DOI: 10.20350/digitalcsic/16556
title: Molecular analysis of atypical GC donors of the breast cancer susceptibility genes ATM, BRIP1 and PALB2

description: [Description of methods used for collection/generation of data] - Sanger sequencing. - Fluorescent Fragment Analysis.
description: This dataset contains fragment analysis and sequencing files of a comprehensive study of GC splice sites of the breast/ovarian cancer susceptibility genes ATM, BRIP1 and PALB2. The non-canonical GC-5’ splice-sites (5’ss) are the most common exception (~1%) to the classical GT/AG splicing rule. They constitute weak 5’ss and can be regulated by splicing factors, so they are especially sensitive to genetic variations inducing misrecognition of their respective exons. We aimed at investigating GC-5’ss of the breast/ovarian cancer susceptibility genes ATM (exon 50), BRIP1 (exon 1) and PALB2 (exon 12) and their dysregulation induced by DNA variants. For this purpose, we have used three splicing reporter minigenes: mgATM_49-52, mgBRIP1_1-2 and mgPALB2_5-12. We identified three regions of ATM exon 50 and PALB2 exon 12 enriched in splicing regulatory elements. We selected and assayed 23 variants located at these positive intervals, 12 of which impaired recognition of their respective exons.
description: File List: • Folder: ATM ex50 - Sub-folder: Fragment_Analysis. Fluorescent Fragment Analysis: Sub-folder Microdeletions: 35 *.fsa files of fluorescent fragment analysis of RT-PCRs of microdeletions Sub-folder Variants and control: 53 *.fsa files of fluorescent fragment analysis of RT-PCRs of variants - Sub-folder: Sequences. Sub-folder cDNA. Transcript Sequencing. Sub-folder Microdeletions: 14 *.ab1 files of transcripts generated by microdeletions. Sub-folder Variants and control: 30 *.ab1 files of transcripts generated by variants. Sub-folder: Minigenes. Sequence files of wild type and mutant constructs: Sub-folder Microdeletions: 12 *.ab1 files. Sub-folder Variants and control: 18 *.ab1 files - Sub-folder: WT. Fragment analysis and sequencing files of the wild type minigene. Fragment_Analysis: 3 *.fsa files of fluorescent fragment analysis of RT-PCRs of the wild type construct. Sequences: 4 *.ab1 files of RT-PCRs and the construct sequences of the wild type minigene. • Folder: BRIP1 - Sub-folder: Sequences. Sub-folder cDNA. Transcript Sequencing. 8 *.ab1 files of transcripts generated by microdeletions. Sub-folder: Minigene. Sequence files of mutant constructs: 4 *.ab1 files. - Sub-folder: WT. Fragment analysis and sequencing files of the wild type minigene. Fragment_Analysis: 3 *.fsa files of fluorescent fragment analysis of RT-PCRs of the wild type construct. Sequences: 3 *.ab1 files of RT-PCRs and the construct sequences of the wild type minigene. • Folder: PALB2 ex12 - Sub-folder: Fragment_Analysis. Fluorescent Fragment Analysis: Sub-folder Microdeletions: 33 *.fsa files of fluorescent fragment analysis of RT-PCRs of microdeletions Sub-folder Variants: 30 *.fsa files of fluorescent fragment analysis of RT-PCRs of variants - Sub-folder: Sequences. Sub-folder cDNA. Transcript Sequencing: 25 *.ab1 files of transcripts generated by microdeletions. Sub-folder: Minigenes. Sequence files of wild type and mutant constructs: Sub-folder Microdeletions: 11 *.ab1 files. Sub-folder Variants: 11 *.ab1 files - Sub-folder: WT. Fragment analysis and sequencing files of the wild type minigene. Fragment_Analysis: 3 *.fsa files of fluorescent fragment analysis of RT-PCRs of the wild type construct. Sequences: 11 *.ab1 files of RT-PCRs and the construct sequences of the wild type minigene.