Analysis of 51 breast cancer susceptibility genes in BRCA1 and BRCA2 mutation-negative individuals from a South Australian cohort

These files contain individually sequenced and pooled sequencing data for the analysis of 51 hereditary and putative breast cancer susceptibility genes in BRCA1/2 mutation-negative individuals. All individuals included in this study had familial (or suspected inherited) breast and/or ovarian cancer and had been referred for genetic screening. Screening did not identify any pathogenic mutations within BRCA1/2. All sequencing was carried out using the Ion Torrent Personal Genome Machine or Ion Torrent using a custom AmpliSeq gene panel. The BED files for the designed gene panel have been provided. The individually sequenced data folder contains deidentified raw sequencing data for 42 individuals. The pooled data folders contains sequencing data from 4 pools, each containing 25 individuals. Sequencing data was either provided as .fastq or .BAM, so files of each sequencing format have been provided for the initial analysis.

Data can be analysed using any genomics analysis programs or algorithms (CLC Genomics Workbench and Ion Reporter were used successfully in this study). An additional 89 individually sequenced files and 4 pooled samples are available by emailing library@flinders.edu.au.

Data consists of 3 zip files (6.5Gb compressed (zipped) to 3.34Gb), plus a text ReadMe file:

- BED_files - 3x .bed files (26Kb)
- Individual_Data - 4 Folders (1.7Gb)
* Run 1 (3 samples) .fastq files
* Run 2 (10 samples) .fastq files
* Run 3 (29 samples) .fastq files
* Run 6 (1 sample) .bam file

- Pooled_data (1.8Gb)
* Pool 1 (fastq) .fastq
* Pool 6 (fastq) .fastq
* Pool 11 (fastq) .fastq
* Pool 7 (BAM) .bam

- ReadMe.txt (2Kb)


Additional 89 individually sequenced files and 4 pooled samples is approximately 44Gb (uncompressed).

Genes included in the custom AmpliSeq panel were : ATF1, ATM, BARD1, BRCA1, BRCA2, BRCC3, BRIP1, CDH1,CDKN1A, CDKN2A, CHEK1, CHEK2, CKS1B, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, EP300, FAM175A, GADD45A, HLTF, HMMR, KAT2B, MRE11A, NBN, NQO2, PALB2, PKMYT1, PRKDC, RAD50, RAD51, RAD51C, RAD51D, RBL1, RBL2, RFC2, RFC3, RFC4, RFC5, RPA1, RPRM, RPS6KA1, SFN, SLC19A1, SMARCD2, TP53, UIMC1, WEE1, XRCC2

Date coverage: 2005-06 - 2014-06