The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

The present invention includes compositions and methods useful for the detection of a mutational change, SNP, translocation, inversion, deletion, change in copy number, or other genetic variation within a sample of cellular genomic DNA or cell-free DNA (cfDNA). In some embodiments, the compositions and methods of the present invention provide an extremely high level of resolution that is particularly useful in detecting copy number variations in a small fraction of the total cfDNA from a biological sample (e.g., blood).

The present invention relates to the field of allergies. More specifically, the present invention provides compositions and methods useful for identifying anti-allergen antibodies in a patient sample using phage display. In one embodiment, a method for detecting the presence of an antibody against an allergen in subject includes the steps of (a) contacting a reaction sample comprising a display library with a biological sample comprising antibodies, wherein the display library includes a plurality of peptides derived from a plurality of allergens; and (b) detecting at least one antibody bound to at least one peptide expressed by the display library, thereby detecting an antibody against the at least one peptide in the biological sample.

The present invention relates to the field of allergies. More specifically, the present invention provides compositions and methods useful for identifying anti-allergen antibodies in a patient sample using phage display. In one embodiment, a method for detecting the presence of an antibody against an allergen in subject includes the steps of (a) contacting a reaction sample comprising a display library with a biological sample comprising antibodies, wherein the display library includes a plurality of peptides derived from a plurality of allergens; and (b) detecting at least one antibody bound to at least one peptide expressed by the display library, thereby detecting an antibody against the at least one peptide in the biological sample.

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 is a method of detecting and quantifying genomic and gene expression alterations using RNA in a biological sample. The disclosed method may include determining presence or absence of the genomic alteration and/or determining presence or absence of the gene expression and/or quantifying the level of the gene expression, by performing variant calling of the sequence alignment obtained from the disclosed method. Variant calling may comprise the steps of identifying differences between a consensus read and a reference genome based on the sequence alignment from the disclosed method; and determining the read count of sequence alignments comprising genomic alteration. The genomic alteration may be an insertion (such as a duplication), a deletion, a single nucleotide variant, or combinations thereof. Also disclosed is a kit for detecting and quantifying genomic and gene expression alterations using RNA in a biological sample.

Disclosed is a method of detecting and quantifying genomic and gene expression alterations using RNA in a biological sample. The disclosed method may include determining presence or absence of the genomic alteration and/or determining presence or absence of the gene expression and/or quantifying the level of the gene expression, by performing variant calling of the sequence alignment obtained from the disclosed method. Variant calling may comprise the steps of identifying differences between a consensus read and a reference genome based on the sequence alignment from the disclosed method; and determining the read count of sequence alignments comprising genomic alteration. The genomic alteration may be an insertion (such as a duplication), a deletion, a single nucleotide variant, or combinations thereof. Also disclosed is a kit for detecting and quantifying genomic and gene expression alterations using RNA in a biological sample.

A method for obtaining a single-cell mRNA sequence, including: (1) capturing mRNA of a cell by using a cell tag carrier, and performing reverse transcription to obtain cDNA having a cell tag; (2) obtaining multiple cDNA fragments having molecular tags by using a transposase complex and a molecular tag carrier; (3) performing high-throughput sequencing; (4) performing sequence assembly according to the molecular tags to obtain the sequence of each mRNA; and (5) obtaining the sequence of all mRNAs of each single cell according to the cell tags.

A method for obtaining a single-cell mRNA sequence, including: (1) capturing mRNA of a cell by using a cell tag carrier, and performing reverse transcription to obtain cDNA having a cell tag; (2) obtaining multiple cDNA fragments having molecular tags by using a transposase complex and a molecular tag carrier; (3) performing high-throughput sequencing; (4) performing sequence assembly according to the molecular tags to obtain the sequence of each mRNA; and (5) obtaining the sequence of all mRNAs of each single cell according to the cell tags.