Cell-Free DNA Fragmentomes in the Diagnostic Evaluation of Patients With Symptoms Suggestive of Lung Cancer

BACKGROUND

The diagnostic workup of individuals suspected of having lung cancer can be complex and protracted because conventional symptoms of lung cancer have low specificity and sensitivity.

RESEARCH QUESTION

Among individuals with symptoms of lung cancer, can a blood-based approach to analyze cell-free DNA (cfDNA) fragmentation (the DNA evaluation of fragments for early interception [DELFI] score) enhance evaluation for the possible presence of lung cancer?

STUDY DESIGN AND METHODS

Adults were referred to Bispebjerg Hospital (Copenhagen, Denmark) for diagnostic evaluation of initial imaging anomalies and symptoms consistent with lung cancer. Numbers and types of symptoms were extracted from medical records. cfDNA from plasma samples obtained at the prediagnostic visit was isolated, sequenced, and analyzed for genome-wide cfDNA fragmentation patterns. The relationships among clinical presentation, cancer status, and DELFI score were examined.

RESULTS

A total of 296 individuals were analyzed. Median DELFI scores were higher for those with lung cancer (n = 98) than those without cancer (n = 198; 0.94 vs 0.19; P < .001). In a multivariate model adjusted for age, smoking history, and presenting symptoms, the addition of the DELFI score improved the prediction of lung cancer for those who demonstrated symptoms (area under the receiver operating characteristic curve, 0.74-0.94).

INTERPRETATION

The DELFI score distinguishes individuals with lung cancer from those without cancer better than suspicious symptoms do. These results represent proof-of-concept support that fragmentation-based biomarker approaches may facilitate diagnostic resolution for patients with concerning symptoms of lung cancer.

Abstract 5714: Cell-free DNA fragmentation profiling for monitoring therapeutic response in metastatic colorectal cancer

BACKGROUND: Cell-free circulating tumor DNA (ctDNA) assays have been adopted to monitor therapeutic response in both early- and late-stage cancer. However, tests currently available require deep-targeted sequencing to detect cancer-specific mutations at low mutant allele frequency (MAF) levels in the circulation. Recently, we developed a tumor-agnostic approach called DELFI Tumor Fraction (DELFI-TF), a Bayesian probabilistic model designed to predict plasma tumor fractions based on genome-wide fragmentation-related features.

METHODS: Overall, 692 longitudinal plasma samples collected from 153 patients with initially unresectable colorectal cancer (CRC) liver-only metastases participating in the phase III study CAIRO5 (NCT02162563) were split across a training (RAS/BRAF mutant) and a validation cohort (RAS/BRAF wildtype). For all cell-free DNA (cfDNA) samples of patients within the training cohort (n=312), the tumor burden was quantified as the MAF of the tumor-tissue-proven RAS/BRAF variant measured by digital droplet PCR (ddPCR). Using cfDNA fragment-sequencing statistics from low-coverage WGS data, a Bayesian regression model was trained against the MAF of the tumor-specific driver RAS/BRAF variant in all longitudinal timepoints in the training cohort. Changes in DELFI-TF scores during first-line FOLFOX/FOLFIRI and bevacizumab therapy were assessed to predict disease response. A tissue-informed approach was applied to detect minimal residual disease in the subgroup of patients treated with curative intent (complete resection of the primary tumor and liver metastases).

RESULTS: In the training cohort, DELFI-TF scores strongly correlated with RAS/BRAF MAF measured by ddPCR (r=0.85, p&lt;0.001). DELFI-TF captured plasma tumor fractions associated with copy number changes when ddPCR failed to detect RAS/BRAF mutations. Before treatment initiation, DELFI-TF correlated with the sum of the largest diameters on CT scans according to RECIST1.1 (r=0.49, p&lt;0.001). Patients with negative and positive changes in DELFI-TF more often exhibited response and progressive disease based on consecutive RECIST assessments, respectively. Median progression-free survival was 9.9 and 12.8 months for patients with DELFI-TF low versus DELFI-TF high, respectively (p=0.007). Overall survival was 28.8 and 58.9 months for patients with DELFI-TF low versus DELFI-TF high, respectively (p=0.001). In patients treated with curative intent, tissue-informed focal and arm-level copy number changes were detected 4-12 weeks after metastasectomy. Most patients presenting molecular relapse were later diagnosed with clinical recurrence by conventional CT imaging.

CONCLUSIONS: DELFI-TF demonstrates the ability to use cfDNA fragmentomes to estimate cfDNA tumor burden with a performance comparable to standard approaches for treatment response monitoring and clinical outcome prediction.

Citation Format: Bahar Alipanahi, Iris van 't Erve, Keith Lumbard, Laurel K. Millberg, Zach Skidmore, Lorenzo Rinaldi, Jacob Carey, Jennifer Tom, Cornelis J. A. Punt, Nicholas C. Dracopoli, Gerrit A. Meijer, Robert B. Scharpf, Victor E. Velculescu, Remond Fijneman, Alessandro Leal. Cell-free DNA fragmentation profiling for monitoring therapeutic response in metastatic colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5714.

A Unusual Case of Classic Hodgkin Lymphoma (cHL) with Aberrant T-Antigens Expression

Introduction/Objective

T-cell-associated antigens (TCA) are rarely expressed by Hodgkin/Reed-Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) and is associated with uncertain clinical significance.

