Abstract: The disclosure provides a synthetic standard which includes polynucleotides (e.g., DNA or RNA) containing multiple clinically important germline and somatic variants. These materials are utilized to calibrate, evaluate, and/or validate the performance of polynucleotide-based genetic analysis assays, such as NGS assays. In one aspect the disclosure provides a method for validating assay performance including generating synthetic variant DNA fragments comprising variants with known allele frequencies, wherein the fragments comprise a molecular tag; combining the synthetic variant DNA with wild-type DNA to create test samples; preparing one or more dilutions of the test samples; performing an assay of interest on the one or more dilutions of test samples; and comparing the outcome of the assay with the test samples with known allele frequencies of interest, thereby validating the performance of the assay.

Abstract: The present disclosure provides methods and systems that utilize analysis of cell-free DNA (cfDNA) fragmentation profiles in a sample obtained from a patient, determining a ratio of short to long fragments and a fragment size distribution from the fragmentation profile and determining a divergence score based on the ratio of short to long fragments in the sample as correlated to a ratio from a sample from a healthy patient, and determining, by the machine learning model, a monitoring score for the sample based on the fragmentation score, the divergence score, and the model weights, the monitoring score being indicative of a level of a tumor-derived nucleic acid in the cfDNA of the sample to detect, monitor, diagnose, predict cancer status, determine the likelihood of the presence of cancer and administer treatment to the patient.

Abstract: The disclosure provides a synthetic standard which includes polynucleotides (e.g., DNA or RNA) containing multiple clinically important germline and somatic variants. These materials are utilized to calibrate, evaluate, and/or validate the performance of polynucleotide-based genetic analysis assays, such as NGS assays. In one aspect the disclosure provides a method for validating assay performance including generating synthetic variant DNA fragments comprising variants with known allele frequencies, wherein the fragments comprise a molecular tag; combining the synthetic variant DNA with wild-type DNA to create test samples; preparing one or more dilutions of the test samples; performing an assay of interest on the one or more dilutions of test samples; and comparing the outcome of the assay with the test samples with known allele frequencies of interest, thereby validating the performance of the assay.