Abstract: The present disclosure provides methods of assessing tumor progression in a subject. In an aspect, a method for assessing tumor progression of a subject can comprise: measuring a count of a plurality of cell-free DNA (cfDNA) molecules at each of a plurality of genomic regions, wherein the plurality of cfDNA molecules is obtained or derived from a bodily fluid sample of the subject; processing the counts measured at each of the genomic regions to obtain quantitative measures of deviation of the counts relative to a plurality of reference values, to produce deviation scores; determining a difference between the deviation scores and a plurality of reference deviation scores to produce changes in deviation (CID) values, and calculating a CID score based on the CID values; and detecting a tumor progression of the subject when the CID score satisfies a pre-determined criterion.

Abstract: The present disclosure provides methods of assessing tumor progression in a subject. In an aspect, a method for assessing tumor progression of a subject can comprise: measuring a count of a plurality of cell-free DNA (cfDNA) molecules at each of a plurality of genomic regions, wherein the plurality of cfDNA molecules is obtained or derived from a bodily fluid sample of the subject; processing the counts measured at each of the genomic regions to obtain quantitative measures of deviation of the counts relative to a plurality of reference values, to produce deviation scores; determining a difference between the deviation scores and a plurality of reference deviation scores to produce changes in deviation (CID) values, and calculating a CID score based on the CID values; and detecting a tumor progression of the subject when the CID score satisfies a pre-determined criterion.

Abstract: The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided.

Abstract: The present disclosure provides methods of assessing tumor progression in a subject. In an aspect, a method for assessing tumor progression of a subject can comprise: measuring a count of a plurality of cell-free DNA (cfDNA) molecules at each of a plurality of genomic regions, wherein the plurality of cfDNA molecules is obtained or derived from a bodily fluid sample of the subject; processing the counts measured at each of the genomic regions to obtain quantitative measures of deviation of the counts relative to a plurality of reference values, to produce deviation scores; determining a difference between the deviation scores and a plurality of reference deviation scores to produce changes in deviation (CID) values, and calculating a CID score based on the CID values; and detecting a tumor progression of the subject when the CID score satisfies a pre-determined criterion.

Abstract: The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided.

Abstract: The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided.

Abstract: The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided.