New York University

Bioarray Solutions Ltd.

Vera Cherepinsky

Bhubaneswar Mishra

Michael Seul

Ghazala Hashmi

The present invention relates generally to systems, methods, storage media, and software arrangements for genotyping and/or haplotyping a sequence of polymorphic genetic loci in a deoxyribonucleic acid (DNA) sample or identifying a strain variant from the DNA sample. Exemplary embodiments of systems, methods, storage media, and software arrangements may perform the optimization of the design of one or more microarrays, each containing a set of oligonucleotide probes capable of detecting one or more known genotypes and/or haplotypes at given polymorphic genetic loci or identifying the strain variant, by optimizing the set of oligonucleotides to be incorporated into the microarrays and by optimizing the arrangement of a set of oligonucleotides on the microarrays. The optimization may be achieved through the application of one or more optimization procedures. The instant invention may be useful in typing individuals at the HLA loci or other polymorphic genetic loci, or may be employed to quickly identify viral or bacterial pathogens from which genome sequence information is available.

Methods, software arrangements, storage media, and systems for genotyping or haplotyping polymorphic genetic loci or strain identification

Disclosed is an analysis method useful in multiplexed hybridization-mediated analysis of polymorphisms, i.e., wherein a labeled nucleic acid of interest ('target') interacts with two or more pairs of immobilized degenerate capture probes. In one embodiment, one member of each pair has a sequence that is complementary to the normal ('wild-type') sequence in a designated location of the target, while the other member of each pair has a sequence that is complementary to an anticipated variant (&#x201c;mutant&#x201d; or &#x201c;polymorph&#x201d;) sequence in that location of the target. These methods permit selection of two or more probe pairs such that, for each pair of probes interacting with a given target strand, interaction of the target with a preferred member of the probe pair is optimized. Also interpreting results obtained by multiplexed hybridization of the target to two or more pairs of probes under conditions permitting competitive hybridization is disclosed.

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Sandy Hook, CT, United States of America

Vera Cherepinsky