Genome-wide high-resolution screening in Dupuytren's disease reveals common regions of DNA copy number alterations.
OBJECTIVE
Dupuytren's disease (DD) is a familial disorder with a high genetic susceptibility in white people; however, its etiopathogenesis remains unknown. Previous comparative genomic hybridization studies using lower-resolution, 44-k oligonucleotide-based arrays revealed no copy number variation (CNV) changes in DD. In this study, we used a higher-resolution genome-wide screening (next-generation microarrays) comprising 963,331 human sequences (3 kb spacing between probes) for whole genome DNA variation analysis. The objective was to detect cryptic chromosomal imbalances in DD.


METHODS
Agilent SurePrint G3 microarrays, one million format (Agilent Technologies, Santa Clara, CA), were used to detect CNV regions (CNVRs) in DNA extracted from nodules of 4 white men with DD (age, 69 +/- 4 y). Reference samples were from the DNA of 10 men who served as control patients. Copy number variations that were common to greater than 3 assessed DD individuals (p < .05) were selected as candidate loci for DD etiology. In addition, quantitative polymerase chain reactions (qPCR) assays were designed for selected CNVRs on DNA from 13 DD patients and 11 control patients. Independent t-tests and Fisher's exact tests were carried out for statistical analysis.


RESULTS
Three novel CNVs previously unreported in the phenotypically normal population were detected in 3 DD cases, located at 10q22, 16p12.1, and 17p12. Nine polymorphic CNVRs potentially associated with DD were determined using our strategic selection criteria, locating to chromosomes 1q31, 6p21, 7p14, 8p11, 12p13, 14q11, 17q21 and 20p13. More than 3 of the DD cases tested had a CNVR located to a small region on 6p21 and 4 CNVRs within 6p21-22 of the human leukocyte antigen (HLA) genes.


CONCLUSIONS
Three novel copy number alterations were observed in 3 unrelated patients with sporadic (no known family history) DD. Nine polymorphic CNVRs were found to be common among the DD cases. These variants might contain genes involved in DD formation, indicating that important gene networks expressed within the palmar fascia might contribute to genetic susceptibility of DD.
Shih
Barbara B
BB
Plastic and Reconstructive Surgery Research, School of Translational Medicine, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M17ND, UK.
Tassabehji
May
M
Watson
James S
JS
McGrouther
Angus D
AD
Bayat
Ardeshir
A
D000368:Aged; D016022:Case-Control Studies; D055028:Comparative Genomic Hybridization; D004247:DNA / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D004387:Dupuytren Contracture / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008297:Male; D046228:Microarray Analysis; D016133:Polymerase Chain Reaction / Q000379:methods; D012016:Reference Values
D004247:DNA