Population Screening for Hemoglobinopathy Profiling: Is the Development of a Microarray Worthwhile?

Abstract

In order to perform affordable and expedient whole population scans for the single nucleotide polymorphisms (SNPs) involved in hemoglobinopathies, microarrays based on single nucleotide extension (SNE) might prove advantageous to whole genome/exome sequencing in terms of cost, speed, interpretation and discretion as they focus on a very small part of the tested genome. The development of a microarray assay entails most of the cost, to be deferred by the massive use of the end product. A microarray assay development project, involving multiplex polymerase chain reaction (PCR), labeling, hybridization and scanning/scoring steps is presented as a paradigm of objective bug ratios expected to such procedures and of ways to cope with them. Qualification of the microarray genotypes needs a reference method, which may still be restriction digestion or other, as sequencing remains an expensive commodity. Optimization of wet steps should also be followed by careful and perhaps individualized dye excitation and in silico scoring rules, taking into consideration decay and bleaching effects that perplex development. The strategy of successive elimination of problems, a top-bottom procedure, which had been used and is usually preferred by developing agencies, might have been erroneous; a bottom-up course to delineate issues in different levels, although more laborious, might be the correct choice, especially as software and robotic hardware, high throughput tools become more mature and available. The testing for interlocus compatibility, specificity and robustness is demanding and warranted only in the case of steady, high volume use of an assay for territorial, national or international use.

Keywords:

• Hemoglobinopathies
• microarray development
• microarrays
• multiplex polymerase chain reaction (PCR)
• population screening
• single nucleotide polymorphims (SNPs)

Acknowledgements

The author wishes to thank Drs. Xiangfeng Cui, Sreemanta Pramanik and Hui-Yun Wang of the Cancer Institute of New Jersey, New Brunswick, NJ, USA, for their active and consulting assistance with the array development procedures.

Declaration of interest

The author wishes to thank Assistant Professor Dr. Honghua Li of The Cancer Institute of New Jersey, New Brunswick, NJ, USA, under whose patronage, guidance and support (National Human Genome Research Institute grant R01 HG02094, and the National Cancer Institute grants R01 CA77363 and R33 CA 96309) the array experiments were implemented. The author reports no conflicts of interest. The author alone is responsible for the content and writing of this article.