Table 2 Ten questions that help during the SNP genotyping triage process

[2]

Is the SNP located inside of a DNA repeat?

This SNP could be a sequencing artefact.

[3]

Has a particular SNP been submitted by at least two reliable sources?

The genomic sequence may not be polymorphic.

[4]

Is the SNP seen jointly in different public (dbSNP, HGBASE) and private (ALLSNPS, REALSNP, CELERA) databases?

The SNP may not exist.

[5]

Are allele frequencies available in the target population?

The SNP may not exist in the target population.

[6]

Is the SNP located in a known functional motif?

This will increase the likelihood of a causative mutation.

[7]

Is the SNP situated in a region that is conserved in other species?

Highly conserved regions have an increased likelihood of being functionally important.

[8]

Are there more SNPs in the neighborhood?

These SNPs may interfere with primer design.

[9]

Is the SNP seen also in paralogous genomic regions ("multiple genome hitters">)?

These SNPs could interfere at genotyping by creating artificial alleles.

[10]

Does the SNP tag any specific haplotype?

Tagging SNP can help to capture effects of neighboring SNPs in linkage disequilibrium.