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Familial breast cancer targeted sequencing with ONT

A large cohort of 600 cases with familial breast cancer as classified by the Spanish Society of Medical Oncology (SEOM) Clinical Guidelines Update that were recruited during 6 years at Hospital Universitario Morales Meseguer (Murcia, Spain) were retrospectively evaluated to select 16 cases with no positive finding in NGS analysis of 20 genes implicated in this disease. These 16 cases were selected for further investigation using nanopore sequencing. This method involved the use of adaptive sampling enrichment, targeting a panel of 18 human genome regions, which contained the 20 genes (PTEN, ATM, BRCA2, PALB2, CDH1, TP53, NF1, RAD51D, BRCA1, RAD51C ,BRIP1, STK11, CHEK2, EPCAM, MSH2, MSH6, BARD1, MLH1, PMS2, NBN). In 5 samples (P1, P2, P4, P15 and P16) no selection of long reads was performed. Additionally, in 3 samples (P7, P9 and P10), both procedures were performed in two independent runs, and for the second run of P7, the DNA was previously fragmented using g-TUBE Covaris® (ref 520079) according to the protocol for 6 kb fragments.

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Genomic Data Access Policy: This policy outlines the guidelines and procedures established by Fundación para la Formación e Investigación Sanitarias de la Región de Murcia (FFIS) for accessing and using genomic data. It specifically addresses the data uploaded to the EGA (European Genome-phenome Archive), ensuring responsible and secure handling of the data for research and educational purposes.

1. Purpose: The purpose of this genomic data access policy is to establish guidelines and procedures for accessing and using genomic data collected and stored by Funciación para la Formación e Investigación Sanitarias de la Región de Murcia (FFIS)/IMIB. It ensures that genomic data is handled in a responsible, ethical, and secure manner, while promoting scientific research and advancements. 2. Scope: This policy applies to all individuals, including researchers, employees, and external collaborators, who want to access or use genomic data held by Fundación para la Formación e Investigación Sanitarias de la Región de Murcia (FFIS)/IMIB and stored in EGA (European Genome-phenome Archive). 3. Data Access Requests and EGA Data Submission: a. Access to genomic data in EGA shall be granted only to authorized individuals who have a legitimate need to conduct scientific research or fulfill their professional responsibilities. b. All individuals involved in the data submission process must follow the EGA data submission guidelines and comply with any additional requirements specified by FFIS and EGA. 4. Data Use and Sharing: a. Genomic data accessed and uploaded to the EGA database must be used solely for the purposes specified in the approved Data Access Agreement (DAA) and in accordance with the EGA data sharing policies. b. Researchers and individuals involved in the data submission process shall not share, disclose, or transfer genomic data to third parties without explicit permission from the Data Access Committee (DAC). c. When publishing research findings based on the genomic data, researchers should acknowledge the data source and comply with any data sharing policies or publication guidelines set by FFIS. 5. Data Security and Confidentiality: a. Genomic data must be stored and transmitted in a secure manner, using appropriate encryption and access controls, to prevent unauthorized access, loss, or theft. b. Individuals accessing genomic data shall comply with all relevant data protection laws and regulations, maintaining strict confidentiality and privacy of the data. 6. Compliance and Monitoring: a. Compliance with this policy shall be regularly monitored by the DAC. b. Non-compliance with this policy may result in disciplinary actions, including revocation of data access privileges, as deemed appropriate.

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
EGAS00001007375 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
EGAF00008116886 fq.gz 1.8 GB
EGAF00008116887 fq.gz 8.9 GB
EGAF00008116888 fq.gz 997.5 MB
EGAF00008116889 fq.gz 9.9 GB
EGAF00008116890 fq.gz 538.3 MB
EGAF00008116891 fq.gz 4.6 GB
EGAF00008116892 fq.gz 292.7 MB
EGAF00008116893 fq.gz 2.0 GB
EGAF00008116894 fq.gz 164.6 MB
EGAF00008116895 fq.gz 3.3 GB
EGAF00008116896 fq.gz 314.3 MB
EGAF00008116897 fq.gz 3.0 GB
EGAF00008116898 fq.gz 692.4 MB
EGAF00008116899 fq.gz 6.2 GB
EGAF00008116900 fq.gz 374.1 MB
EGAF00008116901 fq.gz 5.8 GB
EGAF00008116902 fq.gz 374.8 MB
EGAF00008116903 fq.gz 6.1 GB
EGAF00008116904 fq.gz 817.6 MB
EGAF00008116905 fq.gz 7.7 GB
EGAF00008116906 fq.gz 782.7 MB
EGAF00008116907 fq.gz 8.0 GB
EGAF00008116908 fq.gz 867.4 MB
EGAF00008116909 fq.gz 6.6 GB
EGAF00008116910 fq.gz 1.8 GB
EGAF00008116911 fq.gz 6.7 GB
EGAF00008116912 fq.gz 631.9 MB
EGAF00008116913 fq.gz 6.3 GB
EGAF00008116914 fq.gz 786.7 MB
EGAF00008116915 fq.gz 8.2 GB
EGAF00008116916 fq.gz 881.6 MB
EGAF00008116917 fq.gz 10.9 GB
EGAF00008116918 fq.gz 725.4 MB
EGAF00008116919 fq.gz 11.2 GB
EGAF00008116920 fq.gz 594.0 MB
EGAF00008116921 fq.gz 5.4 GB
EGAF00008116922 fq.gz 1.0 GB
EGAF00008116923 fq.gz 7.4 GB
38 Files (142.7 GB)