The present invention relates to a primer for PCR obtained by, directly or through inosine as a linker, linking a complementary nucleotide sequence or a complementary nucleotide sequence including a mis-matched nucleotide sequence to the 5′-terminal of a forward or reverse primer; and to a PCR method including a step of mixing a nucleic acid template in a PCR composition including the primer and then performing PCR on the mixture. The primer for PCR of the present invention includes a complementary nucleotide sequence or a mis-matched nucleotide sequence in a complementary nucleotide sequence, which is linked to the 5′-terminal thereof directly or via a linker, thereby lowering the sensitivity increase due to the increase in amplification products and reducing non-specifically occurring reactions in PCR.

The present invention relates to a primer for PCR obtained by, directly or through inosine as a linker, linking a complementary nucleotide sequence or a complementary nucleotide sequence including a mis-matched nucleotide sequence to the 5′-terminal of a forward or reverse primer; and to a PCR method including a step of mixing a nucleic acid template in a PCR composition including the primer and then performing PCR on the mixture. The primer for PCR of the present invention includes a complementary nucleotide sequence or a mis-matched nucleotide sequence in a complementary nucleotide sequence, which is linked to the 5′-terminal thereof directly or via a linker, thereby lowering the sensitivity increase due to the increase in amplification products and reducing non-specifically occurring reactions in PCR.

Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).

Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).

Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).

Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).

This invention provides ultra-sensitive methods and compositions for detecting patient-specific mutations from cell free nucleic acids (cfDNA) without sequencing. Methods of the invention make use of fluidic partitions for multiplex amplification of cfDNA and thereby create a library of uniformly amplified amplicons. The uniformly amplified amplicons can be split into any number of different detection reactions (while maintaining detection sensitivity) for single-plex detection of mutations present in cfDNA. These methods provide substantially improved signal to noise ratio and easier discrimination of low-abundance mutations.

This invention provides ultra-sensitive methods and compositions for detecting patient-specific mutations from cell free nucleic acids (cfDNA) without sequencing. Methods of the invention make use of fluidic partitions for multiplex amplification of cfDNA and thereby create a library of uniformly amplified amplicons. The uniformly amplified amplicons can be split into any number of different detection reactions (while maintaining detection sensitivity) for single-plex detection of mutations present in cfDNA. These methods provide substantially improved signal to noise ratio and easier discrimination of low-abundance mutations.

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.

Provided herein are methods and composition for processing samples that contain nucleic acids, or cells containing nucleic acids, of a microbiome, using amounts of primers within a range of mole values and rounds of polymerase chain reaction (PCR) within a range of numbers of rounds.