HLA class II typing of whole genome amplified mouth swab DNA

Postal collection of mouth swabs provides a cheap and convenient means of D NA sampling but hitherto has not provided sufficient genetic material for H LA typing by polymerase chain reaction using sequence-specific primers (PCR -SSP). This study examined the feasibility of collecting mouth swabs from a test population by post, amplifying the DNA by whole genome amplification and genotyping for selected HLA class II alleles. We optimised a strategy f or whole genome amplification or primer extension preamplification using a random 15 base pair primer which resulted in a 1,000-fold increase in DNA t emplate. The amplified DNA was of sufficient quality for analysis of select ed HLA Class II alleles by PCR-SSP and PCR using sequence-specific oligonuc leotide probes. To test the reliability of our data, blood DNA from 30 indi viduals in 10 families, previously tested for all DRB1 alleles in a routine diagnostic laboratory, was then tested in our laboratory for DRB1 *03 and *04 following whole genome amplification. Further whole genome amplified pr oduct from another 10 families was tested for DRB1 *03, *04 in our laborato ry and then tested for all DRB1 alleles in a routine diagnostic laboratory. One repeat typing was required to achieve 100% concordance between laborat ories. Amplification of whole genome amplified DNA by PCR-SSP was then exte nded successfully to low-resolution HLA DRB1, DQA1, DQB1 and DPB1 typing. M outh swab collection by post, followed by whole genome amplification of DNA provides an effective strategy for genetic analysis of large cohorts. We h ave optimised conditions for HLA class II typing on whole genome amplified DNA collected by mouth swab, but this method could potentially be applied t o low concentrations of DNA from other sources.