Allele Drop Out Conferred by a Frequent CYP2D6 Genetic Variation For Commonly Used CYP2D6*3 Genotyping Assays

Background/Aim: Accurate genotyping of CYP2D6 is challenging due to its inherent genetic variation, copy number variation (duplications and deletions) and hybrid formation with highly homologous pseudogenes. Because a relatively high percentage (∼25%) of clinically prescribed drugs are substrates for this enzyme, accurate determination of its genotype for phenotype prediction is essential. Methods: A cohort of 365 patient samples was genotyped for CYP2D6 using Sanger sequencing (as the gold standard), hydrolysis probe assays or pyrosequencing. Results: A discrepant result between the three genotyping methods for the loss of function CYP2D6*3 (g.2549delA, rs35742686) genetic variant was found in one of the samples. This sample also contained the CYP2D6 g.2470T>C (rs17002852) variation, which had an allele frequency of 2.47% in our cohort. Redesign of the CYP2D6*3 pyrosequencing and hydrolysis probe assays to avoid CYP2D6 g.2470 corrected the anomaly. Conclusion: To evidence allele drop out and increase the accuracy of genotyping, intra-patient validation of the same genetic variation with at least two separate methods should be considered.

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On the Trail of Spatial Patterns of Genetic Variation

Evolutionary Biology ◽

10.1007/s11692-021-09552-y ◽

2021 ◽

Author(s):

José A. Peña ◽

Luis Gómez-Pérez ◽

Miguel A. Alfonso-Sánchez

Keyword(s):

Genetic Variation ◽

Evolutionary Biology ◽

Isolation By Distance ◽

Accurate Determination ◽

Data Entry ◽

Centroid Method ◽

Genome Wide ◽

Genome Wide Data ◽

History Of

AbstractThe accurate determination of the spatial trends on the variability of a species’ gene pool is essential to elucidate the underlying demographic-evolutionary events, thus helping to unravel the microevolutionary history of the population under study. Herein we present a new software called GenoCline, mainly addressed to detect genetic clines from allele, haplotype, and genome-wide data. This program package allows identifying the geographic orientation of clinal genetic variation through a system of iterative rotation of a virtual coordinate axis. Besides, GenoCline can perform complementary analyses to explore the potential origin of the genetic clines observed, including spatial autocorrelation, isolation by distance, centroid method, multidimensional scaling and Sammon projection. Among the advantages of this software is the ease in data entry and potential interconnection with other programs. Genetic and geographic data can be entered in spreadsheet table formatting (.xls), whereas genome-wide data can be imported in Eigensoft format. Genetic frequencies can also be exported in a format compatible with other programs dealing with population genetic and evolutionary biology analyses. All illustrations of results are saved in.svg format so that there will be high quality and easily editable vectorial graphs available for the researcher. Being implemented in Java, GenoCline is highly portable, thus working in different operating systems.

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Can estimated glomerular filtration rate (eGFR) replace isotopic measurement of GFR for carboplatin dosing in stage 1 seminoma?

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.2589 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 2589-2589

Author(s):

Scott T.C. Shepherd ◽

Gerry Gillen ◽

Paula Morrison ◽

Carla Forte ◽

Iain R. MacPherson ◽

...

Keyword(s):

Gold Standard ◽

Accurate Determination ◽

Gold Standard Method ◽

Isotopic Methods ◽

51Cr Edta ◽

Isotope Studies ◽

Clinically Significant ◽

Stage 1 ◽

Carboplatin Dose

2589 Background: Accurate determination of GFR is essential for correct dosing of carboplatin, the standard adjuvant therapy for stage 1 seminoma. Isotopic methods (e.g. 51Cr-EDTA) remain the gold standard for determination of GFR. However, the use of eGFR could reduce the need for such isotope studies. As novel formulae to estimate GFR such as CKD-EPI and MDRD4 have improved the assessment of renal function in non-oncological settings, we investigated their utility for carboplatin dosing. Methods: 115 patients (pts) (mean age 40.3, std dev. 10.1) who received adjuvant carboplatin for stage 1 seminoma at our institution between 2007-2012 were identified. All pts underwent 51Cr-EDTA measurement of GFR with carboplatin dose calculated using the Calvert formula, based on GFR uncorrected for body surface area (BSA). Theoretical carboplatin doses were then calculated using eGFR values obtained using the CKD-EPI and MDRD4 formulae with additional calculation to uncorrect for BSA. Creatinine clearance was calculated by Cockcroft-Gault (CG) formula. For each pt the carboplatin doses calculated by eGFR were compared with the actual dose calculated by the gold-standard method; a difference of less than 10% was considered acceptable. Results: The Table shows the percentage of pts who would have received an equivalent carboplatin dose using each eGFR formula compared to the dose calculated using 51Cr-EDTA. The CKD-EPI formula performed best with 58.9% of pts receiving within 10% of the correct dose. Pts predicted to be underdosed by CKD-EPI eGFR were more likely to be obese (BMI >30) (p=0.01); there were no predictors of the 18.8% who would have received an excess dose. Conclusions: Our data support further evaluation of the CKD-EPI formula but highlight the clinically significant variances in carboplatin dosing when using non-isotopic methods of GFR estimation. [Table: see text]

