News Column

Patent Application Titled "Method of Improving Microarray Performance by Strand Elimination" Published Online

May 26, 2014



By a News Reporter-Staff News Editor at Cancer Gene Therapy Week -- According to news reporting originating from Washington, D.C., by NewsRx journalists, a patent application by the inventor NAKAO, AKI (SUNNYVALE, CA), filed on October 30, 2013, was made available online on May 15, 2014 (see also Roche Molecular Systems, Inc.).

The assignee for this patent application is Roche Molecular Systems, Inc.

Reporters obtained the following quote from the background information supplied by the inventors: "Oligonucleotide microarrays (chips) are an economical way of analyzing multiple nucleic acid targets in one experiment. These arrays are commonly used to analyze multiple genes, for example in a gene expression assay. However, oligonucleotide microarrays are also gaining popularity as an economical and convenient alternative to sequencing in somatic and germline mutation detection assays. Certain genes are well known as somatic mutation and polymorphism hotspots. For such genes, many of the somatic mutations and polymorphisms are associated with a disease or an altered phenotype. For example, multiple mutations in the TP53 and EGFR genes are relevant to cancer. Somatic mutations in TP53 gene are known to cause loss of p53 function, associated with an increase of cancers occurring in various tissues. The TP53 mutation status is also useful for prognosis and predicting response to therapy. Similarly, multiple polymorphisms in CYP450 gene effectively predict the pattern of drug metabolism. Because of the large number of mutations, targeting each mutation with a separate assay becomes impractical. Thus microarrays capable of at once probing multiple mutated base positions (or even every base position within the gene) offer a useful alternative.

"A typical microarray (chip) is a collection of microscopic spots each containing millions of nucleic acid probes attached to a solid surface. The probes are capable of hybridizing to the labeled DNA fragments from a sample under suitable conditions. Probe-target hybridization is detected and optionally quantified by detection of a label conjugated to the target molecule. Microarrays as a mutation detection tool have been validated in several systems (reviewed in Schwartz, S., Clinical Utility of Single Nucleotide Polymorphism Arrays (2011) Clin. Lab. Med. 31:581.) Unfortunately, studies involving microarrays report that the sensitivity and specificity of microarrays are not yet ideal compared to existing technologies (see e.g. Zin R., et al., SNP-based arrays complement classic cytogenetics in the detection of chromosomal aberrations in Wilms' tumor (2012) Cancer Genetics 205:80. In practice, it appears that performance of microarrays is not uniform throughout the probed sequence. Some positions within the sequence are subject to error more than others. The use of better mathematical or statistical tools for data analysis that identify such special sites holds the promise of improving sensitivity and specificity of mutation detection microarrays."

In addition to obtaining background information on this patent application, NewsRx editors also obtained the inventor's summary information for this patent application: "In some embodiments, the invention is a method of interrogating a sequence of a target nucleic acid having a sense and an anti-sense strands by a microarray analysis comprising a sequence determination computation, comprising omitting from the computation a signal from one of the sense and anti-sense strands for one or more nucleotide positions in the target nucleic acid sequence. In variations of this embodiment, omitting the signal from one of the sense and anti-sense strands at a nucleotide position comprises the steps of using a plurality of microarrays, measuring hybridization signals at the nucleotide position using one or more probe sets for each of the sense and the anti-sense strands; for each probe set, determining base discrimination ability by comparing the hybridization signals within each probe set; for each nucleotide position, computing discrimination ability for sense and antisense strand separately using the computed discrimination ability from each of the probe sets; for each nucleotide position, comparing the computed discrimination ability between the sense and the anti-sense strands; omitting the signal from the strand with lower base discrimination ability. In variations of this embodiment, the base discrimination is measured using Formula 1. In further variations of this embodiment, the discrimination ability for sense and antisense strand is computed as a percentile of the discrimination ability for probe sets in the strand at the base position. In yet further variations of this embodiment, the discrimination ability between sense and antisense starnd is compared using Formula 3.

