
Lyle John PalmerUniversity of Adelaide
Lyle John Palmer
PhD
About
629
Publications
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Introduction
Additional affiliations
June 2011 - March 2014
June 2010 - March 2014
Publications
Publications (629)
Deformable brain templates are an important tool in many neuroimaging analyses. Conditional templates (e.g., age-specific templates) have advantages over single population templates by enabling improved registration accuracy and capturing common processes in brain development and degeneration. Conventional methods require large, evenly-spread cohor...
Deformable brain templates are an important tool in many neuroimaging analyses. Conditional templates (e.g., age-specific templates) have advantages over single population templates by enabling improved registration accuracy and capturing common processes in brain development and degeneration. Conventional methods require large, evenly-spread cohor...
Obstructive sleep apnea (OSA) is a multifactorial sleep disorder characterized by a strong genetic basis. Excessive daytime sleepiness (EDS) is a symptom that is reported by a subset of OSA patients, persisting even after treatment with continuous positive airway pressure (CPAP). It is recognized as a clinical subtype underlying OSA carrying alarmi...
Obstructive sleep apnea (OSA) is a multifactorial sleep disorder characterized by a strong genetic basis. Excessive daytime sleepiness (EDS) is a symptom that is reported by a subset of OSA patients, persisting even after treatment with continuous positive airway pressure (CPAP). It is recognized as a clinical subtype underlying OSA carrying alarmi...
Background
Accurate outcome predictions for patients who had ischaemic stroke with successful reperfusion after endovascular thrombectomy (EVT) may improve patient treatment and care. Our study developed prediction models for key clinical outcomes in patients with successful reperfusion following EVT in an Australian population.
Methods
The study...
"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could aff...
Objective
In this prospective cohort study, we provide several prognostic models to predict functional status as measured by the modified Health Assessment Questionnaire (mHAQ). The early adoption of the treat-to-target strategy in this cohort offered a unique opportunity to identify predictive factors using longitudinal data across 20 years.
Meth...
Introduction: We aimed to analyze long-term trends in characteristics of patients undergoing diagnostic polysomnography (PSG) and subsequently diagnosed with obstructive sleep apnea (OSA) to inform delivery of sleep services.
Material and Methods: We studied 24,510 consecutive patients undergoing PSG at a tertiary-care sleep service between 1989 an...
Background
Obstructive sleep apnoea (OSA) is a heterogeneous disorder with certain phenotypes at increased risk of major adverse cardiovascular events (MACE). We investigated whether symptom subtypes and/or symptom burden are useful predictors of MACE risk in severe OSA.
Method
In a longitudinal sleep clinic cohort with apnoea-hypopnoea index ≥30...
While acute ischemic stroke due to large vessel occlusion (LVO) may be life-threatening or permanently disabling, timely intervention with endovascular thrombectomy (EVT) can prove life-saving for affected patients. Appropriate patient selection based on prognostic prediction is vital for this costly and invasive procedure, as not all patients will...
Genetic association studies of many heritable traits resulting from physiological testing often have modest sample sizes due to the cost and burden of the required phenotyping. This reduces statistical power and limits discovery of multiple genetic associations. We present a strategy to leverage pleiotropy between traits to both discover new loci a...
Rheumatoid arthritis is an autoimmune condition that predominantly affects the synovial joints, causing joint destruction, pain, and disability. Historically, the standard for measuring the long-term efficacy of disease-modifying antirheumatic drugs has been the assessment of plain radiographs with scoring techniques that quantify joint damage. How...
Background
Obstructive sleep apnoea (OSA) is a complex heterogeneous disorder, and patients with similar disease severity present with different symptom profiles and outcomes. It is unclear whether OSA symptom subtypes independently predict incident major adverse cardiovascular events (MACE).
Method
Consecutive patients attending a tertiary sleep...
Introduction
Machine learning (ML) methods are being increasingly applied to prognostic prediction for stroke patients with large vessel occlusion (LVO) treated with endovascular thrombectomy. This systematic review aims to summarize ML-based pre-thrombectomy prognostic models for LVO stroke and identify key research gaps.
Methods
Literature searc...
Why was the cohort set up?
The prevalences of many chronic diseases—including cancer, cardiovascular disease, asthma and type 2 diabetes—have increased in Canada and many other countries over the past 30 years.1–4 In 2020, cancer and heart disease were the leading causes of death for Canadians, accounting for 48% of all deaths.⁵ About 37% of senior...
Objective:
To characterise the clinical phenotypes and genetic variants of hereditary pancreatitis in people diagnosed in South Australia.
