Isolation of human simple repeat loci by hybridization selection

Abstract

We have isolated short tandem repeat arrays from the human genome, using a rapid method involving filter hybridization to enrich for tri- or tetranucleotide tandem repeats. About 30% of clones from the enriched library cross-hybridize with probes containing trimeric or tetrameric tandem arrays, facilitating the rapid isolation of large numbers of clones. In an initial analysis of 54 clones, 46 different tandem arrays were identified. Analysis of these tandem repeat loci by PCR showed that 24 were polymorphic in length; substantially higher levels of polymorphism were displayed by the tetrameric repeat loci isolated than by the trimeric repeats. Primary mapping of these loci by linkage analysis showed that they derive from 17 chromosomes, including the X chromosome. We anticipate the use of this strategy for the efficient isolation of tandem repeats from other sources of genomic DNA, including DNA from flow-sorted chromosomes, and from other species.

Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal

“…An enriched library was made from size selected genomic DNA ligated into SAULA/SAULB-linker [51] and enriched by magnetic bead selection with biotinlabelled (GT) 13 , (CT) 13 , (GTAT) 7 and (GATA) 7 oligonucleotide repeats [52,53]. Of 562 recombinant colonies screened, 142 gave a positive signal after hybridization.…”

Abundant variation in microsatellites of the parasitic nematode Trichostrongylus tenuis and linkage to a tandem repeat

“…Two genomic DNA libraries were prepared following a standard enrichment protocol [29]. For the first library genomic DNA was purified from bulked male and female adult nematodes (approximately a 200-µl volume of compressed tissue, probably containing well over 1000 individuals) taken from a single red grouse from a grouseshooting estate in North Yorkshire, England in September 2001.…”

Characterization of ten polymorphic microsatellite markers for the endemic Chapman's ringlet, Erebia palarica (Lepidoptera: Nymphalidae)

“…Genomic DNA was extracted from the thorax of E. palarica using the QIAGEN DNeasy® Tissue Kit (Qiagen Iberia S.L., Madrid, Spain). An enriched library was made by Ecogenics GmbH (Zurich, Switzerland) from size selected genomic DNA ligated into SAULA/SAULB-linker (Armour et al, 1994) and enriched by magnetic bead selection with biotinlabelled (GTAT)7, (GATA)7, (GT)13 and (CT)13 oligonucleotide repeats (Gautschi et al, 2000a, b). Of 1126 recombinant colonies screened, 208 gave a positive signal after hybridization.…”