Dysmorphology at a distance: results of a web-based diagnostic service

In 2007, the DYSCERNE pilot project funded by the European Commission Public Health Executive Agency (EU DG Sanco) aimed at setting up a network of expertise for patients with rare dysmorphic disorders. As part of DYSCERNE, a Dysmorphology Diagnostic System (DDS) was set up to enable clinicians throughout the EU to submit cases electronically for diagnosis using a secure, web-based interface, hosted at specified access points (Submitting nodes), in 26 different European countries. We report the outcome of this service for 200 cases submitted consecutively between January 2010 and 2012. Each case was reviewed by an average of five expert reviewers. An average of three possible syndromic diagnoses was suggested per case. In 22.5% of the cases, a consensus clinical diagnosis was reached. Genetic testing was suggested in 70.5% of the cases, whereas other laboratory investigations and diagnostic imaging were recommended in 35.5 and 26% of the cases, respectively. Further specialized opinions were suggested in 23.5% of the cases. Overall, a total of 181 very rare or extremely rare genetic syndromes were considered in the differential diagnosis of the 200 cases. In two cases, the reviewers suggested that the findings represented a new syndrome, and in one of these syndromes the underlying genetic cause was subsequently identified. Other benefits of the submission process included the possibility of directing the case submitters to specific centres for diagnostic testing or participation in research and educational benefit derived for both case submitters and reviewers.

Gene expression analysis of early stage endometrial cancers reveals unique transcripts associated with grade and histology but not depth of invasion

Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least fourfold (univariate t-test, p < 0.001) between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis.

Congenital hypothyroidism with goiter in Tenterfield terriers

BACKGROUND

A cluster of cases of congenital hypothyroidism with goiter (CHG) in Tenterfield Terriers was identified and hypothesized to be dyshormonogenesis of genetic etiology with autosomal recessive inheritance.

OBJECTIVES

To describe the phenotype, thyroid histopathology, biochemistry, mode of inheritance, and causal mutation of CHG in Tenterfield Terriers.

ANIMALS

Thyroid tissue from 1 CHG-affected Tenterfield Terriers, 2 affected Toy Fox Terriers, and 7 normal control dogs. Genomic DNA from blood or buccal brushings of 114 additional Tenterfield Terriers.

METHODS

Biochemical and genetic segregation analysis of functional gene candidates in a Tenterfield Terrier kindred. Thyroid peroxidase (TPO) iodide oxidation activity was measured, and TPO protein and SDS-resistant thyroglobulin aggregation were assessed on western blots. TPO cDNA was amplified from thyroid RNA and sequenced. Exons and flanking splice sites were amplified from genomic DNA and sequenced. Variant TPO allele segregation was assessed by restriction enzyme digestion of PCR products.

RESULTS

Thyroid from an affected pup had lesions consistent with dyshormonogenesis. TPO activity was absent, but normal sized immunocrossreactive TPO protein was present. Affected dog cDNA and genomic sequences revealed a homozygous TPO missense mutation in exon 9 (R593W) that was heterozygous in all obligate carriers and in 31% of other clinically normal Tenterfield Terriers.

CONCLUSIONS

The mutation underlying CHG in Tenterfield Terriers was identified, and a convenient carrier test made available for screening Tenterfield Terriers used for breeding.

Phase II trial of oral 1,25-dihydroxyvitamin D (calcitriol) in hormone refractory prostate cancer

Epidemiologic and experimental data support a role for 1,25-dihydroxyvitamin D(3) in the growth regulation of prostate cancer. We conducted a phase II clinical trial evaluating calcitriol (1,25(OH)(2)D(3)) in patients with hormone refractory prostate cancer. We enrolled 14 patients in this study. 1,25(OH)(2)D(3) was initiated at a daily oral dose of 0.5 μg and escalated to 1.5 μg daily. No objective responses were observed. However, in two patients decreases of 25% and 45% in prostate specific antigen levels were seen. Hypercalcemia was the predominant toxicity. We conclude that 1,25(OH)(2)D(3) given in this manner is inactive in advanced prostate cancer. Dose escalation of oral 1,25(OH)(2)D(3) is limited by hypercalcemia.

