The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Methods for designing and producing a fluorescent-labeled detection probe and a competitive probe combination are provided to improve detection by reducing noise. A method for designing the fluorescent-labeled detection probe and a competitive probe combination includes, for example, determining the base length and the base sequence of each of the fluorescent-labeled detection probe and the competitive probe. The determining can include experimentally determining the amount to be added to the nucleic acid sample of each of the fluorescent-labeled detection probe and the competitive probe. The methods provide a functional result of a first order derivative curve for the control target reaction sample having a substantial peak (maximum value), but a first order derivative curve for the control non-target reaction sample not having a substantial peak, the functional result improving detection by reducing noise.

Methods for designing and producing a fluorescent-labeled detection probe and a competitive probe combination are provided to improve detection by reducing noise. A method for designing the fluorescent-labeled detection probe and a competitive probe combination includes, for example, determining the base length and the base sequence of each of the fluorescent-labeled detection probe and the competitive probe. The determining can include experimentally determining the amount to be added to the nucleic acid sample of each of the fluorescent-labeled detection probe and the competitive probe. The methods provide a functional result of a first order derivative curve for the control target reaction sample having a substantial peak (maximum value), but a first order derivative curve for the control non-target reaction sample not having a substantial peak, the functional result improving detection by reducing noise.

Kits for detecting a mutated target base sequence are provided. For example, the kits can be for detecting a target base sequence (A) containing a nucleotide with a mutated base from a nucleic acid sample. The kits contain a fluorescent-labeled detection probe and a competitive probe combination that is to improve detection by reducing noise. The probe combination is produced using a process that includes, for example, determining the base length and the base sequence of each of the fluorescent-labeled detection probe and the competitive probe. The determining can include experimentally determining the amount to be added to the nucleic acid sample of each of the fluorescent-labeled detection probe and the competitive probe. The kits provide a functional result of a first order derivative curve for the control target reaction sample having a substantial peak (maximum value), but a first order derivative curve for the control non-target reaction sample not having a substantial peak, the functional result improving detection by reducing noise.

Kits for detecting a mutated target base sequence are provided. For example, the kits can be for detecting a target base sequence (A) containing a nucleotide with a mutated base from a nucleic acid sample. The kits contain a fluorescent-labeled detection probe and a competitive probe combination that is to improve detection by reducing noise. The probe combination is produced using a process that includes, for example, determining the base length and the base sequence of each of the fluorescent-labeled detection probe and the competitive probe. The determining can include experimentally determining the amount to be added to the nucleic acid sample of each of the fluorescent-labeled detection probe and the competitive probe. The kits provide a functional result of a first order derivative curve for the control target reaction sample having a substantial peak (maximum value), but a first order derivative curve for the control non-target reaction sample not having a substantial peak, the functional result improving detection by reducing noise.

This disclosure provides oligomers, compositions, and kits for detecting and quantifying Hepatitis C virus (HCV), including different genotypes and variants thereof, and related methods and uses. In some embodiments, oligomers target the 5′ untranslated region of HCV and are configured to provide substantially equivalent quantification of different genotypes and variants of HCV.

The present disclosure provides, among other things, systems, methods, and kits include internal amplification controls. Provided internal amplification controls are or include non-target sequences that are amplified during nucleic acid amplification. Provided internal amplification controls are linearly amplified. Provided internal amplification controls are useful for systems, methods and kits for nucleic acid amplification.

The present disclosure provides, among other things, systems, methods, and kits include internal amplification controls. Provided internal amplification controls are or include non-target sequences that are amplified during nucleic acid amplification. Provided internal amplification controls are linearly amplified. Provided internal amplification controls are useful for systems, methods and kits for nucleic acid amplification.

Methods and compositions for the detection and quantification of nucleic acids are provided. In certain embodiments, methods involve the use of cleavable probes capable of forming double-stranded structures, such as hairpin structures, which probes can be distinguished from one another on the basis of reporter signal, melt properties, or both.

Disclosed is a method for amplifying and detecting polynucleotides which can provide sensitive, specific detection of multiple targets from a clinical specimen within a relatively short time.