NGS Database Infrastructure

Data from whole exome sequencing of 287 clinically well-characterized Parkinson disease patients from southern Sweden is now available in the MultiPark NGS database.

Patients had been recruited within the PARkinsonLUnd (PARLU) study and MultiPark’s biobank sample collection(MPBC). Great care has been taken to ensure the patients have Parkinson disease, using clinical examinations and longitudinal follow up within the PARLU research study and Parkinson registry data. The database is enriched for groups where the genetic component to the disease cause likely is increased - patients who reported that family members also had Parkinson disease and patients younger than the average age at disease onset. An exact description of the studied population is provided in the table below. 

Whole exome sequencing has been performed on an Illumina platform at the Medical faculty’s core sequencing facility, the Center for translational genomics. The database lists all genetic variants that have been identified in any of the patients’ exomes. Variants have been annotated with a wide range of bioinformatical and database information, in an attempt to make the database useful for many MultiPark researchers. The added information includes various standardized nomenclatures for variant designation, the variant’s frequency in large international databases as well as within the MultiPark NGS database, locus conservation between species, and predictions of the variants’ biological effect on the protein level from a large number of prediction tools. It is easily readable and available in the form of an excel/txt file for MultiPark PIs on request to Andreas [dot] Puschmann [at] med [dot] lu [dot] se (Andreas Puschmann).

Within the NGS database infrastructure, also whole genome datasets have been obtained from 12 patients/families with frontotemporal dementia of unknown cause.

Additional searches and/or individual-level genetic data can be made available to interested researchers through contact with Andreas Puschmann; ethics approval and approval for sharing of individual-level patient data are usually required.     

The summary data also includes data obtained in individual research projects without / prior to MultiPark support to maximize the numbers of patients sequenced. 

This infrastructure forms a collaboration with Region Skåne who are responsible for individual patient-related data.