This README.txt file was generated on 2022-04-16 by Chai-Ann Ng GENERAL INFORMATION 1. Title of Dataset: Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome 2. Date of data collection: 2021 3. Recommended citation for this dataset: (a) Jiang et al. A calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome. American Journal of Human Genetics (2022); (b) Jiang et al. Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome. https://doi.org/10.5061/dryad.m905qfv38 DATA & FILE OVERVIEW 1. Description of dataset The aim of this study was to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in the KCNH2 gene. The assay was designed according to recommendations proposed by the ClinGen Sequence Variant Interpretation Working Group. Thirty-one variants (17 pathogenic/likely pathogenic, 14 benign/likely benign) were classified internally as variant controls. They were heterozygously expressed in Flp-In HEK293 cells for assessing the effects of variant on current density and channel gating in order to determine the sensitive and specificity of the assay. All 17 pathogenic variant controls had reduced current density and 13/14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying moderate or supporting evidence strength for VUS reclassification. Inclusion of KCNH2 functional assay evidence enabled us to reclassify 6 out of 44 VUS as likely pathogenic. The high-throughput patch clamp assay can provide moderate strength evidence for clinical interpretation of clinical KCNH2 variants and demonstrates the value of developing automated patch clamp assays for functional characterisation of ion channel gene variants. 2. File List: SyncroPatch data files: (2.1) SyncroPatch_data.zip: 24 electrophysiology dataset collected in 2021 (2.2) CSV_files_zip: Exported CSV files that contain patch clamp current traces (2.3) variant location.xlsx: plate ID and column location for different variants investigated for the above electrophysiology dataset Data file specific for SyncroPatch_data.zip After unzipping, each folder (e.g. 01042021_CJ) contains 7 folders and 1 zip file. These were the original folders and files generated by the Patch Control software during data acquisition using the SyncroPatch 384PE (Nanion Technologies). Option (A) If you have access to the software 'DataControl' (Nanion Technologies), simply point your path to the directory (SyncroPatch_data) to inspect or analyse the data. Option (B) If you do not have access to the software 'DataControl', a seperate CSV files have been exported for each of the three protocols ((a) hERG_ssDeact_3s_AN (b) hERG_ssAct_1s_AN; (c) hERG_Inact_Onset_AN)) in CSV_files.zip. These csv files can be analysed using your prefer electrophysiology software. Data file specific for CSV_files.zip These CSV files are the current traces recorded on SyncroPatch 384PE using the following voltage protocols: (a) hERG_ssDeact_3s_AN (b) hERG_ssAct_1s_AN; (c) hERG_Inact_Onset_AN). Detail explanation of these protocols can be found at Ng et al. 2021 (PMID: 33884304). Data file specific for variant location.xlsx Each SyncroPatch assay plate (e.g. 01042021_CJ) contains 24 columns, which corresponding to 12 different cell lines (WT, 10 KCNH2 variant and negative control). Every 2 columns corresponds to a specific cell line (e.g. columns 1-2 for WT, columns 3-4 for variant I31M, etc). This excel file contains the number of plate, Plate ID and the name of the variants denoted by their respective column numbers.