Diagnostic screening workflow for mutations in the BRCA1 and BRCA2 genes

Screening for mutations in large genes is challenging in a molecular diagnostic environment. Sanger-based DNA sequencing methods are largely used; however, massively parallel sequencing [MPS] can accommodate increasing test demands and financial constraints. This study aimed to establish a simple workflow to amplify and screen all coding regions of the BRCA1 and BRCA2 [BRCA1/2] genes by Sanger-based sequencing as well as to assess a MPS approach encompassing multiplex polymerase chain reaction [PCR] and pyrosequencing. This study was conducted between July 2011 and April 2013. A total of 20 patients were included in the study who had been referred to Genetic Health Services New Zealand [Northern Hub] for BRCA1/2 mutation screening. Patients were randomly divided into a MPS evaluation and validation cohort [n = 10 patients each]. Primers were designed to amplify all coding exons of BRCA1/2 [28 and 42 primer pairs, respectively]. Primers overlying known variants were avoided to circumvent allelic drop-out. The MPS approach necessitated utilisation of a complementary fragment analysis assay to eliminate apparent false-positives at homopolymeric regions. Variants were filtered on the basis of their frequency and sequence depth. Sanger-based sequencing of PCR amplified coding regions was successfully achieved. Sensitivity and specificity of the combined MPS/homopolymer protocol was determined to be 100% and 99.5%, respectively. In comparison to traditional Sangerbased sequencing, the MPS workflow led to a reduction in both cost and analysis time for BRCA1/2 screening. MPS analysis achieved high analytical sensitivity and specificity, but required complementary fragment analysis combined with Sanger-based sequencing confirmation in some instances

Array-based identification of copy number changes in a diagnostic setting. Simultaneous gene-focused and low resolution whole human genome analysis

The aim of this study was to develop and validate a comparative genomic hybridisation [CGH] array that would allow simultaneous targeted analysis of a panel of disease genes and low resolution whole genome analysis. A bespoke Roche NimbleGen 12x135K CGH array [Roche NimbleGen Inc., Madison, Wisconsin, USA] was designed to interrogate the coding regions of 66 genes of interest, with additional widelyspaced backbone probes providing coverage across the whole genome. We analysed genomic deoxyribonucleic acid [DNA] from 20 patients with a range of previously characterised copy number changes and from 8 patients who had not previously undergone any form of dosage analysis. The custom-designed Roche NimbleGen CGH array was able to detect known copy number changes in all 20 patients. A molecular diagnosis was also made for one of the additional 4 patients with a clinical diagnosis that had not been confirmed by sequence analysis, and carrier testing for familial copy number variants was successfully completed for the remaining four patients. The custom-designed CGH array described here is ideally suited for use in a small diagnostic laboratory. The method is robust, accurate, and cost-effective, and offers an ideal alternative to more conventional targeted assays such as multiplex ligation-dependent probe amplification

Iceberg in Small Pulmonary Embolism

No abstract available.

Exploring orthostatic hypotension in patients with multiple system atrophy by a non-invasive cardiac output system

Objective: To detect early subclinical signs of autonomic dysfunction in the cardiovascular system and explore the mechanism of orthostatic hypotension (OH) in patients with multiple system atrophy (MSA). Methods: Eighteen male patients with possible MSA and 10 healthy men were recruited. The hemodynamic responses to head-up tilt and tilt-reversal were studied by an electrically-powered tilt table and a non-invasive cardiac output measurement (NICOM) system. Results: At supine, there was no signifi cant difference in blood pressure, heart rate (HR), stroke volume, cardiac output and total peripheral resistance between MSA patients and healthy controls. During tilting upright, OH developed in 5 MSA patients, with a 23.7±4.8 mmHg drop in systolic blood pressure. Patients with OH were older and exhibited higher scores in unifi ed Multiple System Atrophy Rating Scale part I than patients without OH. The stroke volume, cardiac output and total peripheral resistance did not differ between groups. The controls had the most signifi cant HR elevation (6.5±2.5 bpm) during tiltup, followed by patients without OH (2.8±1.6 bpm) and those with OH (-0.2±2.2 bpm). A similar trend of HR decrease was observed during return to supine posture. The process of tilt-reversal altered HR more signifi cantly than head-up tilt in controls (8.0±2.9 vs 6.5±2.5 bpm; P=0.031) and patients without OH (4.2±2.1 vs 2.8±1.6 bpm; P=0.032), but not in patients with OH (1.2±1.5 vs -0.2±2.2 bpm; P=0.380). Conclusions: The HR change during postural challenge showed signifi cant difference between MSA patients and healthy controls. Impaired HR responsiveness contributed to OH in MSA. Monitoring HR during the tilt table test may be a practical and useful method to detect early autonomic dysfunction in patients with MSA.