Design, setting, participants:
Cross-sectional study of people who received molecular diagnoses of hereditary pancreatitis from one of four major diagnostic services in South Australia, 1 January 2006 - 30 Ju...
Background
Previous studies in medical imaging have shown disparate abilities of artificial intelligence (AI) to detect a person's race, yet there is no known correlation for race on medical imaging that would be obvious to human experts when interpreting the images. We aimed to conduct a comprehensive evaluation of the ability of AI to recognise a...
Background
Proximal femoral fractures are an important clinical and public health issue associated with substantial morbidity and early mortality. Artificial intelligence might offer improved diagnostic accuracy for these fractures, but typical approaches to testing of artificial intelligence models can underestimate the risks of artificial intelli...
Background
Sleep-disordered breathing is a common disorder associated with significant morbidity. The genetic architecture of sleep-disordered breathing remains poorly understood. Through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, we performed the first whole-genome sequence analysis of sleep-disordered breathing.
Methods
The s...
Objective
To assess longitudinal, population-based data regarding the prevalence and impact of chronic pancreatitis on children.
Study design
Administrative data linkage was used to ascertain an index cohort consisting of all individuals who had an initial diagnosis of chronic pancreatitis before the age of 19 years in the South Australian public...
Long and short sleep duration are associated with elevated blood pressure (BP), possibly through effects on molecular pathways that influence neuroendocrine and vascular systems. To gain new insights into the genetic basis of sleep-related BP variation, we performed genome-wide gene by short or long sleep duration interaction analyses on four BP tr...
Genetic and epidemiologic investigations into obstructive sleep apnoea (OSA) have been limited by a scarcity of sizeable well-characterised sleep clinic cohorts with laboratory-based polysomnography (PSG). This profile reports the characteristics of a prospective clinic cohort study exploring the genotypic and phenotypic features of OSA with ongoin...
Aim
To assess the generalisability of a deep learning (DL) system for screening mammography developed at New York University (NYU), USA (1,2) in a South Australian (SA) dataset.
Methods and Materials
Clients with pathology-proven lesions (n=3,160) and age-matched controls (n=3,240) were selected from women screened at BreastScreen SA from January 2...
Background:
This study aimed to describe the clinical outcomes of total pancreatectomy with islet autotransplantation (TP-IAT) in Australia.
Methods:
Individuals selected for TP-IAT surgery according to the Minnesota Criteria (Appendix) without evidence of diabetes were evaluated including time to transplantation from pancreatectomy, islet numbe...
Artificial intelligence technology has advanced rapidly in recent years and has the potential to improve healthcare outcomes. However, technology uptake will be largely driven by clinicians, and there is a paucity of data regarding the attitude that clinicians have to this new technology. In June–August 2019 we conducted an online survey of fellows...
Long and short sleep duration are associated with elevated blood pressure (BP), possibly through effects on molecular pathways that influence neuroendocrine and vascular systems. To gain new insights into the genetic basis of sleep-related BP variation, we performed genome-wide gene by short or long sleep duration interaction analyses on four BP tr...
Study Objectives
Sleep duration is an important marker of sleep quality and overall sleep health. Both too little and too much sleep are associated with poorer health outcomes. We hypothesized that ethnicity-specific differences in sleep duration exist.
Methods
This cross-sectional study utilized questionnaire data from the Ontario Health Study (O...
Objective:
Despite evidence of a relationship among obstructive sleep apnea (OSA), metabolic dysregulation, and diabetes, it is uncertain whether OSA treatment can improve metabolic parameters. We sought to determine effects of long-term continuous positive airway pressure (CPAP) treatment on glycemic control and diabetes risk in patients with car...
Study objectives:
Obstructive sleep apnea (OSA) is a common condition with significant symptoms and long-term adverse cognitive, mental health, vascular, and respiratory sequelae. Physical activity has been recognised as a key determinant for good health and has been associated with lower risk of these sequelae. We hypothesized that that increased...
Genetic association studies of many heritable traits resulting from physiological testing often have modest sample sizes due to the cost and burden of the required phenotyping. This reduces statistical power and limits discovery of multiple genetic associations. We present a strategy to leverage pleiotropy between traits to both discover new loci a...
Average arterial oxyhemoglobin saturation during sleep (AvSpO2S) is a clinically relevant measure of physiological stress associated with sleep-disordered breathing, and this measure predicts incident cardiovascular disease and mortality. Using high-depth whole-genome sequencing data from the National Heart, Lung, and Blood Institute (NHLBI) Trans-...
Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved are not fully understood. Here, we combine genome-wide association studies with modeling of longitudinal growth traits to study the genetics of infant and child growth, followed by functional, pathway, genetic correlation,...
