title: Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.
abstract: Although oligonucleotide probes complementary to single nucleotide substitutions are commonly used in microarray-based screens for genetic variation, little is known about the hybridization properties of probes complementary to small insertions and deletions. It is necessary to define the hybridization properties of these latter probes in order to improve the specificity and sensitivity of oligonucleotide microarray-based mutational analysis of disease-related genes. Here, we compare and contrast the hybridization properties of oligonucleotide microarrays consisting of 25mer probes complementary to all possible single nucleotide substitutions and insertions, and one and two base deletions in the 9168 bp coding region of the ATM (ataxia telangiectasia mutated) gene. Over 68 different dye-labeled single-stranded nucleic acid targets representing all ATM coding exons were applied to these microarrays. We assess hybridization specificity by comparing the relative hybridization signals from probes perfectly matched to ATM sequences to those containing mismatches. Probes complementary to two base substitutions displayed the highest average specificity followed by those complementary to single base substitutions, single base deletions and single base insertions. In all the cases, hybridization specificity was strongly influenced by sequence context and possible intra- and intermolecular probe and/or target structure. Furthermore, single nucleotide substitution probes displayed the most consistent hybridization specificity data followed by single base deletions, two base deletions and single nucleotide insertions. Overall, these studies provide valuable empirical data that can be used to more accurately model the hybridization properties of insertion and deletion probes and improve the design and interpretation of oligonucleotide microarray-based resequencing and mutational analysis.
authors.affiliation: The Institute for Genetic Medicine, University of Southern California Los Angeles, CA 90089, USA.
authors.forename: Mazen W
authors.initials: MW
authors.lastname: Karaman
authors.forename: Susan
authors.initials: S
authors.lastname: Groshen
authors.forename: Chi-Chiang
authors.initials: CC
authors.lastname: Lee
authors.forename: Brian L
authors.initials: BL
authors.lastname: Pike
authors.forename: Joseph G
authors.initials: JG
authors.lastname: Hacia
mesh_terms: D064007:Ataxia Telangiectasia Mutated Proteins; D020137:Base Pair Mismatch; D001483:Base Sequence; D018797:Cell Cycle Proteins / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D004268:DNA-Binding Proteins / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry*; D017354:Point Mutation; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; D015345:Oligonucleotide Probes; D025521:Tumor Suppressor Proteins; C576324:ATM protein, human; D064007:Ataxia Telangiectasia Mutated Proteins; D017346:Protein Serine-Threonine Kinases
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