Mono- and biallelic variant effects on disease at biobank scale

Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics¹. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance^2,3. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.

Clinical and genetic markers of prehypertension in North-Western Russian population

Introduction

Prehypertension is a medical classification for patients with above normal blood pressure (BP) but insufficient for confirming hypertension diagnosis. Condition is often asymptomatic as it gradually develops over the years, yet recent meta-analyses suggest that prehypertension is a significant risk factor for stroke and other cardiovascular diseases.

Methods

We analyzed phenotypic data from 879 (age 25–64) individuals without hypertension from a population based-sampling cohort of St. Petersburg region in the North-West of Russia to identify clinical risk factors associated with prehypertension condition. All patients were divided in two groups – optimal BP (systolic BP <120 mmHg and diastolic BP <80; N=426) and prehypertension (systolic BP in range 120–140 mmHg and diastolic BP in range 80–90 and not on antihypertensive therapy; N=453).

Results

Phenotypic analysis with linear regression was corrected for age, sex, smoking status, BMI and levels of LDL and HDL cholesterol (Figure 1). Interestingly, blood level of insulin was significantly associated with prehypertension status along with insulin resistance index, however, presence of diabetes diagnosis in medical history was not significant. Phenotypes associated with prehypertension suggest that prehypertension is often developing along with hyperinsulinemia.

Finally, we estimated polygenic risk scores (PRS) for hypertension using UK biobank GWAS summary statistics and confirmed that prehypertension is more frequent at earlier age in patients with higher genetic susceptibility (Figure 1, Figure 2).

Conclusions

Hyperinsulinemia and genetic susceptibility to hypertension are strong risk factors for prehypertension.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This work was financially supported by the Ministry of Science and Higher Education of the Russian Federation (Agreement No. 075-15-2020-901) to Al.K. Figure 1. Clinical markers of prehypertensionFigure 2. Genetic markers of prehypertension

Genetic influences on eight psychiatric disorders based on family data of 4 408 646 full and half-siblings, and genetic data of 333 748 cases and controls

BACKGROUND

Most studies underline the contribution of heritable factors for psychiatric disorders. However, heritability estimates depend on the population under study, diagnostic instruments, and study designs that each has its inherent assumptions, strengths, and biases. We aim to test the homogeneity in heritability estimates between two powerful, and state of the art study designs for eight psychiatric disorders.

METHODS

We assessed heritability based on data of Swedish siblings (N = 4 408 646 full and maternal half-siblings), and based on summary data of eight samples with measured genotypes (N = 125 533 cases and 208 215 controls). All data were based on standard diagnostic criteria. Eight psychiatric disorders were studied: (1) alcohol dependence (AD), (2) anorexia nervosa, (3) attention deficit/hyperactivity disorder (ADHD), (4) autism spectrum disorder, (5) bipolar disorder, (6) major depressive disorder, (7) obsessive-compulsive disorder (OCD), and (8) schizophrenia.

RESULTS

Heritability estimates from sibling data varied from 0.30 for Major Depression to 0.80 for ADHD. The estimates based on the measured genotypes were lower, ranging from 0.10 for AD to 0.28 for OCD, but were significant, and correlated positively (0.19) with national sibling-based estimates. When removing OCD from the data the correlation increased to 0.50.

CONCLUSIONS

Given the unique character of each study design, the convergent findings for these eight psychiatric conditions suggest that heritability estimates are robust across different methods. The findings also highlight large differences in genetic and environmental influences between psychiatric disorders, providing future directions for etiological psychiatric research.

Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability

The Psychiatric Genomics Consortium-Posttraumatic Stress Disorder group (PGC-PTSD) combined genome-wide case-control molecular genetic data across 11 multiethnic studies to quantify PTSD heritability, to examine potential shared genetic risk with schizophrenia, bipolar disorder, and major depressive disorder and to identify risk loci for PTSD. Examining 20 730 individuals, we report a molecular genetics-based heritability estimate (h2SNP) for European-American females of 29% that is similar to h2SNP for schizophrenia and is substantially higher than h2SNP in European-American males (estimate not distinguishable from zero). We found strong evidence of overlapping genetic risk between PTSD and schizophrenia along with more modest evidence of overlap with bipolar and major depressive disorder. No single-nucleotide polymorphisms (SNPs) exceeded genome-wide significance in the transethnic (overall) meta-analysis and we do not replicate previously reported associations. Still, SNP-level summary statistics made available here afford the best-available molecular genetic index of PTSD-for both European- and African-American individuals-and can be used in polygenic risk prediction and genetic correlation studies of diverse phenotypes. Publication of summary statistics for ∼10 000 African Americans contributes to the broader goal of increased ancestral diversity in genomic data resources. In sum, the results demonstrate genetic influences on the development of PTSD, identify shared genetic risk between PTSD and other psychiatric disorders and highlight the importance of multiethnic/racial samples. As has been the case with schizophrenia and other complex genetic disorders, larger sample sizes are needed to identify specific risk loci.

ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties

Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic of schizophrenia do not appear before early adulthood. We investigated whether overlap in common genetic influences between these clinical conditions and impairments in social communication depends on the developmental stage of the assessed trait. Social communication difficulties were measured in typically-developing youth (Avon Longitudinal Study of Parents and Children, N⩽5553, longitudinal assessments at 8, 11, 14 and 17 years) using the Social Communication Disorder Checklist. Data on clinical ASD (PGC-ASD: 5305 cases, 5305 pseudo-controls; iPSYCH-ASD: 7783 cases, 11 359 controls) and schizophrenia (PGC-SCZ2: 34 241 cases, 45 604 controls, 1235 trios) were either obtained through the Psychiatric Genomics Consortium (PGC) or the Danish iPSYCH project. Overlap in genetic influences between ASD and social communication difficulties during development decreased with age, both in the PGC-ASD and the iPSYCH-ASD sample. Genetic overlap between schizophrenia and social communication difficulties, by contrast, persisted across age, as observed within two independent PGC-SCZ2 subsamples, and showed an increase in magnitude for traits assessed during later adolescence. ASD- and schizophrenia-related polygenic effects were unrelated to each other and changes in trait-disorder links reflect the heterogeneity of genetic factors influencing social communication difficulties during childhood versus later adolescence. Thus, both clinical ASD and schizophrenia share some genetic influences with impairments in social communication, but reveal distinct developmental profiles in their genetic links, consistent with the onset of clinical symptoms.

The iPSYCH2012 case-cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders

The Integrative Psychiatric Research (iPSYCH) consortium has established a large Danish population-based Case-Cohort sample (iPSYCH2012) aimed at unravelling the genetic and environmental architecture of severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005, including 1 472 762 persons. This paper introduces the iPSYCH2012 sample and outlines key future research directions. Cases were identified as persons with schizophrenia (N=3540), autism (N=16 146), attention-deficit/hyperactivity disorder (N=18 726) and affective disorder (N=26 380), of which 1928 had bipolar affective disorder. Controls were randomly sampled individuals (N=30 000). Within the sample of 86 189 individuals, a total of 57 377 individuals had at least one major mental disorder. DNA was extracted from the neonatal dried blood spot samples obtained from the Danish Neonatal Screening Biobank and genotyped using the Illumina PsychChip. Genotyping was successful for 90% of the sample. The assessments of exome sequencing, methylation profiling, metabolome profiling, vitamin-D, inflammatory and neurotrophic factors are in progress. For each individual, the iPSYCH2012 sample also includes longitudinal information on health, prescribed medicine, social and socioeconomic information, and analogous information among relatives. To the best of our knowledge, the iPSYCH2012 sample is the largest and most comprehensive data source for the combined study of genetic and environmental aetiologies of severe mental disorders.

Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia

This corrects the article DOI: 10.1038/mp.2016.97.

Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia

This corrects the article DOI: 10.1038/mp.2016.97.

[Generic and biosimilar drug substitution: a panacea?]

Drugs are the third largest source of expenditure under Switzerland's compulsory basic health insurance. Generics, the price of which should be at least 30 per cent less than the cost of the original drugs, can potentially allow substantial savings. Their approval requires bioequivalence studies and their use is safe, although some factors may influence patients' and physicians' acceptance. The increased substitution of biosimilar drugs for more expensive biotech drugs should allow further cost savings. In an attempt to extend the monopoly granted by the original drug patent, some pharmaceutical companies implement "evergreening" strategies including small modifications of the original substance for which the clinical benefit is not always demonstrated.

Guidelines for investigating causality of sequence variants in human disease

The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.

The effects of electrode misplacement on clinicians' interpretation of the standard 12-lead electrocardiogram

INTRODUCTION

This study investigates how a particular incorrect electrode configuration affects the 12-lead Electrocardiogram (ECG).

METHODS

A correct and an incorrect 12-lead ECG were extracted from a 192-lead BSPM. This was done for 232 BSPMs yielding 464 12-lead ECGs. The particular incorrect ECG involved displacing electrodes V1 and V2 in the second intercostal space whilst also offsetting the remaining electrodes. These ECGs were examined in two stages: (a) analysis of the effects of electrode misplacement on signal morphology and (b) analysis of how often the incorrect electrode configuration changed the diagnosis of two clinicians in a random sample of 75 patients.

RESULTS

According to the Root Mean Square Error (RMSE) of the difference between PQRST intervals in the correct and incorrect ECGs, lead V2 is the most affected lead (mean: 185 μV ± 82 μV), followed by lead V4 (mean: 114 μV ± 59 μV) and lead V1 (mean: 100 μV ± 47 μV). It was found that if the incorrect electrode configuration is applied, there is a 17% to a 24% chance the diagnostic interpretation will be different. Quantified using Similarity Coefficient (SC) leads V1 and V2 were found to be more alike when misplaced in the second intercostal space. The average SC between these leads when correctly placed was 0.08 (± 0.65), however when incorrectly placed, the average SC was 0.43 (± 0.3).

CONCLUSION

There is a reasonable chance this particular incorrect electrode configuration will change the diagnosis of the 12-lead ECG. This highlights the importance of developing algorithms to detect electrode misplacement along with better education regarding ECG acquisition.

Improving superficial target delineation in radiation therapy with endoscopic tracking and registration

PURPOSE

Target delineation within volumetric imaging is a critical step in the planning process of intensity modulated radiation therapy. In endoluminal cancers, endoscopy often reveals superficial areas of visible disease beyond what is seen on volumetric imaging. Quantitatively relating these findings to the volumetric imaging is prone to human error during the recall and contouring of the target. We have developed a method to improve target delineation in the radiation therapy planning process by quantitatively registering endoscopic findings contours traced on endoscopic images to volumetric imaging.

