Biomedical subjects

Daniel Z Wetmore

Publications and source records attributed to Daniel Z Wetmore.

3 recordsLinked to original sources

PubMed2004

Increased measurement accuracy for sequence-verified microarray probes.

Microarrays have been extensively used to investigate genome-wide expression patterns. Although this technology has been tremendously successful, it has suffered from suboptimal individual measurement precision. Significant improvements in this respect have been recently made. In an effort to further explore the underlying variability, we have attempted to globally assess the accuracy of individual probe sequences used to query gene expression. For mammalian Affymetrix microarrays, we identify an unexpectedly large number of probes (greater than 19% of the probes on each platform) that do not correspond to their appropriate mRNA reference sequence (RefSeq). Compared with data derived from inaccurate probes, we find that data derived from sequence-verified probes show 1) increased precision in technical replicates, 2) increased accuracy translating data from one generation microarray to another, 3) increased accuracy translating data from oligonucleotide to cDNA microarrays, and 4) improved capture of biological information in human clinical specimens. The logical conclusion of this work is that probes containing the most reliable sequence information provide the most accurate results. Our data reveal that the identification and removal of inaccurate probes can significantly improve this technology.

Breast↗

PubMed2004

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.

Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms.

Breast↗

PubMed2004

Post-spike distance-to-threshold trajectories of neurones in monkey motor cortex.

A recently developed method permits calculation of the post-spike distance-to-threshold trajectory from an extracellularly recorded spontaneous spike train, using a transform of the interspike interval histogram. We applied this method to 61 single neurones recorded from the primary motor cortex of an awake behaving monkey; 39 cells were antidromically identified as pyramidal tract neurones (PTNs). The cells fell into three categories. Fifty-three trajectories (37 from PTNs) had statistically significant peaks 10-60 ms after the preceding spike. Six neurones (2 PTNs) had non-peaked trajectories which rose exponentially towards threshold. Two cells (both unidentified) had trajectories which declined monotonically away from threshold with increasing post-spike latency. The peaked trajectories were unlikely simply to be an artefact of changing firing rate, which potentially can invalidate this method. Firstly, computer simulations confirmed that the method could accurately re-create both exponential and peaked trajectories, even in the presence of the same rate modulation as seen experimentally. Secondly, the responses of eight cells to weak single pulse intracortical microstimulation (20 microA) through a nearby electrode were measured. For each cell, including representatives of all three trajectory shapes, the modulation of response probability with post-spike latency was consistent with the trajectory computed from the spontaneous discharge. We also demonstrated that cells showed a peaked trajectory during periods with either high or low spontaneous network oscillations, so that the peaks were likely to be generated in part by single cell properties rather than exclusively by network activity. We conclude that many single neurones in motor cortex have an increased probability of firing a spike around 30 ms after the previous action potential. This could act to enhance synchronized oscillatory discharge among populations of cells at functionally relevant frequencies.

Action Potentials↗