| Title: |
Patch clamp dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2 |
| Authors: |
Ng, Chai-Ann; Ullah, Rizwan; Farr, Jessica; Hill, Adam; Kozek, Krystian; Vanags, Loren; Mitchell, Devyn; Kroncke, Brett; Vandenberg, Jamie |
| Publisher Information: |
Zenodo |
| Publication Year: |
2022 |
| Collection: |
Zenodo |
| Description: |
Many genes, including KCNH2, contain 'hotspot' domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of KCNH2, a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death. Forty-two percent of KCNH2 exon 2 variants caused at least 50 % reduction in protein trafficking and 65% of these trafficking defective variants exerted a dominant-negative effect when co-expressed with a WT KCNH2 allele as assessed using a calibrated patch clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this 'hotspot' domain is necessary. Our massively parallel trafficking assay can provide this information prospectively. ; The raw SyncroPatch datafiles (obtained after unzipping the Patch_Clamp_Dataset_1.zip, Patch_Clamp_Dataset_2.zip, Patch_Clamp_Dataset_3.zip and Patch_Clamp_Dataset_4.zip file) can be opened using DataControl software (Nanion). Data can be reanalysed directly in DataControl and a copy of these data for each protocol have been exported as csv files and can be analysed using Python scripts available at https://git.victorchang.edu.au/projects/SADA/repos/syncropatch_automated_analysis/browse. The list of variants assayed on each plate are available in the "compound editor" tab of each dataset. This information is also provided in the excel spreadsheet: ... |
| Document Type: |
dataset |
| Language: |
unknown |
| Relation: |
https://zenodo.org/communities/dryad/; https://zenodo.org/records/6507250; oai:zenodo.org:6507250; https://doi.org/10.5061/dryad.zpc866t9x |
| DOI: |
10.5061/dryad.zpc866t9x |
| Availability: |
https://doi.org/10.5061/dryad.zpc866t9x; https://zenodo.org/records/6507250 |
| Rights: |
Creative Commons Zero v1.0 Universal ; cc0-1.0 ; https://creativecommons.org/publicdomain/zero/1.0/legalcode |
| Accession Number: |
edsbas.A08DBC0E |
| Database: |
BASE |