METHODS

Using electromagnetic sensors embedded in an endoscope, 2D endoscopic images were registered to computed tomography (CT) volumetric images by tracking the position and orientation of the endoscope relative to a CT image set. Regions-of-interest (ROI) in the 2D endoscopic view were delineated. A mesh created within the boundary of the ROI was projected onto the 3D image data, registering the ROI with the volumetric image. This 3D ROI was exported to clinical radiation treatment planning software. The precision and accuracy of the procedure was tested on two solid phantoms with superficial markings visible on both endoscopy and CT images. The first phantom was T-shaped tube with X-marks etched on the interior. The second phantom was an anatomically correct skull phantom with a phantom superficial lesion placed on the pharyngeal surface. Markings were contoured on the endoscope images and compared with contours delineated in the treatment planning system based on the CT images. Clinical feasibility was tested on three patients with early stage glottic cancer. Image-based rendering using manually identified landmarks was used to improve the registration.

RESULTS

Using the T-shaped phantom with X-markings, the 2D to 3D registration accuracy was 1.5-3.5 mm, depending on the endoscope position relative to the markings. Intraobserver standard variation was 0.5 mm. Rotational accuracy was within 2°. Using the skull phantom, registration accuracy was assessed by calculating the average surface minimum distance between the endoscopy and treatment planning contours. The average surface distance was 0.92 mm with 93% of all points in the 2D-endoscopy ROI within 1.5 mm of any point within the ROI contoured in the treatment planning software. This accuracy is limited by the CT imaging resolution and the electromagnetic (EM) sensor accuracy. The clinical testing demonstrated that endoscopic contouring is feasible. With registration based on em tracking only, accuracy was 5.6-8.4 mm. Image-based registration reduced this error to less than 3.5 mm and enabled endoscopic contouring in all cases.

CONCLUSIONS

Registration of contours generated on 2D endoscopic images to 3D planning space is feasible, with accuracy smaller than typical set-up margins. Used in addition to standard 3D contouring methods in radiation planning, the technology may improve gross tumour volume (GTV) delineation for superficial tumors in luminal sites that are only visible in endoscopy.

Improved detection of acute myocardial infarction in patients with chest pain and significant left main stem coronary stenosis

BACKGROUND

Non-invasive diagnosis of acute myocardial infarction (AMI) associated with significant left main stem (LMS) stenosis remains challenging.

METHODS

Consecutive patients presenting with acute ischaemic-type chest pain from 2000 to 2010 were analysed. Entry criteria: 12-lead ECG and Body Surface Potential Map (BSPM) at presentation, cardiac troponin T (cTnT) ≥12 h and coronary angiography during admission. cTnT ≥0.03 µg/l defined AMI. ECG abnormalities assessed: STEMI by Minnesota criteria; ST elevation (STE) aVR ≥0.5 mm; ST depression (STD) ≥0.5 mm in ≥2 contiguous leads (CL); T-wave inversion (TWI) ≥1 mm in ≥2 CL. BSPM STE was ≥2 mm in anterior, ≥1 mm in lateral, inferior, right ventricular or high right anterior and ≥0.5 mm in posterior territories. Significant LMS stenosis was ≥70%.

RESULTS

Enrolled were 2810 patients (aged 60 ± 12 years; 71% male). Of these, 116 (4.1%) had significant LMS stenosis with AMI occurring in 92 (79%). STEMI by Minnesota criteria occurred in 13 (11%) (sensitivity 12%, specificity 92%), STE in lead aVR in 23 (20%) (sensitivity 23%, specificity 92%), TWI in 38 (33%) (sensitivity 34%, specificity 71%) and STD in 51 (44%) (sensitivity 49%, specificity 75%). BSPM STE occurred in 85 (73%): sensitivity 88%, specificity 83%, positive predictive value 95% and negative predictive value 65%. Of those with AMI, 74% had STE in either the high right anterior or right ventricular territories not identified by the 12-lead ECG. C-Statistic for AMI diagnosis using BSPM STE was 0.800 (P < 0.001).

CONCLUSION

In patients with significant LMS stenosis presenting with chest pain, BSPM STE has improved sensitivity (88%), with specificity 83%, over 12-lead ECG in the diagnosis of AMI.

Genome-wide association study of serious blistering skin rash caused by drugs

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are rare but severe, potentially life threatening adverse drug reactions characterized by skin blistering. Previous studies have identified drug-specific and population-specific genetic risk factors with large effects. In this study, we report the first genome-wide association study (GWAS) of SJS/TEN induced by a variety of drugs. Our aim was to identify common genetic risk factors with large effects on SJS/TEN risk. We conducted a genome-wide analysis of 96 retrospective cases and 198 controls with a panel of over one million single-nucleotide polymorphisms (SNPs). We further improved power with about 4000 additional controls from publicly available datasets. No genome-wide significant associations with SNPs or copy number variants were observed, although several genomic regions were suggested that may have a role in predisposing to drug-induced SJS/TEN. Our GWAS did not find common, highly penetrant genetic risk factors responsible for SJS/TEN events in the cases selected.

Demons deformable registration for CBCT-guided procedures in the head and neck: convergence and accuracy

PURPOSE

The accuracy and convergence behavior of a variant of the Demons deformable registration algorithm were investigated for use in cone-beam CT (CBCT)-guided procedures of the head and neck. Online use of deformable registration for guidance of therapeutic procedures such as image-guided surgery or radiation therapy places trade-offs on accuracy and computational expense. This work describes a convergence criterion for Demons registration developed to balance these demands; the accuracy of a multiscale Demons implementation using this convergence criterion is quantified in CBCT images of the head and neck.

