A noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family

Whitney Besse, Jungmin Choi, Dina Ahram, Shrikant Mane, Simone Sanna-Cherchi, Vicente Torres, Stefan Somlo

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Expanded mutation detection and novel gene discovery for isolated polycystic liver disease (PCLD) are necessary as 50% of cases do not have identified mutations in the seven published disease genes. We investigated a family with five affected siblings for which no loss-of-function variants were identified by whole exome sequencing analysis. SNP genotyping and linkage analysis narrowed the candidate regions to ∼8% of the genome, which included two published PCLD genes in close proximity to each other, GANAB and LRP5. Based on these findings, we re-evaluated the exome sequencing data and identified a novel intronic nine base pair deletion in the vicinity of the GANAB exon 24 splice donor that had initially been discarded by the sequence analysis pipelines. We used a minigene assay to show that this deletion leads to skipping of exon 24 in cell lines and primary human cholangiocytes. These findings prompt genomic evaluation beyond the coding region to enhance mutation detection in PCLD and to avoid premature implication of other genes in linkage disequilibrium.

Original languageEnglish (US)
Pages (from-to)378-382
Number of pages5
JournalHuman Mutation
Volume39
Issue number3
DOIs
StatePublished - Mar 1 2018

Fingerprint

Exome
Mutation
Exons
Genes
Linkage Disequilibrium
Genetic Association Studies
Base Pairing
Single Nucleotide Polymorphism
Sequence Analysis
Genome
Cell Line
Polycystic liver disease

Keywords

  • GANAB
  • LRP5
  • minigene
  • polycystic liver disease
  • splice assay

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

A noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family. / Besse, Whitney; Choi, Jungmin; Ahram, Dina; Mane, Shrikant; Sanna-Cherchi, Simone; Torres, Vicente; Somlo, Stefan.

In: Human Mutation, Vol. 39, No. 3, 01.03.2018, p. 378-382.

Research output: Contribution to journalArticle

Besse, W, Choi, J, Ahram, D, Mane, S, Sanna-Cherchi, S, Torres, V & Somlo, S 2018, 'A noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family', Human Mutation, vol. 39, no. 3, pp. 378-382. https://doi.org/10.1002/humu.23383
Besse, Whitney ; Choi, Jungmin ; Ahram, Dina ; Mane, Shrikant ; Sanna-Cherchi, Simone ; Torres, Vicente ; Somlo, Stefan. / A noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family. In: Human Mutation. 2018 ; Vol. 39, No. 3. pp. 378-382.
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