Methods/Case Report

We present a very recent case of a 68 year-old female with no significant past medical history presented with a large right groin mass for 1 month. She denied any fever, night sweats, fatigue or weight loss. CT abdomen/pelvis showed inguinal/pelvic lymphadenopathy. Resection showed effaced nodal architecture with a vague nodular appearance and with large, atypical nucleolated cells in a background of small, mature lymphocytes and histiocytes. Eosinophils are conspicuously absent in the background. The large cells were polylobated lymphocyte and histiocyte rich (L & H) like, classic HRS cells as well as multinucleated in appearance. The morphologic features overlapped between Classic Hodgkin Lymphoma, and Nodular Lymphocyte Predominant Hodgkin Lymphoma. Given the immunohistochemical (IHC) features of the neoplastic cells [CD45 negative, PAX5+ (weak), CD30+ (strong), CD15+ (majority) and MUM1 +] the diagnosis was most compatible with CHL. Interestingly, a subset of the Hodgkin cells (10-20%) aberrantly expressed a number of T-cell markers (CD2, CD3, CD4, and CD8). However, the background smaller T-cells did not show cytologic atypia or aberrancies of T-cell antigen markers. The large cells were negative for CD43 and ALK1. TCR gamma gene rearrangement was also negative for clonal T-lymphocytes, thus excluding the possibility of peripheral T-cell lymphoma with Hodgkin-like cells. Based on the morphology and IHC profile, this case proves to be CHL with multiple TCA expression including CD2, CD3, CD4 and CD8. She was planned for chemotherapy. Four months after the initial diagnosis and after completion of 2 cycles of chemotherapy, her PET CT scan showed improvement with right inguinal adenopathy being smaller in size and decreased avidity, indicating a response to treatment. She is due for 2 more cycles. Till todate she is doing well with no further symptoms.

Results (if a Case Study enter NA)

NA.

Conclusion

So far reported cases of classic Hodgkin lymphoma (CHL) with aberrant T-cell antigen (TCA) expression were associated with decreased event-free survival and overall survival when compared with TCA-negative CHLs. Our finding contributes to the literature and improves our knowledge of the disease.

Abstract 5159: Towards population-scale screening of human cancer using genome-wide fragmentation profiles of cell-free DNA

Introduction: Earlier detection is a critical clinical intervention to reduce cancer-related mortality. The DELFI liquid biopsy approach (DNA evaluation of fragments for early interception) utilizing low coverage (1-2x) whole genome sequencing (WGS) to analyze cell-free DNA (cfDNA) fragmentation provides a promising avenue for cancer detection. As sequencing costs remain a barrier to adoption of liquid biopsy approaches for early detection, we evaluated WGS for DELFI using 2-channel Illumina NovaSeq sequencing as a more affordable (~7-fold cost savings) alternative to 4-channel HiSeq instruments.

Methods: We performed WGS on the prospectively collected LUCAS cohort of 365 individuals at risk for lung cancer using both HiSeq and NovaSeq platforms (Mathios et. al., Nature Communications 2021). Genome-wide fragmentation was summarized in non-overlapping 5 Mb bins by ratio of short (100-150 bp) to long (151-220 bp) fragments.To measure within-sequencer repeatability, we compared fragmentation profiles of non-cancer individuals to the median non-cancer fragmentation profile by Spearman correlation. Principal component analyses were performed to assess the extent to which the sequencer explains variation of fragmentation profiles across samples.For cancer prediction, we used a penalized logistic regression model with fragmentation profiles and other genome-wide characteristics as features. Machine learning performance was assessed by cross-validation and area under the receiver operator characteristic curve (AUC). To evaluate whether we could have developed the classifier from a combination of NovaSeq with HiSeq sequenced samples, we evaluated performance trained on 90:10%, 75:25%, 50:50%, 25:75%, and 10:90% HiSeq:NovaSeq mixtures, respectively.

Results: cfDNA fragmentation profiles were highly concordant among non-cancer individuals for both platforms with median correlations of 0.96 (IQR: 0.95 - 0.97) and 0.95 (IQR: 0.94 - 0.96). Visualization of fragmentation principal components did not reveal separation by sequencing platform. The DELFI approach applied to samples sequenced by NovaSeq recapitulated previously published performance measures based on HiSeq (AUC 0.90, 95% CI 0.86 - 0.94). In simulations of mixed-platform datasets, we found the same qualitative performance (AUC range: 0.893-0.902).

Conclusions: cfDNA fragmentation profiles were similar between HiSeq and NovaSeq platforms, and classification accuracies from machine learning models trained on these platforms were equivalent. Our results indicate HiSeq and NovaSeq sequenced samples can be combined in models with no discernible loss in classification accuracy provided a balance of non-cancers and cancers are sequenced on both platforms. The lower cost of NovaSeq sequencing may enable wider adoption of genome-wide fragmentation-based approaches for cancer detection.

Citation Format: Akshaya V. Annapragada, Dimitrios Mathios, Stephen Cristiano, Jamie E. Medina, Vilmos Adleff, Noushin Niknafs, Jacob Carey, Nic Dracopoli, Peter Bach, Jillian Phallen, Victor E. Velculescu, Robert B. Scharpf. Towards population-scale screening of human cancer using genome-wide fragmentation profiles of cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5159.

Abstract 2224: DELFI as a real-time treatment response assessment for patients with cancer

Introduction: Measurement of tumor-derived DNA molecules in the plasma (ctDNA) has become a useful tool to determine the overall tumor burden in patients with cancer. The ctDNA burden may change over time, decreasing after treatment response and increasing with development of resistance to therapy. Monitoring the dynamics of ctDNA burden over the course of treatment with a rapid, non-invasive test enables physicians to make timely treatment decisions. Using the DNA evaluation of fragments for early interception (DELFI) approach, we have developed the DELFI Monitoring Score (DMS) to longitudinally assess ctDNA burden during therapy of cancer patients.

Methods: We performed low coverage whole genome sequencing on 302 cfDNA libraries of 76 treatment-naive metastatic colorectal cancer (mCRC) patients with at least one blood draw prior to and after treatment initiation. Mutations in KRAS, NRAS, or BRAF were independently measured by digital droplet PCR (ddPCR) for all timepoints evaluated. We trained a Bayesian regression model with the mutant allele fraction (MAF) of KRAS, NRAS, or BRAF as response and fragmentation-related features as predictors as well as a random intercept. To avoid overfitting and assess generalizability, we used cross-validation, wherein each patient’s samples were held out of the dataset and a model was trained on the samples of all other patients to generate predictions for the held-out samples. Patients with DMS below and above a detectability threshold at the first blood draw post-treatment (between 4-12 weeks) were classified as molecular responders and non-responders, respectively. Progression-free survival outcomes, defined as time to progression by RECIST 1.1 or death, were evaluated using a Kaplan-Meier estimator in these two groups.