METHODS

Using an open-source "symmetric" Demons registration algorithm, a convergence criterion based on the change in the deformation field between iterations was developed to advance among multiple levels of a multiscale image pyramid in a manner that optimized accuracy and computation time. The convergence criterion was optimized in cadaver studies involving CBCT images acquired using a surgical C-arm prototype modified for 3D intraoperative imaging. CBCT-to-CBCT registration was performed and accuracy was quantified in terms of the normalized cross-correlation (NCC) and target registration error (TRE). The accuracy and robustness of the algorithm were then tested in clinical CBCT images of ten patients undergoing radiation therapy of the head and neck.

RESULTS

The cadaver model allowed optimization of the convergence factor and initial measurements of registration accuracy: Demons registration exhibited TRE=(0.8+/-0.3) mm and NCC =0.99 in the cadaveric head compared to TRE=(2.6+/-1.0) mm and NCC=0.93 with rigid registration. Similarly for the patient data, Demons registration gave mean TRE=(1.6+/-0.9) mm compared to rigid registration TRE=(3.6+/-1.9) mm, suggesting registration accuracy at or near the voxel size of the patient images (1 x 1 x 2 mm3). The multiscale implementation based on optimal convergence criteria completed registration in 52 s for the cadaveric head and in an average time of 270 s for the larger FOV patient images.

CONCLUSIONS

Appropriate selection of convergence and multiscale parameters in Demons registration was shown to reduce computational expense without sacrificing registration performance. For intraoperative CBCT imaging with deformable registration, the ability to perform accurate registration within the stringent time requirements of the operating environment could offer a useful clinical tool allowing integration of preoperative information while accurately reflecting changes in the patient anatomy. Similarly for CBCT-guided radiation therapy, fast accurate deformable registration could further augment high-precision treatment strategies.

A case of ST-elevation and nystagmus--when coronary thrombosis is not to blame

We present the case of a post-menopausal female who, following a prolonged period of vomiting and diarrhoea, presented acutely with Wernicke's; encephalopathy, chest pain, ST-segment elevation and congestive cardiac failure associated with hypotension. Coronary angiography demonstrated no abnormality. Haemodynamics improved significantly in the short-term following intravenous thiamine replacement, with complete resolution of all ST-segment abnormalities and normalization of left ventricular function at six-week follow-up. Shoshin beriberi in the context of metabolic alkalosis, secondary to severe electrolyte depletion, is exceptional and is a differential diagnosis to be considered in all malnourished patients presenting with symptoms and signs suggestive of an acute coronary syndrome, especially those with a history of alcohol-dependence.

Automatic image-to-world registration based on x-ray projections in cone-beam CT-guided interventions

Intraoperative imaging offers a means to account for morphological changes occurring during the procedure and resolve geometric uncertainties via integration with a surgical navigation system. Such integration requires registration of the image and world reference frames, conventionally a time consuming, error-prone manual process. This work presents a method of automatic image-to-world registration of intraoperative cone-beam computed tomography (CBCT) and an optical tracking system. Multimodality (MM) markers consisting of an infrared (IR) reflective sphere with a 2 mm tungsten sphere (BB) placed precisely at the center were designed to permit automatic detection in both the image and tracking (world) reference frames. Image localization is performed by intensity thresholding and pattern matching directly in 2D projections acquired in each CBCT scan, with 3D image coordinates computed using backprojection and accounting for C-arm geometric calibration. The IR tracking system localized MM markers in the world reference frame, and the image-to-world registration was computed by rigid point matching of image and tracker point sets. The accuracy and reproducibility of the automatic registration technique were compared to conventional (manual) registration using a variety of marker configurations suitable to neurosurgery (markers fixed to cranium) and head and neck surgery (markers suspended on a subcranial frame). The automatic technique exhibited subvoxel marker localization accuracy (< 0.8 mm) for all marker configurations. The fiducial registration error of the automatic technique was (0.35 +/-0.01) mm, compared to (0.64 +/- 0.07 mm) for the manual technique, indicating improved accuracy and reproducibility. The target registration error (TRE) averaged over all configurations was 1.14 mm for the automatic technique, compared to 1.29 mm for the manual in accuracy, although the difference was not statistically significant (p = 0.3). A statistically significant improvement in precision was observed-specifically, the standard deviation in TRE was 0.2 mm for the automatic technique versus 0.34 mm for the manual technique (p = 0.001). The projection-based automatic registration technique demonstrates accuracy and reproducibility equivalent or superior to the conventional manual technique for both neurosurgical and head and neck marker configurations. Use of this method with C-arm CBCT eliminates the burden of manual registration on surgical workflow by providing automatic registration of surgical tracking in 3D images within approximately 20 s of acquisition, with registration automatically updated with each CBCT scan. The automatic registration method is undergoing integration in ongoing clinical trials of intraoperative CBCT-guided head and neck surgery.

Reversible dilated cardiomyopathy associated with post-partum thyrotoxic storm

The following case of a young mother presenting with post-partum pulmonary oedema, highlights a singular and life-threatening complication of a common condition (thyrotoxicosis). While thyrotoxic heart disease is well described, thyrotoxic storm in the post-partum period associated with dilated cardiomyopathy, congestive cardiac failure and ventricular fibrillation is exceptional.

Microdeletion/duplication at 15q13.2q13.3 among individuals with features of autism and other neuropsychiatric disorders

BACKGROUND

Segmental duplications at breakpoints (BP4-BP5) of chromosome 15q13.2q13.3 mediate a recurrent genomic imbalance syndrome associated with mental retardation, epilepsy, and/or electroencephalogram (EEG) abnormalities.

