Genome wide analysis identifies mitotic recombination as cause of somatic loss of heterozygosity in cysts
from polycystic liver disease patients.
M.J. Janssen1,*, R. Pfundt2, J.P.H. Drenth1
1
Department of Gastroenterology & Hepatology, 2 Department of Human Genetics Radboud University
Nijmegen Medical Centre, Nijmegen, The Netherlands. *mj.janssen@mdl.umcn.nl
Somatic mutations play an important role in the progression of many diseases, including inheritable cancers,
and benign disorders such as polycystic liver disease (PCLD). We recently found in PCLD patients that carry a
PRKCSH germline mutation, that 76% of the liver cysts had lost the wild type PRKCSH allele through loss of
heterozygosity (LOH). The aim of this study was to determine the nature and the extent of the underlying
somatic genomic changes.
We isolated cyst epithelial cells from liver tissue which was obtained during laporoscopic cyst fenestration from
a PCLD patient carrying a c.292+1G>C PRKCSH germline mutation. Cells were isolated from adjacent liver tissue
using EDTA and trypsin. Identity of the cells was confirmed using CK19 staining. We performed a genome wide
cytogenetic array analysis (Affymetrix CytoScanTM HD with 2.7 Million probes of which 750.000 SNP probes) for
high resolution imaging of both copy number variations and LOH regions from 2 cysts.
Using this approach we found that the LOH region leading to loss of the wild type PRKCSH allele was in both
cysts the result of terminal copy number neutral LOH on the short arm of chromosome 19. We could identify in
each cyst a single breakpoint from where the LOH continued to the end of the p arm, covering a region of 14
Mb (megabases) in the first and 18 Mb in the second cyst. The location of the breakpoint was different in each
cyst, thereby indicating these cysts developed independently and resulted from a different somatic event. No
other genomic abnormalities were found.
In conclusion, these data shows that a single breakpoint in the p arm of chromosome 19 is responsible for the
LOH which leads to loss of the wide type PRKCSH allele in these cysts. As the LOH is not caused by a deletion, a
mitotic recombination event must have occurred leading to copy number neutral LOH. These data provide
important insights in the mechanisms behind somatic mutations in a benign disorder.
Keywords: polycystic liver disease (PCLD); somatic mutations; loss of heterozygosity; genome wide; mitotic
recombination