Predictions of Cu, Zn, and Cd Concentrations in Soil Using Portable X-Ray Fluorescence Measurements.

Portable X-ray fluorescence (PXRF) measurements on 1520 soil samples were used to create national prediction models for copper (Cu), zinc (Zn), and cadmium (Cd) concentrations in agricultural soil. The models were validated at both national and farm scales. Multiple linear regression (MLR), random forest (RF), and multivariate adaptive regression spline (MARS) models were created and compared. National scale cross-validation of the models gave the following R2 values for predictions of Cu (R2 = 0.63), Zn (R2 = 0.92), and Cd (R2 = 0.70) concentrations. Independent validation at the farm scale revealed that Zn predictions were relatively successful regardless of the model used (R2 > 0.90), showing that a simple MLR model can be sufficient for certain predictions. However, predictions at the farm scale revealed that the non-linear models, especially MARS, were more accurate than MLR for Cu (R2 = 0.94) and Cd (R2 = 0.80). These results show that multivariate modelling can compensate for some of the shortcomings of the PXRF device (e.g., high limits of detection for certain elements and some elements not being directly measurable), making PXRF sensors capable of predicting elemental concentrations in soil at comparable levels of accuracy to conventional laboratory analyses.

A novel assay for evaluating fragile X locus repeats.

We have developed a novel fragile X locus repeat assay that is a simple and high-throughput method that, with clinical validation, may be suitable for screening. It uses amplification of the FMR1 trinucleotide repeat region, followed by a hybridization assay to quantify the number of repeats in the amplicons. To our knowledge, this is the first repeat-counting assay that uses fluorescent signals rather than electrophoresis or mass spectrometry as the signaling mechanism. We also report the development of a simple microfluidic electrophoresis reflex test that uses the same amplicons and reduces the need for Southern blots to differentiate homozygous female normal samples from full mutations. The new assay, which is based on a suspension-array hybridization method, was tested on a series of male and female reference samples spanning the range from normal to full mutations. It was also tested on DNA from 1008 dried blood spot samples from pregnant women in their first trimester. The hybridization assay identified 51 of those as potentially expanded alleles of ≥45 repeats or as intermediate or higher in FMR1 repeat classification. Of these screen-positive samples, eight were confirmed by microfluidic electrophoresis as premutations consisting of ≥55 repeats. The FMR1 repeat assay is straightforward to run in high throughput, and the results are in the form of numerical ratios for ease of initial interpretation.

The development of a rapid assay for prenatal testing of common aneuploidies and microdeletion syndromes.

OBJECTIVE: To develop a novel, rapid prenatal assay for pregnancies with high likelihood of normal karyotypes, using BACs-on-Beads(™) technology, a suspension array-based multiplex assay that employs Luminex(®) xMAP(®) technology, for the detection of gains and losses in chromosomal DNA. METHODS: Fifteen relatively common microdeletions were selected that are not detectable, or may be missed, by karyotyping and usually do not present with abnormal ultrasound findings. Chromosomes 13, 18, 21, X, and Y were included. We validated the assay with 430 samples. RESULTS: All microdeletions and aneuploidies were correctly identified, except for a 69,XXX incorrectly identified as a normal female and a male with ∼20% maternal cell contamination (MCC) that could not be distinguished from 69,XXY. MCC became apparent at 20 to 30%. Mosaicism was identified at 30 to 35% abnormal cells. CONCLUSION: We have developed an alternative to fluorescence in situ hybridization (FISH) aneuploidy screening and microarray analysis in otherwise normal pregnancies undergoing invasive testing. We demonstrated that the assay will detect all microdeletions and aneuploidies of regions covered on the assay. We developed analytical software that displays results for well-characterized syndromes but not abnormalities of unclear clinical significance. This assay is likely to be preferred by women seeking testing beyond routine karyotyping but who desire more information than provided by aneuploidy FISH.