According to one embodiment, a detection method is a method for detecting a plurality of target nucleic acids in a sample. The method includes (a) preparing a chain-elongation nucleic acid set group, a primer set, and a probe immobilized substrate, (b) obtaining the target nucleic acid and a long-chain nucleic acid group containing a first sub-chain-elongation nucleic acid and a second sub-chain-elongation nucleic acid, (c) obtaining an amplification product group by maintaining the long-chain nucleic acid group and the primer set under amplification conditions, (d) detecting presence/absence and/or an amount of hybridization, and (e) detecting the plurality of target nucleic acids.

The subject invention pertains to the rapid amplification and real-time monitoring of nucleic acid sequences at a constant temperature. Specifically, fluorescent or electroactive-labeled loop probes and primers are designed to be specific to identified regions of a target nucleic acid sequences and subsequently amplify and permit the identification of the presence of the target sequence. In this method, a DNA polymerase with no 5′ to 3′ exonuclease activity is added to extend the primers and probes, while a nicking endonuclease is added to specifically identify the amplified nucleic acid product and cleave the label from the loop probe-extended DNA duplex.

The subject invention pertains to the rapid amplification and real-time monitoring of nucleic acid sequences at a constant temperature. Specifically, fluorescent or electroactive-labeled loop probes and primers are designed to be specific to identified regions of a target nucleic acid sequences and subsequently amplify and permit the identification of the presence of the target sequence. In this method, a DNA polymerase with no 5′ to 3′ exonuclease activity is added to extend the primers and probes, while a nicking endonuclease is added to specifically identify the amplified nucleic acid product and cleave the label from the loop probe-extended DNA duplex.

The present disclosure provides methods and systems for processing nucleic acid molecules. The methods may comprise performing one or more extension or amplification processes to provide libraries for subsequent analysis using nucleic acid sequencing. Logical partitioning and directionality considerations may facilitate efficient and cost-effective amplification of target nucleic acid sequences.

The present disclosure provides methods and systems for processing nucleic acid molecules. The methods may comprise performing one or more extension or amplification processes to provide libraries for subsequent analysis using nucleic acid sequencing. Logical partitioning and directionality considerations may facilitate efficient and cost-effective amplification of target nucleic acid sequences.

Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a 3-fold or greater increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Modified bases can be employed in primers to provide this base-3 or greater amplification with satisfactory PCR cycle times, which are improved, as compared to those observed in the absence of modified bases.

Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a 3-fold or greater increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Modified bases can be employed in primers to provide this base-3 or greater amplification with satisfactory PCR cycle times, which are improved, as compared to those observed in the absence of modified bases.

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.

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.

The present invention provides methods, compositions and kits for enriching and determining nucleotide sequences of a plurality of target loci from a sample comprising nucleic acids. The methods comprise one or more cycles of primer extension followed by PCR amplification of target sequences using nested target-specific primers.