Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory diseaseReport as inadecuate

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BMC Genomics

, 17:299

Non-human and non-rodent vertebrate genomics


BackgroundDissecting the role copy number variants CNVs play in disease pathogenesis is directly reliant on accurate methods for quantification. The Shar-Pei dog breed is predisposed to a complex autoinflammatory disease with numerous clinical manifestations. One such sign, recurrent fever, was previously shown to be significantly associated with a novel, but unstable CNV CNV 16.1. Droplet digital PCR ddPCR offers a new mechanism for CNV detection via absolute quantification with the promise of added precision and reliability. The aim of this study was to evaluate ddPCR in relation to quantitative PCR qPCR and to assess the suitability of the favoured method as a genetic test for Shar-Pei Autoinflammatory Disease SPAID.

ResultsOne hundred and ninety-six individuals were assayed using both PCR methods at two CNV positions CNV 14.3 and CNV 16.1. The digital method revealed a striking result. The CNVs did not follow a continuum of alleles as previously reported, rather the alleles were stable and pedigree analysis showed they adhered to Mendelian segregation. Subsequent analysis of ddPCR case-control data confirmed that both CNVs remained significantly associated with the subphenotype of fever, but also to the encompassing SPAID complex p < 0.001. In addition, harbouring CNV 16.1 allele five CNV 16.1|5 resulted in a four-fold increase in the odds for SPAID p < 0.001. The inclusion of a genetic marker for CNV 16.1 in a genome-wide association test revealed that this variant explained 9.7 % of genetic variance and 25.8 % of the additive genetic heritability of this autoinflammatory disease.

ConclusionsThis data shows the utility of the ddPCR method to resolve cryptic copy number inheritance patterns and so open avenues of genetic testing. In its current form, the ddPCR test presented here could be used in canine breeding to reduce the number of homozygote CNV 16.1|5 individuals and thereby to reduce the prevalence of disease in this breed.

KeywordsCopy number variation Autoinflammation Droplet digital PCR Quantitative PCR AbbreviationsaCGHarray comparative genomic hybridisation

AMY2Bamylase, alpha 2B

AUCarea under the curve

CNVcopy number variant

DAMPdanger associated molecular pattern

ddPCRdroplet digital polymerase chain reaction

FDRFalse discovery rate

FGF3, FGF4 and FGF19Fibroblast Growth Factor 3, 4 and 19

FISHfluorescence in situ hybridisation

GWASgenome wide association analysis


HAS2Hyaluronan Synthase 2

HWEHardy-Weinberg Equilibrium


LDlinkage disequilibrium

MLPAmultiplex ligation-dependent probe amplification


PCRpolymerase chain reaction

qPCRquantitative polymerase chain reaction

RFrandom forest

SNPsingle nucleotide polymorphisms

SPAIDShar-Pei Autoinflammatory Disease

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-2619-0 contains supplementary material, which is available to authorized users.

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Author: M. Olsson - M. Kierczak - Å. Karlsson - J. Jabłońska - P. Leegwater - M. Koltookian - J. Abadie - C. Dufaure De Citres

Source: https://link.springer.com/


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