1. Longitudinal change in collagen degradation biomarkers in idiopathic pulmonary fibrosis: an analysis from the prospective, multicentre PROFILE study 
R Gisli Jenkins, PhD, Juliet K Simpson, PhD, Gauri Saini, MD, Jane H Bentley, PhD, Anne-Marie Russell, MSc, Rebecca Braybrooke, RGN, Philip L Molyneaux, MD, Tricia M McKeever, PhD, Athol U Wells, MD, Aiden Flynn, PhD, Prof Richard B Hubbard, MD, Diana J Leeming, PhD, Richard P Marshall, PhD, Morten A Karsdal, PhD, Pauline T Lukey, PhD, Dr Toby M Maher, PhD 
The Lancet Respiratory Medicine 
Volume 3, Issue 6, Pages (June 2015)
DOI: /S (15)00048-X
Copyright © 2015 Elsevier Ltd Terms and Conditions

2. Figure 1 Study population
A discovery cohort of 55 patients, based on disease severity as determined by composite physiological index (mildest, n=21 [39%]; moderate, n=14 [25%]; severest, n=20 [37%]) was drawn from the first 100 participants. The validation cohort (n=134) comprised 15% mild (n=20), 72% moderate (n=96), and 14% (n=18) severe participants based on the criteria applied to the discovery cohort consisted of the subsequent 114 participants plus the remaining participants with idiopathic pulmonary fibrosis from the first 100 patients. Three participants were excluded from the validation cohort (one was missing a baseline serum sample and two were lost to follow-up).
The Lancet Respiratory Medicine 2015 3, DOI: ( /S (15)00048-X)
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3. Figure 2
Baseline comparison of neoepitope concentrations in healthy controls and participants with idiopathic pulmonary fibrosis with stable or progressive disease in the discovery cohort
Biomarker data from the discovery cohort are mean and 95% CI (error bars) adjusted for age and sex. Disease progression was defined as all-cause mortality or 10% or more decline in forced vital capacity at 12 months. For ELM2, 4% of values were imputed. For all other epitopes, the imputation rate was less than 1%. *Healthy control compared with stable idiopathic pulmonary fibrosis. †Healthy control compared with progressive idiopathic pulmonary fibrosis. ‡Stable idiopathic pulmonary fibrosis compared with progressive idiopathic pulmonary fibrosis.
The Lancet Respiratory Medicine 2015 3, DOI: ( /S (15)00048-X)
Copyright © 2015 Elsevier Ltd Terms and Conditions

4. Figure 3
Baseline comparison of neoepitope concentrations in healthy controls and participants with idiopathic pulmonary fibrosis in the validation cohort
At baseline, there were 50 healthy age-matched and sex-matched controls and 134 participants with idiopathic pulmonary fibrosis (one of whom was missing a baseline blood sample, so 133). Error bars are 95% CIs, adjusted for age and sex. For C5M, 2% of values were imputed. For all other epitopes the imputation rate was less than 1%.
The Lancet Respiratory Medicine 2015 3, DOI: ( /S (15)00048-X)
Copyright © 2015 Elsevier Ltd Terms and Conditions

5. Figure 4
Comparison of neoepitope concentrations in healthy controls, participants with stable idiopathic pulmonary fibrosis, and participants with progressive idiopathic pulmonary fibrosis at baseline and at 1 month, 3 months, and 6 months after baseline in the validation cohort
Biomarker data are mean (ng/mL) and 95% CI. The number of evaluable samples available for analysis at each time point are provided at the foot of each panel. Two participants were excluded from analysis because of missing longitudinal follow-up data and one participant because of missing baseline samples. For C5M, 2% of values were imputed. For all other neoepitopes, the imputation rate was less than 1%.
The Lancet Respiratory Medicine 2015 3, DOI: ( /S (15)00048-X)
Copyright © 2015 Elsevier Ltd Terms and Conditions

6. Figure 5
Effect of 3 month change in neoepitope concentrations on overall survival
The number of deaths in each group is shown for every biomarker. Hazard ratio represents the mortality risk in participants with rising neoepitope concentrations relative to those with stable or falling concentrations. p values presented are those for association between the individual, dichotomous marker, and survival.
The Lancet Respiratory Medicine 2015 3, DOI: ( /S (15)00048-X)
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7. Figure 6
Effect of the magnitude of change from baseline to 3 months in neoepitope concentrations on overall survival
The effect of different rates of neoepitope concentration change was explored by use of a range of threshold values of the biomarker gradient to dichotomise the patients into a high (gradient above threshold) or low (gradient below threshold) group. The effect, on the hazard ratio (HR), of dichotomising participants at different available thresholds of 3-month neoepitope change is presented. The x-axis represents the threshold of the slope of the biomarker change that was used to dichotomise the patient population. The y-axis represents the HR plotted as base 2 log transformation of the unitary data. The data are expressed as mean HR with 95% CIs for all thresholds. For every threshold value on the x-axis, the HR plotted represents the risk for participants with idiopathic pulmonary fibrosis in the high group versus the low group. The upper and lower extremes for every neoepitope have been limited to comparisons for which there are at least five deaths in both the high and low groups.
The Lancet Respiratory Medicine 2015 3, DOI: ( /S (15)00048-X)
Copyright © 2015 Elsevier Ltd Terms and Conditions