Abstract: Disclosed herein are methods of reducing and/or preventing “greening” in sunflower-containing food products.

Abstract: Methods, systems, and software are provided for validating a somatic sequence variant in a subject having a cancer condition. Sequence reads are obtained from sequencing cell-free DNA fragments in a liquid biopsy sample of the subject. Sequence reads are aligned to a reference sequence. A variant allele fragment count and locus fragment count are identified for a candidate variant that maps to a locus in the reference sequence. The variant allele fragment count is compared against a dynamic variant count threshold for the locus. The threshold is based on a pre-test odds of a positive variant call for the locus, based on the prevalence of variants in a genomic region including the locus in a cohort of subjects having the cancer condition. The somatic sequence variant in the subject is validated, or rejected, when the variant allele fragment count for the candidate variant satisfies, or does not satisfy, the threshold.

Abstract: Methods, systems, and software are provided for monitoring a cancer condition of a test subject. The method includes obtaining a liquid biopsy sample from the subject at a second time point, occurring after a first time point, containing cell-free DNA fragments. Low-pass whole genome methylation sequencing of the cell-free DNA fragments is performed to obtain nucleic acid sequences having a methylation pattern for a corresponding cell-free DNA fragment. The nucleic acid sequences are mapped to a location on a reference genome. Methylation metrics are determined based on the methylation patterns and mapped locations of the nucleic acid sequences. A circulating tumor fraction is estimated from the methylation metrics, and the estimate is compared to an estimate of the circulating tumor fraction for the test subject at the first time point.

Abstract: Methods, systems, and software are provided for validating a somatic sequence variant in a subject having a cancer condition. Sequence reads are obtained from sequencing cell-free DNA fragments in a liquid biopsy sample of the subject. Sequence reads are aligned to a reference sequence. A variant allele fragment count and locus fragment count are identified for a candidate variant that maps to a locus in the reference sequence. The variant allele fragment count is compared against a dynamic variant count threshold for the locus. The threshold is based on a pre-test odds of a positive variant call for the locus, based on the prevalence of variants in a genomic region including the locus in a cohort of subjects having the cancer condition. The somatic sequence variant in the subject is validated, or rejected, when the variant allele fragment count for the candidate variant satisfies, or does not satisfy, the threshold.

Abstract: Methods, systems, and software are provided for estimating a circulating tumor fraction for a test subject. Sequence reads are obtained from a panel-enriched sequencing reaction, including sequences for a first plurality of cfDNA fragments corresponding to probe sequences and a second plurality of cfDNA fragments not corresponding to probe sequences. Bin-level coverage ratios are determined from the sequences. Segments are formed by grouping adjacent bins based on similar coverage ratios and segment-level coverage ratios are determined based on bin-level coverage ratios for bins in the segment. For each simulated circulating tumor fraction in a plurality of circulating tumor fractions, segments are fitted to an integer copy state by identifying the integer copy state that best matches the segment-level coverage ratio.

Abstract: Methods, systems, and software are provided for estimating a circulating tumor fraction for a test subject. Sequence reads are obtained from a panel-enriched sequencing reaction, including sequences for a first plurality of cfDNA fragments corresponding to probe sequences and a second plurality of cfDNA fragments not corresponding to probe sequences. Bin-level coverage ratios are determined from the sequences. Segments are formed by grouping adjacent bins based on similar coverage ratios and segment-level coverage ratios are determined based on bin-level coverage ratios for bins in the segment. For each simulated circulating tumor fraction in a plurality of circulating tumor fractions, segments are fitted to an integer copy state by identifying the integer copy state that best matches the segment-level coverage ratio.

Abstract: Methods, systems, and software are provided for monitoring a cancer condition of a test subject. The method includes obtaining a liquid biopsy sample from the subject at a second time point, occurring after a first time point, containing cell-free DNA fragments. Low-pass whole genome methylation sequencing of the cell-free DNA fragments is performed to obtain nucleic acid sequences having a methylation pattern for a corresponding cell-free DNA fragment. The nucleic acid sequences are mapped to a location on a reference genome. Methylation metrics are determined based on the methylation patterns and mapped locations of the nucleic acid sequences. A circulating tumor fraction is estimated from the methylation metrics, and the estimate is compared to an estimate of the circulating tumor fraction for the test subject at the first time point.

Abstract: Methods, systems, and software are provided for validating a somatic sequence variant in a subject having a cancer condition. Sequence reads are obtained from sequencing cell-free DNA fragments in a liquid biopsy sample of the subject. Sequence reads are aligned to a reference sequence. A variant allele fragment count and locus fragment count are identified for a candidate variant that maps to a locus in the reference sequence. The variant allele fragment count is compared against a dynamic variant count threshold for the locus. The threshold is based on a pre-test odds of a positive variant call for the locus, based on the prevalence of variants in a genomic region including the locus in a cohort of subjects having the cancer condition. The somatic sequence variant in the subject is validated, or rejected, when the variant allele fragment count for the candidate variant satisfies, or does not satisfy, the threshold.

Abstract: Methods, systems, and software are provided for estimating a circulating tumor fraction for a test subject. Sequence reads are obtained from a panel-enriched sequencing reaction, including sequences for a first plurality of cfDNA fragments corresponding to probe sequences and a second plurality of cfDNA fragments not corresponding to probe sequences. Bin-level coverage ratios are determined from the sequences. Segments are formed by grouping adjacent bins based on similar coverage ratios and segment-level coverage ratios are determined based on bin-level coverage ratios for bins in the segment. For each simulated circulating tumor fraction in a plurality of circulating tumor fractions, segments are fitted to an integer copy state by identifying the integer copy state that best matches the segment-level coverage ratio.

Abstract: Novel agents acting as co-factors for replacement of NAD(P)+/NAD(P)H co-enzyme systems in enzymatic oxido-reductive reactions. Agents mimicking the action of NAD(P)+/NAD(P)H system in enzymatic oxidation/reduction of substrates into reduced or oxidized products. A method for selection and preparation of the mimicking agents for replacement of NAD(P)+/NAD(P)H system and a device comprising co-factors for replacement of NAD(P)+/NAD(P)H system.