I enjoyed the article on the controversy concerning the utility of haplotypes in human disease understanding.1 My assessment is more in line with Ken Kidd's than with the fervent advocates of the HapMap.

My interest in this area dates from the 1970s and culminated in 1989–1990 with two patents concerning the utility of haplotypes marked by noncoding sequence variant markers exhibiting linkage disequilibrium http://www.SimonsJunkDNA.com. Those articles indicate that HLA scientists have understood the haplotype phenomenon since 1967. The notion of haplotype blocks is not as recent as some think, being first reported in 1983. In the genomic mapping patent, filed July 1990, I predicted that haplotypic structure would be a general feature of eukaryotic organisms, sufficient to dispense with the requirement for pedigree-based linkage for gene identification and fine mapping.

Malcolm Simons


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