PATIENTS

DNA samples from 1445 unrelated patients submitted consecutively for clinical array comparative genomic hybridisation (CGH) testing at Children's Hospital Boston and DNA samples from 1441 individuals with autism from 751 families in the Autism Genetic Resource Exchange (AGRE) repository.

RESULTS

We report the clinical features of five patients with a BP4-BP5 deletion, three with a BP4-BP5 duplication, and two with an overlapping but smaller duplication identified by whole genome high resolution oligonucleotide array CGH. These BP4-BP5 deletion cases exhibit minor dysmorphic features, significant expressive language deficits, and a spectrum of neuropsychiatric impairments that include autism spectrum disorder, attention deficit hyperactivity disorder, anxiety disorder, and mood disorder. Cognitive impairment varied from moderate mental retardation to normal IQ with learning disability. BP4-BP5 covers approximately 1.5 Mb (chr15:28.719-30.298 Mb) and includes six reference genes and 1 miRNA gene, while the smaller duplications cover approximately 500 kb (chr15:28.902-29.404 Mb) and contain three reference genes and one miRNA gene. The BP4-BP5 deletion and duplication events span CHRNA7, a candidate gene for seizures. However, none of these individuals reported here have epilepsy, although two have an abnormal EEG.

CONCLUSIONS

The phenotype of chromosome 15q13.2q13.3 BP4-BP5 microdeletion/duplication syndrome may include features of autism spectrum disorder, a variety of neuropsychiatric disorders, and cognitive impairment. Recognition of this broader phenotype has implications for clinical diagnostic testing and efforts to understand the underlying aetiology of this syndrome.

Multigenic control of tuberculosis resistance: analysis of a QTL on mouse chromosome 7 and its synergism with sst1

Tuberculosis remains a significant global health problem: one-third of the human population is infected with Mycobacterium tuberculosis (MTB) and 10% of those are at lifetime risk of developing tuberculosis. In the majority of individuals infected, genetic determinants of susceptibility remain largely unknown due to complex multigenic control and the influence of genes--environment interactions. Genetic variation of host resistance to MTB in animal models reflects heterogeneity among humans. Stepwise dissection of these interactions will permit the deciphering of MTB's complex virulence strategy. Previously, we have characterized a mouse supersusceptibility locus (sst1) controlling antituberculosis immunity. In this study, eight host resistance quantitative trait loci (QTLs) were mapped that counter-balance the devastating effect of sst1, among which a QTL on chromosome 7 (Chr7) was most prominent. The Chr7 and sst1 loci independently control distinct resistance mechanisms to MTB, but their effects apparently converge on macrophages in remarkable synergy. Combining these resistance alleles on a C3HeB/FeJ-susceptible background reduced the lung pathology and improved survival after MTB challenge accounting for half of the difference between susceptible and resistant parental strains. These data reveal novel gene interactions controlling MTB resistance and will enable the identification of resistance gene(s) encoded within Chr7 locus.

Image quality and localization accuracy in C-arm tomosynthesis-guided head and neck surgery

The image quality and localization accuracy for C-arm tomosynthesis and cone-beam computed tomography (CBCT) guidance of head and neck surgery were investigated. A continuum in image acquisition was explored, ranging from a single exposure (radiograph) to multiple projections acquired over a limited arc (tomosynthesis) to a full semicircular trajectory (CBCT). Experiments were performed using a prototype mobile C-arm modified to perform 3D image acquisition (a modified Siemens PowerMobil). The tradeoffs in image quality associated with the extent of the source-detector arc (theta(tot)), the number of projection views, and the total imaging dose were evaluated in phantom and cadaver studies. Surgical localization performance was evaluated using three cadaver heads imaged as a function of theta(tot). Six localization tasks were considered, ranging from high-contrast feature identification (e.g., tip of a K-wire pointer) to more challenging soft-tissue delineation (e.g., junction of the hard and soft palate). Five head and neck surgeons and one radiologist participated as observers. For each localization task, the 3D coordinates of landmarks pinpointed by each observer were analyzed as a function of theta(tot). For all tomosynthesis angles, image quality was highest in the coronal plane, whereas sagittal and axial planes exhibited a substantial decrease in spatial resolution associated with out-of-plane blur and distortion. Tasks involving complex, lower-contrast features demonstrated steeper degradation with smaller tomosynthetic arc. Localization accuracy in the coronal plane was correspondingly high, maintained to < 3 mm down to theta(tot) approximately 30 degrees, whereas sagittal and axial localization degraded rapidly below theta(tot) approximately 60 degrees. Similarly, localization precision was better than approximately 1 mm within the coronal plane, compared to approximately 2-3 mm out-of-plane for tomosynthesis angles below theta(tot) approximately 45 degrees. An overall 3D localization accuracy of approximately 2.5 mm was achieved with theta(tot) approximately 90 degrees for most tasks. The high in-plane spatial resolution, short scanning time, and low radiation dose characteristic of tomosynthesis may enable the surgeon to collect near real-time images throughout the procedure with minimal interference to surgical workflow. Therefore, tomosynthesis could provide a useful addition to the image-guided surgery arsenal, providing on-demand, high quality image updates, complemented by CBCT at critical milestones in the surgical procedure.

