Automated deep phenotyping of the cardiovascular system using magnetic resonance imaging

Across a lifetime, the cardiovascular system must adapt to a great range of demands from the body. The individual changes in the cardiovascular system that occur in response to loading conditions are influenced by genetic susceptibility, and the pattern and extent of these changes have prognostic value. Brachial blood pressure (BP) and left ventricular ejection fraction (LVEF) are important biomarkers that capture this response, and their measurements are made at high resolution. Relatively, clinical analysis is crude, and may result in lost information and the introduction of noise. Digital information storage enables efficient extraction of information from a dataset, and this strategy may provide more precise and deeper measures to breakdown current phenotypes into their component parts. The aim of this thesis was to develop automated analysis of cardiovascular magnetic resonance (CMR) imaging for more detailed phenotyping, and apply these techniques for new biological insights into the cardiovascular response to different loading conditions. I therefore tested the feasibility and clinical utility of computational approaches for image and waveform analysis, recruiting and acquiring additional patient cohorts where necessary, and then applied these approaches prospectively to participants before and after six-months of exercise training for a first-time marathon. First, a multi-centre, multi-vendor, multi-field strength, multi-disease CMR resource of 110 patients undergoing repeat imaging in a short time-frame was assembled. The resource was used to assess whether automated analysis of LV structure and function is feasible on real-world data, and if it can improve upon human precision. This showed that clinicians can be confident in detecting a 9% change in EF or a 20g change in LV mass. This will be difficult to improve by clinicians because the greatest source of human error was attributable to the observer rather than modifiable factors. Having understood these errors, a convolutional neural network was trained on separate multi-centre data for automated analysis and was successfully generalizable to the real-world CMR data. Precision was similar to human analysis, and performance was 186 times faster. This real-world benchmarking resource has been made freely available (thevolumesresource.com). Precise automated segmentations were then used as a platform to delve further into the LV phenotype. Global LVEFs measured from CMR imaging in 116 patients with severe aortic stenosis were broken down into ~10 million regional measurements of structure and function, represented by computational three-dimensional LV models for each individual. A cardiac atlas approach was used to compile, label, segment and represent these data. Models were compared with healthy matched controls, and co-registered with follow-up one year after aortic valve replacement (AVR). This showed that there is a tendency to asymmetric septal hypertrophy in all patients with severe aortic stenosis (AS), rather than a characteristic specific to predisposed patients. This response to AS was more unfavourable in males than females (associated with higher NT-proBNP, and lower blood pressure), but was more modifiable with AVR. This was not detected using conventional analysis. Because cardiac function is coupled with the vasculature, a novel integrated assessment of the cardiovascular system was developed. Wave intensity theory was used to combine central blood pressure and CMR aortic blood flow-velocity waveforms to represent the interaction of the heart with the vessels in terms of traveling energy waves. This was performed and then validated in 206 individuals (the largest cohort to date), demonstrating inefficient ventriculo-arterial coupling in female sex and healthy ageing. CMR imaging was performed in 236 individuals before training for a first-time marathon and 138 individuals were followed-up after marathon completion. After training, systolic/diastolic blood pressure reduced by 4/3mmHg, descending aortic stiffness decreased by 16%, and ventriculo-arterial coupling improved by 14%. LV mass increased slightly, with a tendency to more symmetrical hypertrophy. The reduction in aortic stiffness was equivalent to a 4-year reduction in estimated biological aortic age, and the benefit was greater in older, male, and slower individuals. In conclusion, this thesis demonstrates that automating analysis of clinical cardiovascular phenotypes is precise with significant time-saving. Complex data that is usually discarded can be used efficiently to identify new biology. Deeper phenotypes developed in this work inform risk reduction behaviour in healthy individuals, and demonstrably deliver a more sensitive marker of LV remodelling, potentially enhancing risk prediction in severe aortic stenosis

