Ordering three DNA polymorphisms on human chromosome 3 by sperm typing.

Three loci on the short arm of human chromosome 3 were ordered by sperm typing to expand the limited genetic map of this region. Almost 300 individual sperm from a donor triply heterozygous at D3S2, D3S11, and D3S12 were amplified by PCR using primers flanking the polymorphic site at each locus. Primary PCR product was reamplified using allele-specific primers of different lengths, allowing the allelic state at each locus to be determined by gel electrophoresis. Maximum likelihood analysis of the sperm-typing data showed that the most likely order was D3S2-D3S11-D3S12 with an odds ratio of almost 5000:1 when compared to the next most likely order. This finding should be useful in interpreting loss of heterozygosity on 3p in a variety of cancers. Our results also demonstrate the practicality of ordering DNA polymorphisms using sperm typing.