MAST3: a novel IBD risk factor that modulates TLR4 signaling

Inflammatory bowel disease (IBD) is a chronic disorder caused by multiple factors in a genetically susceptible host. Significant advances in the study of genetic susceptibility have highlighted the importance of the innate immune system in this disease. We previously completed a genome-wide linkage study and found a significant locus (IBD6) on chromosome 19p. We were interested in identifying the causal variant in IBD6. We performed a two-stage association mapping study. In stage 1, 1530 single-nucleotide polymorphisms (SNPs) were selected from the HapMap database and genotyped in 761 patients with IBD. Among the SNPs that passed the threshold for replication, 26 were successfully genotyped in 754 additional patients (stage 2). One intronic variant, rs273506, located in the microtubule-associated serine/threonine-protein kinase gene-3 (MAST3), was found to be associated in both stages (pooled P=1.8 x 10(-4)). We identified four MAST3 coding variants, including a non-synonymous SNP rs8108738, correlated to rs273506 and associated with IBD. To test whether MAST3 was expressed in cells of interest, we performed expression assays, which showed abundant expression of MAST3 in antigen-presenting cells and in lymphocytes. The knockdown of MAST3 specifically decreased Toll-like receptor-4-dependent NF-kappaB activity. Our findings are additional proofs of the pivotal role played by modulators of NF-kappaB activity in IBD pathogenesis.

Geometric calibration of a mobile C-arm for intraoperative cone-beam CT

A geometric calibration method that determines a complete description of source-detector geometry was adapted to a mobile C-arm for cone-beam computed tomography (CBCT). The non-iterative calibration algorithm calculates a unique solution for the positions of the source (X(s), Y(s), Z(s)), detector (X(d), Y(d), Z(d)), piercing point (U(o), V(o)), and detector rotation angles (phi, theta, eta) based on projections of a phantom consisting of two plane-parallel circles of ball bearings encased in a cylindrical acrylic tube. The prototype C-arm system was based on a Siemens PowerMobil modified to provide flat-panel CBCT for image-guided interventions. The magnitude of geometric nonidealities in the source-detector orbit was measured, and the short-term (approximately 4 h) and long-term (approximately 6 months) reproducibility of the calibration was evaluated. The C-arm exhibits large geometric nonidealities due to mechanical flex, with maximum departures from the average semicircular orbit of deltaU(o) = 15.8 mm and deltaV(o) = 9.8 mm (for the piercing point), deltaX and deltaY = 6-8 mm and deltaZ = 1 mm (for the source and detector), and deltaphi approximately 2.9 degrees, deltatheta approximately 1.9 degrees, and delta eta approximately 0.8 degrees (for the detector tilt/rotation). Despite such significant departures from a semicircular orbit, these system parameters were found to be reproducible, and therefore correctable by geometric calibration. Short-term reproducibility was < 0.16 mm (subpixel) for the piercing point coordinates, < 0.25 mm for the source-detector X and Y, < 0.035 mm for the source-detector Z, and < 0.02 degrees for the detector angles. Long-term reproducibility was similarly high, demonstrated by image quality and spatial resolution measurements over a period of 6 months. For example, the full-width at half-maximum (FWHM) in axial images of a thin steel wire increased slightly as a function of the time (delta) between calibration and image acquisition: FWHM=0.62, 0.63, 0.66, 0.71, and 0.72 mm at delta = 0 s, 1 h, 1 day, 1 month, and 6 months, respectively. For ongoing clinical trials in CBCT-guided surgery at our institution, geometric calibration is conducted monthly to provide sufficient three-dimensional (3D) image quality while managing time and workflow considerations of the calibration and quality assurance process. The sensitivity of 3D image quality to each of the system parameters was investigated, as was the tolerance to systematic and random errors in the geometric parameters, showing the most sensitive parameters to be the piercing point coordinates (U(o), V(o)) and in-plane positions of the source (X(s), Y(s)) and detector (X(d), Y(d)). Errors in the out-of-plane position of the source (Z(s)) and detector (Z(d)) and the detector angles (phi, theta, eta) were shown to have subtler effects on 3D image quality.

Whole-genome association study of bipolar disorder

We performed a genome-wide association scan in 1461 patients with bipolar (BP) 1 disorder, 2008 controls drawn from the Systematic Treatment Enhancement Program for Bipolar Disorder and the University College London sample collections with successful genotyping for 372,193 single nucleotide polymorphisms (SNPs). Our strongest single SNP results are found in myosin5B (MYO5B; P=1.66 x 10(-7)) and tetraspanin-8 (TSPAN8; P=6.11 x 10(-7)). Haplotype analysis further supported single SNP results highlighting MYO5B, TSPAN8 and the epidermal growth factor receptor (MYO5B; P=2.04 x 10(-8), TSPAN8; P=7.57 x 10(-7) and EGFR; P=8.36 x 10(-8)). For replication, we genotyped 304 SNPs in family-based NIMH samples (n=409 trios) and University of Edinburgh case-control samples (n=365 cases, 351 controls) that did not provide independent replication after correction for multiple testing. A comparison of our strongest associations with the genome-wide scan of 1868 patients with BP disorder and 2938 controls who completed the scan as part of the Wellcome Trust Case-Control Consortium indicates concordant signals for SNPs within the voltage-dependent calcium channel, L-type, alpha 1C subunit (CACNA1C) gene. Given the heritability of BP disorder, the lack of agreement between studies emphasizes that susceptibility alleles are likely to be modest in effect size and require even larger samples for detection.

