Abstract: Methods for interpreting absolute copy number of complex tumors and for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. In certain aspects, genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

Abstract: Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.

Abstract: Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

Abstract: Methods for interpreting absolute copy number of complex tumors and for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. In certain aspects, genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

Abstract: After DNA fragments are sequenced and mapped to a reference, various hypotheses for the sequences in a variant region can be scored to find which sequence hypotheses are more likely. A hypothesis can include a specific variable fraction for the plurality of alleles that comprise the sequence hypothesis in the region. A likelihood of each hypothesis can be determined using a probability that accounts for the fraction of the alleles specified in the respective sequence hypothesis. Thus, other hypotheses besides standard homozygous and equal heterozygous (i.e., one chromosome with A and one with B in a cell) can be explored by explicitly including the variable fractions of the alleles as a parameter in the optimization. Also, a variant score can be determined for a variant relative to a reference. The variant score can be used to determine a variant calibrated score indicating a likelihood that the variant call is correct.

Abstract: Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.