Results: Molecular responders based on DMS assessment experienced longer progression-free survival than molecular non-responders (p &lt; 0.01), similar to a MAF-based approach. Additionally, in the 43 patients for whom the MAF of the KRAS, NRAS, or BRAF variants was 0% at the first blood draw post-treatment, we observed further separation on progression-free survival by the DELFI Monitoring Score (p = 0.014).

Conclusions: We developed a novel quantitative measure of ctDNA burden using cell-free DNA fragmentation patterns that is estimable from low coverage whole genome sequencing. The DMS appears to be useful for measuring ctDNA burden and enabling a non-invasive approach to treatment monitoring, as it distinguishes therapeutic responses in a mCRC cohort. Our ability to detect differences in progression-free survival among patients with undetectable ddPCR MAFs suggests that DMS may be more sensitive and predictive than conventional mutation-based approaches for treatment response monitoring.

Citation Format: Keith Lumbard, Laurel A. Keefer, Iris van't erve, Jacob Carey, Bryan Chesnick, Denise Butler, Michael Rongione, Cornelis J. Punt, Nicholas C. Dracopoli, Remond J. Fijneman, Gerrit A. Meijer, Robert B. Scharpf, Victor E. Velculescu, Alessandro Leal. DELFI as a real-time treatment response assessment for patients with cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2224.

Cell-free DNA (cfDNA) fragmentomes predict tumor burden in metastatic colorectal cancer (mCRC)

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Background: Measurement of plasma mutant allele fraction (MAF) in patients with cancer provides prognostic information, but this approach typically relies on prior tumor tissue analyses or knowledge of specific mutations. There is a clinical need to develop rapid and accurate noninvasive plasma-only approaches to estimate disease burden dynamics. Comprehensive genome-wide analyses of cfDNA fragmentomes has become a useful tool for noninvasive cancer characterization. Here we present a novel application to predict MAF from genome-wide fragmentation-related profiles (fMAF) as a prognostic marker in mCRC patients with initially unresectable liver-only metastases enrolled in the phase III CAIRO5 study (NCT02162563). Methods: 693 longitudinal plasma cfDNA samples were obtained from patients with RAS/BRAF-mutant mCRC (training arm, N = 78) and patients with RAS/BRAF wild-type mCRC (validation arm, N = 75) treated with first-line fluoropyrimidine-based chemotherapy were collected. MAFs as measured by digital droplet PCR (ddPCR) were obtained for patients in the training arm. We trained an initial regression model to predict MAFs with genome-wide fragmentation features using subject-level random intercepts. Out of sample predictions for participants in the RAS/BRAF-mutant mCRC arm were obtained through cross-validation. Cox proportional hazards models were used to evaluate the association between fMAF and PFS and overall survival (OS) at pre- and first post-treatment blood draws. Standardized hazard ratios (sHR) and 95% confidence intervals (CI) are reported. Results: There were 68 and 61 evaluable participants with median (range) age of 62 y (41-79 y) and 58 y (27-76 y), and 38% and 36% female in the training and testing arms, respectively. Median time between pre- and post-treatment blood draw was 8 weeks. In the training cohort, median fMAFs dropped from pre- to post-treatment initiation (17.8% to 1.8%). Median PFS was 9 months. For both fMAFs and RAS/BRAF MAFs, the association with PFS was stronger for the pre-treatment than the post-treatment timepoint (Table). Post-treatment fMAFs were not associated with PFS in the training cohort and similar trends were observed for OS. Conclusions: Initial modeling demonstrates the ability of cfDNA fragmentomes to estimate cell-free DNA tumor burden with performance comparable to standard approaches. Ongoing modeling efforts will result in evaluation of a final model in the testing arm. The development of a noninvasive tissue-independent diagnostic approach that does not rely on mutation detection in the circulation has the potential to expand the use of liquid biopsies for advanced disease monitoring. Clinical trial information: NCT02162563. [Table: see text]

1438 The Past, Present and Future Management of Complex Chyle Fistulae

Background

Chyle leak/fistula is a rare complication of oesophageal surgery, usually consequent on an unintended breach of the thoracic duct, its tributaries, or the cisterna chyli. For high volume persistent leaks further surgery has been the traditional approach, however two cases have resulted in a new management approach at this Centre.

Case Series

The first patient, a 49-year-old, developed high volume drain output post three stage oesophagectomy. His jejunostomy feeding was discontinued, total parenteral nutrition and a somatostatin analogue, were commenced. Despite these measures, the drain output remained &gt;1.5litres per day and an exploratory thoracotomy was performed. The second patient, an 81-year-old underwent a transhiatal-oesophagectomy. On postoperative day 10 he developed acute onset shortness of breath, CXR demonstrated a large left sided pleural effusion. CT thorax demonstrated multiloculated complex pleural effusions. US guided pig tail drain was placed in the largest targetable effusion. The fluid was chylous in appearance. In both cases, an interventional radiological approach, not previously performed at this centre, provided definitive management. Lymphangiography was performed via injection of 1mL of Lipoidol® every 5 minutes into the inguinal lymph nodes to identify the cisterna chyli. A guidewire was advanced via the cisterna chyli with coils and glue used to embolize the leaking tracts.

Discussion

The lessons from this experience provide an algorithm for the management of chyle leaks, that will change practice at this centre. Embolization or disruption of thoracic duct and cisterna chyli leaks will be first line therapy for complex chyle leaks, with surgery reserved for where this fails.

Detection and characterization of lung cancer using cell-free DNA fragmentomes

Non-invasive approaches for cell-free DNA (cfDNA) assessment provide an opportunity for cancer detection and intervention. Here, we use a machine learning model for detecting tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation in a prospective study of 365 individuals at risk for lung cancer. We validate the cancer detection model using an independent cohort of 385 non-cancer individuals and 46 lung cancer patients. Combining fragmentation features, clinical risk factors, and CEA levels, followed by CT imaging, detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. Genome-wide fragmentation profiles across ~13,000 ASCL1 transcription factor binding sites distinguished individuals with small cell lung cancer from those with non-small cell lung cancer with high accuracy (AUC = 0.98). A higher fragmentation score represented an independent prognostic indicator of survival. This approach provides a facile avenue for non-invasive detection of lung cancer.

