Predicting Human Minisatellite Polymorphism Export

@article{citeulike:6090851, abstract = {10.1101/gr.574403 We seek to define sequence-based predictive criteria to identify polymorphic and hypermutable minisatellites in the human genome. Polymorphism of a representative pool of minisatellites, selected from human chromosomes 21 and 22, was experimentally measured by PCR typing in a population of unrelated individuals. Two predictive approaches were tested. One uses simple repeat characteristics (e.g., unit length, copy number, nucleotide bias) and a more complex measure, termed HistoryR, based on the presence of variant motifs in the tandem array. We find that HistoryR and percentage of GC are strongly correlated with polymorphism and, as predictive criteria, reduce by half the number of repeats to type while enriching the proportion with heterozygosity \^{a}‰¥0.5, from a background level of 43\% to 59\%. The second approach uses length differences between minisatellites in the two releases of the human genome sequence (from the public consortium and Celera). As a predictor, this similarly enriches the number of polymorphic minisatellites, but fails to identify an unexpectedly large number of these. Finally, typing of the highly polymorphic minisatellites in large families identified one new hypermutable minisatellite, located in a predicted coding sequence. This may represent the first coding human hypermutable minisatellite. [Supplemental material is available online at .]}, author = {Denoeud, France and Vergnaud, Gilles and Benson, Gary}, citeulike-article-id = {6090851}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.574403}, citeulike-linkout-1 = {http://genome.cshlp.org/content/13/5/856.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/13/5/856.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/12695323}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=12695323}, day = {1}, doi = {10.1101/gr.574403}, journal = {Genome Research}, keywords = {minisatellites, polymorphism, tandem, tandem-repeats}, month = {May}, number = {5}, pages = {856--867}, posted-at = {2009-11-09 23:00:39}, priority = {2}, title = {Predicting Human Minisatellite Polymorphism}, url = {http://dx.doi.org/10.1101/gr.574403}, volume = {13}, year = {2003} }

TY - JOUR ID - citeulike:6090851 L3 - citeulike-article-id:6090851 N2 - 10.1101/gr.574403 We seek to define sequence-based predictive criteria to identify polymorphic and hypermutable minisatellites in the human genome. Polymorphism of a representative pool of minisatellites, selected from human chromosomes 21 and 22, was experimentally measured by PCR typing in a population of unrelated individuals. Two predictive approaches were tested. One uses simple repeat characteristics (e.g., unit length, copy number, nucleotide bias) and a more complex measure, termed HistoryR, based on the presence of variant motifs in the tandem array. We find that HistoryR and percentage of GC are strongly correlated with polymorphism and, as predictive criteria, reduce by half the number of repeats to type while enriching the proportion with heterozygosity ≥0.5, from a background level of 43% to 59%. The second approach uses length differences between minisatellites in the two releases of the human genome sequence (from the public consortium and Celera). As a predictor, this similarly enriches the number of polymorphic minisatellites, but fails to identify an unexpectedly large number of these. Finally, typing of the highly polymorphic minisatellites in large families identified one new hypermutable minisatellite, located in a predicted coding sequence. This may represent the first coding human hypermutable minisatellite. [Supplemental material is available online at .] IS - 5 JF - Genome Research EP - 867 TI - Predicting Human Minisatellite Polymorphism VL - 13 SP - 856 KW - minisatellites KW - polymorphism KW - tandem KW - tandem-repeats AU - Denoeud, France AU - Vergnaud, Gilles AU - Benson, Gary PY - 2003/05/01/ UR - http://dx.doi.org/10.1101/gr.574403 ER -