High host density favors greater virulence: a model of parasite-host dynamics based on multi-type branching processes

We use a multitype continuous time Markov branching process model to describe the dynamics of the spread of parasites of two types that can mutate into each other in a common host population. While most mathematical models for the virulence of infectious diseases focus on the interplay between the dynamics of host populations and the optimal characteristics for the success of the pathogen, our model focuses on how pathogen characteristics may change at the start of an epidemic, before the density of susceptible hosts decline. We envisage animal husbandry situations where hosts are at very high density and epidemics are curtailed before host densities are much reduced. The use of three pathogen characteristics: lethality, transmissibility and mutability allows us to investigate the interplay of these in relation to host density. We provide some numerical illustrations and discuss the effects of the size of the enclosure containing the host population on the encounter rate in our model that plays the key role in determining what pathogen type will eventually prevail. We also present a multistage extension of the model to situations where there are several populations and parasites can be transmitted from one of them to another. We conclude that animal husbandry situations with high stock densities will lead to very rapid increases in virulence, where virulent strains are either more transmissible or favoured by mutation. Further the process is affected by the nature of the farm enclosures.

Directional limits on persistent gravitational waves using LIGO S5 science data

The gravitational-wave (GW) sky may include nearby pointlike sources as well as stochastic backgrounds. We perform two directional searches for persistent GWs using data from the LIGO S5 science run: one optimized for pointlike sources and one for arbitrary extended sources. Finding no evidence to support the detection of GWs, we present 90% confidence level (C.L.) upper-limit maps of GW strain power with typical values between 2-20×10(-50)  strain(2) Hz(-1) and 5-35×10(-49)  strain(2) Hz(-1) sr(-1) for pointlike and extended sources, respectively. The latter result is the first of its kind. We also set 90% C.L. limits on the narrow-band root-mean-square GW strain from interesting targets including Sco X-1, SN 1987A and the Galactic center as low as ≈7×10(-25) in the most sensitive frequency range near 160 Hz.

A state observer for the Virgo inverted pendulum

We report an application of Kalman filtering to the inverted pendulum (IP) of the Virgo gravitational wave interferometer. Using subspace method system identification techniques, we calculated a linear mechanical model of Virgo IP from experimental transfer functions. We then developed a Kalman filter, based on the obtained state space representation, that estimates from open loop time domain data, the state variables of the system. This allows the observation (and eventually control) of every resonance mode of the IP mechanical structure independently.

Proteomic analysis of stage I endometrial cancer tissue: identification of proteins associated with oxidative processes and inflammation

OBJECTIVE

The present study aimed to identify differentially expressed proteins employing a high resolution mass spectrometry (MS)-based proteomic analysis of endometrial cancer cells harvested using laser microdissection.

METHODS

A differential MS-based proteomic analysis was conducted from discrete epithelial cell populations gathered by laser microdissection from 91 pathologically reviewed stage I endometrial cancer tissue samples (79 endometrioid and 12 serous) and 10 samples of normal endometrium from postmenopausal women. Hierarchical cluster analysis of protein abundance levels derived from a spectral count analysis revealed a number of proteins whose expression levels were common as well as unique to both histologic types. An independent set of endometrial cancer specimens from 394 patients were used to externally validate the differential expression of select proteins.

RESULTS

209 differentially expressed proteins were identified in a comparison of stage I endometrial cancers and normal post-menopausal endometrium controls (Q<0.005). A number of differentially abundant proteins in stage I endometrial cancer were identified and independently validated by western blot and tissue microarray analyses. Multiple proteins identified with elevated abundance in stage I endometrial cancer are functionally associated with inflammation (annexins) and oxidative processes (peroxiredoxins). PRDX1 and ANXA2 were both confirmed as being overexpressed in stage I cancer compared to normal endometrium by independent TMA (Q=0.008 and Q=0.00002 respectively).

CONCLUSIONS

These data provide the basis for further investigation of previously unrecognized novel pathways involved in early stage endometrial carcinogenesis and provide possible targets for prevention strategies that are inclusive of both endometrioid and serous histologic subtypes.

