Quality metrics for enhanced performance of an NGS panel using single-vial amplification technology

AIMS

Targeted next-generation sequencing (NGS) panels, which identify genomic alterations, are the stronghold of molecular oncology laboratories. In spite of technological advances, the quantity and quality of DNA from formalin-fixed paraffin-embedded tissue and paucicellular specimens are barriers to successful sequencing. Here, we describe an NGS assay employing single tube stem-loop inhibition mediated amplification technology that delivers highly accurate results with low input DNA. Rigorous quality metrics, regular monitoring and in-depth validation make the test attractive for clinical laboratories.

METHODS

The study used a customised NGS panel, targeting 48 genes across several solid tumour types. Validation, in accordance with guidelines from New York State, sequenced patient samples harbouring 136 known variants, including single-nucleotide variants (SNVs) and indels. Specimen types included formalin-fixed paraffin embedded blocks, core biopsies and cytology material. Neoplastic cellularity of the tumours ranged from 10% to 80%.

RESULTS

The assay was highly specific and sensitive with excellent accuracy, reproducibility and repeatability/precision. Concordant results for identification of SNVs and indels were obtained from specimens with DNA input of 2-3 ng, tissue with 10% neoplastic cellularity and variant allelic frequencies of 2.5%-3%. Over 99% of the target areas are shown to achieve at least 500X coverage when parsed through two bioinformatics pipelines. With over 2000 clinical specimens analysed, the success of the panel for reporting of results is 95.3% CONCLUSIONS: The advanced technology enables accurate identification of clinically relevant variants with uniformity of coverage and an impressive turn-around-time. The overall workflow and cost-effectiveness provide added value.

Ovarian Malignant Mixed Germ Cell Tumor With Prominent Embryoid Bodies (Polyembryoma Background): A Case Report and Literature Review

Ovarian malignant mixed germ cell tumors are rare tumors occurring in young women. The presence of prominent embryoid bodies in these tumors is extremely uncommon. Herein, we report such a case, with a histomorphologic description and immunohistochemical and fluorescence in situ hybridization analyses.

Comparison of older people with psychosis living in the community and in care homes

Aims and Method

To compare two groups of older people with chronic schizophrenia or delusional disorder living in the community and in care homes, along the domains of morbidity suggested by prior research. From the case-load of one old age psychiatrist, 22 individuals with chronic psychosis residing in care homes were compared to 23 living in their own homes. The measures used were: the Positive and Negative Symptom Score (PANSS; Kay et al, 1987); the Mini Mental State Examination (MMSE; Folstein et al, 1975); the Burvill Physical Illness Scale (Burvill et al, 1990); and an Activities of Daily Living Scale (IADL; Lawton et al, 1969).

Results

Those in care homes had significantly higher PANSS scores (38.9 v. 21.0, P<0.01), largely accounted for by significantly more deficit symptoms (14.2 v. 5.6, P<0.01). They also had poorer cognition and significantly greater impairment in daily-life activities but their medical condition was not significantly worse. Most were seen only by a psychiatrist.

Clinical Implications

The greater morbidity and disablement of older people with chronic schizophrenia or delusional disorder living in care homes is likely to be intrinsic to the disorder but does not appear to be taken into account in current service planning or delivery.

Ultrasensitive microarray bioassays using cyanine5 dye-doped silica nanoparticles

Herein we report the use of high brightness Cyanine5-doped silica nanoparticles (NPs) for the detection of antibodies or DNA in microarray bioassays. NP labels showed negligible non-specific binding, greater sensitivity and lower limits of detection when compared to free dye-labelled biomolecules. Moreover, the spotted microarrays used in this study required low NP and antibody concentrations to generate large data sets with improved statistical accuracy. These NPs have significant potential for use in biosensing for disease detection.

Multivalent linkers for improved covalent binding of oligonucleotides to dye-doped silica nanoparticles

This paper describes the fabrication of oligonucleotide-coated Cy5-doped silica nanoparticles using a combination of multivalent linkers and their use in surface-based DNA sandwich hybridization assays. Dipodal silane is introduced as a means to fabricate amine-coated silica nanoparticles and its advantages compared to monopodal silanes are discussed. The use of dipodal silane in conjunction with three different polymer linkers (oxidized dextran, linear and 8-arm polyethylene glycol (PEG)) to immobilize single-stranded DNA to Cy5-doped nanoparticles is investigated and dynamic light scattering measurements and Fourier transform infrared spectroscopy are used to follow the progression of the functionalization of the nanoparticles. We observe a significant improvement in the binding stability of the single-stranded DNA when the dipodal silane and 8-arm PEG are used in combination, when compared to alternative conjugation strategies. Both 8mer and 22mer oligonucleotides are securely conjugated to the high-brightness nanoparticles and their availability to hybridize with a complementary strand is confirmed using solution-based DNA hybridization experiments. In addition, a full surface-based sandwich assay demonstrates the potential these nanoparticles have in the detection of less than 500 femtomolar of a DNA analogue of micro RNA, miR-451.

Subtle alternating electrocardiographic morphology as an indicator of decreased cardiac electrical stability

Observations from finite-element computer models, together with analytic developments based on percolation theory have suggested that subtle fluctuations of ECG morphology might serve as an indicator diminished cardiac electrical stability. With fixed-rate atrial pacing in canines, we have previously observed a pattern of alternation in T wave energy which correlated with cardiac electrical stability. We report here on a series of 20 canine experiments in which cardiac electrical stability (measured via Ventricular Fibrillation Threshold determination) was compared to a non-degenerate, multidimensional measurement of the degree of alternating activity present in the ECG complex morphology. The decrease in cardiac electrical stability brought on by both coronary artery occlusion and systemic hypothermia was consistently accompanied by subtle alternation in ECG morphology, with the absolute degree of alternating activity being significantly (negatively) correlated with cardiac electrical stability.

Client donation program for acquiring dogs and cats to teach veterinary gross anatomy

A donor program for procuring dogs and cats to meet the needs of anatomical instruction was initiated six years ago at Tufts University School of Veterinary Medicine. The program was initiated in order to comply with state regulations that preclude the use of shelter animals and to satisfy ethical objections of students and faculty. The donor program has successfully met the animal needs for teaching gross anatomy and, in addition, provides opportunities to integrate clinical perspectives and ethics beginning from the first year of veterinary education.

Quantitative assessment of four men using above-elbow prosthetic control

We studied the relationship between kinematically unconstrained activities of daily living (ADL) tasks and a kinematically constrained task in above-elbow (AE) amputee subjects using myoelectrically controlled prostheses. Four men, 24 to 49 years old, with unilateral AE amputation wore a prosthesis interfaced to a programmable controller to emulate two different elbow control schemes, conventional velocity and a new "natural" controller. Subjects were timed during three ADL tasks--cutting meat, donning socks, and rolling dough--with both controllers. The prosthesis emulator was then connected to a crank device with a handle, and the subjects turned the crank from bottom to top positions in a vertical plane using each controller. Synergistic shoulder-elbow joint coordination required for crank turning was quantified as the maximum slope of the change in elbow torque versus the change in crank-angle. Performance between the two controllers differed significantly for the crank test but not for ADL tasks. One subject did not complete all crank turning tests. Positive canonical correlation of 0.77 was found between time and crank domain measures. We conclude that biomechanical assessments should be integrated with time-based clinical tests to comprehensively evaluate performance of AE amputee subjects with a myoelectric device.