DNA from tumour cells can be detected in the blood of cancer patients. Here, the authors show that cell free DNA fragmentation patterns can identify lung cancer patients and when this information is further interrogated it can be used to predict lung cancer histological subtype.

Abstract 570: Detecting cancer using genome-wide cfDNA nucleosomal fragmentation in a prospective multi cancer cohort

Genome-wide cfDNA fragmentation patterns have previously been demonstrated to distinguish with high sensitivity and specificity between plasma samples from individuals with and without cancer. To further evaluate cfDNA fragmentation as a blood-based screening test for cancer, we have used low coverage whole genome sequencing to analyze plasma samples from 280 patients referred to an advanced diagnostic center due to non-organ specific signs and symptoms of cancer. Within three months of inclusion, 74 of these patients were diagnosed with one of 16 different solid cancers while 206 patients did not have cancer. Using an improved version of our genome-wide cfDNA fragmentation analyses, we observed high performance in distinguishing cancer and non-cancer samples (AUC=0.92, 95% CI 0.88-0.96), including lung cancer (n=12, AUC=0.91, 95% CI 0.80-1.00) and colorectal cancer (n=12, AUC=0.94, 95% CI 0.89-0.99). Although many of the patients in this cohort had other common illnesses including cardiovascular, autoimmune, and inflammatory diseases, the machine learning models of cfDNA fragmentation were able to detect cancer with high sensitivity and specificity. These data support the development of genome-wide cfDNA fragmentation analyses as a non-invasive detection screening approach for both single and multiple cancers.

Citation Format: Jacob Carey, Alessandro Leal, Bryan Chesnick, Denise Butler, Michael Rongione, Sian Jones, Rob Scharpf, Mette Villadsen, Stig E. Bojesen, Julia S. Johansen, Claus L. Feltoft, Victor E. Velculescu, Nicholas C. Dracopoli. Detecting cancer using genome-wide cfDNA nucleosomal fragmentation in a prospective multi cancer cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 570.

Modeling cell-free DNA fragment size densities for non-invasive detection of cancer

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Background: Circulating cell-free DNA (cfDNA) is largely nucleosomal in origin with typical fragment lengths of 167 base-pairs reflecting the length of DNA wrapped around-the histone and H1 linker. Given the nucleosomal origin of cfDNA, we have previously used low coverage whole genome sequencing to evaluate DNA fragmentation profiles to sensitively and specifically detect tumor-derived DNA with altered fragment lengths or coverage. Methods: Here we evaluate the use of Bayesian finite mixtures to model the fragment length distribution and demonstrate how the parameters from these models can be useful to distinguish between individuals with and without cancer. We examined the number of cfDNA fragments by size ranging from 100-220bp and approximated the mixture component location, scale, and weight using Markov Chain Monte Carlo. The performance of the method was determined using a ten-fold, ten repeat cross-validation of Gradient Boosted Machine model using 1) our previously described genome-wide fragmentation profile approach, 2) the parameters from the mixture model and 3) a combination of approaches 1) and 2) as features. Results: In this study of 215 cancer patients and 208 cancer-free individuals, we observed cross-validated AUCs of 1) 0.94, 2) 0.95, and 3) 0.97 among the three approaches. Conclusions: Our findings indicate that parsimonious mixture models may improve detection of cancer in conjunction with fragmentation profile analyses across the genome.

Genome-wide cfDNA fragmentation in patients with cancer and other diseases

3136

Background: Genome-wide cfDNA fragmentation patterns have previously been demonstrated to distinguish with high sensitivity and specificity between plasma samples from individuals with and without cancer. Methods: To further evaluate cfDNA fragmentation as a blood-based screening test for cancer, we have evaluated these genomic features in patients with and without cancer who have been diagnosed with other common comorbidities. For this study, we have used low coverage (1-2x) whole genome sequencing to analyze plasma samples from 412 patients referred to an advanced diagnostic center due to unexplained signs and symptoms associated with cancer. Results: Seventy-seven of these patients were ultimately diagnosed with one of sixteen different solid cancers, 68 with cardiovascular disease, 48 with diabetes, as well as other comorbidities. We used the DELFI approach (DNA evaluation of fragments for early interception) to measure the cfDNA fragmentation in plasma from all 412 patients included in the study using a cross-validated machine learning model. Patients with cancer could be distinguished from non-cancer individuals with high sensitivity and specificity (AUC = 0.92), including for common cancers such as colorectal and lung cancer. Conclusions: These data support the hypothesis that abnormal cfDNA fragmentation is a consequence of unregulated mitoses in cancer cells and can be distinguished from fragmentation patterns of individuals with co-morbidities.

POS1162 PREDICTORS OF HOSPITALISATION IN PATIENTS WITH RHEUMATIC DISEASE AND COVID-19 IN IRELAND: DATA FROM THE COVID-19 GLOBAL RHEUMATOLOGY ALLIANCE PHYSICIAN-REPORTED REGISTRY

Background:

There is limited data regarding the risk of hospitalisation in patients with rheumatic disease and COVID-19 in Ireland.

Objectives:

We used the COVID-19 Global Rheumatology Alliance (GRA) registry data to study outcomes and their predictors.

Methods:

We examined data on patients and their disease-related characteristics entered into the COVID-19 GRA provider registry from Ireland (24th March 2020 to 31st August 2020). Multivariable logistic regression was used to assess the association of demographic and clinical characteristics with hospitalisation.

Results:

Of 105 patients, 47 (45.6%) were hospitalised and 10 (9.5%) died. Multivariable logistic regression analysis showed age (OR=1.06, 95%CI 1.01 to 1.10), number of comorbidities (OR=1.93, 95%CI 1.11 to 3.35), and glucocorticoid use (OR=15.01, 95%CI 1.77 to 127.16) were significantly associated with hospitalisation. A diagnosis of inflammatory arthritis was associated with a lower odds of hospitalisation (OR=0.09, 95%CI 0.02 to 0.32).

