High-Throughput Genomic and Proteomic Analysis Using Microarray Technology

Abstract

Background: High-density microarrays are ideally suited for analyzing thousands of genes against a small number of samples. The next step in the discovery process is to take the resulting genes of interest and rapidly screen them against thousands of patient samples, tissues, or cell lines to further investigate their involvement in disease risk or the response to medication. Methods: We used a microarray technology platform for both single-nucleotide polymorphisms (SNPs) and protein expression. Each microarray contains up to 250 elements that can be customized for each application. Slides contained either a 16- or 96-microarray format (4000–24 000 elements per slide), allowing the corresponding number of samples to be rapidly processed in parallel. Results: Results for SNP genotyping and protein profiling agreed with results of restriction fragment length polymorphism (RFLP) analysis or ELISA, respectively. Genotyping analyses, using the microarray technology, on large sample sets over multiple polymorphisms in the NAT2 gene were in full agreement with traditional methodologies, such as sequencing and RFLP analysis. The multiplexed protein microarray had correlation coefficients of 0.82–0.99 (depending on analyte) compared with ELISAs. Conclusions: The integrated microarray technology platform is adaptable and versatile, while offering the high-throughput capabilities needed for drug development and discovery applications.

Cancer Statistics, 2002

“…Mortality data were obtained from the National Center for Health Statistics (NCHS) 1 . Incidence data, including five‐year relative survival rate data and data on lifetime probability of developing cancer, were obtained from the Surveillance, Epidemiology, and End Results (SEER) program of the National Cancer Institute (NCI) covering about 10 percent of the US population 2 .…”

“…We estimated the number of cancer deaths expected to occur in the United States and in each state in the year 2002 using underlying cause‐of‐death data from death certificates as reported to the National Center for Health Statistics 1 . The recorded numbers of cancer deaths occurring annually from 1979 to 1999 in the United States and in each state were fitted with autoregressive quadratic models 7 in order to forecast the number of cancer deaths expected to occur in 2002.…”

An oligonucleotide-tagged microarray for routine diagnostics of colon cancer by genotyping KRAS mutations

“…Identification of mutations of host specific cellular gene is of considerable importance for the diagnosis of serious diseases such as CRC. DNA microarray has emerged as a promising tool for large-scale genetic analysis (39,40). The World Health Organization (WHO) estimates that there are over 940,000 CRC cases annually worldwide, with almost 500,000 deaths (41).…”

Potential Breast Anticancer Drug Targets Revealed by Differential Gene Regulatory Network Analysis and Molecular Docking: Neoadjuvant Docetaxel Drug as a Case Study

“…Recent advances in high-throughput DNA microarray technologies have fostered a growing interest in genomics, 1 proteomics, 2 and drug discovery, 3 offering a platform for a deeper understanding of gene-gene interaction and shedding light on previously uncharted avenues for understanding protein-protein and drug-protein interactions. However, a framework for understanding the causal relationship between gene-gene interactions and protein-protein interactions (PPIs) is yet to be developed.…”