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

Andrew T. DeWan, Antonio R. Parrado, Tara C. Matise, Suzanne M. Leal

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


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 assembled nonredundant human genome sequence from the Human Genome Project-Santa Cruz (HGP-sc; October 2000 and April 2001 releases) and Celera (CEL; February 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 ≥3 (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 inconsistent markers, the genetic order was supported by a likelihood ratio of ≥3, and the physical order in the other assembly matched the genetic order. The majority of the inconsistencies between the physical- and genetic-map order point to errors in the physical-map order. A Web site is made available that displays inconsistencies for genetic markers from Marshfield panels 9 and 10 between their genetic-map positions and sequence-based physical-map positions, as well as inconsistencies between their sequence-based physical position. This Web site also contains genetic-map distances, physical-map positions from the Celera and Human Genome Project sequence, and likelihood-ratio support for the genetic maps.

Original languageEnglish (US)
Pages (from-to)101-107
Number of pages7
JournalAmerican Journal of Human Genetics
Issue number1
StatePublished - 2002

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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