Abstract: Methods for determining an arm aneuploidy score in a tumor sample genome include selectively amplifying nucleic acid sequences at specific locations in the tumor genome using a targeted panel to generate sequence reads. Next, divide the genome locations into segments with homogeneous copy numbers based on log odds of heterozygous SNPs and CNV log ratios of the sequence reads. Identify gain and loss segments relative to a reference copy number and intersecting respective chromosome arms. Compare the cellularities of these segments to a minimum threshold. Retain the longest segment for the arm that meets the minimum cellularity and sum its total bases. Divide this total by the number of bases in the arm to yield a fraction. If this fraction meets a minimum threshold, filter the segment based on fold changes and determine gains or losses. Count the arms with called gains or losses to generate the arm aneuploidy score.

Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.

Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.

Abstract: The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.

Abstract: The disclosure provides compositions, kits, and methods for detecting a plurality of genes and associated variants in a sample from a subject with cancer (e.g., lung cancer). The compositions, kits, and methods include a set of oligonucleotides, typically primers and/or probes that can hybridize to identify a gene variant. The methods disclosed herein provide for a mutation status of a tumor to be determined and subsequently associated with a report comprising an actionable treatment recommendation (e.g., a report comprising an actionable treatment recommendation).

Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.

Abstract: Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.

Abstract: Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.

Abstract: The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.

Abstract: The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: The disclosure provides compositions, kits, and methods for detecting a plurality of genes and associated variants in a sample from a subject with cancer. The compositions, kits, and methods include a set of oligonucleotides, typically primers and/or probes that can hybridize to identify a gene variant. The methods disclosed herein provide for a mutation status of a tumor to be determined and subsequently associated with a report comprising an actionable treatment recommendation.

Abstract: The disclosure provides gene fusion variants and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: The disclosure provides gene fusion variants and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: The disclosure provides compositions, kits, and methods for detecting a plurality of genes and associated variants in a sample from a subject with lung cancer. The compositions, kits, and methods include a set of oligonucleotides, typically primers and/or probes that can hybridize to identify a gene variant. The methods disclosed herein provide for a mutation status of a tumor to be determined and subsequently associated with an actionable treatment recommendation.

Abstract: The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.

Abstract: The disclosure provides compositions, kits, and methods for detecting a plurality of genes and associated variants in a sample from a subject with cancer. The compositions, kits, and methods include a set of oligonucleotides, typically primers and/or probes that can hybridize to identify a gene variant. The methods disclosed herein provide for a mutation status of a tumor to be determined and subsequently associated with a report comprising an actionable treatment recommendation.

Abstract: Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.