Copy number variation and association over T-cell receptor genes—influence of DNA source

Abstract

Genomic copy number variants (CNVs) are a common, heritable source of inter-individual differences in genomic sequence. Their influence on phenotypic variability and their involvement in the pathogenesis of several common diseases is well established and the object of many current studies. In the course of examining CNV association to various quantitative traits in a general population, we have detected a strong association of CNVs over the four TCR genes to lymphocyte and neutrophil numbers in blood. In a small replication series, we have further characterized the nature of these CNVs and found them not to be germline, but dependent on the origin of analysed DNA. Germline deletion and rearrangement around the T-cell receptor (TCR) genes naturally occurs in white blood cells. Blood DNA derived from persons with high lymphocyte counts generates variable intensity signals which behave like germline CNVs over these genes. As DNA containing a relative high proportion of these CNV-like events involving the TCR genes has the ability to influence genotype counts of SNPs in the regions of these genes, care should be taken in interpreting and replicating association signals on variants within these genes when blood-derived DNA is the only source of data.

Rare CNVs in Suicide Attempt include Schizophrenia-Associated Loci and Neurodevelopmental Genes: A Pilot Genome-Wide and Family-Based Study

“…FBAT-CNV associations. As our source of DNA was blood, the TCR-associations observed here likely reflect inter-individual variation in somatic rearrangements and/or proportions of lymphocytes, rather than association with SA [32, 44]. This problem has been highlighted by others previously, e.g.…”

“…Using SNPs to complement the testing of CNV-markers, five genome-wide significant CNV-signals ( P ≤ 5 x 10 −8 ; S2 Table) were also observed (Table A in S1 File); four at chromosome 14 (rs8010032, rs10143357, rs17116313 and rs8016619) in the proximity of the significant CNV markers, and one on chromosome 7 (rs1860517). But these associations all mapped to consensus CNVs located in T-cell receptor (TCR) regions (TCR alpha at chromosome 14 and TCR gamma at chromosome 7; Table A in S1 File), and such associations likely reflect somatic, non-inherited alterations rather than association with the SA outcome (see Discussion) [32, 34, 44, 45]. Fig A in S1 File depicts the quantiles vs quantiles (Q-Q) plots of the FBAT-CNV P -values for the 88,450 CNV markers, with or without the TCR regions included.…”

“…This problem has been highlighted by others previously, e.g. comparing CNV-associations between different sources of DNA and performing confirmatory PCRs [44]. Furthermore, it has also been previously reported about spurious CNV-associations of TCRs on chromosome 14 and 7 when using the FBAT-CNV methodology, involving age-dependent effects with regard to signal intensity in TCRs [34].…”

Copy number variations in multiple sclerosis and neuromyelitis optica

“…39 Although the pathogenic role of cd T cells in MS has not been well documented, cd T cell clones expressing a certain TCR gamma chain as a result of deletion within TRG may be involved in the pathophysiology through the regulation of cytokine and chemokine expression of CNSinfiltrating cells. 41 Therefore, we adjusted the DNA of all samples to be equal and then performed the CNV analysis for each white blood cell subset. The BAF findings from a multiple sclerosis (MS) patient carrying the most significant copy number variation (CNV) within TRG suggest that the CNV is a hemizygous deletion (A).…”

“…Thus, it is important to assess the gene copy number within the TCR loci, which may be influenced by the DNA source or sample lymphocyte counts. 41 Therefore, we adjusted the DNA of all samples to be equal and then performed the CNV analysis for each white blood cell subset. LRR and BAF data of T cell subsets from MS patients indicated that the deletion-type CNV at TRG involves the entire J gene segment, as well as part of the V gene segment.…”