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SweGen whole-genome sequencing from the Northern Sweden Population Health Study

The dataset contains whole-genome sequencing data (aligned read files) in CRAM-format (lossless compression) for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

Request Access

Uppsala University Data Access Agreement

Uppsala University FEGA Access guide Requests for data Requests for access to these data will be assessed based on Swedish laws and regulations. Requests must include an explicit acceptance of the conditions stated below and information about the following aspects: - The requester must attach an approval from an ethics committee or equivalent body that allows the data to be handled in accordance to the laws and ethical guidelines in the receiving country. - For researchers in the European Union – specify the legal basis according to GDPR to use the data. - Information about how the data will be stored and managed with regards to information security procedures. Requests for data are only accepted if the recipient adheres to the following conditions: Purpose - The recipient agrees to use data only for research. Confidentiality -The recipient agrees to preserve, at all times, the confidentiality of data pertaining to identifiable data subjects. Data protection - Recipients in EU agrees that it, and its registered users, are covered by and shall comply with the obligations contained in the General Data Protection Regulation (EU) 2016/679 ("GDPR"). Upon receipt of the data, the recipient will become controller of the personal data as defined in the GDPR. Recipients outside EU shall comply with relevant national laws concerning the protection of personal data. Uppsala University reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures. The recipient agrees that it, and its registered users, shall not analyse or make any use of the data in such a way that has the potential to: (a) lead to the identification of any data subject; or (b) compromise the protected identity of any data subject in any way. Access and Governance - The recipient agrees that it shall take all reasonable security precautions to keep the data confidential. The recipient agrees to, under no circumstances, give access to data to any third party, except to registered users (as described below). The recipient agrees to only give access to data, in whole or part, or any identifiable material derived from the data, to a registered user. The recipient agrees that before it gives any registered user access to data, it shall first inform about the conditions stated in this text and that he or she must comply with the obligations. The recipient shall only give registered users that are not researchers (including but not limited to students or new researchers to the field) access to the data if they are supervised by a researcher who will take responsibility for such registered users’ use of the data. The recipient must make sure that: - Data is processed in a way that ensures the confidentiality and integrity of the data. - Analysis and storage of the data must be performed in a secure environment that ensures that only registered users have access to the data. - Transfer of data must be done through encrypted channels. - There are standard operating routines that ensure that registered users handle the data in accordance with information security and legal requirements. - In the case of a personal data breach, the recipient must immediately inform Uppsala University, and the appropriate national data protection authority, of such an incident. Errors - The recipient must notify the Uppsala University of any errors detected in the data. Acknowledgement of data use - The recipient agrees to acknowledge the creators and source of the data in any work based in whole or part on the Data. Definitions: “Research” shall mean research that is seeking to advance the understanding of the research purpose stated in the ethics approval or equivalent document. “Registered User” shall mean a researcher (or an individual conducting research under the supervision of a researcher) that is employed by the recipient and is bound by confidentiality and has been informed of the conditions stated above. For the avoidance of doubt, “Registered User” may also include students, visiting academics, contractors, sub-contractors or independent consultants provided that any such individual is bound by confidentiality and non-use obligations no less onerous than those binding the recipient’s employees.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000000906 Whole Genome Sequencing