Novel imaging techniques for assessing disease affecting the right heart

Right ventricular (RV) size and function are prognostic in congenital and acquired heart disease. Two-dimensional echocardiography (2DE) is the most readily available modality for RV assessment, but is limited by its complex shape. Furthermore, biventricular function is intimately related through a shared septum and pericardium. The simplest metric of left ventricular (LV) function is ejection fraction (LVEF). However, LVEF is often maintained in pulmonary hypertension (PH), for example. Therefore better indicators of LV function are required to identify patients at risk of deterioration. In this thesis, novel imaging techniques for assessing cardiac function in right heart disease are investigated. The first experiment tested the hypothesis that single-beat threedimensional echocardiography (3DE) accurately and reproducibly quantifies RV volumes. 3DE traditionally acquires sub-volumes over consecutive heartbeats, whereas novel 3DE transducers can acquire datasets in a single cardiac cycle. Single-beat 3DE was compared against CMRI in 100 subjects including patients with PH and carcinoid heart disease. Single-beat 3DE was feasible and accurate for RV volumetric quantification, but with limitations of test-retest reproducibility. The second experiment tested the hypothesis that 2D knowledge-based reconstruction (2DKBR) accurately and reproducibly quantifies RV volumes. 2DKBR involves 2DE-acquired RV coordinates localized in 3D space and connected by reference to a disease-specific RV catalogue. This was validated against CMRI in 28 PH patients, and test-retest reproducibility was assessed. 2DKBR was feasible and accurate for RV volumetric quantification in PH, and more reproducible than conventional 2DE. The final experiment tested the hypothesis that multi-directional myocardial velocities could be assessed in PH by CMRI. A tissue phase mapping sequence was utilized in 40 PH patients and 20 healthy volunteers. Over a median follow-up period of 20 months, LV early diastolic wave velocities were the only independent predictors of functional capacity and clinical worsening in a model that includes conventional metrics of biventricular function

My future and I:cardiovascular risk stratification of asymptomatic individuals

In the coming decades, a continuing increase in the number of cases of coronary heart disease (CHD) is expected. This is caused by, amongst others, the increasing prevalence of obesity and diabetes, and the rising numbers of elderly citizens. The morbidity and mortality toll of CHD is high. In many cases, a coronary event occurs acutely, without earlier signs suggesting CHD. So how can we identify individuals in the asymptomatic population at high risk of CHD, and prevent coronary events? Cardiovas- cular risk estimation in the general population is based on determining risk factors such as hypertension and smoking. Risk factor levels can be used to calculate a risk-scoring algorithm, like the European SCORE, and guide medical therapy. Unfortunately, risk factor based algorithms are neither highly sensitive nor specific. Accurate identification of asymptomatic indi- viduals who will develop a coronary event is challenging

