Genetic Maps: Integration

Abstract

Genetic maps describe the order of polymorphisms along a chromosome; however, unlike physical maps, the map distances are related to recombination. The level of recombination varies with position along the chromosome and between the sexes. It is important to integrate genetic and physical or sequence‐based maps to identify regions of elevated or reduced recombination. The presence of recombination hot and cold spots has a bearing on efforts to map disease genes and for the understanding of the biological properties of chromosome location.

Keywords: linkage mapping; recombination; interference; map integration

Figure 1.

Relationship between the male (mcM) and female (fcM) genetic maps for chromosome 22.

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References

Collins A, Frezal J, Teague J and Morton NE (1996) A metric map of humans: 23,500 loci in 850 bands. Proceedings of the National Academy of Sciences of the United States of America 93: 14771–14775.

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Further Reading

Cardon LR and Bell JI (2001) Association study designs for complex diseases. Nature Reviews Genetics 2: 91–99. Good review of linkage disequilibrium mapping of disease genes.

Collins A (2000) Mapping in the sequencing era. Human Heredity 50: 76–84. This article makes the case for maps and map integration to continue postsequencing. Linkage disequilibrium maps were not fully anticipated at this stage.

Ennis S, Maniatis N and Collins A (2001) Allelic association and disease mapping. Briefings in Bioinformatics 2: 375–387. Reviews different measures of LD, diplotype analysis and the background to LD maps.

Morton NE (1991) Parameters of the human genome. Proceedings of the National Academy of Sciences of the United States of America 88: 7474–7476. Perhaps the first paper to give credible genome map lengths on different map scales. Still in use today since large tracts of the genome remain unsequenced for various reasons.

Morton NE and Collins A (1997) The future of gene mapping. Genetic Analysis: Biomolecular Engineering 14: 25–27. This article makes the case for maps and map integration to continue postsequencing. Linkage disequilibrium maps were not fully anticipated at this stage.

Olivier M, Aggarwal A, Allen J, et al. (2001) A high resolution radiation hybrid map of the human genome draft sequence. Science 291: 1298. Radiation hybrid maps remain useful for connectivity and orientation of sequenced contigs.

Patil N, Berno AJ, Hinds DA, et al. (2001) Blocks of limited haplotype diversity revealed by high‐resolution scanning of human chromosome 21. Science 294: 1719–1723. The haplotype structure for a human chromosome established using 24047 SNPs. The first whole‐chromosome LD maps may not be far away.

Taillon‐Miller P, Bauer‐Sardina I, Saccone NL, et al. (2000) Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nature Genetics 25: 324–328. One of the first papers to demonstrate substantial variation in patterns of LD, a forerunner of LD ‘blocks’.

Yu A, Zhao C, Fan Y, et al. (2001) Comparison of human genetic and sequence‐based maps. Nature 409: 951–953. Preliminary assessment of genetic and sequence map relationships based largely on draft sequence.

Web Links

CEPH (version 9) Genotype Database. Genotypes for genetic markers typed in the CEPH reference panel http://www.cephb.fr/cephdb

Center for Medical Genetics. Marshfield maps http://research.marshfieldclinic.org/genetics/

Genetic Location Database (LDB). Locations for expressed sequences and polymorphic markers http://cedar.genetics.soton.ac.uk/public_html/ldb.html

Sequence‐based integrated maps of the human genome http://cedar.genetics.soton.ac.uk/public_html/LDB2000.html/ LDB2000.

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How to Cite close
Collins, Andrew(Jan 2006) Genetic Maps: Integration. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005405]