Type 2 diabetes (T2D) affects the health of millions of people worldwide. The identification of genetic determinants associated with changes in glycemia over time might illuminate biological features that precede the development of T2D. Here we conducted a genome-wide association study of longitudinal fasting glucose changes in up to 13,807 non-dia...
Sleep-disordered breathing (SDB) is a common disorder associated with significant morbidity. Through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program we report the first whole-genome sequence analysis of SDB. We identified 4 rare gene-based associations with SDB traits in 7,988 individuals of diverse ancestry and 4 replicated common va...
Sleep disordered breathing (SDB)-related overnight hypoxemia is associated with cardiometabolic disease and other comorbidities. Understanding the genetic bases for variations in nocturnal hypoxemia may help understand mechanisms influencing oxygenation and SDB-related mortality. We conducted genome-wide association tests across 10 cohorts and 4 po...
Minimum oxygen saturation discovery cohorts manhattan and QQ plots.
Top: African-Americans; Middle: European-Americans; Bottom: Multi-ethnic (2 or more populations for each variant).
(PDF)
Average oxygen saturation regional plot (European ancestry males, 10q22).
(PDF)
Average oxygen saturation regional plot (European ancestry males, 5q21).
(PDF)
Minimum oxygen saturation regional plot (Combined discovery/replication African-American ancestry, 6q25).
(PDF)
Minimum oxygen saturation regional plot (Combined discovery/replication European ancestry, 17p13).
(PDF)
Multi-variate MTAG (p < 10 x 10–6) results.
MTAG analysis was performed on European ancestry samples using our summary statistics for the three traits simultaneously. Lead results (p < 1 x 10–6) are shown.
(XLS)
MetaXcan gene-level results for lung in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
MetaXcan gene-level results for skeletal muscle in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
MetaXcan gene-level results for DGN whole blood in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
GIGSEA transcription factor binding site enrichment in whole blood analyses.
MetaXcan gene-level results for DGN whole blood (S19 Table, all p-values) were used as input. Transcription factor binding sites are curated by the Molecular Signatures Database (http://software.broadinstitute.org/gsea/msigdb/index.jsp).
(XLS)
Multi-ethnic discovery cohorts minimum oxygen saturation miami plots.
Top: Females; Bottom: Males.
(PDF)
Average oxygen saturation regional plot (European ancestry males, 12q14).
(PDF)
Average oxygen saturation regional plot (European ancestry males, 2p21).
(PDF)
Average oxygen saturation regional plot (Combined discovery/replication African-American ancestry, 22q11).
(PDF)
Minimum oxygen saturation regional plot (Combined discovery/replication European ancestry, 2p12).
(PDF)
Phenotype and covariate correlations.
Spearman correlations between phenotypes and covariates across all discovery cohorts and ethnic groups are shown. Correlations with the spirometry measures FEV1 and FVC are also shown. Correlations were pooled using Fisher Z-transformations weighted by sample size. 95% confidence intervals are listed in parenth...
Lead loci results for other phenotypes.
Each lead SNP from the “Original Phenotype” and “Original Model” columns was analyzed using equivalent individuals and models for different phenotypes. Available sample size will vary depending on the availability of the phenotype. AHI values are taken from Chen, Cade, et al. (submitted) “Locus Class” indicat...
Lead loci results adjusted for additional covariates.
Lead variants were re-analyzed with standard models and additional covariates as listed. As these covariates were not collected in all cohorts and individuals, the analysis were also performed with the same individuals for direct comparisons (matched N control columns).
(XLS)
Top locus SNP (p < 1 x 10–6) Blueprint and Vermunt epigenetic evidence.
Blueprint cell lines are a non-cancerous sub-set of largely blood cells. Vermunt brain region samples were not assayed for promoter regions. “Locus Class” indicates “Discovery/Replication” for main analyses or “Combined meta-analysis” for regions not clearing initial discovery...
GIGSEA micro RNA enrichment in whole blood analyses.
MetaXcan gene-level results for DGN whole blood (S19 Table, all p-values) were used as input. MicroRNAs are curated by the Molecular Signatures Database (http://software.broadinstitute.org/gsea/msigdb/index.jsp).
(XLS)
Per90 discovery cohorts manhattan and QQ plots.
Top: African-Americans; Middle: European-Americans; Bottom: Multi-ethnic (2 or more populations for each variant).
(PDF)
Multi-ethnic discovery cohorts Per90 saturation miami plots.
Top: Females; Bottom: Males.
(PDF)
Average oxygen saturation regional plot (European ancestry, 10q22).
