Abstract: The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.

Abstract: The invention provides methods of comparing a target nucleic acid with a reference nucleic acid using nucleic acid arrays.

Abstract: Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene expression arrays.

Abstract: Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.

Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.

Abstract: The invention provides chips of immobilized probes, and methods employing the chips, for comparing a reference polynucleotide sequence of known sequence with a target sequence showing substantial similarity with the reference sequence, but differing in the presence of e.g., mutations.

Abstract: Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.

Abstract: Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.

Abstract: Methods, computer software and systems are provided for biological data analysis. In one embodiment, a probe logarithmic intensity error resolver is provided to analyze gene expression data obtained using multiprobes.

Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.

Abstract: Methods and computer software products are provided for analyzing gene expression data In one embodiment, multiple probes are used to detect a single transcript The hybridization intensities of each probe is adjusted by dividing the intensities by the affinities of the probes The minimal adjusted hybridization intensity may be used as the measurement of the gene expression

Abstract: Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.

Abstract: Systems and methods of synthesizing probes on a substrate are provided. One or more shift reticles are utilized to uniformly add monomers to the substrate at specified locations. The shift reticles are shifted relative to the substrate between monomer addition steps. Additionally, characteristics of the desired probes may be specified at synthesis time.

Abstract: Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.

Abstract: Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.

Abstract: Techniques for designing polymer probes to verify the integrity of the probe synthesis are provided. Multiple probes with identical sequences are designed so that the probes will be formed utilizing at least one different monomer addition cycle. Based on the probes affinity to a control target, variations (e.g., errors) in probe synthesis may be identified.

Abstract: Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.