All significant variable modelMost parsimonious modelUnadjusted OR (95% CI)Adjusted OR (95%CI)*Adjusted p-value*Adjusted OR (95%CI)&Adjusted p-value&Female0.45 (0.20-1.02)0.33 (0.05-2.23)0.34 (0.09-1.36)0.128Age (years)1.08 (1.05-1.11)1.04 (0.97-1.10)0.2241.06 (1.01-1.10)0.010Inflammatory arthritis0.11 (0.05-0.28)0.14 (0.02-0.95)0.0440.09 (0.02-0.32)<0.001Connective Tissue Disease and Other1.56 (0.62 - 3.92)No comorbidities0.11 (0.04-0.30)0.76 (0.09-6.58)0.802Most common comorbiditiesCOPD / asthma4.77 (1.23-18.54)3.09 (0.16-60.07)0.456CVD3.40 (1.31-8.85)0.11 (0.01-1.88)0.129Hypertension3.71 (1.52-9.08)0.56 (0.04-7.94)0.668Obesity0.58 (0.10-3.30)Number of comorbidities (Median, IQR)3.01 (1.92-4.72)2.99 (0.59-15.02)0.1841.93 (1.11-3.35)0.020Never Smokerref.0.889Ever Smoker3.17 (1.18-8.89)1.19 (0.10-13.68)Medication prior to COVID-19 diagnosisGlucocorticoids9.26 (1.95-43.89)18.14 (1.13-290.81)0.04115.01 (1.77-127.16)0.013csDMARD monotherapy0.42 (0.17-1.00)b/tsDMARD (monotherapy or in combination with csDMARD)0.24 (0.10-0.58)1.36 (0.19-9.72)0.557

Conclusion:

Increasing age, comorbidity burden, and glucocorticoid use were associated with hospitalisation, while a diagnosis of inflammatory arthritis was associated with lower odds of hospitalization.

Disclosure of Interests:

Richard Conway Speakers bureau: Janssen, Roche, Sanofi, Abbvie, Elena Nikiphorou Speakers bureau: AbbVie, Eli-Lilly, Gilead, Celltrion, Pfizer, Sanofi, Christiana Demetriou: None declared, Candice Low: None declared, Kelly Leamy: None declared, John Ryan: None declared, Ronan Kavanagh: None declared, Alexander Fraser: None declared, John Carey: None declared, Paul O’Connell: None declared, Rachael Flood: None declared, Ronan Mullan: None declared, David Kane: None declared, Philip Robinson Speakers bureau: UCB, Roche, Pfizer, Gilead, Janssen, Novartis, Eli Lilly, Abbvie, Grant/research support from: Abbvie, UCB, Novartis, Janssen, Pfizer, Jean Liew Grant/research support from: Pfizer, Rebecca Grainger Speakers bureau: Pfizer, Cornerstones, Janssen, Novartis, Abbvie, Geraldine McCarthy: None declared.

Bayesian copy number detection and association in large-scale studies

BACKGROUND

Germline copy number variants (CNVs) increase risk for many diseases, yet detection of CNVs and quantifying their contribution to disease risk in large-scale studies is challenging due to biological and technical sources of heterogeneity that vary across the genome within and between samples.

METHODS

We developed an approach called CNPBayes to identify latent batch effects in genome-wide association studies involving copy number, to provide probabilistic estimates of integer copy number across the estimated batches, and to fully integrate the copy number uncertainty in the association model for disease.

RESULTS

Applying a hidden Markov model (HMM) to identify CNVs in a large multi-site Pancreatic Cancer Case Control study (PanC4) of 7598 participants, we found CNV inference was highly sensitive to technical noise that varied appreciably among participants. Applying CNPBayes to this dataset, we found that the major sources of technical variation were linked to sample processing by the centralized laboratory and not the individual study sites. Modeling the latent batch effects at each CNV region hierarchically, we developed probabilistic estimates of copy number that were directly incorporated in a Bayesian regression model for pancreatic cancer risk. Candidate associations aided by this approach include deletions of 8q24 near regulatory elements of the tumor oncogene MYC and of Tumor Suppressor Candidate 3 (TUSC3).

CONCLUSIONS

Laboratory effects may not account for the major sources of technical variation in genome-wide association studies. This study provides a robust Bayesian inferential framework for identifying latent batch effects, estimating copy number, and evaluating the role of copy number in heritable diseases.

CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network

Patients with oncogene driven tumors are treated with targeted therapeutics including EGFR inhibitors. Genomic data from The Cancer Genome Atlas (TCGA) demonstrates molecular alterations to EGFR, MAPK, and PI3K pathways in previously untreated tumors. Therefore, this study uses bioinformatics algorithms to delineate interactions resulting from EGFR inhibitor use in cancer cells with these genetic alterations. We modify the HaCaT keratinocyte cell line model to simulate cancer cells with constitutive activation of EGFR, HRAS, and PI3K in a controlled genetic background. We then measure gene expression after treating modified HaCaT cells with gefitinib, afatinib, and cetuximab. The CoGAPS algorithm distinguishes a gene expression signature associated with the anticipated silencing of the EGFR network. It also infers a feedback signature with EGFR gene expression itself increasing in cells that are responsive to EGFR inhibitors. This feedback signature has increased expression of several growth factor receptors regulated by the AP-2 family of transcription factors. The gene expression signatures for AP-2alpha are further correlated with sensitivity to cetuximab treatment in HNSCC cell lines and changes in EGFR expression in HNSCC tumors with low CDKN2A gene expression. In addition, the AP-2alpha gene expression signatures are also associated with inhibition of MEK, PI3K, and mTOR pathways in the Library of Integrated Network-Based Cellular Signatures (LINCS) data. These results suggest that AP-2 transcription factors are activated as feedback from EGFR network inhibition and may mediate EGFR inhibitor resistance.

Combined rTMS and virtual reality brain-computer interface training for motor recovery after stroke

OBJECTIVE

Combining repetitive transcranial magnetic stimulation (rTMS) with brain-computer interface (BCI) training can address motor impairment after stroke by down-regulating exaggerated inhibition from the contralesional hemisphere and encouraging ipsilesional activation. The objective was to evaluate the efficacy of combined rTMS  +  BCI, compared to sham rTMS  +  BCI, on motor recovery after stroke in subjects with lasting motor paresis.

APPROACH

Three stroke subjects approximately one year post-stroke participated in three weeks of combined rTMS (real or sham) and BCI, followed by three weeks of BCI alone. Behavioral and electrophysiological differences were evaluated at baseline, after three weeks, and after six weeks of treatment.

