Introduction

Single nucleotide polymorphisms (SNPs) are common variants in the human genome (and other genomes). There are approximately 5 million validated reference SNPs (RefSNPs) at the NCBI SNP database, dbSNP. SNP analysis facilitates large-scale studies of changes in chromosomal copy number, changes in genotype, as well as association studies. You can read an introduction to SNPs at the NCBI and ORNL websites.

SNPscan is a web-accessible tool that allows users to upload large-scale SNP datasets obtained from the Affymetrix 10K, 50K Xba, 50K Hind or 100K (combined 50K Xba/Hind) SNP array platforms. SNPscan provides data analysis and data visualization.

We developed SNPscan as a way to identify chromosomal variations in DNA samples from individuals with childhood brain disorders. There are several kinds of information we can obtain from SNP array data as analyzed and visualized by SNPscan:

• SNP intensity data reveal chromosomal copy number changes such as microdeletions, microduplications, and aneuploidies (change in chromosome number)
• SNP genotype data show positions that are heterozygous (AB call), homozygous (AA or BB call), or have no call. A stretch of autosomal homozygous calls (also called a region of "loss of heterozygosity," or LOH) may correspond to a region of deletion. Such phenomena are relatively common in conditions ranging from some forms of cancer to mental retardation.
• A region of homozygosity in which the chromosome number is unchanged (disomic) may reflect uniparental disomy (UPD), in which two copies of a particular chromosome are inherited from the same parent. If the pair of chromosomes from one parent are identical, the condition is uniparental isodisomy; this is easily observable using SNPscan.
• With SNPscan, pairs of array data can be compared. For example, some researchers compare SNP profiles in cancerous versus unaffected samples from the same individual.

The National Center of Toxicogenomics (NCT) at the National Institutes of Health offers an on-line glossary with the following terms of interest:

Allele: An alternative form of a gene or any other segment of a chromosome.

Genotype: The genetic composition of an organism or a group of organisms; a group or class of organisms having the same genetic constitution.

Microarray: A tool used to sift through and analyze the information contained within a genome. A microarray consists of different nucleic acid probes that are chemically attached to a substrate, which can be a microchip, a glass slide or a microsphere-sized bead.

Polymorphism: The quality or character of occurring in several different forms.

Single nucleotide polymorphism (SNP): A change in which a single base in the DNA differs from the usual base at that position.