Carpenter et al. BMC Genomics 2011, 12:418 http://www.biomedcentral.com/1471-2164/12/418 RESEARCH ARTICLE Open Access Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders Danielle Carpenter1, Susan Walker1, Natalie Prescott2, Joost Schalkwijk3 and John AL Armour1* Abstract Background: Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn’s disease, rheumatoid arthritis and psoriasis clinical cohorts. Results: We evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn’s disease, rheumatoid arthritis or psoriasis. Conclusions: Differential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion. Background genotyping are robust for all copy number classes and Within the last few years there have been significant do not result in the systematic rejection of samples with developments in our understanding of copy number var- high copy number. Repeated exclusion of particular gen- iation (CNV) and its contribution to human genetic var- otypes will lead to mis-representation of copy number iation. It is now apparent that CNVs are both a frequent variation at a particular locus in a given population due form of variation throughout the human genome, and to an artificially reduced apparent mean copy number. are implicated in disease susceptibility [1,2]. To define the full variation at a particular copy number In general, three forms of CNVs can be defined; inser- variable locus it is critical that these technical challenges tion, deletion and multi-allelic, but accurate and stan- are overcome successfully. dardised measurement of individual copy numbers is Furthermore, and perhaps most importantly, accurate technically challenging. In particular the measurement CNV measurement is essential in the context of case of multi-allelic CNVs is the most problematic, more control association studies. Critically, inaccurate copy specifically those with higher copy numbers, where it is number measurements can lead to differential bias essential that the technical challenges of copy number between cases and controls and result in false positive findings [3]. In SNP based studies differential bias can * Correspondence: [email protected] lead to differences in allele frequency estimates between 1Centre for Genetics and Genomics and School of Biology, University of batches of samples. In the context of CNVs bias can be Nottingham, Nottingham NG7 2UH, UK seen as a systematic shift in the raw measurement Full list of author information is available at the end of the article © 2011 Carpenter et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Carpenter et al. BMC Genomics 2011, 12:418 Page 2 of 9 http://www.biomedcentral.com/1471-2164/12/418 around integer values for cases and controls, leading to ThecopyvariablegenesCCL3L1 and CCL4L1 located differential mis-classification of samples by either over- on chromosome 17q12 lie in a 90 kb repeat unit, neigh- or under-estimation of the integer copy number. Differ- bouring the paralogous, but copy invariant, genes CCL3 ences in DNA source and quality can cause small and CCL4 [12]. CCL3L1 and CCL4L1 show 96% changes in the measured copy number distribution of sequence similarity at both the nucleotide and protein case and control samples [2]. Furthermore, the power to level with their respective paralogues [13,14]. All four detect disease associations in case control studies is also genes (CCL3, CCL3L1, CCL4 and CCL4L1) encode che- reduced with inaccurate genotyping of copy number [4]. mokines, chemotactic cytokines, which play an impor- Thus accurate determination of copy number is limited tant role in the immune response by attracting by the precision of the methodology used, which needs lymphocytes and macrophages to sites of infection and to be robust and replicable to give maximum power and inflammation. Furthermore they are all natural ligands reduce spurious disease associations. forCCR5,theco-receptorusedbyHIV-1forcellentry New whole-genome genotyping platforms now incor- [15,16], with CCL3L1 being the most potent [17]. As porate probes to interrogate multiple CNVs [5], and such there have been a number of association studies have begun to yield associations between such variants focused on CCL3L1 copy number variation and HIV-1 and disease phenotypes [2]. However, even these meth- susceptibility [7,18,19]. However, the reported associa- ods are sensitive to DNA quality [6] and are limited in tions are under dispute and the accuracy of CCL3L1 their accuracy to genotype multiallelic loci. The recent measurement is a major factor in the debate [20-23]. report by the Wellcome Trust Case Control Consor- Here we report a modification of a previously tium [2] discusses in detail the potential artefactual described PRT method to measure CCL3L1/CCL4L1 influences on copy number determination and demon- copy number making it more efficient, cost effective and strates the potential for reporting spurious associations convenient. As CCL3L1 and CCL4L1 function as an with CNVs, especially multiallelic regions. To comple- attractant of inflammatory mediators we have performed ment whole genome approaches, particularly for com- three case control studies with autoimmune phenotypes plex diseases where effect sizes are likely to be small, (Crohn’s disease, rheumatoid arthritis and psoriasis). We locus specific methods are also required for investigat- subsequently discuss in detail the accuracy of the PRT ing multiallelic CNV loci. Such targeted methods can methodology used, the precision in CCL3L1/CCL4L1 provide sufficiently accurate data to limit the potential copy number measurement and highlight the implica- for false positive or negative results as a result of dif- tions of differential bias with copy number variation. ferential bias. Locus specific methods are generally PCR-based, and perhaps the most widely used is Real- Results Time quantitative PCR, which depends upon the quan- CCL3L1 copy number measurement tification of a copy variable test locus in comparison The paralogue ratio test was used to genotype the copy with an unrelated reference locus [7]. However, differ- number of the CCL3L1/CCL4L1 copy variable region in ential amplification efficiencies between test and refer- a total of 1661 samples of European origin. The copy ence loci can generate inaccuracies, particularly for number measures generated with the “CCL3A” and high copy number measurements where the relative “CCL3C” measurement systems were shown to be difference in ratio between test and reference products equivalent in accuracy (see additional file 1, Figure S1). is smaller for neighbouring copy number classes. An In the majority of cases (1550/1661) the three indepen- alternative locus specific method with improved relia- dent PRT assays assigned concordant measurements of bility for CNV determination is the paralogue ratio test copy number for samples (to within 0.5 of the integer (PRT)[8].Thismethodusesasinglepairsofprimers value for 85% of samples and to within 0.75 for 93% of to amplify specifically two products simultaneously, samples) (see table 1). Samples showing a higher level of one from a copy-constant reference locus and the discordance between the integer copy numbers assigned other from the copy variable test locus of interest. The by the PRT systems were assayed for two microsatellites copy number of the test locus is then estimated from that are present within the repeat unit [11]. The micro- the ratio of test to reference products. Recently, the satellite genotyping allowed confident integer copy num- accuracy of the PRT method has been directly com- ber calling for 31 of the discordant samples, leaving 2 pared with a Real-Time quantitative PCR method of samplesforwhichthecopynumbercannotbeconfi- copy number measurement for b-defensins and shown dently resolved, and these have therefore been excluded to be the more accurate and robust approach [9]. The from further analysis. PRT method has previously been used to successfully