Genotypic analysis of flow-sorted and microdissected head and neck squamous lesions by whole-genome amplification

To investigate the utility of primer extension preamplification (PEP) in th e genetic analysis of head and neck squamous tumorigenesis, microsatellite analysis was performed on matched deoxyribonucleic acid (DNA) samples extra cted from 32 flow-sorted and microdissected specimens before and after PEP. Eighteen fresh and nine archival specimens were taken from invasive carcin omas, and five specimens were obtained from microdissected archival premali gnant squamous epithelial lesions. Identical microsatellite patterns were o bserved in 276 (87%) of the 319 paired PEP and non-PEP genotypes with suffi cient DNA. Overall, 13 (4%) of the PEP and 28 (8.8%) of the non-PEP fresh t issue samples failed specific microsatellite amplification. All 14 PEP-arch ival specimens were successfully amplified. Sorted cells showed a higher in cidence (42.8%) of loss of heterozygosity (LOH) in both PEP and non-PEP sam ples compared with their unsorted counterparts. The results of this study i ndicate that (a) PEP is a simple and reliable technique for enhancing the D NA yield from small specimens; (b) flow sorting, in certain cases, improves the interpretation of genetic results; and (c) PEP may be used to compensa te for PCR failure of unamplified DNA specimens in these lesions.