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A quantitative approach to inner shell losses

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010010977x ◽

1978 ◽

Vol 36 (1) ◽

pp. 526-527 ◽

Cited By ~ 2

Author(s):

R.D. Leapman ◽

P. Rez ◽

D.F. Mayers

Keyword(s):

Energy Transfer ◽

Cross Section ◽

Cross Sections ◽

Accurate Determination ◽

Background Intensity ◽

Core Excitation ◽

Quantitative Basis ◽

Cross Section Differential ◽

Bound Electrons

Microanalysis by EELS has been developing rapidly and though the general form of the spectrum is now understood there is a need to put the technique on a more quantitative basis (1,2). Certain aspects important for microanalysis include: (i) accurate determination of the partial cross sections, σx(α,ΔE) for core excitation when scattering lies inside collection angle a and energy range ΔE above the edge, (ii) behavior of the background intensity due to excitation of less strongly bound electrons, necessary for extrapolation beneath the signal of interest, (iii) departures from the simple hydrogenic K-edge seen in L and M losses, effecting σx and complicating microanalysis. Such problems might be approached empirically but here we describe how computation can elucidate the spectrum shape.The inelastic cross section differential with respect to energy transfer E and momentum transfer q for electrons of energy E0 and velocity v can be written as

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Fast calibration of CBED patterns for quantitative analysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100149209 ◽

1993 ◽

Vol 51 ◽

pp. 674-675

Author(s):

M.A. Gribelyuk ◽

M. Rühle

Keyword(s):

Reciprocal Lattice ◽

Accurate Determination ◽

Incident Beam ◽

Crystal Thickness ◽

Structure Model ◽

Beam Direction ◽

Transmitted Beam ◽

Reciprocal Vector ◽

On Line

A new method is suggested for the accurate determination of the incident beam direction K, crystal thickness t and the coordinates of the basic reciprocal lattice vectors V1 and V2 (Fig. 1) of the ZOLZ plans in pixels of the digitized 2-D CBED pattern. For a given structure model and some estimated values Vest and Kest of some point O in the CBED pattern a set of line scans AkBk is chosen so that all the scans are located within CBED disks.The points on line scans AkBk are conjugate to those on A0B0 since they are shifted by the reciprocal vector gk with respect to each other. As many conjugate scans are considered as CBED disks fall into the energy filtered region of the experimental pattern. Electron intensities of the transmitted beam I0 and diffracted beams Igk for all points on conjugate scans are found as a function of crystal thickness t on the basis of the full dynamical calculation.

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Computer-Assisted High-Re Solution TEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100179567 ◽

1990 ◽

Vol 48 (1) ◽

pp. 162-163

Author(s):

F.A. Ponce ◽

H. Hikashi

Keyword(s):

Signal To Noise Ratio ◽

Accurate Determination ◽

Computer Software ◽

Video Camera ◽

Image Contrast ◽

Objective Lens ◽

Computer Assisted ◽

Optical Parameters ◽

Astigmatism Correction

The determination of the atomic positions from HRTEM micrographs is only possible if the optical parameters are known to a certain accuracy, and reliable through-focus series are available to match the experimental images with calculated images of possible atomic models. The main limitation in interpreting images at the atomic level is the knowledge of the optical parameters such as beam alignment, astigmatism correction and defocus value. Under ordinary conditions, the uncertainty in these values is sufficiently large to prevent the accurate determination of the atomic positions. Therefore, in order to achieve the resolution power of the microscope (under 0.2nm) it is necessary to take extraordinary measures. The use of on line computers has been proposed [e.g.: 2-5] and used with certain amount of success.We have built a system that can perform operations in the range of one frame stored and analyzed per second. A schematic diagram of the system is shown in figure 1. A JEOL 4000EX microscope equipped with an external computer interface is directly linked to a SUN-3 computer. All electrical parameters in the microscope can be changed via this interface by the use of a set of commands. The image is received from a video camera. A commercial image processor improves the signal-to-noise ratio by recursively averaging with a time constant, usually set at 0.25 sec. The computer software is based on a multi-window system and is entirely mouse-driven. All operations can be performed by clicking the mouse on the appropiate windows and buttons. This capability leads to extreme friendliness, ease of operation, and high operator speeds. Image analysis can be done in various ways. Here, we have measured the image contrast and used it to optimize certain parameters. The system is designed to have instant access to: (a) x- and y- alignment coils, (b) x- and y- astigmatism correction coils, and (c) objective lens current. The algorithm is shown in figure 2. Figure 3 shows an example taken from a thin CdTe crystal. The image contrast is displayed for changing objective lens current (defocus value). The display is calibrated in angstroms. Images are stored on the disk and are accessible by clicking the data points in the graph. Some of the frame-store images are displayed in Fig. 4.

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