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Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays.

TitleBranch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays.
Publication TypeJournal Article
Year of Publication2007
AuthorsPourmand N, Caramuta S, Villablanca A, Mori S, Karhanek M, Wang SX, Davis RW
JournalProc Natl Acad Sci U S A
Volume104
Issue15
Pagination6146-51
Date Published2007 Apr 10
ISSN0027-8424
KeywordsDNA, Forensic Genetics, Microsatellite Repeats, Neural Networks (Computer), Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotides
Abstract

The analysis of short tandem repeats (STRs) plays an important role in forensic science, human identification, genetic mapping, and disease diagnostics. Traditional STR analysis utilizes gel- or column-based approaches to analyze DNA repeats. Individual STR alleles are separated and distinguished according to fragment length; thus the assay is generally hampered by its low multiplex capacity. However, use of DNA microarray would employ a simple hybridization and detection for field forensics and biology. Here we demonstrate a rapid, highly sensitive method for STR analysis that utilizes DNA microarray technology. We describe two adaptations to accomplish this: the use of competitive hybridization to remove unpaired ssDNA from an array and the use of neural network classification to automate the analysis. The competitive displacement technique mimics the branch migration process that occurs during DNA recombination. Our technique will facilitate the rapid deduction of identity, length, and number of repeats for the multiple STRs in an unknown DNA sample.

DOI10.1073/pnas.0700921104
Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID17389407
PubMed Central IDPMC1838402
Grant ListP01-HG000205 / HG / NHGRI NIH HHS / United States