Molecular diagnosis of Wilson disease using prevalent mutations and informative single-nucleotide polymorphism markers.
BACKGROUND
Wilson disease (WD) is an autosomal recessive disorder caused by defects in the ATPase, Cu(2+) transporting, beta-polypeptide gene (ATP7B) resulting in accumulation of copper in liver and brain. WD can be thwarted if detected at a presymptomatic stage, but occasional recombination during carrier detection with dinucleotide repeat markers flanking the WD locus may lead to faulty diagnosis. We examined the use of intragenic single-nucleotide polymorphism (SNP) markers to avoid this limitation.


METHODS
We prepared genomic DNA from the peripheral blood of Indian WD patients. By use of PCR, we amplified the exons and flanking regions of the WD gene and then performed sequencing to identify the nucleotide variants. We genotyped the SNPs in 1871 individuals by use of the Sequenom mass array system. We made linkage disequilibrium plots using Haploview software.


RESULTS
We identified 1 mutation accounting for 11% (19 of 174) of WD chromosomes among patients in addition to 4 prevalent mutations characterized previously. Among 24 innocuous allelic variants identified, we selected 3 SNPs found to have high heterozygosity (>0.40) for the detection of mutant WD chromosomes. On analyzing these SNPs in 28 test individuals, who were sibs to 17 unrelated WD patients, we obtained unequivocal genotyping in 25 cases (approximately 89%). The remaining 3 cases were genotyped by dinucleotide repeat marker (D13S133).


CONCLUSIONS
Sets of SNP markers are highly heterozygous across most world populations and could be used in combination with analysis of prevalent mutations as a comprehensive strategy for determining presymptomatic and carrier sibs of WD patients.
Gupta
Arnab
A
Molecular and Human Genetics Division, Indian Institute of Chemical Biology, Kolkata, India.
Maulik
Mahua
M
Nasipuri
Poonam
P
Chattopadhyay
Ishita
I
Das
Shyamal K
SK
Gangopadhyay
Prasanta K
PK
Ray
Kunal
K
D000251:Adenosine Triphosphatases / Q000235:genetics*; D027682:Cation Transport Proteins / Q000235:genetics*; D000073840:Copper-Transporting ATPases; D005819:Genetic Markers; D005838:Genotype; D006527:Hepatolenticular Degeneration / Q000175:diagnosis* / Q000208:ethnology / Q000235:genetics*; D006579:Heterozygote; D006801:Humans; D007194:India / Q000453:epidemiology; D015810:Linkage Disequilibrium; D025202:Molecular Diagnostic Techniques; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D010375:Pedigree; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D044382:Population Groups; D035781:Siblings
D027682:Cation Transport Proteins; D005819:Genetic Markers; D000251:Adenosine Triphosphatases; C000612464:ATP7B protein, human; D000073840:Copper-Transporting ATPases