Guardant Health, Inc.

This disclosure provides, among other things, methods for compiling and using a database for identifying one or more therapeutic interventions for a cancer and/or the efficacy of a therapeutic intervention for subjects with a tumor genomic profile. The database may include, for each of a plurality of subjects having cancer: (i) tumor genomic testing data, including somatic alterations, collected at two or more time intervals per subject via serial biopsy of cell-free DNA, (ii) one or more therapeutic interventions administered to each of the subjects at one or more times; and (iii) efficacy of the therapeutic interventions.

The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample. The state may include a somatic homozygous deletion, a somatic heterozygous deletion, a copy number variation, or other states. A computer system may generate competing probabilistic models that each output a probability that the genetic material is in a certain state. Each model may be trained on a training sample set to output a probability that the genetic material is in a respective state. In some embodiments, the computer system may use various probabilistic distributions to generate the models. For example, the computer system may use a beta-binomial distribution, a binomial distribution, a normal (also referred to as “Gaussian”) distribution, or other type of probabilistic modeling techniques.

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.

Provided herein is a DNA analysis method comprising partitioning a sample into at least a first subsample and a second subsample, wherein the first subsample comprises DNA (e.g., cell-free DNA) with a cytosine modification in a greater proportion; the first subsample undergoes a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the first subsample; and DNA is sequenced to distinguish the first nucleobase from the second nucleobase. Also provided is a combination comprising first and second populations of captured DNA, wherein the first population comprises or was derived from DNA with a cytosine modification in a greater proportion than the second population, and wherein the first population comprises a form of a first nucleobase originally present in the DNA with altered base pairing specificity and a second nucleobase without altered base pairing specificity.

Provided herein are methods of analyzing DNA comprising partitioning the DNA into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified cytosine in the DNA, and sequencing the DNA of at least one of the plurality of subsamples in a modification-sensitive manner. Such methods facilitate detection of an epigenetic modification status of at least a portion of the nucleobases of the DNA.

Described herein are methods and composition related to detection of unmethylated DNA regions with high sensitivity and low costs compared to current methods. This approach involves tagging CpG in unmethylated DNA with reagents that provides both handle for immobilization/enrichments, and blocking of CpG deamination by deaminases (e.g. APOBEC3A). By leveraging methods involving methyltransferase-based transfer of unnatural substrates to unmodified cytosines (in CpGs only), one can adapt such steps into various workflow sequences involving hyper-and hypo-methylated DNA with flexible deployment of tagging steps as suited for the analyte of interest.

Provided herein are methods for selectively depleting a target nucleic acid comprising a sequence that does not comprise a nucleotide variant of interest. In some embodiments, a concentration of the target nucleic acid comprising the variant sequence is increased relative to a concentration of the target nucleic acid comprising the wild-type sequence, a concentration of the target nucleic acid comprising a converted nucleotide is increased relative to a concentration of the target nucleic acid that does not comprise the converted nucleotide, or a concentration of the target nucleic acid that does not comprise the converted nucleotide is increased relative to a concentration of the target nucleic acid comprising the converted nucleotide. In some embodiments, the target nucleic acids are sequenced.

Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, Methods and compositions for determining cancer and subtypes, including breast cancer are described and specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at identifying candidates for responsiveness and overcoming resistance mechanisms.

Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, Methods and compositions for determining cancer and subtypes, including breast cancer are described and specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at identifying candidates for responsiveness and overcoming resistance mechanisms.

Disclosed herein are compositions and methods for isolating DNA, such as cell-free DNA (cfDNA). In some embodiments, the cell-free DNA is from a subject having or suspected of having cancer and/or the cell-free DNA comprises DNA produced by a tumor. In some embodiments, the DNA isolated by the method is captured using a sequence-variable target region set and an epigenetic target region set, wherein the sequence-variable target region set is captured with a greater capture yield than the epigenetic target region set. In some embodiments, captured cfDNA of the sequence-variable target region set is sequenced to a greater depth of sequencing than captured cfDNA of the epigenetic target region set.