Abstract: High throughput methods and compositions (e.g., kits) for the amplification of RNA fragments, including in particular, for the detection of fusion mutations in a high volume of samples, e.g., by high throughput sequencing method. These methods may include barcoding cDNA preparations with template switching reactions, indexing pools of libraries and intensive use of automatic liquid handling, and providing a ready-to-sequence library mix.

Abstract: Laboratory-based high throughput methods and compositions (e.g., kits) for the detection of pathogen mRNA, including in particular, for the detection of SARS-CoV-2 RNA from up to 85,000 samples in one Illumina NovaSeq sequencing run. These methods may include barcoding cDNA, indexing pools of libraries and intensive use of automatic liquid handling, providing a ready-to-sequence library mix. These methods and compositions may allow a very inexpensive per sample cost and an assay that may be performed in about one day or less.

Abstract: Methods, compositions, systems and kits to amplify or improve amplification of target-specific amplification products by reducing non-specific amplification products (e.g., primer-dimers) when amplifying multiple different nucleotide regions. The methods, compositions, systems and kits described herein may include, or include the use of, one or more resolvases that recognize and bind to and/or cut an aberrant DNA structure.

Abstract: Methods, compositions, systems and kits to introduce a controlled-number of molecular barcodes onto DNA fragments by reducing redundant molecular barcodes formed in template-dependent primer extension reactions, and to find variant frequencies from both strands of DNA. The methods, compositions, systems and kits described herein may include, or include the use of, one or more single-stranded DNA specific nucleases that cleave the single-stranded regions containing unmatched base pairs in amplification products.

Abstract: Methods, compositions, systems and kits to introduce a controlled-number of molecular barcodes onto DNA fragments by reducing redundant molecular barcodes formed in template-dependent primer extension reactions, and to find variant frequencies from both strands of DNA. The methods, compositions, systems and kits described herein may include, or include the use of, one or more single-stranded DNA specific nucleases that cleave the single-stranded regions containing unmatched base pairs in amplification products.

Abstract: Methods, compositions, systems and kits to amplify or improve amplification of target-specific amplification products by reducing non-specific amplification products (e.g., primer-dimers) when amplifying multiple different nucleotide regions. The methods, compositions, systems and kits described herein may include, or include the use of, one or more resolvases that recognize and bind to and/or cut an aberrant DNA structure.

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: 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 for novel methods and kits for determining the methylation status of a cytosine in a nucleic acid sample. The methylation status of a plurality of cytosines may be determined simultaneously. In one embodiment methylation status is determined using methylation specific modification of cytosines followed by locus specific amplification, single base extension at the interrogation position and identification of the extended base by array hybridization. In another embodiment methylation specific modification of a cytosine is detected by hybridization to an array of probes that are perfectly complementary to either the methylated product of modification or the unmethylated product of modification. In another embodiment methylation status is determined using methylation specific restriction enzymes coupled with hybridization to an array.

Abstract: Methods of identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.

Abstract: Methods of identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.

Abstract: The present invention provides for novel methods and kits for determining the methylation status of a cytosine in a nucleic acid sample. The methylation status of a plurality of cytosines may be determined simultaneously. In one embodiment methylation status is determined using methylation specific modification of cytosines followed by locus specific amplification, single base extension at the interrogation position and identification of the extended base by array hybridization. In another embodiment methylation specific modification of a cytosine is detected by hybridization to an array of probes that are perfectly complementary to either the methylated product of modification or the unmethylated product of modification. In another embodiment methylation status is determined using methylation specific restriction enzymes coupled with hybridization to an array.

Abstract: A genomic portal system receives from a user a selection of one or more probe-set identifiers associated with one or more probe sets. The probe-set identifiers may be submitted in a batch file and may include one or more annotation terms. The system also correlates the user-selected probe-set identifiers with one or more biological sequences, and correlates the one or more biological sequences with a first set of probe sets. A network server identifies the first set of probe sets to the user. The genomic portal system may also receive from a user a selection of one or more probe-set identifiers associated with one or more probe sets, wherein the probe-set identifiers include one or more biological sequences. The system periodically update one or more local genomic databases, clusters the one or more biological sequences based on the local genomic databases, and provide the clustered data to a user.