Analysis of immune regulatory genes' copy number variants in Graves' disease.
BACKGROUND
Copy number variants (CNVs) have recently been reported to be associated with several autoimmune conditions. Moreover, loci involved in immunity are enriched in CNVs. Therefore, we hypothesized that CNVs in immune genes associated with Graves' disease (GD) may contribute to the etiology of disease.


METHODS
One hundred ninety-one North American Caucasian GD patients and 192 Caucasian controls were analyzed for CNVs in three major immune regulatory genes: CD40, PTPN22, and CTLA-4. Copy number was determined using quantitative-PCR (Q-PCR) assays specifically designed for determining copy numbers in genomic DNA. Additionally, a well-characterized CNV in the amylase gene was typed in a separate dataset of DNA samples that were derived from cell lines or blood.


RESULTS
No CNVs could be confirmed in the CD40 and CTLA-4 genes, even though a CD40 CNV is cataloged in the Database of Genomic Variants. Only the PTPN22 CNV was confirmed in our cohort, but it was rare and appeared in only two individuals. A key finding was that the source of DNA has a significant effect on CNV typing. There was a statistically significant increase in amylase locus deletions in cell line-derived DNA compared to blood-derived DNA samples.


CONCLUSIONS
We conclude that CNV analysis should be performed only using blood-derived DNA Samples. Additionally, the CTLA-4, CD40, and PTPN22 loci do not harbor CNVs that play a role in the etiology of GD.
Division of Endocrinology, Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA. amanda.huber@mssm.edu
Amanda K
AK
Huber
Erlinda S
ES
Concepcion
Alisha
A
Gandhi
Francesca
F
Menconi
Eric P
EP
Smith
Mehdi
M
Keddache
Yaron
Y
Tomer
D000328:Adult; D000681:Amylases / Q000235:genetics; D015703:Antigens, CD / Q000235:genetics*; D019013:CD40 Antigens / Q000235:genetics*; D060908:CTLA-4 Antigen; D016022:Case-Control Studies; D002460:Cell Line; D018628:Gene Dosage; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human; D006111:Graves Disease / Q000235:genetics* / Q000276:immunology*; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods; D054596:Protein Tyrosine Phosphatase, Non-Receptor Type 22 / Q000235:genetics*; D017422:Sequence Analysis, DNA
D015703:Antigens, CD; D019013:CD40 Antigens; D060908:CTLA-4 Antigen; C556706:CTLA4 protein, human; C516765:PTPN22 protein, human; D054596:Protein Tyrosine Phosphatase, Non-Receptor Type 22; D000681:Amylases