Abstract: Systems, methods, and devices for generating synthetic genomic datasets and validating bioinformatic pipelines for genomic analysis are disclosed. In preferred embodiments, synthetic maternal and paternal datasets with known variants are used with matched normal synthetic datasets to validate various bioinformatic pipelines. Bioinformatic pipelines are evaluated using the synthetic datasets to assess design changes and improvements. Accuracy, PPV, specificity, sensitivity, reproducibility, and limit of detection of the pipelines in calling variants in synthetic datasets is reported.

Abstract: Improved accuracy of SNV-based genetic tests is performed using DNA sequencing data from a tumor sample and a matched normal sample to determine SNVs, and RNA sequencing data from the tumor sample are used to ascertain expression of so identified SNVs.

Abstract: Molecular profiles of metastatic tumors can be more accurately determined using combination of DNA mutational profiles and RNA expression profiles of selected genes that show substantial changes upon anti-tumor treatment. Such combinatorial information can be used to determine differential pathway activity that may be related to the sensitivity or resistance to the anti-tumor treatment.

Abstract: A unique hash representing patient omics data is constructed using results for known SNP positions and their respective allele frequencies in the patient's omics data. In most preferred aspects, the known SNP positions are selected for specific factors (e.g., ethnicity, sex, etc.) and the allele fraction is represented in values of a non-linear scale. Typically, the hash comprises a header/metadata relating to the known SNP positions and non-linear scale and further includes the actual hash string.

Abstract: A unique hash representing patient omics data is constructed using results for known SNP positions and their respective allele frequencies in the patient's omics data. In most preferred aspects, the known SNP positions are selected for specific factors (e.g., ethnicity, sex, etc.) and the allele fraction is represented in values of a non-linear scale. Typically, the hash comprises a header/metadata relating to the known SNP positions and non-linear scale and further includes the actual hash string.

Abstract: Systems, methods, and devices for generating synthetic genomic datasets and validating bioinformatic pipelines for genomic analysis are disclosed. In preferred embodiments, synthetic maternal and paternal datasets with known variants are used with matched normal synthetic datasets to validate various bioinformatic pipelines. Bioinformatic pipelines are evaluated using the synthetic datasets to assess design changes and improvements. Accuracy, PPV, specificity, sensitivity, reproducibility, and limit of detection of the pipelines in calling variants in synthetic datasets is reported.