"In other embodiments, the invention is a method of detecting the presence or absence of a target nucleic acid having a sense and an anti-sense strands in a test sample using a microarray analysis including a sequence determination or mutation detection computation, comprising omitting from the computation a signal from one of the sense and anti-sense strands for one or more nucleotide positions in the target nucleic acid sequence. In variations of this embodiment, omitting the signal from one of the sense and anti-sense strands at a nucleotide position comprises the steps of: using a plurality of microarrays, measuring hybridization signals at the nucleotide position using one or more probe sets for each of the sense and the anti-sense strands; for each probe set, determining base discrimination by comparing the hybridization signals within each probe set; for each nucleotide position, computing discrimination ability for sense and antisense strand separately using discrimination ability from each of the probe sets; for each nucleotide position, comparing discrimination ability between the sense and the anti-sense strands; omitting the signal from a strand with lower base discrimination ability. In variations of this embodiment, the base discrimination is measured using Formula 1. In further variations of this embodiment, the discrimination ability of the sense and anti-sense strand is computed as a percentile of the discrimination ability for probe sets in the strand at the base position measured using a plurality of microarrays.

"In yet another embodiment, the invention is a computer readable medium including code for controlling one or more processors to detect the presence or absence of a target nucleic acid having a sense and an anti-sense strands in a test sample using a microarray analysis that includes a sequence determination or mutation detection computation, comprising omitting from the computation a signal from one of the sense and anti-sense strands for one or more nucleotide positions in the target nucleic acid sequence. In variations of this embodiment, the computer readable medium comprises a code controlling the steps of: using a plurality of microarrays, measuring hybridization signals at the nucleotide position using one or more probe sets for each of the sense and the anti-sense strands; for each probe set, determining base discrimination ability by comparing the hybridization signals within each probe set; for each nucleotide position, computing discrimination ability for sense and antisense strand separately using discrimination ability from each of the probe sets; for each nucleotide position, comparing discrimination ability between the sense and the anti-sense strands; omitting the signal from a strand with lower base discrimination ability.

"In yet another embodiment, the invention is a system for detecting a target nucleic acid in a test sample comprising: a data acquisition module configured to acquire hybridization data from a microarray; a data processing unit configured to process the data to determine a target nucleotide sequence by omitting the signal from one of the sense and anti-sense strands at one or more nucleotide positions in the target sequence via the steps of: using a plurality of microarrays, measuring hybridization signals at the nucleotide position using one or more probe sets for each of the sense and the anti-sense strands; for each probe set, determining base discrimination ability by comparing the hybridization signals within each probe set; for each nucleotide position, computing discrimination ability for sense and antisense strand separately using discrimination ability from each of the probe sets; for each nucleotide position, comparing discrimination ability between the sense and the anti-sense strands; omitting the signal from a strand with lower base discrimination ability; and a display module configured to display the data produced by the data processing unit.

"In yet another embodiment, the invention is a method of detecting the presence or absence of a mutation in the p53 gene in a test sample using a microarray analysis including a mutation detection computation, comprising omitting from the computation a signal from one of the sense and anti-sense strands for one or more nucleotide positions in the target nucleic acid sequence. In variations of this embodiment, the nucleotide positions are selected from codon 273, position 1 and codon 220, position 2 within the p53 gene.

BRIEF DESCRIPTION OF THE FIGURES

"FIG. 1. Selecting strands for elimination by comparing discriminating ability of sense and antisense probes using Q.sub.75 value."

For more information, see this patent application: NAKAO, AKI. Method of Improving Microarray Performance by Strand Elimination. Filed October 30, 2013 and posted May 15, 2014. Patent URL: http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&u=%2Fnetahtml%2FPTO%2Fsearch-adv.html&r=1954&p=40&f=G&l=50&d=PG01&S1=20140508.PD.&OS=PD/20140508&RS=PD/20140508

Keywords for this news article include: Antisense Technology, Biotechnology, Genetics, p53 Gene, Bioengineering, Cancer Gene Therapy, Information Technology, Roche Molecular Systems Inc., Information and Data Processing.

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Source: Cancer Gene Therapy Week


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