Chromosomal SVs are often difficult to interrogate using microarrays or short-read NGS-based methods.
Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs).
Given the current DNA microarray technologies (long or short oligonucleotide arrays and cDNA arrays), which allow simultaneous monitoring of thousands of genes, the PCR amplified cDNA array is the most accessible for studies in non-model organisms (but see [ 6] for oligonucleotide strategies).
Neither oligonucleotide microarrays nor short high-throughput sequencing reads preserve long-range exon connectivity within individual mRNA molecules.
The properties of short unmodified oligonucleotide arrays provide a considerable cost-saving alternative in barcode or short oligonucleotide DNA microarray fabrication, particularly amenable to large-scale in-house synthesis efforts (in our case, forgoing oligonucleotide modification confers an approximately 75% savings in synthesis costs; Supplementary Table S1).
Due to the high sequence identity of 22q11.2 SDs, which may cause cross-hybridization signals, we only considered genome-wide CNVs detected using relatively high-resolution technology (either using microarray with short probes or based on direct sequencing).
Our results demonstrate that a simple TP53 microarray employing short (7-mer) probes, used in combination with single or double tandem hybridization approach and a simple or multiplex target preparation method, can identify common TP53 missense mutations from a variety of DNA sources with good specificity.
These results suggest that the current format of this microarray falls short of adding diagnostic value beyond the customary testing of GJB2, perhaps reflecting the array's limitations on the number of mutations included for each gene, but more likely resulting from unknown genetic contributors to this phenotype.
Our results demonstrate that a simple TP53 microarray using short (7-mer) probes, used in combination with a double tandem hybridization approach and a simple multiplex fragment preparation method, can identify common TP53 point mutations from different DNA sources.