MAIN RESULTS

Motor improvements were observed in both real rTMS  +  BCI and sham groups, but only the former showed significant alterations in inter-hemispheric inhibition in the desired direction and increased relative ipsilesional cortical activation from fMRI. In addition, significant improvements in BCI performance over time and adequate control of the virtual reality BCI paradigm were observed only in the former group.

SIGNIFICANCE

When combined, the results highlight the feasibility and efficacy of combined rTMS  +  BCI for motor recovery, demonstrated by increased ipsilesional motor activity and improvements in behavioral function for the real rTMS  +  BCI condition in particular. Our findings also demonstrate the utility of BCI training alone, as shown by behavioral improvements for the sham rTMS  +  BCI condition. This study is the first to evaluate combined rTMS and BCI training for motor rehabilitation and provides a foundation for continued work to evaluate the potential of both rTMS and virtual reality BCI training for motor recovery after stroke.

Traumatic pulmonary pseudocyst: An underreported entity

BACKGROUND

Traumatic pulmonary pseudocysts (TPP) are underreported cavitary lesions of the pulmonary parenchyma that can develop following blunt chest trauma. Although the occurrence of traumatic pulmonary pseudocyst is rare, this condition should be considered in the differential diagnosis of any cavitary lesion. Awareness of this injury and its clinical significance is important for successful management in order to avoid medical errors in the course of treatment.

METHODS

A literature search was conducted through Medline using the key phrases "traumatic pulmonary pseudocyst" and "traumatic pneumatocele." Relevant articles, especially those with focus on diagnosis and management of traumatic pneumatocele in adults, were selected. Due to the scarcity of literature and lack of Level I evidence on this subject, studies published in any year were considered.

RESULTS

A search of "traumatic pulmonary pseudocyst" and "traumatic pneumatocele" yielded 114 studies. Most of these were excluded based on inclusion and exclusion criteria. Thirty-five articles were reviewed. The majority of these were individual case studies; only eight articles were considered large case studies (greater than eight patients).

CONCLUSION

Traumatic pulmonary pseudocysts are lesions that occur secondary to blunt chest trauma. Diagnosis is based on a history of trauma and appearance of a cystic lesion on CT. Accurate diagnosis of traumatic pulmonary pseudocyst is imperative to achieve successful outcomes. Failure to do so may lead to unnecessary procedures and complications.

Genome-Wide Association of Copy Number Polymorphisms and Kidney Function

Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea. We used hidden Markov models (HMMs) to identify copy number polymorphic regions (CNPs) from high-throughput SNP arrays for 2,514 African (AA) and 8,645 European ancestry (EA) participants in the Atherosclerosis Risk in Communities (ARIC) study. Separately for the EA and AA cohorts, we used Bayesian Gaussian mixture models to estimate copy number at regions identified by the HMM or previously reported in the HapMap Project. We identified 312 and 464 autosomal CNPs among individuals of EA and AA, respectively. Multivariate models adjusted for SNP-derived covariates of population structure identified one CNP in the EA cohort near genome-wide statistical significance (Bonferroni-adjusted p = 0.067) located on chromosome 5 (876-880kb). Overall, our findings suggest a limited role of CNPs in explaining eGFR variability.

Whole exome association of rare deletions in multiplex oral cleft families

By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood. To identify putative structural variants underlying risk, we developed a pipeline for rare hemizygous deletions in families from whole exome sequencing and statistical inference based on rare variant sharing. Among 56 multiplex families with 115 individuals, we identified 53 regions with one or more rare hemizygous deletions. We found 45 of the 53 regions contained rare deletions occurring in only one family member. Members of the same family shared a rare deletion in only eight regions. We also devised a scalable global test for enrichment of shared rare deletions.

Post-combustion carbon dioxide capture cost reduction to 2030 and beyond

Post-combustion CO₂ capture (PCC) can be achieved using a variety of technologies. Importantly it is applicable to a wide range of processes and may also be retrofitted in certain cases. This paper covers the use of PCC for low carbon power generation from new natural gas combined cycle (NGCC) plants that are expected to be built in the UK in the 2020s and 2030s and that will run into the 2050s. Costs appear potentially comparable with other low carbon and controllable generation sources such as nuclear or renewables plus storage, especially with the lower gas prices that can be expected in a carbon-constrained world. Non-fuel cost reduction is still, however, desirable and, since CO₂ capture is a new application, significant potential is likely to exist. For the NGCC+PCC examples shown in this paper, moving from ‘first of a kind’ (FOAK) to ‘nth of a kind’ (NOAK) gives significant improvements through both reduced financing costs and capital cost reductions. To achieve this the main emphasis needs to be on ‘commercial readiness’, rather than on system-level ‘technical readiness’, and on improvements through innovation activities, supported by underpinning research, that develop novel sub-processes; this will also maintain NOAK status for cost-effective financing. Feasible reductions in the energy penalty for PCC capture have much less impact, reflecting the inherently high levels of efficiency for modern NGCC+PCC plants.

Multiobjective optimization framework for landmark measurement error correction in three-dimensional cephalometric tomography

The purpose of this study is to minimize errors that occur when using a four vs six landmark superimpositioning method in the cranial base to define the co-ordinate system. Cone beam CT volumetric data from ten patients were used for this study. Co-ordinate system transformations were performed. A co-ordinate system was constructed using two planes defined by four anatomical landmarks located by an orthodontist. A second co-ordinate system was constructed using four anatomical landmarks that are corrected using a numerical optimization algorithm for any landmark location operator error using information from six landmarks. The optimization algorithm minimizes the relative distance and angle between the known fixed points in the two images to find the correction. Measurement errors and co-ordinates in all axes were obtained for each co-ordinate system. Significant improvement is observed after using the landmark correction algorithm to position the final co-ordinate system. The errors found in a previous study are significantly reduced. Errors found were between 1 mm and 2 mm. When analysing real patient data, it was found that the 6-point correction algorithm reduced errors between images and increased intrapoint reliability. A novel method of optimizing the overlay of three-dimensional images using a 6-point correction algorithm was introduced and examined. This method demonstrated greater reliability and reproducibility than the previous 4-point correction algorithm.

