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 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 > or = 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 > or = 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.
DeWan
Andrew T
AT
The Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021-6399, USA.
Parrado
Antonio R
AR
Matise
Tara C
TC
Leal
Suzanne M
SM
D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics*; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D030561:Databases, Nucleic Acid; D023061:Gene Order / Q000235:genetics*; D008040:Genetic Linkage / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D016045:Human Genome Project; D006801:Humans; D020407:Internet; D016013:Likelihood Functions; D016017:Odds Ratio; D020161:Physical Chromosome Mapping; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D005819:Genetic Markers