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| Status |
Public on Jun 30, 2016 |
| Title |
Chromosomal abnormalities in hepatic cysts point to novel polycystic liver disease genes |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
Autosomal dominant polycystic liver disease (ADPLD) is caused by mutations in PRKCSH, SEC63, and LRP5, while autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1, and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild type allele in the developing cyst. We hypothesize that we can use this mechanism to identify novel disease genes that reside in LOH regions. In this study, we aim to map abnormal genomic regions using high-density SNP microarrays to find novel polycystic liver disease genes.
We collected 46 cysts from 23 patients with polycystic or sporadic hepatic cysts, and analyzed DNA from those cysts using high-resolution microarray (n=24) or Sanger sequencing (n=22). We here focused on regions of homozygosity on the autosomes (>3.0Mb), and large CNVs (>1.0Mb).
We found frequent LOH in PRKCSH (22/29), and PKD1/PKD2 (2/3) cysts of patients with known heterozygous germline variants in the respective genes. In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, chromosome 9q copy number loss, and LOH on chromosome 3p. The latter region was overlapping with an LOH region identified in two other cysts.
Unique germline and somatic abnormalities occur frequently in and outside of known genes underlying cysts. Each liver cyst has a unique genetic makeup. LOH driver gene BUB1 may imply germline causes of genetic instability in PLD.
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| Overall design |
24 liver cysts from 23 patients
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| Contributor(s) |
Wills ES, Cnossen WR, Veltman JA, Woestenenk R, Steehouwer M, Salomon J, te Morsche RH, Huch M, Hehir-Kwa JY, Banning MJ, Pfundt R, Roepman R, Hoischen A, Drenth PJ |
| Citation(s) |
27552964 |
| Submission date |
Mar 01, 2016 |
| Last update date |
Mar 27, 2020 |
| Contact name |
Edgar Wills |
| E-mail(s) |
edgar.wills@gmail.com
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| Phone |
+31617411834
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| Organization name |
RadboudUMC
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| Department |
Gastroenterology & Hepatology
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| Street address |
Andrej Sacharowstraat 37
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| City |
The Hague |
| ZIP/Postal code |
2552HK |
| Country |
Netherlands |
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| Platforms (1) |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
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| Samples (27)
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| Relations |
| BioProject |
PRJNA313973 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE78808_RAW.tar |
2.9 Gb |
(http)(custom) |
TAR (of CEL, CYCHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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