The supplemental regional plot order corresponds to the order found in S2, S3 and S4 Tables, minus the associations shown in Figs 1 and 2.
(PDF)
Minimum oxygen saturation regional plot (European ancestry males, 10q22).
(PDF)
Significant and suggestive meta-analysis results.
Lead SNPs are shown for regions with significant (p < 5.0 × 10–8) and suggestive (p < 1.0 × 10–6) p-values. Discovery regions were carried forward if the combined discovery and replication analysis results indicated a lower p-value, retained genome-level significance, or replication was unavailable...
All top locus SNP results (p < 1 x 10–6; full sleep combined-sex and sex-stratified analyses).
“Locus Class” indicates “Discovery/Replication” for main analyses or “Combined meta-analysis” for regions not clearing initial discovery p-value thresholds (i.e. S7 Table loci).
(XLS)
Significant combined discovery/replication cohort meta-analysis results.
Lead SNPs are shown for regions with significant (p < 5.0 x 10–8) combined-analysis p-values with p > 1 x 10–6 in the discovery phase. SNPs denotes the count of regional SNPs with p < 1.0 x 10–6. Genes indicates overlapping Ensembl genes within 5 kb of the p < 1 x 10–6 SNPs. C...
MetaXcan gene-level results for visceral omentum adipose tissue in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
Study-level variant counts.
Cohort-level information is shown for the three primary analyses, including discovery/replication category, the number of individuals with available phenotyping and genotyping, genotyping platform, imputation panel, and the number of imputed variants tested in each analysis following info score, MAC, and MAF filtering.
(...
Average oxygen saturation discovery cohorts manhattan and QQ plots.
Top: African-Americans; Middle: European-Americans; Bottom: Multi-ethnic. Variants in the multi-ethnic results had to have results from cohorts in two or more populations.
(PDF)
Multi-ethnic discovery cohorts average oxygen saturation miami plots.
Top: Females; Bottom: Males.
(PDF)
Per90 regional plot (African-American ancestry, 3p24).
(PDF)
Per90 regional plot (African-American ancestry, 4p35).
(PDF)
Per90 regional plot (European ancestry, 10q22).
(PDF)
Average oxygen saturation regional plot (European ancestry males, 5p15).
(PDF)
Minimum oxygen saturation regional plot (European ancestry males, 23p21).
(PDF)
Per90 regional plot (Combined discovery/replication, 7q22).
(PDF)
Sex-stratified comparison of top locus SNPs (p < 1 x 10–6).
Sex-stratified samples with n < 1000 are included here for comparison but were not included in the main analyses. An individual variant present in the combined-sex analysis for a given cohort may be missing from the equivalent sex-stratified analysis due to analysis-specific minor allele c...
Suggestive sex-stratified meta-analysis results.
Lead SNPs are shown for regions with suggestive (p < 1.0 × 10–6) p-values. Discovery regions were carried forward if the combined discovery and replication analysis results indicated a lower p-value, retained genome-level significance, or replication was unavailable (i.e. due to frequency or imputati...
Top locus SNP (p < 1 x 10–6) HaploReg (Roadmap Epigenomics and ENCODE) epigenetic evidence.
Data were obtained from HaploReg 4.1 (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) using exact SNPs (LD threshold = NA) and a ChromHMM 15-state model, followed by extraction from HTML. “Locus Class” indicates “Discovery/Replication” for mai...
Top locus SNP (p < 1 x 10–6) eQTL evidence.
Data were obtained from Fairfax et al. (monocytes), Geuvadis (LCLs), GTEx, Hao et al. (lung), Muther (adipose, LCLs, skin), Raj et al. (CD4, monocytes), Westra et al. (whole blood), and Zeller et al. (monocytes). “Locus Class” indicates “Discovery/Replication” for main analyses or “Combined meta-analysis”...
MetaXcan gene-level results for subcutaneous adipose tissue in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
MetaXcan gene-level results for hypothalamus in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
MetaXcan gene-level results for liver in European-Americans.
Lead results (p < 0.05) are shown. Note that Ensembl IDs obtained from MetaXcan are occasionally unavailable.
(XLS)
GIGSEA KEGG pathway enrichment in whole blood analyses.
MetaXcan gene-level results for DGN whole blood (S19 Table, all p-values) were used as input.
(XLS)
There has been a vast expansion in the volume of artificial intelligence (AI) research in biomedicine over the last several years. Simultaneously, we have begun to see the first medical AI systems rapidly translating from research into clinical practice. Evaluating AI systems for clinical tasks can be quite different than for other applications of...