Variant calling analysis of cfDNA whole exome sequencing in neuroblastoma
This dataset contains VCF files from a variant calling analysis of 19 neuroblastoma patients. WES or WGS data of the primary tumor were compared to WES cfDNA analysis at the time of diagnosis and at a 2nd timepoint (complete remission, partial remission, disease progression or relapse). For 4 patients, WGS of germline, tumor at diagnosis and tumor at relapse DNA was performed on Illumina HiSeq2500, with 100-bp paired-end reads. For the other patients, WES was performed using either an AgilentSureSelect Human All Exon v5 or a Roche Nimblegen SeqCap EZ Exome V3 kit on Illumina HiSeq2000, with 100-bp paired-end reads. SNVs observed in any of the primary tumors or cfDNA samples studied by WES were targeted using a capture sequencing panel at all intermediate time points.
- 14/12/2017
- 146 samples
- DAC: EGAC00001000319
Institut Curie Neuroblastoma DAC policy
DAC NAME AND ACCESSIONThis document specifies the policy for granting access to the European Genome-phenome Archive (EGA) secure Web based tools for managing data access permissions to the data stored in the EGA database. Access is granted to those Data Access Committee members named in this document by Paul Flicek, head of Genes, Genomes and Variation.Conditions of access:The account holder will abide by all current and future policies of the EBI for computer use as well as computer use policies of the European Molecular Biology Laboratory (EMBL), of which the EBI is a part. All EGA specific policies and standard operating procedures (SOPs) must also be followed. All applicable policies will be provided to the authorized users. Method of access:The EBI will create a personal account for the authorized person. The account username and password together with a RSA key provide access to the secure EGA infrastructure. A separate document with detailed guidelines on how to access and use these tools is provided to each account holder. The EGA help-desk provides training when needed.Review:All individuals will access to the EGA user authorization tools will be reviewed annually by Paul Flicek. Any staff changes affecting the authorized person must be provided immediately to Paul Flicek (flicek@ebi.ac.uk).Authorized Data Access Committee user:Gudrun SchleiermacherDépartement d'Oncologie Pédiatrique et INSERM U830 Institut Curie26 rue d'Ulm75248 Paris Cedex 05Francegudrun.schleiermacher@curie.frOlivier DelattreInstitut Curie – Centre de recherche – Unité U830 Inserm26 rue d'Ulm – 75248 Paris Cedex 05 Franceolivier.delattre@curie.frSupervisor of Authorized user:Olivier DelattreDirector of the Unit 830 Insermolivier.delattre@curie.fr
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 |
---|---|---|
EGAS00001002705 | Other |
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 | Located in | |
---|---|---|---|---|
EGAF00001781265 | vcf | 2.6 kB | ||
EGAF00001781266 | vcf | 5.4 kB | ||
EGAF00001781267 | vcf | 4.7 kB | ||
EGAF00001781268 | vcf | 8.4 kB | ||
EGAF00001781269 | vcf | 15.1 kB | ||
EGAF00001781270 | vcf | 8.7 kB | ||
EGAF00001781271 | vcf | 6.3 kB | ||
EGAF00001781272 | vcf | 3.0 kB | ||
EGAF00001781273 | vcf | 2.6 kB | ||
EGAF00001781274 | vcf | 2.8 kB | ||
EGAF00001781275 | vcf | 2.5 kB | ||
EGAF00001781276 | vcf | 3.7 kB | ||
EGAF00001781277 | vcf | 4.6 kB | ||
EGAF00001781278 | vcf | 2.7 kB | ||
EGAF00001781279 | vcf | 3.1 kB | ||
EGAF00001781280 | vcf | 3.1 kB | ||
EGAF00001781281 | vcf | 2.1 kB | ||
EGAF00001781282 | vcf | 2.3 kB | ||
EGAF00001781283 | vcf | 2.6 kB | ||
19 Files (86.4 kB) |