Pilot study on schizophrenia in Sardinia.

OBJECTIVE: Based on a small sample of cases with schizophrenia and control individuals from an isolated population, a genome-wide association study was undertaken to find variants conferring susceptibility to this disease. METHODS: Standard association tests were employed, followed by newer multilocus association methods (genotype patterns). RESULTS: Individually, no variant produced a significant result. However, the best two variants (rs1360382 on chromosome 9 and rs1303 on chromosome 14) showed significantly different genotype pattern distributions between patients and control individuals. The risk genotype pattern AA-TT is highly predictive of schizophrenia, with estimated sensitivity and specificity of 1 and 0.96, respectively. CONCLUSIONS: These findings support the hypothesis that schizophrenia is partly due to multiple genetic variants, each with a relatively small effect.

AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts.

An increasing number of eukaryotic and prokaryotic genes are being found to have natural antisense transcripts (NATs). There is also growing evidence to suggest that antisense transcription could play a key role in many human diseases. Consequently, there have been several recent attempts to set up computational procedures aimed at identifying novel NATs. Our group has developed the AntiHunter program for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, the program requires a genomic sequence plus an associated list of transcript names and coordinates of the genomic region. After masking the repeated regions, the program carries out a BLASTN search of this sequence in the selected EST database, reporting via email the EST entries that reveal an antisense transcript according to the user-supplied list. Here, we present the newly developed version 2.0 of the AntiHunter tool. Several improvements have been added to this version of the program in order to increase its ability to detect a larger number of antisense ESTs. As a result, AntiHunter can now detect, on average, >45% more antisense ESTs with little or no increase in the percentage of the false positives. We also raised the maximum query size to 3 Mb (previously 1 Mb). Moreover, we found that a reasonable trade-off between the program search sensitivity and the maximum allowed size of the input-query sequence could be obtained by querying the database with the MEGABLAST program, rather than by using the BLAST one. We now offer this new opportunity to users, i.e. if choosing the MEGABLAST option, users can input a query sequence up to 30 Mb long, thus considerably improving the possibility to analyze longer query regions. The AntiHunter tool is freely available at http://bioinfo.crs4.it/AH2.0.

Real-Time Tele-Mentored Low Cost "Point-of-Care US" in the Hands of Paediatricians in the Emergency Department: Diagnostic Accuracy Compared to Expert Radiologists.

BACKGROUND: The use of point-of-care ultrasonography (POC US) in paediatrics is increasing. This study investigated the diagnostic accuracy of POC US in children accessing the emergency department (ED) when performed by paediatricians under the remote guidance of radiologists (TELE POC). METHODS: Children aged 0 to 18 years accessing the ED of a third level research hospital with eight possible clinical scenarios and without emergency/severity signs at the triage underwent three subsequent US tests: by a paediatrician guided remotely by a radiologist (TELE POC); by the same radiologist (UNBLIND RAD); by an independent blinded radiologist (BLIND RAD). Tele-radiology was implemented using low cost "commercial off-the-shelf" (COTS) equipment and open-source software. Data were prospectively collected on predefined templates. RESULTS: Fifty-two children were enrolled, for a total of 170 ultrasound findings. Sensitivity, specificity, positive and negative predictive values of TELE POC were: 93.8, 99.7, 96.8, 99.4 when compared to UNBLIND RAD and 88.2, 99.7, 96.8, 98.7 when compared to BLIND RAD. The inter-observers agreement between the paediatricians and either the unblind or blind radiologist was excellent (k = 0.93). The mean duration of TELE POC was 6.3 minutes (95% CI 4.1 to 8.5). Technical difficulties occurred in two (3.8%) cases. Quality of the transmission was rated as fair, good, very good and excellent in 7.7%, 15.4%, 42.3% and 34.6% of cases respectively, while in no case was it rated as poor. CONCLUSIONS: POC US performed by paediatricians in ED guided via tele-radiology by an expert radiologist (TELE POC) produced reliable and timely diagnoses. Findings of this study, especially for the rarer conditions under evaluation, need further confirmation. Future research should investigate the overall benefits and the cost savings of using tele-ultrasound to perform US "at children's bedsides", under remote guidance of expert radiologists.

Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia.

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.

COTS technologies for telemedicine applications.

PURPOSE: To demonstrate a simple low-cost system for tele-echocardiology, focused on paediatric cardiology applications. METHODS: The system was realized using open-source software and COTS technologies. It is based on the transmission of two simultaneous video streams, obtained by direct digitization of the output of an ultrasound machine and by a netcam showing the examination that is taking place. These streams are then embedded into a web page so they are accessible, together with basic video controls, via a standard web browser. The system can also record video streams on a server for further use. RESULTS: The system was tested on a small group of neonatal cases with suspected cardiopathies for a preliminary assessment of its features and diagnostic capabilities. Both the clinical and technological results were encouraging and are leading the way for further experimentation. CONCLUSIONS: The presented system can transfer clinical images and videos in an efficient way and in real time. It can be used in the same hospital to support internal consultancy requests, in remote areas using Internet connections and for didactic purposes using low cost COTS appliances and simple interfaces for end users. The solution proposed can be extended to control different medical appliances in those remote hospitals.

Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.