Comparison of T-cell receptor diversity of people with myalgic encephalomyelitis versus controls

BMC Research Notes

Table 4 Variables tested as potential confounders with MDS plot x-axis using a generalised linear model fit

Variable	Estimate	Std. Error	t-value	\(\varvec{P}\varvec{r}(>\|\varvec{t}\left\|\right)\)	Significance
(Intercept)	1.25E + 11	2.22E + 11	0.564	0.574
ME(mm)	1.89E + 02	3.20E + 02	0.590	0.556
ME(sa)	4.51E + 01	3.68E + 02	0.123	0.903
MS	4.73E + 01	3.23E + 02	0.147	0.884
Age	-1.36E + 03	4.29E + 02	-3.16	0.00199	**
PBMC Number	1.35E + 02	1.02E + 02	1.32	0.190
CD8+ % Input	-4.54E + 01	2.87E + 01	-1.58	0.116
CD8 + Cells Post-selection	-7.90E + 02	7.85E + 02	-1.01	0.316
Purity	6.47E + 00	8.34E + 00	0.776	0.439
DNA Extracted (µg)	-9.18E + 01	1.51E + 02	-0.608	0.544
DNA Yield (ng)	6.11E-03	3.90E-01	0.016	0.988
Demultiplexed Reads (641)	1.23E-04	5.47E-05	2.25	0.0263	*
PEAR Assembled (641)	1.19E + 01	1.69E + 01	0.701	0.485
Demultiplexed Reads (782)	-1.56E-05	4.27E-05	-0.366	0.715
PEAR Assembled (782)	-1.39E + 01	1.87E + 01	-0.741	0.460
α Coding Junctions	5.74E-01	2.38E-01	2.41	0.0174	*
β Coding Junctions	-4.18E-01	3.32E-01	-1.26	0.211
γ Coding Junctions	-8.88E-01	3.07E-01	-2.90	0.00452	**
α %	-1.25E + 11	2.22E + 11	-0.564	0.574
β %	-1.25E + 11	2.22E + 11	-0.564	0.574
γ %	-1.25E + 11	2.22E + 11	-0.564	0.574

Significance levels for the t-test statistic are shown: for \(p<0.001\) (***), \(p<0.01\) (**), and \(p<0.05\) (*). ME(sa), ME(mm) and MS were testing whether being a member of the given subgroup was correlated with the axis, relative to healthy controls (HC). Age (binned by decade) was the linear term of the model t for that covariate. Other covariates: PBMC Number, total number of cells per sample; CD8⁺% Input, percentage of input PBMCs that were CD8⁺ cells; CD8⁺ cells post-selection, number of CD8⁺ cells after the SureSelect process; Purity, corresponding CD8⁺ purity at this stage; DNA Extracted (µg), total amount of DNA initially recovered from each sample; DNA Yield (ng), amount remaining after size selection; Demultiplexed Reads [Library], total number of reads recovered for the two Illumina flowcells of sufficient quality (library numbers 641 and 782); PEAR Assembled [Library], percentages assembled into clonotypes for the same libraries using the Paired-End Read Merger tool [37]; α/β/γ Coding Junctions, total numbers of coding junctions for each chain type; α/β/γ %, percentages of each chain type, relative to the other two types (such that the sum was 100%)

ISSN: 1756-0500