HAPPY Mapping

Abstract

HAPPY mapping is a versatile in vitro method for making genome maps. Genomic deoxyribonucleic acid (DNA) is broken randomly and diluted to the point where samples contain only a few molecules. If two sequences (‘markers’) are then found together in the same sample, this implies that they are on the same DNA fragment and therefore adjacent in the genome.

Keywords: genome mapping; single‐molecule analysis; linkage analysis; polymerase chain reaction

Figure 1.

Principle of HAPPY mapping. The example shows the mapping of just three sequence‐tagged site (STS) markers (A, B and Z), although typically many hundreds are mapped in parallel. Genomic deoxyribonucleic acid (DNA) is prepared from cells (a), and is broken randomly to give a pool of fragments (b). The fragments are dispensed into a series of samples (c) constituting the mapping panel; each sample contains less than a genome's worth of fragments and hence only a subset of the markers. Polymerase chain reaction (PCR) is used to ascertain which markers are present in each member of the panel (d). Linked markers such as A and B, because they tend to lie on the same DNA fragments after breakage, tend to cosegregate (as in samples 1, 3 and 96 of this mapping panel). Cosegregation frequencies reflect the distances between markers, which allows a map (e) to be deduced.

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References

Dear PH (1997) HAPPY Mapping in Genome Mapping: A Practical Approach, pp. 95–123. Oxford, UK: IRL Press.

Dear PH, Bankier AT and Piper MB (1998) A high‐resolution metric HAPPY map of human chromosome 14. Genomics 48: 232–241.

Dear PH and Cook PR (1989) HAPPY mapping – a proposal for linkage mapping the human genome. Nucleic Acids Research 17: 6795–6807.

Dear PH and Cook PR (1993) HAPPY mapping – linkage mapping using a physical analog of meiosis. Nucleic Acids Research 21: 13–20.

Konfortov BA, Cohen HM, Bankier AT and Dear PH (2000) A high‐resolution HAPPY map of Dictyostelium discoideum chromosome 6. Genome Research 10: 1737–1742.

Piper MB, Bankier AT and Dear PH (1999) A HAPPY map of Cryptosporidium parvum. Genome Research 8: 1299–1307.

Zhang L, Cui XF, Schmitt K, et al. (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proceedings of the National Academy of Sciences of the United States of America 89: 5847–5851.

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How to Cite close
Dear, Paul H(Sep 2005) HAPPY Mapping. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005362]