Fluorescence Intensity Normalisation: Correcting for Time Effects in Large-Scale Flow Cytometric Analysis

A next step to interpret the findings generated by genome-wide association studies is to associate molecular quantitative traits with disease-associated alleles. To this end, researchers are linking disease risk alleles with gene expression quantitative trait loci (eQTL). However, gene expression at the mRNA level is only an intermediate trait and flow cytometry analysis can provide more downstream and biologically valuable protein level information in multiple cell subsets simultaneously using freshly obtained samples. Because the throughput of flow cytometry is currently limited, experiments may need to span over several weeks or months to obtain a sufficient sample size to demonstrate genetic association. Therefore, normalisation methods are needed to control for technical variability and compare flow cytometry data over an extended period of time. We show how the use of normalising fluorospheres improves the repeatability of a cell surface CD25-APC mean fluorescence intensity phenotype on CD4+ memory T cells. We investigate two types of normalising beads: broad spectrum and spectrum matched. Lastly, we propose two alternative normalisation procedures that are usable in the absence of normalising beads

Effect of Genetic Variants, Especially CYP2C9 and VKORC1, on the Pharmacology of Warfarin

The genes encoding the cytochrome P450 2C9 enzyme (CYP2C9) and vitamin K-epoxide reductase complex unit 1 (VKORC1) are major determinants of anticoagulant response to warfarin. Together with patient demographics and clinical information, they account for approximately one-half of the warfarin dose variance in individuals of European descent. Recent prospective and randomized controlled trial data support pharmacogenetic guidance with their use in warfarin dose initiation and titration. Benefits from pharmacogenetics-guided warfarin dosing have been reported to extend beyond the period of initial dosing, with supportive data indicating benefits to at least 3 months. The genetic effects of VKORC1 and CYP2C9 in African and Asian populations are concordant with those in individuals of European ancestry; however, frequency distribution of allelic variants can vary considerably between major populations. Future randomized controlled trials in multiethnic settings using population-specific dosing algorithms will allow us to further ascertain the generalizability and cost-effectiveness of pharmacogenetics-guided warfarin therapy. Additional genome-wide association studies may help us to improve and refine dosing algorithms and potentially identify novel biological pathways

Fluorescence intensity normalisation: correcting for time effects in large-scale flow cytometric analysis.

A next step to interpret the findings generated by genome-wide association studies is to associate molecular quantitative traits with disease-associated alleles. To this end, researchers are linking disease risk alleles with gene expression quantitative trait loci (eQTL). However, gene expression at the mRNA level is only an intermediate trait and flow cytometry analysis can provide more downstream and biologically valuable protein level information in multiple cell subsets simultaneously using freshly obtained samples. Because the throughput of flow cytometry is currently limited, experiments may need to span over several weeks or months to obtain a sufficient sample size to demonstrate genetic association. Therefore, normalisation methods are needed to control for technical variability and compare flow cytometry data over an extended period of time. We show how the use of normalising fluorospheres improves the repeatability of a cell surface CD25-APC mean fluorescence intensity phenotype on CD4(+) memory T cells. We investigate two types of normalising beads: broad spectrum and spectrum matched. Lastly, we propose two alternative normalisation procedures that are usable in the absence of normalising beads.Peer Reviewe

Evidence of Associations Between Feto-Maternal Vitamin D Status, Cord Parathyroid Hormone and Bone-Specific Alkaline Phosphatase, and Newborn Whole Body Bone Mineral Content

In spite of a high prevalence of vitamin D inadequacy in pregnant women and neonates, relationships among vitamin D status (25(OH)D), parathyroid hormone (PTH), bone specific alkaline phosphatase (BALP), and whole body bone mineral content (WBBMC) in the newborn are poorly characterized. The purpose of the present study was to investigate the relationships between maternal and cord 25(OH)D, PTH, BALP, and WBBMC in newborns in a multiethnic population in Oakland, California and to evaluate the predictive value of the biochemical indices as indicators of WBBMC. Maternal and cord blood were collected from 80 mother-infant pairs and infant WBBMC was measured by dual energy X-ray absorptiometry 8–21 days post-birth. Cord PTH and BALP were each inversely correlated with infant WBBMC (r = −0.28, p = 0.01 and r = −0.26, p = 0.02) and with cord 25(OH)D (r = −0.24, p = 0.03 and r = −0.34, p = 0.002), while cord 25(OH)D and unadjusted or weight-adjusted WBBMC were not significantly correlated with one other. In multivariate regression modeling, infant WBBMC was most strongly predicted by infant weight (p < 0.0001), while either PTH or BALP contributed modestly but significantly to the model (p = 0.006 and p = 0.03 respectively). Cord 25(OH)D was not a significant predictor of infant WBBMC. This study provides evidence of associations between feto-maternal 25(OH)D, cord PTH and BALP, and early infant WBBMC, though neither feto-maternal 25(OH)D nor the measured biochemical indices were suitable indicators of WBBMC

Mapping the categories of the Swedish primary health care version of ICD-10 to SNOMED CT concepts: Rule development and intercoder reliability in a mapping trial

<p>Abstract</p> <p>Background</p> <p>Terminologies and classifications are used for different purposes and have different structures and content. Linking or mapping terminologies and classifications has been pointed out as a possible way to achieve various aims as well as to attain additional advantages in describing and documenting health care data.</p> <p>The objectives of this study were:</p> <p>• to explore and develop rules to be used in a mapping process</p> <p>• to evaluate intercoder reliability and the assessed degree of concordance when the 'Swedish primary health care version of the International Classification of Diseases version 10' (ICD-10) is matched to the Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT)</p> <p>• to describe characteristics in the coding systems that are related to obstacles to high quality mapping.</p> <p>Methods</p> <p>Mapping (interpretation, matching, assessment and rule development) was done by two coders. The Swedish primary health care version of ICD-10 with 972 codes was randomly divided into an allotment of three sets of categories, used in three mapping sequences, A, B and C. Mapping was done independently by the coders and new rules were developed between the sequences. Intercoder reliability was measured by comparing the results after each set. The extent of matching was assessed as either 'partly' or 'completely concordant'</p> <p>Results</p> <p>General principles for mapping were outlined before the first sequence, A. New mapping rules had significant impact on the results between sequences A - B (p < 0.01) and A - C (p < 0.001). The intercoder reliability in our study reached 83%. Obstacles to high quality mapping were mainly a lack of agreement by the coders due to structural and content factors in SNOMED CT and in the current ICD-10 version. The predominant reasons for this were difficulties in interpreting the meaning of the categories in the current ICD-10 version, and the presence of many related concepts in SNOMED CT.</p> <p>Conclusion</p> <p>Mapping from ICD-10-categories to SNOMED CT needs clear and extensive rules. It is possible to reach high intercoder reliability in mapping from ICD-10-categories to SNOMED CT. However, several obstacles to high quality mapping remain due to structure and content characteristics in both coding systems.</p