Abstract: Provided herein are systems, software media, networks, kits, and methods for performing computational analyses on sequencing data of samples from an individual. An analysis can extract germline and somatic information and compare both types of information to identify sequence variants based on probabilistic modeling and statistical inferences. The analysis can comprise distinguishing between germline variants, e.g., private variants, and somatic mutations. The identified variants can be used by clinics to provide better health care.

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: The present teachings describe methods for selecting informative genetic markers including single nucleotide polymorphisms (SNPs) that may be used in the design and execution of genome wide association studies. These methods are distinguished from other methods relying on a predefined haplotype block structure and may be configured to make use of correlations that occur across neighboring haplotype blocks. The disclosed methods may further be implemented across chromosomal regions having both high and low local linkage disequilibrium. Informative genetic marker selection, as described, provides an alternative and potentially more efficient mechanism to select genetic markers such as SNPs using block-based and random approaches.

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: 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.

Abstract: A method for displaying genomic information includes displaying a first axis representing a chromosome with units of basepairs. It also includes displaying on the first axis first and second sets of gene reference marks identifying genes located on forward and reverse strands of the chromosome. One or more sets of additional reference marks are further displayed, including genetic marker reference marks and haplotype reference marks. Each set of haplotype reference marks identifies one or more haplotype blocks for a population.

Abstract: A numerical approach used to select a reduced subset of single nucleotide polymorphisms (SNPs) from a larger superset and useful for efficiently identifying haplotype blocks or other genetic loci. In general, the methods may be configured to select for the reduced SNP subset with little or no loss of haplotype diversity information. The methods may also be adapted to operate in a more aggressive mode to further reduce the SNP set while maintaining diversity of haplotype blocks with minimal loss of information. Computation of the reduced SNP subset is generally rapid and the methods perform well even when applied to large data sets spanning significant genomic distances.