Abstract: Methods, systems, and software are provided for determining copy number variation status of a subject. A first plurality of nucleic acid sequences generated by whole genome sequencing at an average depth of 0.5× to 5× is obtained from a first sample. A second plurality of nucleic acid sequences generated by panel-targeted sequencing is obtained from a second sample. A first mapped dataset is obtained by mapping the first plurality of sequences to positions within a reference genome for the species of the subject. A second mapped dataset is obtained by mapping the second plurality of sequences to positions within a reference construct for genomic regions targeted by the panel-targeted sequencing. A model is applied to all or a portion of the first mapped dataset and all or a portion of the second mapped dataset, or dimensionality reduction components thereof.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Aspects of the disclosure relate to methods and kits for assessing cancer. Some aspects of the disclosure relate to methods and kits for preparing a sample library for sequencing. Some aspects of the disclosure relate to methods and kits for allele detection. Some aspects of the disclosure relate to high efficiency ligation methods and kits. Some aspects of the disclosure relate to sensitive detection of amplicons.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: A visual tool facilitates selecting SNPs for genotyping experiments comprises a first memory containing a datastore of pre-calculated linkage disequilibrium map information; a second memory containing a datastore of haplotype block information; and a third memory containing at least one set of tagging SNPs. A graphical user interface provides visualization of SNPs, integrated with a physical genome map. A stepwise selection tool associated with the graphical user interface facilitates selection of tagging SNPs by selectively using the information in at least one of the first, second and third memories.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Methods for determining the binding affinity of a probe to a target or targets in a polynucleotide composite using an automated system. Such methods determine relative binding sites based on thermodynamic principles, using a thermodynamic alphabet and a thermodynamic scoring matrix, with appropriate computer software, such as BLASTP. The invention also provides methods for designing polynucleotide probes to be used in hybridization assays, and minimizing the occurrence of cross-hybridization.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Methods for determining the binding affinity of a probe to a target or targets in a polynucleotide composite using an automated system. Such methods determine relative binding sites based on thermodynamic principles, using a thermodynamic alphabet and a thermodynamic scoring matrix, with appropriate computer software, such as BLASTP. The invention also provides methods for designing polynucleotide probes to be used in hybridization assays, and minimizing the occurrence of cross-hybridization.

Abstract: Libraries of assays and methods of compiling the libraries are provided. The assays can identify Single Nucleotide Polymorphisms (SNPs). Methods of validating SNPs are provided. Methods of constructing linkage disequilibrium maps using sets or subsets of SNPs are also provided.