Intraoperative cone-beam CT for image-guided tibial plateau fracture reduction

OBJECTIVES

A mobile isocentric C-arm was modified in our laboratory in collaboration with Siemens Medical Solutions to include a large-area flat-panel detector providing multi-mode fluoroscopy and cone-beam CT (CBCT) imaging. This technology is an important advance over existing intraoperative imaging (e.g., Iso-C(3D)), offering superior image quality, increased field of view, higher spatial resolution, and soft-tissue visibility. The aim of this study was to assess the system's performance and image quality in tibial plateau (TP) fracture reconstruction.

METHODS

Three TP fractures were simulated in fresh-frozen cadaveric knees through combined axial loading and lateral impact. The fractures were reduced through a lateral approach and assessed by fluoroscopy. The reconstruction was then assessed using CBCT. If necessary, further reduction and localization of remaining displaced bone fragments was performed using CBCT images for guidance. CBCT image quality was assessed with respect to projection speed, dose and filtering technique.

RESULTS

CBCT imaging provided exquisite visualization of articular details, subtle fragment detection and localization, and confirmation of reduction and implant placement. After fluoroscopic images indicated successful initial reduction, CBCT imaging revealed areas of malalignment and displaced fragments. CBCT facilitated fragment localization and improved anatomic reduction. CBCT image noise increased gradually with reduced dose, but little difference in images resulted from increased projections. High-resolution reconstruction provided better delineation of plateau depressions.

CONCLUSION

This study demonstrated a clear advantage of intraoperative CBCT over 2D fluoroscopy and Iso-C(3D) in TP fracture fixation. CBCT imaging provided benefits in fracture type diagnosis, localization of fracture fragments, and intraoperative 3D confirmation of anatomic reduction.

Association testing of common variants in the insulin receptor substrate-1 gene (IRS1) with type 2 diabetes

AIMS/HYPOTHESIS

Activation of the insulin receptor substrate-1 (IRS1) is a key initial step in the insulin signalling pathway. Despite several reports of association of the G972R polymorphism in its gene IRS1 with type 2 diabetes, we and others have not observed this association in well-powered samples. However, other nearby variants might account for the putative association signal.

SUBJECTS AND METHODS

We characterised the haplotype map of IRS1 and selected 20 markers designed to capture common variations in the region. We genotyped this comprehensive set of markers in several family-based and case-control samples of European descent totalling 12,129 subjects.

RESULTS

In an initial sample of 2,235 North American and Polish case-control pairs, the minor allele of the rs934167 polymorphism showed nominal evidence of association with type 2 diabetes (odds ratio [OR] 1.25, 95% CI 1.03-1.51, p = 0.03). This association showed a trend in the same direction in 7,659 Scandinavian samples (OR 1.16, 95% CI 0.96-1.39, p = 0.059). The combined OR was 1.20 (p = 0.008), but statistical correction for the number of variants examined yielded a p value of 0.086. We detected no differences across rs934167 genotypes in insulin-related quantitative traits.

CONCLUSIONS/INTERPRETATION

Our data do not support an association of common variants in IRS1 with type 2 diabetes in populations of European descent.

The role of the Toll receptor pathway in susceptibility to inflammatory bowel diseases

The intestinal flora has long been thought to play a role either in initiating or in exacerbating the inflammatory bowel diseases (IBD). Host defenses, such as those mediated by the Toll-like receptors (TLR), are critical to the host/pathogen interaction and have been implicated in IBD pathophysiology. To explore the association of genetic variation in TLR pathways with susceptibility to IBD, we performed a replication study and pooled analyses of the putative IBD risk alleles in NFKB1 and TLR4, and we performed a haplotype-based screen for association to IBD in the TLR genes and a selection of their adaptor and signaling molecules. Our genotyping of 1539 cases of IBD and pooled analysis of 4805 cases of IBD validates the published association of a TLR4 allele with risk of IBD (odds ratio (OR): 1.30, 95% confidence interval (CI): 1.15-1.48; P=0.00017) and Crohn's disease (OR: 1.33, 95% CI: 1.16-1.54; P=0.000035) but not ulcerative colitis. We also describe novel suggestive evidence that TIRAP (OR: 1.16, 95% CI: 1.04-1.30; P=0.007) has a modest effect on risk of IBD. Our analysis, therefore, offers additional evidence that the TLR4 pathway - in this case, TLR4 and its signaling molecule TIRAP - plays a role in susceptibility to IBD.

Genetic architecture of tuberculosis resistance in a mouse model of infection

Tuberculosis remains a significant public health problem: one-third of the human population is infected with virulent Mycobacterium tuberculosis (MTB) and 10% of those are at risk of developing tuberculosis during their lifetime. In both humans and experimental animal models, genetic variation among infected individuals contributes to the outcome of infection. However, in immunocompetent individuals (the majority of patients), genetic determinants of susceptibility to tuberculosis remain largely unknown. Mouse models of MTB infection, allowing control of exposure and other potential environmental contributors, have proven extremely useful for examining this genetic component. In a cross of C3HeB/FeJ (susceptible) by C57BL/6J (resistant) inbred mouse strains, we have previously identified one major genetic locus, sst1, the susceptible allele of which did not confer an overt immunodeficiency, but rather specifically affected progression of lung tuberculosis. Having generated and tested the sst1 congenic strains, we have observed that this locus only partially explained the difference in susceptibility of the parental strains to MTB. We now present further studies controlling for the effect of the sst1, identify four additional tuberculosis susceptibility loci and characterize their effects by testing an independent cross, knockout or congenic mice.