Tetralogy of Fallot in Finland

Abstract Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect. Postoperative patients with TOF are mostly compromised by chronic pulmonary regurgitation and chronic right ventricular volume load. These patients suffer from impaired exercise capacity and have an increased risk of sudden cardiac death (SCD) and heart failure. This thesis investigates the long-term outcome of surgically corrected TOF patients in a population-based setting. It also assesses the effects of long-lasting pulmonary regurgitation (PR) in the postoperative state in children and adolescents with TOF and healthy control subjects. During the period from 1962 to 2007 a total of 600 patients with TOF were surgically corrected in Finland before the age of 15 years. The follow-up time of these patients was 23±12.1 years. We observed that: i. 514 (85%) patients were alive and living in Finland; 82 (14%) had died. Primary repair of TOF was found to predict lower mortality and longer event-free survival when compared with two-stage repair. The need for a transannular patch (TAP) in TOF surgery carried a higher risk of re-operation without impact on late survival. In addition to the population-based follow-up study, we conducted a single‑centre cross-sectional study including 45 patients after repair of tetralogy of Fallot (rTOF) and 45 healthy age- and gender-matched paediatric and adolescent volunteers as controls (CO). Cardiac magnetic resonance (CMR) imaging was performed on all the study subjects. We made the following observations: ii. Late gadolinium enhancement (LGE), detected with CMR after gadolinium contrast agent, was also found outside the surgically affected areas in the right ventricle (RV) of TOF patients. Severity of PR correlated with the degree of LGE. LGE is recognized as a marker of fibrosis, scars, or otherwise abnormal myocardium. iii. In children and adolescents with TOF, severe pulmonary regurgitation importantly affects volume flow through the left atrium. Reduction in left ventricular (LV) preload volume may be an additional factor contributing to LV dysfunction. iv. RV longitudinal strain is increased in paediatric TOF patients with severe pulmonary regurgitation. In comparison with healthy volunteers, all TOF patients demonstrated enhanced and delayed RV circumferential strain that was accentuated in the apical region. In conclusion, the late results of TOF surgery are excellent. Patients operated on in the last two decades can expect to have a life expectancy comparable to their healthy peers. Early primary correction and avoidance of TAP if possible are predictors of superior late outcome. Chronic pulmonary regurgitation has deleterious effects on both right and LV filling and function. Novel methods such as LGE analysis, feature tracking (FT), and evaluation of LV preload may prove valuable when assessing the need for pulmonary valve replacement (PVR).Vaikean synnynnäisen sydänvian ennuste on parantunut merkittävästi Nuorimpien potilaiden ennuste lähestyy verrokkiväestöä, mutta sydänlihas ja sen toiminta ovat kuitenkin potilailla poikkeavia terveisiin verrattuna. Sydämen rakennevika on kaikkein yleisin yhteen elimeen kohdistuva rakennevika. Näiden sairauksien ennuste on parantunut huomattavasti viime vuosikymmenien aikana, ja aikuisiän on saavuttanut jo yli 7000 suomalaista sydänlasta. Hyvästä ennusteesta ovat poikkeuksena syanoottiset sydänviat, joilla tarkoitetaan ryhmää synnynnäisiä sydänvikoja, joissa sydämen oikean ja vasemman puolen välillä on oikovirtaus aiheuttaen verenkierron happivajausta ja sinisyyttä. Potilailla, joilla on oikeaa kammiota kuormittava sydänvika, ennuste on edelleenkin merkittävästi verrokkiväestöä huonompi, ja potilailla on normaaliväestöä suurempi riski kuolla joko sydämen vajaatoiminnan tai sydänperäisen äkkikuoleman vuoksi. Yleisyydeltään suurin ja merkittävin syanoottinen sydänvika on Fallot'n tetralogia. Tutkimuksessa käytettiin koko väestön kattavaa synnynnäisten sydänvikojen rekisteriä, jonka avulla kaikkien Suomessa leikattujen Fallot-potilaiden sairastuvuutta, kuolleisuutta sekä erilaisten kirurgisten menetelmien vaikutusta myöhäistätuloksiin voitiin selvittää. Otimme tutkimukseen mukaan kaikki Suomessa alle 15-vuotiaana korjausleikatut Fallot-potilaat, joita oli yhteensä 601. Rekisterin tietoja käyttämällä ja niitä väestörekisteriin ja potilasasiakirjoihin yhdistämällä selvitimme 99,8% kattavuudella potilaiden myöhäistuloksen sekä merkittävältä osalta myös käytetyt kirurgiset menetelmät sekä uusintaleikkausten määrän. Lisäksi tutkimme kliinisessä potilas-verrokkiasetelmassa Fallot-lapsia ja nuoria sekä heidän ikäisiään terveitä verrokkihenkilöitä. Tutkimukseemme osallistui yhteensä 45 potilasta ja 48 tervettä verrokkihenkilöä. Tavoitteena oli selvittää sydämen magneettikuvaksella Fallot-potilaiden sydämen toimintaa ja vajaatoiminnan kehittymislöydöksiä lapsuus- ja nuoruusiässä. Tutkimustemme mukaan Fallot-potilaiden ennuste on parantunut merkittävästi vuosikymmenten aikana. Leikkauskuolleisuutta ei nykyvuosituhannella enää käytännössä ole ollut ja 2000-luvulla syntyneiden Fallot-lasten ennuste näyttää lähestyvän verrokiväestön eliniänennustetta. TOF potilaille kannattaa, mikäli vain mahdollista, tehdä varhaislapsuudessa suora kirurginen korjaus ilman edeltävää oireita lievittävää leikkausta. Potilaiden hankalin myöhäisongelma on vaikea keuhkovaltimoläppävuoto, jonka totesimme vähentävän keuhkojen läpi kiertävän veren määrää ja vaikuttavan haitallisesti sydämen vasemman puolen toimintaan. Tämä on uusi havainto. Löysimme Fallot-potilaiden sydämestä arpeutumiseen viittaavia löydöksiä magneettikuvauksen myöhäistehostuma-tekniikalla ja totesimme löydösten liittyvän seuranta-ajan pituuteen ja keuhkovaltimoläpän vuodon määrään. Magneettikuvauksen strain-analyysilla osoitimme, että TOF-potilaiden sydänlihaksen liikkuvuus on poikkeavaa ja liikehäiriön vaikeusasteella on yhteys keuhkovaltimoläpän vuotoon. Fallot-kirurgian ja jatkohoidon tulokset Suomessa ovat kansainvälistä huippuluokkaa. Toivomme näiden löydösten tuovan lisäinformaatiota Fallot-potilaiden lääketieteelliseen seurantaan, joko suoraan käytettynä tai osana tulevaisuudessa mahdollisesti kehitettäviä ennustemalleja, jotka hyödyntävät ja analysoivat laaja-alaisesti potilaasta tutkittuja muuttujia. Kummassakin tapauksessa ne voisivat auttaa hoitavia lääkäreitä jatkohoitoon ja uusintaleikkauksiin liittyvässä päätöksenteossa

