Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach

Construction of optimal quality control for oligo arrays

MOTIVATION Oligo arrays are important experimental tools for the high throughput measurement of gene expression levels. During production of oligo arrays, it is important to identify any faulty manufacturing step. RESULTS We describe a practical algorithm for the construction of optimal quality control designs that identify any faulty manufacturing step. The algorithm uses hillclimbing, a sea...

Quality Control in Manufa turing Oligo Arrays: A Combinatorial Design Approa h

Equireplicate Balanced Binary Codes for Oligo Arrays

In the manufacture of oligo arrays for DNA hybridization experiments, manufacturing defects must be detected and their position determined. The design of manufacturing protocols for such oligo arrays leads to a combinatorial problem, requiring certain binary codes which have an additional balance property. Constructions using block designs and packings for these codes, within a range of interes...

Fidelity Probes for DNA Arrays

One current approach to quality control in DNA array manufacturing is to synthesize a small set of test probes that detect variation in the manufacturing process. These fidelity probes consist of identical copies of the same probe, but they are deliberately manufactured using different steps of the manufacturing process. A known target is hybridized to these probes, and those hybridization resu...

Human and mouse oligonucleotide-based array CGH

Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array comparative genomic hybridization (CGH). This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well ...