comment: Exact values reported in “Source Data” file.

    42. Source Data

      AssayResult: 25.09

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 3.48

      Comment: Exact values reported in “Source Data” file.

    43. Source Data

      AssayResult: 97.37

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 5.14

      Comment: Exact values reported in “Source Data” file.

    44. Source Data

      AssayResult: 12.77

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 5.34

      Comment: Exact values reported in “Source Data” file.

    45. Source Data

      AssayResult: 78.91

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 6.86

      Comment: Exact values reported in “Source Data” file.

    46. Source Data

      AssayResult: 8.41

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.95

      Comment: Exact values reported in “Source Data” file.

    47. Source Data

      AssayResult: 24.31

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 5.23

      Comment: Exact values reported in “Source Data” file.

    48. Source Data

      AssayResult: 14.78

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 9.34

      Comment: Exact values reported in “Source Data” file.

    49. Source Data

      AssayResult: 81.17

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 9.32

      Comment: Exact values reported in “Source Data” file.

    50. Source Data

      AssayResult: 91.11

      AssayResultAssertion: Not reported

      ReplicateCount: 3

      StandardErrorMean: 17.74

      Comment: Exact values reported in “Source Data” file.

    51. Source Data

      AssayResult: 26.39

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.11

      Comment: Exact values reported in “Source Data” file.

    52. Source Data

      AssayResult: 94.54

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 19.94

      Comment: Exact values reported in “Source Data” file.

    53. Source Data

      AssayResult: 86.26

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 4.22

      Comment: Exact values reported in “Source Data” file.

    54. Source Data

      AssayResult: 7.73

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 2.25

      Comment: Exact values reported in “Source Data” file.

    55. Source Data

      AssayResult: 29.04

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 7.24

      Comment: Exact values reported in “Source Data” file.

    56. Source Data

      AssayResult: 115.45

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 11.81

      Comment: Exact values reported in “Source Data” file.

    57. Source Data

      AssayResult: 78.3

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 11.75

      Comment: Exact values reported in “Source Data” file.

    58. Source Data

      AssayResult: 86.54

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 11.96

      Comment: Exact values reported in “Source Data” file.

    59. Source Data

      AssayResult: 87.96

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 10.31

      Comment: Exact values reported in “Source Data” file.

    60. Source Data

      AssayResult: 78.2

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 7.31

      Comment: Exact values reported in “Source Data” file.

    61. Source Data

      AssayResult: 103.53

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 7.06

      Comment: Exact values reported in “Source Data” file.

    62. Source Data

      AssayResult: 19.46

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 1.75

      Comment: Exact values reported in “Source Data” file.

    63. Source Data

      AssayResult: 64.92

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 8.7

      Comment: Exact values reported in “Source Data” file.

    64. Source Data

      AssayResult: 11.06

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 2.4

      Comment: Exact values reported in “Source Data” file.

    65. Source Data

      AssayResult: 117.58

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 0.81

      Comment: Exact values reported in “Source Data” file.

    66. Source Data

      AssayResult: 10.68

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 0.32

      Comment: Exact values reported in “Source Data” file.

    67. Source Data

      AssayResult: 23.96

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 7.6

      Comment: Exact values reported in “Source Data” file.

    68. Source Data

      AssayResult: 120.54

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 11.09

      Comment: Exact values reported in “Source Data” file.

    69. Source Data

      AssayResult: 74.18

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 6.49

      Comment: Exact values reported in “Source Data” file.

    70. Source Data

      AssayResult: 95.74

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 14.87

      Comment: Exact values reported in “Source Data” file.

    71. Source Data

      AssayResult: 83.96

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 9.89

      Comment: Exact values reported in “Source Data” file.

    72. Source Data

      AssayResult: 94.84

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 20.56

      Comment: Exact values reported in “Source Data” file.

    73. Source Data

      AssayResult: 17.43

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 5.19

      Comment: Exact values reported in “Source Data” file.

    74. Source Data

      AssayResult: 108.51

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 17.71

      Comment: Exact values reported in “Source Data” file.

    75. Source Data

      AssayResult: 67.82

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 10.97

      Comment: Exact values reported in “Source Data” file.

    76. Source Data

      AssayResult: 72.7

      AssayResultAssertion: Not reported

      ReplicateCount: 3

      StandardErrorMean: 9.73

      Comment: Exact values reported in “Source Data” file.

    77. Source Data

      AssayResult: 9.68

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 3.44

      Comment: Exact values reported in “Source Data” file.

    78. Source Data

      AssayResult: 115.71

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 3.09

      Comment: Exact values reported in “Source Data” file.

    79. Source Data

      AssayResult: 11.28

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardDeviation: 1.24

      StandardErrorMean: 0.87

      Comment: Exact values reported in “Source Data” file.

