The map problem: A comparison of genetic and sequence-based physical maps

The genetic order of autosomal genome-scan markers from Marshfield panels 9 and 10 were compared with their physical order, on the basis of the assemb led nonredundant human genome sequence from the Human Genome Project-Santa Cruz (HGP-sc; October 2000 and April 2001 releases) and Celera (CEL; Februa ry 2001 release) databases. The genetic order of 96% of the markers on the Marshfield map for panel 10 is supported by a likelihood ratio of greater t han or equal to3 (odds ratio of 1,000:1). Inconsistencies with the genetic panel 10 map were found for 5% and 2% of the markers in the CEL and HGP-sc sequences, respectively. These inconsistencies consisted of both positional and chromosomal-assignment disagreements. For the majority of these incons istent markers, the genetic order was supported by a likelihood ratio of gr eater than or equal to3, and the physical order in the other assembly match ed the genetic order. The majority of the inconsistencies between the physi cal- and genetic-map order point to errors in the physical-map order. A Web site is made available that displays inconsistencies for genetic markers f rom Marshfield panels 9 and 10 between their genetic-map positions and sequ ence-based physical- map positions, as well as inconsistencies between thei r sequence-based physical position. This Web site also contains genetic-map distances, physical- map positions from the Celera and Human Genome Projec t sequence, and likelihood-ratio support for the genetic maps.