Vitamin D supplementation versus combined calcium and vitamin D in older female patients - an observational study

BACKGROUND

In most developed countries overt vitamin D deficiency, characterized by rickets or osteomalacia, is now uncommon. However, subclinical vitamin D insufficiency is extremely common and may contribute to the development of skeletal and non-skeletal problems. Standard practice involves supplementation with a combination of vitamin D and calcium although the benefit of adding calcium to vitamin D supplements has not been fully established and may reduce adherence due to its bulky and chalky consistency.

PURPOSE OF STUDY

To compare the effects of vitamin D alone versus vitamin D/calcium supplements on vitamin D levels, bone profile and parathyroid hormone level.

POPULATION

Older (> 65 years) female patients living in the community and long term care institutions.

INTERVENTIONS

Either 800 iu of vitamin D3 or a composite supplement of 800 iu vitamin D3 and 1000 mg calcium were given to patients in an open-labelled observational study. Serum 25-hydroxy-vitamin D, parathyroid hormone, calcium, phosphate and alkaline phosphatase levels were assessed at baseline and after 3 months of treatment.

RESULTS

Serum 25-hydroxy-vitamin D levels rose from baseline levels of 25 ± 16 to 79 ± 16 in those treated with vitamin D alone and from 35 ± 24 nmol/L to 70 ± 24 nmol/L in those treated with vitamin D and calcium. Serum PTH levels fell by similar amounts in both groups. In both community dwellers and institutionalised patients, those treated with vitamin D alone were at least as likely to achieve normalisation of serum vitamin D levels as those on combined calcium/vitamin D treatment.

CONCLUSION

Vitamin D alone appears as effective as combined calcium/vitamin D treatment in restoring serum vitamin D levels in older community dwelling and institutionalised patients. A prospective randomised trial would help confirm these findings.

Pasteurization of chicken litter with steam and quicklime to reduce Salmonella Typhimurium

The nursery industry pasteurizes soil with steam and quicklime to reduce plant pathogens. The mechanism of action for quicklime is the resulting exothermic reaction that occurs when the chemical interacts with water and its ability to increase pH levels. These treatments may also reduce pathogens in a commercial poultry house. In this study, a steam sterilization cart simulated conditions used by the nursery industry to treat litter inoculated with Salmonella enterica serovar Typhimurium. A homogenized sample of litter was exposed to steam for 0, 5, 30, or 120 min. Quicklime was used at concentrations of 0 (control), 2.5, 5.0, or 10.0%. All steam treatments, with or without quicklime, significantly reduced Salmonella Typhimurium colonization by at least 3 orders of magnitude. Significant reductions were also observed in the treatments with quicklime alone. Both the steam and the quicklime treatments often reduced colonization to undetectable levels, even when samples were enriched. Therefore, we demonstrated 2 novel techniques for reducing Salmonella Typhimurium in poultry litter. Soil pasteurization potentially offers an environmentally sound means of reducing the pathogens present in used poultry litter.

Sensitivity analysis for plane orientation in three-dimensional cephalometric analysis based on superimposition of serial cone beam computed tomography images

OBJECTIVES

The purpose of this study was to evaluate the potential errors associated with superimposition of serial cone beam CT (CBCT) images utilizing reference planes based on cranial base landmarks using a sensitivity analysis.

METHODS

CBCT images from 62 patients participating in a maxillary expansion clinical trial were analysed. The left and right auditory external meatus (AEM), dorsum foramen magnum (DFM) and the midpoint between the left and right foramen spinosum (ELSA) were used to define a three-dimensional (3D) anatomical reference co-ordinate system. Intraclass correlation coefficients for all four landmarks were obtained. Transformation of the reference system was carried out using the four landmarks and mathematical comparison of values.

RESULTS

Excellent intrareliability values for each dimension were obtained for each landmark. Evaluation of the method to transform the co-ordinate system was first done by comparing interlandmark distances before and after transformations, giving errors in lengths in the order of 10-14% (software rounding error). A sensitivity evaluation was performed by adding 0.25 mm, 0.5 mm and 1 mm error in one axis of the ELSA. A positioning error of 0.25 mm in the ELSA can produce up to 1.0 mm error in other cranial base landmark co-ordinates. These errors could be magnified to distant landmarks where in some cases menton and infraorbital landmarks were displaced 4-6 mm.

CONCLUSIONS

Minor variations in location of the ELSA, both the AEM and the DFM landmarks produce large and potentially clinically significant uncertainty in co-ordinate system alignment.

Effect of object location on the density measurement and Hounsfield conversion in a NewTom 3G cone beam computed tomography unit

OBJECTIVES

The purpose of this study was to determine the effect of an object's location in a cone beam CT imaging chamber (CBCT-NewTom 3G) on its apparent density and to develop a linear conversion coefficient for Hounsfield units (HU) to material density (g cm(-3)) for the NewTom 3G Scanner.

METHODS

Three cylindrical models of materials with different densities were constructed and scanned at five different locations in a NewTom 3G Volume Scanner. The average HU value for each model at each location was obtained using two different types of software. Next, five cylinders of different known densities were scanned at the exact centre of a NewTom 3G Scanner. The collected data were analysed using the same two types of software to determine a standard linear relationship between density and HU for each type of software.

RESULTS

There is no statistical significance of location of an object within the CBCT scanner on determination of its density. A linear relationship between the density of an object and the HU of a scan was rho = 0.001(HU)+1.19 with an R2 value of 0.893 (where density, rho, is measured in g cm(-3)). This equation is to be used on a range between 1.42 g cm(-3) and 0.4456 g cm(-3).

CONCLUSIONS

A linear relationship can be used to determine the density of materials (in the density range of bone) from the HU values of a CBCT scan. This relationship is not affected by the object's location within the scanner itself.