    Tags

    Annotators

    URL

    1. Most Suspected Brugada Syndrome Variants Had (Partial) Loss of Function

      AssayResult: 113.2

      AssayResultAssertion: Normal

      ReplicateCount: 30

      StandardErrorMean: 13.9

      Comment: This variant had normal function (75-125% of wildtype peak current, <1% late current, no large perturbations to other parameters). These in vitro features are consistent with non-disease causing variants. (Personal communication: A. Glazer)

    1. This new quantitative assay, based on both RT-QMPSF and RT-MLPA, was first validated on 31 lymphoblastoid cell lines derived from patients with LFS harbouring different germline heterozygous TP53 variants

      AssayGeneralClass: BAO:0010044 targeted transcriptional assay

      AssayMaterialUsed: BTO:0000773 lymphoblastoid cell line derived from control individuals or individuals with germline TP53 variants

      AssayDescription: Comparative transcriptomic analysis using RNA-Seq to compare EBV cell lines of wild type and pathogenic TP53 in the context of genotoxic stress induced by doxorubicin treatment. p53 RNA levels were evaluated and expressed as a percentage of the mean levels obtained for the three wild-type TP53 individuals.

      AdditionalDocument: PMID: 23172776

      AssayReadOutDescription: The p53 mRNA levels were expressed as a ratio of the normal values obtained for 3 TP53 wild-type control individuals.

      AssayRange: UO:0000187 the p53 RNA levels were evaluated and expressed as a percentage of the mean levels obtained for three wild-type TP53 individuals.

      AssayNormalRange: N/A

      AssayAbnormalRange: N/A

      AssayIndeterminateRange: N/A

      AssayNormalControl: wild type TP53

      AssayAbnormalControl: LFS patient cells

      ValidationControlPathogenic: 8 Individuals with dominant-negative TP53 missense variants, 10 Individuals with null TP53 variants, and 13 Individuals with other TP53 missense variants

      ValidationControlBenign: 3 patients with wild type TP53

      Replication: experiments were performed in triplicates.

      StatisticalAnalysisDescription: Differentially expressed genes between doxorubicin-treated and untreated cells were arbitrarily defined using, as filters, a P<0.01 and fold-change cutoffs >2 or <2, for up and down regulation, respectively. The resultant signal information was analyzed using one-way analysis of variance (ANOVA, P= 0.001), assuming normality but not equal variances with a Benjamani–Hochberg correction for multiple comparisons using three groups: controls, null, and missense mutations.

      SignificanceThreshold: P=0.001

      Comment: statistical analysis and P value from previous publication.

  2. Feb 2021
    1. Supplemental material

      AssayResult: 82

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    2. Supplemental material

      AssayResult: 80

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    3. Supplemental material

      AssayResult: 69

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    4. Supplemental material

      AssayResult: 99

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    5. Supplemental material

      AssayResult: 98

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    6. Supplemental material

      AssayResult: 77

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    7. Supplemental material

      AssayResult: 105

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    8. Supplemental material

      AssayResult: 96

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    9. Supplemental material

      AssayResult: 104

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    10. Supplemental material

      AssayResult: 99

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    11. Supplemental material

      AssayResult: 83

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    12. Supplemental material

      AssayResult: 91

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    13. Supplemental material

      AssayResult: 86

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    14. Supplemental material

      AssayResult: 56

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    15. Supplemental material

      AssayResult: 61

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    16. Supplemental material

      AssayResult: 51

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    17. Supplemental material

      AssayResult: 66

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    18. Supplemental material

      AssayResult: 60

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    19. Supplemental material

      AssayResult: 65

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    20. Supplemental material

      AssayResult: 66

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    21. Supplemental material

      AssayResult: 45

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    22. Supplemental material

      AssayResult: 58

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    23. Supplemental material

      AssayResult: 49

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    24. Supplemental material

      AssayResult: 83

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    25. Supplemental material

      AssayResult: 84

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    26. Supplemental material

      AssayResult: 91

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    27. Supplemental material

      AssayResult: 94

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    28. Supplemental material

      AssayResult: 97

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    29. Supplemental material

      AssayResult: 98

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    30. Supplemental material

      AssayResult: 96

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    31. Supplemental material

      AssayResult: 105

      AssayResultAssertion: Normal

      Comment: See Table S2 for details

    32. Supplemental material

      AssayResult: 88

      AssayResultAssertion: Normal

      ControlType: Normal, wild type TP53 from control 3

      Comment: See Table S2 for details

    33. Supplemental material

      AssayResult: 95

      AssayResultAssertion: Normal

      ControlType: Normal, wild type TP53 from control 2

      Comment: See Table S2 for details

    34. Supplemental material

      AssayResult: 100

      AssayResultAssertion: Normal

      ControlType: Normal, wild type TP53 from control 1

      Comment: See Table S2 for details

    35. Supplemental material

      AssayResult: 7.1

      AssayResultAssertion: Abnormal

      Comment: See Table S2 for details