Characterising Shape Variation in the Human Right Ventricle Using Statistical Shape Analysis: Preliminary Outcomes and Potential for Predicting Hypertension in a Clinical Setting

Variations in the shape of the human right ventricle (RV) have previously been shown to be predictive of heart function and long term prognosis in Pulmonary Hypertension (PH), a deadly disease characterised by high blood pressure in the pulmonary arteries. The extent to which ventricular shape is also affected by non-pathological features such as sex, body mass index (BMI) and age is explored in this thesis. If fundamental differences in the shape of a structurally normal RV exist, these might also impact the success of a predictive model. This thesis evaluates the extent to which non-pathological features affect the shape of the RV and determines the best ways, in terms of procedure and analysis, to adapt the model to consistently predict PH. It also identifies areas where the statistical shape analysis procedure is robust, and considers the extent to which specific, non-pathological, characteristics impact the diagnostic potential of the statistical shape model. Finally, recommendations are made on next steps in the development of a classification procedure for PH. The dataset was composed of clinically-obtained, cardiovascular magnetic resonance images (CMR) from two independent sources; The University of Pittsburgh Medical Center and Newcastle University. Shape change is assessed using a 3D statistical shape analysis technique, which topologically maps heart meshes through an harmonic mapping approach to create a unique shape function for each shape. Proper Orthogonal Decomposition (POD) was applied to the complete set of shape functions in order to determine and rank a set of shape features (i.e. modes and corresponding coefficients from the decomposition). MRI scanning protocol produced the most significant difference in shape; a shape mode associated with detail at the RV apex and ventricular length from apex to base strongly correlated with the MRI sequence used to record each subject. Qualitatively, a protocol which skipped slices produced a shorter RV with less detail at the apex. Decomposition of sex, age and BMI also derives unique RV shape descriptors which correspond to anatomically meaningful features. The shape features are shown to be able to predict presence of PH. The predictive model can be improved by including BMI as a factor, but these improvements are mainly concentrated in identification of healthy subjects

Development of High-speed Optical Coherence Tomography for Time-lapse Non-destructive Characterization of Samples

Optical coherence tomography (OCT) is an established optical imaging modality which can obtain label-free, non-destructive 3D images of samples with micron-scale resolution and millimeter penetration. OCT has been widely adopted for biomedical researches

