Methods for capturing and characterizing low frequency nucleic acid molecules indicative of diseases such as cancer (e.g. adenomas or early stage cancers) are provided. In some aspects, a low complexity capture technique is combined with a high complexity analytical technique. In some aspects, samples may be analyzed using a digital analysis and/or a single molecule sequencing technique.

Methods for capturing and characterizing low frequency nucleic acid molecules indicative of diseases such as cancer (e.g. adenomas or early stage cancers) are provided. In some aspects, a low complexity capture technique is combined with a high complexity analytical technique. In some aspects, samples may be analyzed using a digital analysis and/or a single molecule sequencing technique.

Methods, compositions and kits are described for resequencing, confirming or verifying Next Generation Sequencing (NGS) results with Sanger Sequencing. These methods are particularly useful for samples having very limited quantities such as formalin-fixed, paraffin-embedded (FFPE), Laser Capture Microdissection (LCM), fine needle biopsies or aspirates.

Methods, compositions and kits are described for resequencing, confirming or verifying Next Generation Sequencing (NGS) results with Sanger Sequencing. These methods are particularly useful for samples having very limited quantities such as formalin-fixed, paraffin-embedded (FFPE), Laser Capture Microdissection (LCM), fine needle biopsies or aspirates.

A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.

Methods, compositions, and kits are provided for quantifying RNA molecules in a partitioned sample via multiple reverse transcription reactions.

Methods, compositions, and kits are provided for quantifying RNA molecules in a partitioned sample via multiple reverse transcription reactions.

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.

Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.