The use of semantic distance metrics to support ontology audit

This study explored the possibility that semantic distance metrics can be used to develop methods for auditing biomedical ontologies. We developed and tested an approach using the Foundational Model of Anatomy (FMA) and the body-structure taxonomy of SNOMED CT. We evaluated 190 class pairs in human anatomical structures using three semantic distance metrics: simple edge count, normalized path length, and information content. We applied principal component analysis (PCA) to study relationships between the semantic distance measurements so produced in FMA and SNOMED CT. We found that our application of PCA could detect significant discrepancies, but not necessarily outright mistakes, in the two ontologies. A review of discrepancies revealed that they often relate to multiple design perspectives employed in ontological definitions.

In-vacuum Faraday isolation remote tuning

In-vacuum Faraday isolators (FIs) are used in gravitational wave interferometers to prevent the disturbance caused by light reflected back to the input port from the interferometer itself. The efficiency of the optical isolation is becoming more critical with the increase of laser input power. An in-vacuum FI, used in a gravitational wave experiment (Virgo), has a 20 mm clear aperture and is illuminated by an almost 20 W incoming beam, having a diameter of about 5 mm. When going in vacuum at 10(-6) mbar, a degradation of the isolation exceeding 10 dB was observed. A remotely controlled system using a motorized lambda=2 waveplate inserted between the first polarizer and the Faraday rotator has proven its capability to restore the optical isolation to a value close to the one set up in air.

Adaptive Bayesian design for phase I dose-finding trials using a joint model of response and toxicity

We present a new adaptive Bayesian method for dose-finding in phase I clinical trials based on both response and toxicity. Although clinical responses are usually rare in phase I cancer trials, molecularly targeted therapy may make clinical responses more likely. In addition, biological responses may be common. Thus responses may be frequent enough to help decide how aggressive a phase I escalation should be. The model assumes that response and toxicity events happen depending on respective dose thresholds for the individual, assuming that the thresholds jointly follow a bivariate log-normal distribution or a mixture. The design utilizes prior information about the population threshold distribution as well as accumulated data. The next dose is assigned to maximize a patient-oriented expected utility integrated over the current posterior distribution. The design is evaluated through simulation with population parameters equaling estimates from early Gleevec trials. This exercise provides evidence for the value of the use of the proposed design for future clinical trials.

Are specialist physicians missing out on the e-Health boat?

BACKGROUND

Nationally health systems are making increasing investments in the use of clinical information systems. Little is known about current computer use by specialist physicians, particularly outside the hospital setting.

AIMS

To identify the extent and reasons physician Fellows of the Royal Australasian College of Physicians (RACP) use computers in their work.

METHODS

A self-administered survey was emailed from the RACP to all practising physicians in 2007 that were living in Australia and New Zealand who had consented to email contact with the College.

RESULTS

The survey was sent to a total of 7445 eligible physicians, 2328 physicians responded (31.3% response rate), but only 1266 responses (21.0%) were able to be analysed. Most 97.5% had access to computers at work and 96.5% used home computers for work purposes. Physicians in public hospitals (72.6%) were more likely to use computers for work (65.6%) than those in private hospitals (12.6%) or consulting rooms (27.3%). Overall physicians working in public hospitals used a wider range of applications with 70.5% using their computers for searching the internet, 53.7% for receiving results and 52.7% used their computers to engage in specific educational activities. Physicians working from their consulting rooms (33.6%) were more likely to use electronic prescribing (11%) compared with physicians working in public hospitals (5.7%).

CONCLUSIONS

Fellows have not incorporated computers into their consulting rooms over which they have control. This is in contrast to general practitioners who have embraced computers after the provision of various incentives. The rate of use of computers by physicians for electronic prescribing in consulting rooms (11%) is very low in comparison with general practitioners (98%). One reason may be that physicians work in multiple locations whereas general practitioners are more likely to work from one location.

Improvement in the care of multiple endocrine neoplasia type 1 through a regional multidisciplinary clinic

BACKGROUND

Multiple endocrine neoplasia type 1 (MEN1) is associated with significant morbidity and mortality. Timely detection of MEN1 kindred, together with treatment of associated tumours, results in an improved outcome. We describe how the development of a dedicated multidisciplinary MEN clinic has improved the diagnosis and treatment of MEN1-associated endocrinopathies.

