Medium-sized deletion in the BRCA1 gene: limitations of Sanger sequencing and MLPA analyses

we describe a family with a history of breast and ovarian cancer in which mlpa analysis of the brca1 gene pointed to a deletion including a part of exon 11. further characterization confirmed a loss of 374 bp in a region completely covered by conventional sequencing which had not revealed the deletion. because this alteration was only detected serendipitously with an mlpa probe, we calculated the probabilities of detecting medium-sized deletions in large exons by methods including initial pcr amplification. this showed that a considerable fraction of medium-sized deletions are undetectable by currently used standard methods of mutation analyses. we conclude that long, widely overlapping amplicons should be used to minimize the risk of missing medium-sized deletions. alternatively, large exons could be completely covered by narrow-spaced mlpa probes.