Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 15161964

Increased measurement accuracy for sequence-verified microarray probes.

Brigham H Mecham·Daniel Z Wetmore·Zoltan Szallasi·Yoel Sadovsky·Isaac Kohane·Thomas J Mariani
View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

BreastBreast NeoplasmsCell LineCell Line, TumorDNA ProbesDNA, NeoplasmDatabases, GeneticEpithelial CellsGene Expression ProfilingHumansMolecular Diagnostic TechniquesOligonucleotide Array Sequence AnalysisRNA, MessengerRNA, NeoplasmReproducibility of ResultsSequence Analysis, DNAComparative StudyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Brigham H Mecham, Daniel Z Wetmore, Zoltan Szallasi, Yoel Sadovsky, Isaac Kohane, Thomas J Mariani. 2004-08-11. Increased measurement accuracy for sequence-verified microarray probes.. https://doi.org/10.1152/physiolgenomics.00066.2004

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2004

Frequent mutations in the mitochondrial control region DNA in breast tissue.

It has been suggested that the extent of mitochondrial DNA mutations might be useful in the prognosis of cancer outcome and/or the response to certain therapies. In order to investigate whether a high incidence of mutations exists in mitochondrial DNA of breast cancer tissues, we screened three regions of the mitochondrial genome by PCR amplification followed by DNA sequence analysis. Laser capture microdissection was used to isolate pure populations of both tumor cells and normal cells from paraffin embedded specimens. DNA isolated from these cells was used to amplify hypervariable regions HV1 and HV2 and the D-loop region. We found a high rate of mutation in the cancer cell DNA but also found the mutation rate was high in the corresponding normal DNA as well. While no correlations to any clinical parameters could be drawn from this study, the variation from patient to patient suggests that clinical implications might be established on examination of a larger number of samples.

Breast↗
PubMed2004

Anatomy of the nipple and breast ducts revisited.

BACKGROUND: Increasing interest in the intraductal approach to the breast has necessitated revisiting the anatomy of the breast. METHODS: Using six different complementary in vivo and in vitro approaches, the authors determined the number, distribution, and anatomic properties of the ductal systems of the breast, which extend from the nipple orifices to the terminal duct lobular units. RESULTS: More than 90% of all nipples examined contained 5-9 ductal orifices, generally arranged as a central group and a peripheral group. Each nipple orifice communicated with a separate, nonanastomosing ductal system, which extended to the terminal duct lobular unit. CONCLUSIONS: Increased knowledge of the ductal anatomy of the breast and the ability to access the nipple ductal orifices will provide a foundation for the intraductal approach to the breast.

Breast↗
PubMed2004

Results of a survey regarding irradiation of internal mammary chain in patients with breast cancer: practice is culture driven rather than evidence based.

PURPOSE: To examine the self-reported practice patterns of radiation oncologists in North America and Europe regarding radiotherapy to the internal mammary lymph node chain (IMC) in breast cancer patients. METHODS AND MATERIALS: A survey questionnaire was sent in 2001 to physician members of the American Society for Therapeutic Radiology and Oncology and European Society for Therapeutic Radiology and Oncology regarding their management of breast cancer. Respondents were asked whether they would treat the IMC in several clinical scenarios. RESULTS: A total of 435 responses were obtained from European and 702 responses from North American radiation oncologists. Respondents were increasingly likely to report IMC irradiation in scenarios with greater axillary involvement. Responses varied widely among different European regions, the United States, and Canada (p < 0.01). European respondents were more likely to treat the IMC (p < 0.01) than their North American counterparts. Academic physicians were more likely to treat the IMC than those in nonacademic positions (p < 0.01). CONCLUSION: The results of this study revealed significant international variation in attitudes regarding treatment of the IMC. The international patterns of variation mirror the divergent conclusions of studies conducted in the different regions, indicating that physicians may rely preferentially on evidence from local studies when making difficult treatment decisions. These variations in self-reported practice patterns indicate the need for greater data in this area, particularly from international cooperative trials. The cultural predispositions documented in this study are important to recognize, because they may continue to affect physician attitudes and practices, even as greater evidence accumulates.

Breast↗