What is the general workflow of SNP microarray?

The general workflow of SNP microarray involves 3 steps: array processing, array screening, and data analysis, in that order respectively. Within these steps, there are specific processes that occur to ensure the experiment is carried out properly. 

The first step is SNP chip fabrication, and the pre-designed oligonucleotide or cDNA chips are arranged properly and in high density on the glass to make microarrays or core chips. Fabrication techniques of the chip include light-guided in-situ synthesis, contact dot coating method, or chemical spray method. A total of 4 X 10^5 different DNA molecules are able to be placed on a single 1 cm^2 chip. 

Next, the sample is prepared from DNA samples from individuals or organisms of interest. These samples can be obtained from blood or tissues and then are extracted and amplified by PCR. During the amplification, the DNA is also labeled with fluorescent dyes to enable the detection of specific SNP alleles. 

Next, the labeled DNA samples are mixed with the reference DNA samples and applied to the SNP microarray chip. The hybridization process allows the test samples to bind to its complementary DNA probes on the microarray. The microarray contains thousands to millions of DNA probes which bind to specific SNPs. 

Following hybridization, the microarray is washed to remove any unbound or non specifically bound DNA. After being washed, a specific fluorescent scanner is utilized to scan the fluorescence, which detects the fluorescent signals at each SNP position on the chip. The computer image analysis is then carried out to process the data prior to the target gene data analysis. There is a large amount of data in the form of fluorescent intensities for each SNP probe. The data is analyzed by determining the genotype at each SNP position. An automated clustering algorithm is then used to group each SNP into clusters representing genotypes. If the algorithm fails to find adequately separated genotype clusters, the SNP is not analyzed further.