Abstract: Compositions, kits, and methods are provided for validating patient-specific oligonuclotide assays using spike-in controls. The compositions comprise multiple sets of spike-in oligos, each set including a unique reference sequence and near-neighbor sequences with at least one substitution, insertion, or deletion. Near-neighbor concentrations are less than the reference and collectively span at least four orders of magnitude (e.g., 1:10 to 1:10,000); all sets have the same number of near-neighbors and concentration ratios. Spike-in sequences are unrelated to human sequences and are complementary to synthesis-control oligos at known concentrations. Kits further include synthesis-control oligos and patient-specific oligos for human DNA or RNA targets. Methods involve spiking a sample, co-synthesizing control and patient-specific oligos, assaying by PCR or sequencing, and validating limit of detection and dynamic range by comparing observed counts to known ratios. Applications include ctDNA and cfRNA testing.

Abstract: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: DNA compositions having nucleotide sequences that do not occur in nature. Also provided are fluorescently labeled DNA molecules and complementary DNA on solid substrates, such as microspheres.

Abstract: The invention provides a method of detecting multiple nucleic acid sequences using multiplex substrate elements, each having predetermined sets of independent probes, and using mistures of distinguishably labeled nucleotides.

Abstract: DNA compositions having nucleotide sequences that do not occur in nature. Also provided are fluorescently labeled DNA molecules and complementary DNA on solid substrates, such as microspheres.

Abstract: Probe selection techniques are based, at least in part, on empirical evidence concerning the hybridization of candidate probes across a panel of diverse biological isolates. Various principles concerning the behavior of the most preferable probes across a panel of diverse biological isolates are applied to select from among a set of candidate probes or to eliminate candidate probes from further consideration.