Probe-guided localization of cancer deposits using [18F]fluorodeoxyglucose

In recent years, several probes have been developed to allow for the intraoperative detection of tumour tissue using [18F]fluorodeoxyglucose (FDG). Detector designs include high-energy gamma and beta probes, as well as combination devices with background rejection capabilities. Some laboratory prototypes and commercialized systems have demonstrated reasonable sensitivities for 511 keV photons and /or b particles emitted from 18F for in vivo use. This review focuses on the ability of these devices to detect tumour deposits in the low-contrast environment of the operating room . Important technical and biological factors that influence tumour-to-background contrast are discussed and potential future applications and developments are highlighted. In addition, we evaluate the limited data on absorbed doses resulting from [18F] FDG administration immediately prior to surgery that indicate acceptable levels of radiation exposure to operating room personnel.

MC1R variants correlate with thinhorn sheep colour cline but not individual colour

The melanocortin 1 receptor (MC1R) gene has provided a window on the evolution of colour polymorphisms. Recent studies have demonstrated associations between MC1R and melanism in a number of wildlife species. Thinhorn sheep ( Ovis dalli Nelson, 1884) are a possible species to test for association between MC1R polymorphisms and melanism. Across their range the pelage colour of thinhorn sheep intergrades between all white phenotypes to very dark phenotypes. Most thinhorn sheep are white; however, there is a 1200 km cline from light to dark sheep that occurs over three genetically distinct polymorphic populations. We sequenced the entire MC1R gene from 40 individuals across the range of thinhorn sheep. We found a single nucleotide polymorphism in MC1R at base pair position 921 that coincided with the geographic cline. However, at the individual level we found no relationship between individual melanism and genotype.

Horn growth rate and longevity: implications for natural and artificial selection in thinhorn sheep (Ovis dalli)

We used horn measurements from natural and hunted mortalities of male thinhorn sheep Ovis dalli from Yukon Territory, Canada, to examine the relationship between rapid growth early in life and longevity. We found that rapid growth was associated with reduced longevity for sheep aged 5 years and older for both the hunted and natural mortality data sets. The negative relationship between growth rate and longevity in hunted sheep can at least partially be explained by morphologically biased hunting regulations. The same trend was evident from natural mortalities from populations that were not hunted or underwent very limited hunting, suggesting a naturally imposed mortality cost directly or indirectly associated with rapid growth. Age and growth rate were both positively associated with horn size at death for both data sets, however of the two growth rate appeared to be a better predictor. Large horn size can be achieved both by individuals that grow horns rapidly and by those that have greater longevity, and the trade-off between growth rate and longevity could limit horn size evolution in this species. The similarity in the relationship between growth rate and longevity for hunted and natural mortalities suggests that horn growth rate should not respond to artificial selection. Our study highlights the need for the existence and study of protected populations to properly assess the impacts of selective harvesting.

Density conversion factor determined using a cone-beam computed tomography unit NewTom QR-DVT 9000

OBJECTIVE

The purpose of this study was to determine a conversion coefficient for Hounsfield Units (HU) to material density (g cm(-3)) obtained from cone-beam computed tomography (CBCT-NewTom QR-DVT 9000) data.

METHODS

Six cylindrical models of materials with different densities were made and scanned using the NewTom QR-DVT 9000 Volume Scanner. The raw data were converted into DICOM format and analysed using Merge eFilm and AMIRA to determine the HU of different areas of the models.

RESULTS

There was no significant difference (P = 0.846) between the HU given by each piece of software. A linear regression was performed using the density, rho (g cm(-3)), as the dependent variable in terms of the HU (H). The regression equation obtained was rho = 0.002H-0.381 with an R2 value of 0.986. The standard error of the estimation is 27.104 HU in the case of the Hounsfield Units and 0.064 g cm(-3) in the case of density.

CONCLUSION

CBCT provides an effective option for determination of material density expressed as Hounsfield Units.

Evidence for cryptic glacial refugia from North American mountain sheep mitochondrial DNA

The separation of populations by ice sheets into large refugia can account for much of the genetic diversity found in present day populations. The evolutionary implications of small glacial refugia have not been as thoroughly explored. To examine refugial origins of North American mountain sheep Ovis spp., we analyzed a 604 bp portion of the mitochondrial DNA (mtDNA) control region from 223 O. dalli and O. canadensis. Major refugia were identified in eastern Beringia and southern North America, and we found evidence for two smaller refugia situated between the Laurentide and Cordilleran glaciers. Our results are the first to demonstrate support for survival of any organism in the latter two refugia. These refugia also appear to have conserved a genetic signal that confirms past hybridization of O. dalli and O. canadensis.

Detecting the signature of selection on immune genes in highly structured populations of wild sheep (Ovis dalli)

The confounding effects of population structure complicate efforts to identify regions of the genome under the influence of selection in natural populations. Here we test for evidence of selection in three genes involved in vertebrate immune function - the major histocompatibility complex (MHC), interferon gamma (IFNG) and natural resistance associated macrophage polymorphism (NRAMP) - in highly structured populations of wild thinhorn sheep (Ovis dalli). We examined patterns of variation at microsatellite loci linked to these gene regions and at the DNA sequence level. Simple Watterson's tests indicated balancing selection at all three gene regions. However, evidence for selection was confounded by population structure, as the Watterson's test statistics from linked markers were not outside of the range of values from unlinked and presumably neutral microsatellites. The translated coding sequences of thinhorn IFNG and NRAMP are fixed and identical to those of domestic sheep (Ovis aries). In contrast, the thinhorn MHC DRB locus shows significant evidence of overdominance through both an excess of nonsynonymous substitution and trans-species polymorphism. The failure to detect balancing selection at microsatellite loci linked to the MHC is likely the result of recombination between the markers and expressed gene regions.

Gender- and age-class-specific reactions to human disturbance in a sexually dimorphic ungulate

According to optimality theory, an individual's characteristics should play a major part in determining antipredator strategies. We studied behavioural reactions to human presence of gender and age classes of 35 thinhorn sheep (Ovis dalli Nelson, 1884) in late winter 2001 in Faro, Yukon Territory, Canada. The behaviour of undisturbed sheep was observed from distances of 400–1200 m and compared with the behaviour recorded when one or two people were in close proximity to the sheep. Ewes decreased bedding and increased foraging when humans were present, but there were no changes in these behaviours in rams. Disturbance caused an increase in vigilance and a trend was found for adults to react more strongly to disturbance than juveniles. We demonstrate the importance for disturbance research of gaining detailed information about all different kinds of population members and using applicable statistical tests in the data analyses.