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Marker pattern instabilities as a major cause of reproducibility problems in two‐dimensional DNA fingerprinting
Author(s) -
Hampe Jochen,
Marczinek Karola,
Preuss André,
Nürnberg Peter
Publication year - 1996
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.1150170406
Subject(s) - dna profiling , biology , reproducibility , restriction enzyme , dna , spots , genetics , computational biology , microbiology and biotechnology , chromatography , chemistry , botany
Two‐dimensional (2‐D) DNA fingerprinting is a promising technique for multilocus analysis of eukaryotic genomes. It has been successfully applied to the detection of DNA variation in tumors, to linkage analyses and to genomic comparisons of inbred mouse strains. However, there are still problems with inter‐gel comparisons of 2‐D DNA typing patterns as documented by the intergel reproducibility rates reported in the literature, which range from 84 to 98%. The basis for standardization in almost all of these studies has been a set of lambda fragments (digested separately with the restriction enzymes Hae III, Rsa I, Bg /I) that produces a spot pattern scattered across the gel. These spots are used as markers for gel comparisons. Since we noticed considerable variations in the marker spot paterns, we evaluated the properties of the lambda marker using both computer simulation and an empirical analysis of forty independent consecutive gels from our laboratory. We explain the instabilities of the spot pattern on the basis of the melting properties of the individual lambda fragments. A subset of spots is presented that has been stable in all our experiments. Only this set of spots should be used for gel standardization purposes until a new, completely reproducible marker becomes available. Finally, suggestions for an improved marker system are made.