Whole exome sequencing identifies recessive PKHD1 mutations in a Chinese twin family with Caroli disease

Abstract

Background: Mutations in PKHD1 cause autosomal recessive Caroli disease, which is a rare congenital disorder involving cystic dilatation of the intrahepatic bile ducts. However, the mutational spectrum of PKHD1 and the phenotype-genotype correlations have not yet been fully established.

Methods: Whole exome sequencing (WES) was performed on one twin sample with Caroli disease from a Chinese family from Shandong province. Routine Sanger sequencing was used to validate the WES and to carry out segregation studies. We also described the PKHD1 mutation associated with the genotype-phenotype of this twin.

Results: A combination of WES and Sanger sequencing revealed the genetic defect to be a novel compound heterozygous genotype in PKHD1, including the missense mutation c.2507 T>C, predicted to cause a valine to alanine substitution at codon 836 (c.2507T>C, p.Val836Ala), and the nonsense mutation c.2341C>T, which is predicted to result in an arginine to stop codon at codon 781 (c.2341C>T, p.Arg781*). This compound heterozygous genotype co-segregates with the Caroli disease-affected pedigree members, but is absent in 200 normal chromosomes.

Conclusions: Our findings indicate exome sequencing can be useful in the diagnosis of Caroli disease patients and associate a compound heterozygous genotype in PKHD1 with Caroli disease, which further increases our understanding of the mutation spectrum of PKHD1 in association with Caroli disease.

Figure 1. Partial sequence of exon 23 in the PKHD1 from member of this Caroli disease-affected pedigree.

(a), (b) and (d) Arrowhead indicates the heterozygous C and T at nucleotide 2341 in proband, elder twins and their mother respectively. (c) Arrowhead indicates the C at nucleotide 2341(wild type) in their father.

Figure 2. Partial sequence of exon 24 in the PKHD1 from member of this Caroli disease-affected pedigree.

(b), (c) and (d) Arrowhead indicates the heterozygous T and C at nucleotide 2507 in proband, elder twins and their father respectively. (a) Arrowhead indicates the T at nucleotide 2507 (wild type) in their mother.

Figure 3. DHPLC shows wave pattern of wild type and mutant type PKHD1.

Wild type: from normal individuals. Mutant type : from affected individuals.

Figure 4. Multiple-sequence alignment of the PKHD1 protein including Mus musculus, Rattus norvegicus, Pan paniscus, Xenopus (Silurana) tropicalis, Falco cherrug, Zonotrichia albicollis and Homo sapiens.

The Val 836 residue is located within a highly conserved region.