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
EGAF50000316303 crai 1.3 MB
Federated EGA
EGAF50000316304 crai 1.3 MB
Federated EGA
EGAF50000316305 crai 1.2 MB
Federated EGA
EGAF50000316307 crai 1.7 MB
Federated EGA
EGAF50000316308 crai 1.3 MB
Federated EGA
EGAF50000316309 crai 1.6 MB
Federated EGA
EGAF50000316310 cram 28.7 GB
Federated EGA
EGAF50000316311 crai 1.6 MB
Federated EGA
EGAF50000316312 cram 33.6 GB
Federated EGA
EGAF50000316313 crai 1.2 MB
Federated EGA
EGAF50000316314 cram 32.7 GB
Federated EGA
EGAF50000316315 crai 1.4 MB
Federated EGA
EGAF50000316316 cram 34.3 GB
Federated EGA
EGAF50000316317 crai 1.2 MB
Federated EGA
EGAF50000316318 cram 26.4 GB
Federated EGA
EGAF50000316319 crai 1.3 MB
Federated EGA
EGAF50000316320 cram 28.4 GB
Federated EGA
EGAF50000316321 crai 1.4 MB
Federated EGA
EGAF50000316322 cram 25.9 GB
Federated EGA
EGAF50000316323 crai 1.3 MB
Federated EGA
EGAF50000316324 cram 27.7 GB
Federated EGA
EGAF50000316325 crai 1.3 MB
Federated EGA
EGAF50000316326 cram 27.5 GB
Federated EGA
EGAF50000316327 crai 1.3 MB
Federated EGA
EGAF50000316328 cram 30.4 GB
Federated EGA
EGAF50000316329 crai 1.5 MB
Federated EGA
EGAF50000316330 cram 28.6 GB
Federated EGA
EGAF50000316331 crai 1.4 MB
Federated EGA
EGAF50000316332 cram 27.5 GB
Federated EGA
EGAF50000316333 crai 1.5 MB
Federated EGA
EGAF50000316334 cram 31.9 GB
Federated EGA
EGAF50000316335 crai 1.5 MB
Federated EGA
EGAF50000316336 cram 29.2 GB
Federated EGA
EGAF50000316337 crai 1.5 MB
Federated EGA
EGAF50000316338 cram 31.3 GB
Federated EGA
EGAF50000316339 crai 1.3 MB
Federated EGA
EGAF50000316340 cram 33.3 GB
Federated EGA
EGAF50000316341 crai 1.3 MB
Federated EGA
EGAF50000316342 cram 32.6 GB
Federated EGA
EGAF50000316343 crai 1.5 MB
Federated EGA
EGAF50000316344 cram 28.7 GB
Federated EGA
EGAF50000316345 crai 1.3 MB
Federated EGA
EGAF50000316346 cram 27.3 GB
Federated EGA
EGAF50000316347 crai 1.4 MB
Federated EGA
EGAF50000316348 cram 32.2 GB
Federated EGA
EGAF50000316349 crai 1.3 MB
Federated EGA
EGAF50000316350 cram 29.8 GB
Federated EGA
EGAF50000316351 crai 1.3 MB
Federated EGA
EGAF50000316352 cram 29.1 GB
Federated EGA
EGAF50000316353 crai 1.3 MB
Federated EGA
EGAF50000316354 cram 27.7 GB
Federated EGA
EGAF50000316355 crai 1.3 MB
Federated EGA
EGAF50000316356 cram 27.6 GB
Federated EGA
EGAF50000316357 crai 1.5 MB
Federated EGA
EGAF50000316358 cram 26.8 GB
Federated EGA
EGAF50000316359 crai 1.3 MB
Federated EGA
EGAF50000316360 cram 38.9 GB
Federated EGA
EGAF50000316361 crai 1.2 MB
Federated EGA
EGAF50000316362 cram 31.8 GB
Federated EGA
EGAF50000316363 crai 1.2 MB
Federated EGA
EGAF50000316364 cram 26.4 GB
Federated EGA
EGAF50000316365 crai 1.3 MB
Federated EGA
EGAF50000316366 cram 25.8 GB
Federated EGA
EGAF50000316367 cram 26.7 GB
Federated EGA
EGAF50000316368 crai 1.3 MB
Federated EGA
EGAF50000316369 cram 29.1 GB
Federated EGA
EGAF50000316370 crai 1.4 MB
Federated EGA
EGAF50000316371 cram 28.3 GB
Federated EGA
EGAF50000316372 crai 1.4 MB
Federated EGA
EGAF50000316373 cram 28.3 GB
Federated EGA
EGAF50000316374 crai 1.3 MB
Federated EGA
EGAF50000316375 cram 31.1 GB
Federated EGA
EGAF50000316376 crai 1.3 MB
Federated EGA
EGAF50000316377 cram 29.2 GB
Federated EGA
EGAF50000316378 crai 1.2 MB
Federated EGA
EGAF50000316379 cram 28.4 GB
Federated EGA
EGAF50000316380 crai 1.3 MB
Federated EGA
EGAF50000316381 cram 27.1 GB
Federated EGA
EGAF50000316382 crai 1.4 MB
Federated EGA
EGAF50000316383 cram 27.0 GB
Federated EGA
EGAF50000316384 crai 1.3 MB
Federated EGA
EGAF50000316385 cram 28.4 GB
Federated EGA
EGAF50000316386 cram 28.2 GB
Federated EGA
EGAF50000316387 crai 1.4 MB
Federated EGA
EGAF50000316388 cram 25.7 GB
Federated EGA
EGAF50000316389 crai 1.4 MB
Federated EGA
EGAF50000316390 cram 25.9 GB
Federated EGA
EGAF50000316391 crai 1.4 MB
Federated EGA
EGAF50000316392 cram 29.7 GB
Federated EGA
EGAF50000316393 cram 29.3 GB
Federated EGA
EGAF50000316394 crai 1.4 MB
Federated EGA
EGAF50000316395 cram 28.4 GB
Federated EGA
EGAF50000316396 crai 1.4 MB
Federated EGA
EGAF50000316397 cram 32.9 GB
Federated EGA
EGAF50000316398 crai 1.9 MB
Federated EGA
EGAF50000316399 cram 38.7 GB
Federated EGA
EGAF50000316400 crai 1.3 MB
Federated EGA
EGAF50000316401 cram 37.8 GB
Federated EGA
EGAF50000316402 crai 1.3 MB
Federated EGA
EGAF50000316403 cram 36.0 GB
Federated EGA
EGAF50000316404 crai 1.7 MB
Federated EGA
EGAF50000316405 cram 50.3 GB
Federated EGA
EGAF50000316406 crai 1.7 MB
Federated EGA
EGAF50000316407 cram 36.2 GB
Federated EGA
EGAF50000316408 crai 1.5 MB
Federated EGA
EGAF50000316409 cram 34.4 GB
Federated EGA
EGAF50000316410 crai 1.6 MB
Federated EGA
EGAF50000316411 cram 29.2 GB
Federated EGA
EGAF50000316412 crai 1.6 MB
Federated EGA
EGAF50000316413 cram 44.7 GB
Federated EGA
EGAF50000316414 crai 1.6 MB
Federated EGA
EGAF50000316415 cram 31.8 GB
Federated EGA
EGAF50000316416 crai 1.7 MB
Federated EGA
EGAF50000316431 cram 32.6 GB
Federated EGA
EGAF50000316534 cram 31.1 GB
Federated EGA
EGAF50000316535 cram 32.6 GB
Federated EGA
116 Files (1.8 TB)