Improving the genetic diagnosis of mitochondrial disease using custom next-generation sequencing strategies /

PhD ThesisMitochondrial disease represents one of the most common inborn errors of metabolism with a minimum disease prevalence of ~12.5 per 100,000 (Gorman et al., 2015) in adults and ~4.7 per 100,000 in children (Skladal et al., 2003). Mitochondrial disease affects people of all ages and, although symptoms can sometimes be treated or ameliorated, there is no cure (McFarland et al., 2010). Mitochondrial disease is associated with a diverse spectrum of clinical presentations ranging from isolated symptoms such as seizures or cardiomyopathy, to severe neurological, syndromic presentations such as Leigh syndrome or Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes (MELAS). The underlying genetic defect can be within either the mitochondria's own genome (mtDNA) - a 16.6kb DNA molecule encoding 37 genes (Anderson et al., 1981) - or the nuclear genome, which encodes ~1150 mitochondrial proteins (Calvo et al., 2016). In view of this complexity, the care and diagnostic investigation of mitochondrial patients is part of the NHS Highly Specialised Services for Mitochondrial Diseases of Adults and Children within the UK. The vast genotypic and phenotypic heterogeneity means that the diagnostic algorithm is often complicated; for a large number of patients, the underlying genetic defect remains unknown often in spite of an established respiratory chain enzyme defect. For example, half of all paediatric patients with an isolated complex I deficiency, the most common respiratory chain defect, lack a genetic diagnosis (Swalwell et al., 2011). There is little that can be offered to these families in terms of counselling and recurrence risk prediction for future pregnancies. High-throughput sequencing offers real hope for families affected by massively heterogeneous conditions; the application of these emerging technologies to "undiagnosed" patients maximises the chance of elucidating the underlying genetic defect. My research proposal focuses on improving the genetic diagnostic pathway for predominantly paediatric patients with suspected mitochondrial disease with a view to enabling their parents’ access to reproductive options for future pregnancies. I plan to expand the scope of genetic testing in our Highly Specialised Mitochondrial Diagnostic Service Laboratory by employing three approaches - Sanger sequencing of new disease genes where there are clear genotypephenotype correlations, targeted next-generation sequencing of panels of candidate genes and unbiased whole exome sequencing. Our current strategy permits analysis of <10% of all candidate genes, whereas the system detailed in my proposal will raise this percentage significantly, with scope to incorporate new disease genes as they are described. ii Collaborative research projects with international academic research institutes have meant that a number of NHS patients have already undergone exome sequencing and a molecular diagnosis has been made via this research-reliant pathway. I believe it is vital that we can provide a similar service within the NHS diagnostic framework and my proposal will move conventional diagnostics using Sanger sequencing of single genes to a futureproof high-throughput strategy. I have access to a paediatric patient cohort (n=60) with a proven biochemical defect in muscle and many more with suspected mitochondrial disease for whom our current strategy has failed to identify the causative genetic defect; this proposal aims to obtain a genetic diagnosis for these patients. There will also be a prospective element as the new high-throughput screening strategy will be applied to each new paediatric patient with a biochemical diagnosis of isolated complex I deficiency (n=30/year). Where novel mutations in known disease genes, or novel mutations in unreported candidate genes are identified, functional investigations will be undertaken to establish their pathogenicity. In the absence of a cure for mitochondrial disease, the provision of reproductive counselling is a vital resource for families affected by inherited mitochondrial disease and the current repertoire includes prenatal genetic diagnosis (chorionic villus biopsy; amniocentesis; non-invasive screening) or pre-implantation genetic diagnosis during in vitro fertilisation procedures. Moreover, determining the phenotypic effect of these genetic mutations on mitochondrial function will be vital to understanding the underlying mechanisms and pathways involved. In addition to providing a genetic diagnosis for patients (and their families), it is hoped that advances in knowledge relating to mitochondrial pathology may lead to new treatments