XXII. BIOCHEMICKÝ ZJAZD - Jesseniova lekárska fakulta

Lectures
A method for aUTOMaTED DETECTION of HETErOZYGOUS
INSErTION-DELETION MUTaTIONS
Peter Májek 1 , Vladimír Špitalský 1 , Gabriel Minárik 2 and Tomáš Szemes 2
1
ADINIS s.r.o., Bratislava
2
Department of Molecular Biology, FNS, Comenius University in Bratislava
Structural and insertion-deletion (indel) variants are of considerable importance, mostly
because of their phenotypic consequences. Indels shorter than 30 bp currently constitute
about 24 % of all disease causing mutations reported in Human Gene Mutation Database.
However, typical tools for analysis of sequence traces with indels obtained from diploid
samples do not have sufficient accuracy and therefore extensive manual review of such
samples is needed.
We present here a new algorithm, implemented in software ADINIS IndelFinder, for
automated detection of indel mutations from diploid sequence traces. The algorithm
identifies 95% of indel mutations selected by a human expert with 5% false positives
rate on a set of 39 sequence traces of exon 11 of KIT gene of subjects diagnosed with
gastrointestinal cancer.
The algorithm is based on a parametric digitalization of the electropherogram signal to
a discrete set of nucleotide peaks followed by three rounds of the Needleman-Wunsch
(NW) algorithm. The parameters of electropherogram digitalization as well as the scoring
matrices used in the NW are optimized by a Monte-Carlo sampling to automatically find
the best performing set of parameters.
XXII. Biochemistry Congress, Martin
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