RT Journal Article SR Electronic T1 Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer JF Journal of Medical Genetics JO J Med Genet FD BMJ Publishing Group Ltd SP jmedgenet-2021-108147 DO 10.1136/jmedgenet-2021-108147 A1 Florentine Scharf A1 Rafaela Magalhaes Leal Silva A1 Monika Morak A1 Alex Hastie A1 Julia M A Pickl A1 Kai Sendelbach A1 Christian Gebhard A1 Melanie Locher A1 Andreas Laner A1 Verena Steinke-Lange A1 Udo Koehler A1 Elke Holinski-Feder A1 Dieter A Wolf YR 2021 UL http://jmg.bmj.com/content/early/2021/12/13/jmedgenet-2021-108147.abstract AB Purpose Approximately 20% of patients with clinical familial adenomatous polyposis (FAP) remain unsolved after molecular genetic analysis of the APC and other polyposis genes, suggesting additional pathomechanisms.Methods We applied multidimensional genomic analysis employing chromosomal microarray profiling, optical mapping, long-read genome and RNA sequencing combined with FISH and standard PCR of genomic and complementary DNA to decode a patient with an attenuated FAP that had remained unsolved by Sanger sequencing and multigene panel next-generation sequencing for years.Results We identified a complex 3.9 Mb rearrangement involving 14 fragments from chromosome 5q22.1q22.3 of which three were lost, 1 reinserted into chromosome 5 and 10 inserted into chromosome 10q21.3 in a seemingly random order and orientation thus fulfilling the major criteria of chromothripsis. The rearrangement separates APC promoter 1B from the coding ORF (open reading frame) thus leading to allele-specific downregulation of APC mRNA. The rearrangement also involves three additional genes implicated in the APC–Axin–GSK3B–β-catenin signalling pathway.Conclusions Based on comprehensive genomic analysis, we propose that constitutional chromothripsis dampening APC expression, possibly modified by additional APC–Axin–GSK3B–β-catenin pathway disruptions, underlies the patient’s clinical phenotype. The combinatorial approach we deployed provides a powerful tool set for deciphering unsolved familial polyposis and potentially other tumour syndromes and monogenic diseases.Data are available on reasonable request.