WES and RNA-seq of triple-negative breast cancers from the MyBrCa cohort
The dataset contains a genomics characterization of 35 triple-negative Asian breast tumours from the Malaysian Breast Cancer cohort. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, and RNA-seq of tumour tissue at 40X coverage (>15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a NovaSeq 6000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturer’s instructions and also subjected to paired end 75 sequencing on a NovaSeq 6000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.
- 105 samples
- DAC: EGAC00001001740
- Technology: Illumina NovaSeq 6000
Access to controlled data will follow the guidelines provided by the International Cancer Genome Consortium, subject to the Malaysian Personal Data Protection Act.
Access to controlled data will follow the guidelines provided by the International Cancer Genome Consortium. All individual-level sequence data stored on the EGA are controlled and requires the review of the Data Access Committee before access is permitted, to protect patient privacy. All aggregate data and data that cannot be used to re-identify individuals are considered open, and are accessible through the relevant publications. Given that all patients in the cohort are Malaysian, data access is further subject to the Malaysian Personal Data Protection Act and its various prohibitions.
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 |
|---|---|---|
| EGAS00001006518 | 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.