Intraoperative cone-beam CT for guidance of head and neck surgery: Assessment of dose and image quality using a C-arm prototype

Cone-beam computed tomography (CBCT) with a flat-panel detector represents a promising modality for intraoperative imaging in interventional procedures, demonstrating sub-mm three-dimensional (3D) spatial resolution and soft-tissue visibility. Measurements of patient dose and in-room exposure for CBCT-guided head and neck surgery are reported, and the 3D imaging performance as a function of dose and other acquisition/reconstruction parameters is investigated. Measurements were performed on a mobile isocentric C-arm (Siemens PowerMobil) modified in collaboration with Siemens Medical Solutions (Erlangen, Germany) to provide flat-panel CBCT. Imaging dose was measured in a custom-built 16 cm cylindrical head phantom at four positions (isocenter, anterior, posterior, and lateral) as a function of kVp (80-120 kVp) and C-arm trajectory ("tube-under" and "tube-over" half-rotation orbits). At 100 kVp, for example ("tube-under" orbit), the imaging dose was 0.059 (isocenter), 0.022 (anterior), 0.10 (posterior), and 0.056 (lateral) mGy/ mAs, with scans at approximately 50 and approximately 170 mAs typical for visualization of bony and soft-tissue structures, respectively. Dose to radiosensitive structures (viz., the eyes and thyroid) were considered in particular: significant dose sparing to the eyes (a factor of 5) was achieved using a "tube-under" (rather than "tube-over") half-rotation orbit; a thyroid shield (0.5 mm Pb-equivalent) gave moderate reduction in thyroid dose due to x-ray scatter outside the primary field of view. In-room exposure was measured at positions around the operating table and up to 2 m from isocenter. A typical CBCT scan (10 mGy to isocenter) gave in-air exposure ranging from 29 mR (0.26 mSv) at 35 cm from isocenter, to <0.5 mR (<0.005 mSv) at 2 m from isocenter. Three-dimensional (3D) image quality was assessed in CBCT reconstructions of an anthropomorphic head phantom containing contrast-detail spheres (11-103 HU; 1.6-12.7 mm) and a natural human skeleton. The contrast-to-noise ratio (CNR) was evaluated across a broad range of dose (0.6-23.3 mGy). CNR increased as the square root of dose, with excellent visualization of bony and soft-tissue structures achieved at approximately 3 mGy (0.10 mSv) and approximately 10 mGy (0.35 mSv), respectively. The prototype C-arm demonstrates CBCT image quality sufficient for guidance of head and neck procedures based on soft-tissue and bony anatomy at dose levels low enough for repeat intraoperative imaging, with total dose over the course of the procedure comparable to or less than the effective dose of a typical (2 mSv) diagnostic CT of the head.

A simple, direct method for x-ray scatter estimation and correction in digital radiography and cone-beam CT

X-ray scatter poses a significant limitation to image quality in cone-beam CT (CBCT), resulting in contrast reduction, image artifacts, and lack of CT number accuracy. We report the performance of a simple scatter correction method in which scatter fluence is estimated directly in each projection from pixel values near the edge of the detector behind the collimator leaves. The algorithm operates on the simple assumption that signal in the collimator shadow is attributable to x-ray scatter, and the 2D scatter fluence is estimated by interpolating between pixel values measured along the top and bottom edges of the detector behind the collimator leaves. The resulting scatter fluence estimate is subtracted from each projection to yield an estimate of the primary-only images for CBCT reconstruction. Performance was investigated in phantom experiments on an experimental CBCT bench-top, and the effect on image quality was demonstrated in patient images (head, abdomen, and pelvis sites) obtained on a preclinical system for CBCT-guided radiation therapy. The algorithm provides significant reduction in scatter artifacts without compromise in contrast-to-noise ratio (CNR). For example, in a head phantom, cupping artifact was essentially eliminated, CT number accuracy was restored to within 3%, and CNR (breast-to-water) was improved by up to 50%. Similarly in a body phantom, cupping artifact was reduced by at least a factor of 2 without loss in CNR. Patient images demonstrate significantly increased uniformity, accuracy, and contrast, with an overall improvement in image quality in all sites investigated. Qualitative evaluation illustrates that soft-tissue structures that are otherwise undetectable are clearly delineated in scatter-corrected reconstructions. Since scatter is estimated directly in each projection, the algorithm is robust with respect to system geometry, patient size and heterogeneity, patient motion, etc. Operating without prior information, analytical modeling, or Monte Carlo, the technique is easily incorporated as a preprocessing step in CBCT reconstruction to provide significant scatter reduction.

Subpopulation difference scanning: a strategy for exclusion mapping of susceptibility genes

BACKGROUND

Association mapping is a common strategy for finding disease-related genes in complex disorders. Different association study designs exist, such as case-control studies or admixture mapping.

METHODS

We propose a strategy, subpopulation difference scanning (SDS), to exclude large fractions of the genome as locations of genes for complex disorders. This strategy is applicable to genes explaining disease incidence differences within founder populations, for example, in cardiovascular diseases in Finland.

RESULTS

The strategy consists of genotyping a set of markers from unrelated individuals sampled from subpopulations with differing disease incidence but otherwise as similar as possible. When comparing allele or haplotype frequencies between the subpopulations, the genomic areas with little difference can be excluded as possible locations for genes causing the difference in incidence, and other areas therefore targeted with case-control studies. As tests of this strategy, we use real and simulated data to show that under realistic assumptions of population history and disease risk parameters, the strategy saves efforts of sampling and genotyping and most efficiently detects genes of low risk--that is, those most difficult to find with other strategies.

CONCLUSION

In contrast to admixture mapping that uses the mixing of two different populations, the SDS strategy takes advantage of drift within highly related subpopulations.