Use of Deming regression in method-comparison studies

Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR

Coronavirus Disease-2019 tests require a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR). The viability of the virus is maintained after collection by storing the NP/OP swabs in Viral Transport Media (VTM). We evaluated the performance of four transport media: locally manufactured ("REVITAL") Viral Transport Media (RVTM), Standard Universal Transport Media (SUTM), PBS and 0.9% (w/v) NaCl (normal saline). We used laboratory cultured virus to evaluate: i) viral recovery and maintaining integrity at different time periods and temperatures; ii) stability in yielding detectable RNA consistently for all time points and conditions; and iii) their overall accuracy. Four vials of SARS-CoV-2 cultured virus (2 high and 2 low concentration samples) and 1 negative control sample were prepared for each media type (SUTM, RVTM, PBS and normal saline) and stored at the following temperatures, -80°C, 4°C, 25°C and 37°C for 7 days. Viral RNA extractions and qRT-PCR were performed at 1, 2, 3, 4 and 7 days after inoculation with the cultured virus to assess virus stability and viral recovery. Ct values fell over time at 25°C and 37°C, but normal saline, PBS, RVTM and SUTM all showed comparable performance in maintaining virus integrity and stability allowing for the detection of SARS-CoV-2 RNA. Overall, this study demonstrated that normal saline, PBS and the locally manufactured VTM can be used for COVID-19 sample collection and testing, thus expanding the range of SARS-CoV-2 viral collection media.

Corrigendum to "Validation of a testosterone and dihydrotestosterone liquid chromatography tandem mass spectrometry assay: interference and comparison with established methods" [Steroids Volume 73, Issue 13, 12 December 2008, Pages 1345-1352]

Testosterone (T) and its metabolite dihydrotestosterone (DHT) are androgens with different biologic profiles. T and DHT measurements are required for assessment of patients with ambiguous genitalia, hirsutism, during 5 alpha reductase treatment of prostate disorders, and new androgen formulations. Our laboratory has developed and validated a method to simultaneously measure serum T and DHT with liquid chromatography tandem mass spectrometry (LC-MS/MS) for use in a clinical chemistry laboratory. Analysis of sera from blood collected in tubes containing clot activator gave results of T that were four fold higher than blood collected in plain tubes. Changing the ion pair selected for monitoring eliminated this interference by clot activators. Blood collected in fluoride coated tubes gave serum T and DHT levels that were 20 and 15 percent lower respectively than levels measured in blood collected in plain tubes (no additives). Addition of T enanthate to blood collected in plain tubes caused a dose related increase serum T levels due to the action of non-specific esterases in the red cells. This esterase activity could be avoided by using fluoride tubes for blood collection. Serum DHT levels were consistently lower when measured by LC-MS/MS versus radioimmunoassay. The differences were concentration dependent and the variance for the difference was large when serum DHT concentration was low. Celite chromatograph prior to radioimmunoassay reduced the differences between the two methods, thus confirming that higher levels of DHT obtained by immunoassays were probably due to interfering substances which were partially removed by Celite chromatography.

Comparison of measurement methods with a mixed effects procedure accounting for replicated evaluations (COM3PARE): method comparison algorithm implementation for head and neck IGRT positional verification

Purpose

Comparison of imaging measurement devices in the absence of a gold-standard comparator remains a vexing problem; especially in scenarios where multiple, non-paired, replicated measurements occur, as in image-guided radiotherapy (IGRT). As the number of commercially available IGRT presents a challenge to determine whether different IGRT methods may be used interchangeably, an unmet need conceptually parsimonious and statistically robust method to evaluate the agreement between two methods with replicated observations. Consequently, we sought to determine, using an previously reported head and neck positional verification dataset, the feasibility and utility of a Comparison of Measurement Methods with the Mixed Effects Procedure Accounting for Replicated Evaluations (COM₃PARE), a unified conceptual schema and analytic algorithm based upon Roy’s linear mixed effects (LME) model with Kronecker product covariance structure in a doubly multivariate set-up, for IGRT method comparison.

Methods

An anonymized dataset consisting of 100 paired coordinate (X/ measurements from a sequential series of head and neck cancer patients imaged near-simultaneously with cone beam CT (CBCT) and kilovoltage X-ray (KVX) imaging was used for model implementation. Software-suggested CBCT and KVX shifts for the lateral (X), vertical (Y) and longitudinal (Z) dimensions were evaluated for bias, inter-method (between-subject variation), intra-method (within-subject variation), and overall agreement using with a script implementing COM₃PARE with the MIXED procedure of the statistical software package SAS (SAS Institute, Cary, NC, USA).

Results

COM₃PARE showed statistically significant bias agreement and difference in inter-method between CBCT and KVX was observed in the Z-axis (both p − value<0.01). Intra-method and overall agreement differences were noted as statistically significant for both the X- and Z-axes (all p − value<0.01). Using pre-specified criteria, based on intra-method agreement, CBCT was deemed preferable for X-axis positional verification, with KVX preferred for superoinferior alignment.

Conclusions

The COM₃PARE methodology was validated as feasible and useful in this pilot head and neck cancer positional verification dataset. COM₃PARE represents a flexible and robust standardized analytic methodology for IGRT comparison. The implemented SAS script is included to encourage other groups to implement COM₃PARE in other anatomic sites or IGRT platforms.

Differential proteome analysis of human gliomas stratified for loss of heterozygosity on chromosomal arms 1p and 19q

Combined deletion of chromosomal arms 1p and 19q is an independent prognostic marker in patients with oligodendroglial brain tumors, including oligodendrogliomas and oligoastrocytomas. However, the relevant genes in these chromosome arms and the molecular mechanisms underlying the prognostic significance of 1p/19q deletion are yet unknown. We used two-dimensional difference gel electrophoresis followed by mass spectrometry to perform a proteome-wide profiling of low-grade oligoastrocytomas stratified for the presence or absence of 1p/19q deletions. Thereby, we identified 22 different proteins showing differential expression in tumors with or without combined deletions of 1p and 19q. Four of the differentially expressed proteins, which are vimentin, villin 2 (ezrin), annexin A1, and glial fibrillary acidic protein, were selected for further analysis. Lower relative expression levels of these proteins in 1p/19q-deleted gliomas were confirmed at the protein level by Western blot analysis and immunohistochemistry. Furthermore, sequencing of sodium bisulfite-treated tumor DNA revealed more frequent methylation of 5'-CpG islands associated with the VIM and VIL2 genes in 1p/19q-deleted gliomas when compared with gliomas without these deletions. In summary, we confirm proteome-wide profiling as a powerful means to identify candidate biomarkers in gliomas. In addition, our data support the hypothesis that 1p/19q-deleted gliomas frequently show epigenetic down-regulation of multiple genes due to aberrant methylation of the 5'-CpG islands.

Method comparison of automated matching software-assisted cone-beam CT and stereoscopic kilovoltage x-ray positional verification image-guided radiation therapy for head and neck cancer: a prospective analysis

We sought to characterize interchangeability and agreement between cone-beam computed tomography (CBCT) and digital stereoscopic kV x-ray (KVX) acquisition, two methods of isocenter positional verification currently used for IGRT of head and neck cancers (HNC). A cohort of 33 patients were near-simultaneously imaged by in-room KVX and CBCT. KVX and CBCT shifts were suggested using manufacturer software for the lateral (X), vertical (Y) and longitudinal (Z) dimensions. Intra-method repeatability, systematic and random error components were calculated for each imaging modality, as were recipe-based PTV expansion margins. Inter-method agreement in each axis was compared using limits of agreement (LOA) methodology, concordance analysis and orthogonal regression. 100 daily positional assessments were performed before daily therapy in 33 patients with head and neck cancer. Systematic error was greater for CBCT in all axes, with larger random error components in the Y- and Z-axis. Repeatability ranged from 9 to 14 mm for all axes, with CBCT showing greater repeatability in 2/3 axes. LOA showed paired shifts to agree 95% of the time within +/-11.3 mm in the X-axis, +/-9.4 mm in the Y-axis and +/-5.5 mm in the Z-axis. Concordance ranged from 'mediocre' to 'satisfactory'. Proportional bias was noted between paired X- and Z-axis measures, with a constant bias component in the Z-axis. Our data suggest non-negligible differences in software-derived CBCT and KVX image-guided directional shifts using formal method comparison statistics.

Validation of a testosterone and dihydrotestosterone liquid chromatography tandem mass spectrometry assay: Interference and comparison with established methods

Testosterone (T) and its metabolite dihydrotestosterone (DHT) are androgens with different biologic profiles. T and DHT measurements are required for assessment of patients with ambiguous genitalia, hirsutism, during 5 alpha reductase treatment of prostate disorders, and new androgen formulations. Our laboratory has developed and validated a method to simultaneously measure serum T and DHT with liquid chromatography tandem mass spectrometry (LC-MS/MS) for use in a clinical chemistry laboratory. Analysis of sera from blood collected in tubes containing clot activator gave results of T that were fourfold higher than blood collected in plain tubes. Changing the ion pair selected for monitoring eliminated this interference by clot activators. Blood collected in fluoride-coated tubes gave serum T and DHT levels that were 20 and 15% lower, respectively than levels measured in blood collected in plain tubes (no additives). Addition of T enanthate to blood collected in plain tubes caused a dose related increase serum T levels due to the action of non-specific esterases in the red cells. This esterase activity could be avoided by using fluoride tubes for blood collection. Serum DHT levels were consistently lower when measured by LC-MS/MS versus radioimmunoassay. The differences were concentration dependent and the variance for the difference was large when serum DHT concentration was low. Celite chromatograph prior to radioimmunoassay reduced the differences between the two methods, thus confirming that higher levels of DHT obtained by immunoassays were probably due to interfering substances which were partially removed by Celite chromatography.