DESIGN AND PATIENTS

A dedicated MEN clinic was developed at Aintree University Hospital, Liverpool in 2002 for patients living in Merseyside, Cheshire and North Wales. The multidisciplinary approach adopted, aimed to improve communication and continuity of care. Patients see all clinicians involved in their care (Consultant Endocrinologist, Paediatrician, Clinical Geneticist and Endocrine Surgeon) simultaneously, allowing for a unified, clear approach and a reduction in unnecessary attendances. The clinicians adopt a proactive approach to tracing the relatives of patients, with the aim of identifying kindred with previously asymptomatic disease.

RESULTS

In 2002, 16 patients from 5 families were diagnosed clinically with MEN1. Twenty MEN1-associated endocrinopathies had been diagnosed and 21 surgical procedures had been performed. By the end of 2008, 45 patients from 15 families had been identified, with 83 endocrinopathies diagnosed and 50 surgical procedures performed. Ninety-four known relatives are awaiting screening for MEN1.

CONCLUSION

The successful identification of patients with MEN1 has resulted in an exponential increase in the number of patients attending the clinic. As relatives undergo screening, the diagnosis of MEN is likely to increase. The ever increasing numbers of patients requiring screening, surveillance and treatment has implications in the planning of future service provision.

Abstract LB-414: Variation in base excision repair genes and risk of smoking-related non-small cell lung cancer

Base excision repair (BER) is the primary mechanism responsible for the repair of small base lesions in DNA caused by oxidation and alkylation. Given this role, functionally relevant polymorphisms in BER pathway genes may well affect the risk of smoking-related non-small cell lung cancer (NSCLC). We examined the association between 49 single nucleotide polymorphisms (SNPs) located in or near 5 different BER genes (XRCC1, LIG1, PARP1, MPG, and OGG1) and risk of NSCLC among Caucasians in a large case-control study. The study population consisted of 599 cases and 934 controls; all study participants were Caucasian and current or former cigarette smokers who had smoked at least 10.0 pack-years. SNPs were selected using various resources including literature review and data from the International HapMap project, and genotyping was conducted by Illumina Goldengate assay. Deviation from Hardy-Weinberg equilibrium was evaluated with the exact method. Associations between alleles and genotypes and NSCLC risk were examined using a Pearson Chi-square test and a Cochran-Armitage trend test, respectively. Per (minor) allele odds ratios (OR) and corresponding 95% confidence intervals (95% CI) were also calculated for each SNP. Six SNPs (rs3219073, rs747658, rs3219090, rs2048424, rs2666428, and rs8679) in PARP1 were statistically significantly (P&lt;0.01) associated with NSCLC risk in our study population. SNP rs3219073 was in high linkage disequilibrium (r2≥0.8) with rs747658, as were rs3219090 and rs2048424 with rs2666428. The minor alleles of these SNPs were associated with a decreased risk of developing NSCLC (rs747658, OR: 0.7, 95%CI: 0.6-0.9, Ptrend=0.0005; rs2666428, OR: 0.8, 95%CI: 0.7-0.9, Ptrend =0.005). The C allele of SNP rs8679 (3′ UTR) was associated with an increased risk of NSCLC (OR: 1.3, 95%CI: 1.1-1.5, Ptrend =0.005). Additionally, SNPs rs3213255 and rs1799782 (Arg194Trp) in XRCC1 and SNP rs10500298 in LIG1 were also significantly associated with NSCLC risk. The minor alleles of rs3213255 and rs10500298 were associated with an increased risk (OR: 1.3, 95%CI: 1.1-1.5; OR: 1.2, 95%CI: 1.1-1.4, respectively), while the minor allele of rs1799782 was associated with a decreased risk (OR: 0.6, 95%CI: 0.4-0.9). PARP1 polymorphisms have previously been reported associated with other cancers, including breast cancer and colorectal cancer, but this is the first study to report associations with NSCLC risk. To conclude, our results suggest that common variation in PARP1, XRCC1 and LIG1 may be associated with risk of smoking-related NSCLC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-414.