ObjectiveTo develop a novel prenatal assay based on selective analysis of cell-free DNA in maternal blood for evaluation of fetal Trisomy 21 (T21) and Trisomy 18 (T18).MethodsTwo hundred ninety-eight pregnancies, including 39 T21 and seven T18 confirmed fetal aneuploidies, were analyzed using a novel, highly multiplexed assay, termed digital analysis of selected regions (DANSR™). Cell-free DNA from maternal blood samples was analyzed using DANSR assays for loci on chromosomes 21 and 18. Products from 96 separate patients were pooled and sequenced together. A standard Z-test of chromosomal proportions was used to distinguish aneuploid samples from average-risk pregnancy samples. DANSR aneuploidy discrimination was evaluated at various sequence depths.ResultsAt the lowest sequencing depth, corresponding to 204 000 sequencing counts per sample, average-risk cases where distinguished from T21 and T18 cases, with Z statistics for all cases exceeding 3.6. Increasing the sequencing depth to 410 000 counts per sample substantially improved separation of aneuploid and average-risk cases. A further increase to 620 000 counts per sample resulted in only marginal improvement. This depth of sequencing represents less than 5% of that required by massively parallel shotgun sequencing approaches.ConclusionDigital analysis of selected regions enables highly accurate, cost efficient, and scalable noninvasive fetal aneuploidy assessment. © 2012 John Wiley & Sons, Ltd.

OBJECTIVE -Diabetic nephropathy is a serious complication of both type 1 and type 2 diabetes, and, unless arrested, leads to end-stage renal disease. Current diagnosis consists of urine assays of microalbuminuria, which have inadequate specificity and sensitivity.RESEARCH DESIGN AND METHODS -We used proteomic analyses to identify novel biomarkers of nephropathy in urine from type 2 diabetic patients with demonstrated normo-, micro-, or macroalbuminuria. Samples were analyzed by fluorescence two-dimensional (2-D) differential in-gel electrophoresis (DIGE), and protein identification was performed by liquid chromatography-tandem mass spectrometry.RESULTS -2-D DIGE analysis of the urinary proteome in diabetes with nephropathy identified 195 protein spots representing 62 unique proteins. These proteins belonged to several functional groups, i.e., cell development, cell organization, defense response, metabolism, and signal transduction. Comparisons between control and diabetic subjects with different stages of renal dysfunction revealed the differential expression of several proteins. Spot volume quantification identified 7 proteins that were progressively upregulated with increasing albuminuria and 4 proteins that exhibited progressive downregulation. The majority of these potential candidate biomarkers were glycoproteins.CONCLUSIONS -These data demonstrate the ability of proteomic analyses to reveal potential biomarkers for diabetic nephropathy in urine, an important step forward in advancing accurate diagnosis and our understanding of disease mechanisms. Diabetes Care 30:629 -637, 2007

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To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used.

The chondrogenesis process requires the ordered proliferation and differentiation of chondrocytes. Insulinlike growth factor-binding protein (IGFBP)-3, well characterized as the carrier of insulin-like growth factor (IGF), has been reported to have intrinsic bioactivity that is independent of IGF binding. The mechanisms involved in this IGF-independent action are still unclear. Using the RCJ3.1C5.18 chondrogenic cells, which in culture progresses from undifferentiated to terminally differentiated chondrocytes, we have shown previously that IGFBP-3 has an IGF-independent, antiproliferative effect in undifferentiated and early differentiated but not in terminally differentiated chondrocytes. In the present study, cDNA microarray analysis was used to screen for genes: 1) that were regulated by IGFBP-3 in early but not in terminally differentiated chondrocytes; 2) that were regulated specifically by IGFBP-