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Mutations in Breast Cancer Information Core Database predicted to affect mRNA splicing

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ASSEDA | Shannon human splicing pipeline | Veridical
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Names of mutations for both BRCA1 and BRCA2:            http://cancer.cytognomix.org/BRCA/BIC-Mutation-Naming-Track.txt     

Mutations in

BRCA1 :         Acceptor sites             http://cancer.cytognomix.org/BRCA/BRCA1-BIC-Acceptor-Affected.txt

                        Donor sites                 http://cancer.cytognomix.org/BRCA/BRCA1-BIC-Donor-Affected.txt

BRCA2:         Acceptor sites             http://cancer.cytognomix.org/BRCA/BRCA2-BIC-Acceptor-Affected.txt

                        Donor sites                 http://cancer.cytognomix.org/BRCA/BRCA2-BIC-Donor-Affected.txt

 

Example of the various splice isoforms produced by mutations in exon 5 of BRCA1 (bottom, header “UCSC Genes Based On RefSeq...”, etc). The mutations result in wildtype splicing, exon exclusion and cryptic donor use. To visualize the predicted splicing effects of the BIC mutations, 5 custom tracks are displayed (top to bottom): the BIC mutation naming track (a GFF track, which displays the name of the mutation causing the Ri change at the affected splice site’s coordinate); changes in acceptor site information due to a mutation, changes in donor site due to a mutation (2 BEDGRAPH tracks which display vertical lines on the ordinate at the affected splice site position, and the values of these lines are the ΔRi caused by each BIC mutation); and the predicted strengths of the acceptor and donor sites on the negative strand of the reference sequence (two more BEDGRAPH tracks where the vertical lines represent the predicted splice site strength at that coordinate). The letter symbols indicate: A) The natural donor site (5.9 bits) is abolished (ΔRi = -18.6 bits), by the mutations indicated. Other mutations weaken the site, but not to the same degree. B) A second strong donor site (5.2 bits) can be recognized, and but is weakened by the mutation designated by the box. C) mutations in BIC which abolish the 10.2 bit natural acceptor site of this exon. The image also shows pre-existing and novel cryptic acceptors which could be activated when the natural site is abolished.