Abstract: Present disclosure provides a method including isolating DNA from a source, thereby providing a composition including the isolated DNA. The isolated DNA has at least first and second target regions, where the length of the second target region is greater than the length of the first target region. The method further includes quantifying a total mass of the isolated DNA, quantifying a first quantification cycle (Cq) of the first target region and a second Cq of the second target region, and calculating a Q-ratio for the isolated DNA by dividing the second Cq by the first Cq. The method further includes determining a value for a quality-mass constant (kQm), estimating a required input mass by dividing kQm by the Q-ratio, and preparing the isolated DNA for sequencing if the total mass of the isolated DNA in the composition is equal or greater than the required input mass.

Abstract: The present disclosure provides a method for enrichment of at least one target nucleic acid in a library of nucleic acids. A first oligonucleotide is hybridized to a target nucleic acid in library of nucleic acids having first and second adapters. The hybridized first oligonucleotide is extended with a first polymerase, thereby producing a first primer extension complex including the target nucleic acid and the extended first oligonucleotide. The first primer extension complex is captured, enriched relative to the library of nucleic acids, and a second oligonucleotide is hybridized to the target nucleic acid. The hybridized second oligonucleotide is extended with a second polymerase, thereby producing a second primer extension complex including the target nucleic acid and the extended second oligonucleotide, and further liberating the extended first oligonucleotide from the first primer extension complex.

Abstract: Disclosed are compositions, kits, and methods for detecting gene fusions involving an unknown fusion partner using locked nucleic acid primers. In some embodiments, the compositions include a compound including at least two nucleotide sequences which are joined, directly or indirectly, through a 5? to 5? linkage. In some embodiments, the compound further includes a spacer moiety and/or a cleavage moiety.

Abstract: Disclosed are methods and compositions for detecting structural rearrangements in a genome using rearrangement-specific enrichment probes or rearrangement- specific amplification primers.

Abstract: The present disclosure provides a kit for preparing a library of nucleic acids. The kit includes first and second oligonucleotide, each having a tail sequence, a common sequence, and at least one of a unique identifier sequence, and a variable length punctuation mark. The kit further includes a first primer having a first sample identifier sequence and a first priming sequence at a 3? end of the first primer. The first priming sequence includes the tail sequence of the first oligonucleotide. The kit further includes a second primer having a second sample identifier sequence and a second priming sequence at a 3? end of the second primer. The second priming sequence is complimentary to the second tail sequence of the second oligonucleotide.

Abstract: The invention is a method of predicting response to therapy in a colorectal cancer patient, the method comprising analysis of circulating tumor DNA from a patient's sample.

Abstract: The invention is a method of predicting response to therapy in a colorectal cancer patient, the method comprising analysis of circulating tumor DNA from a patient's sample.

Abstract: The present invention relates generally to classification of biological samples, and more specifically to cell of original classification. In particular, some embodiments of the invention relate to diffuse large B cell lymphoma cell of origin classification using machine learning models. The machine learning models can be based on decision trees such as a random forest algorithm or a gradient boosted decision tree. Features for the models can be determined through analysis of variant data from plasma or blood samples from a plurality of subjects with the disease.

Abstract: The present invention is a method and compositions for forming a library for nucleic acids sequencing simultaneously from DNA and RNA present in a sample.

Abstract: Techniques for cancer patient management, and more particularly, to techniques for ultrasensitive detection of circulating nucleic acid with prior knowledge of variants to be monitored in the blood. An exemplary technique includes detecting one or more variants in a sample of cell free DNA from a subject. The one or more variants are selected from a plurality of variants known to be specific to a tumor or disease area of the subject. The technique further includes counting the detected one or more variants, determining a tumor burden based on the count of the one or more variants, and determining a statistical significance of the tumor burden based on whether the detection of the one or more variants is associate with true signals or background noise.

Abstract: Methods and systems for detecting MSI are provided. Also provided are methods for enriching human genomic DNA for microsatellite loci. Additional, an oligonucleotide array for detecting MSI is provided.

Abstract: Techniques for identification of global cancer-specific sequence features in whole genome sequence data obtained from cell-free DNA (cfDNA) samples. An exemplary technique includes obtaining a plurality of whole genome sequencing reads from a cfDNA sample and determining two or more metrics from at least a majority of the plurality of genome sequencing reads, where a first metric of the two or more metrics is: (i) a fragment size of the cell free DNA, (ii) relative read depth of the plurality of whole genome sequencing reads, or (iii) germline allelic imbalance. The technique further includes inputting the two or more metrics into a classifier to obtain a first prediction for a first class and a second prediction for a second class, and classifying the sample of cell free DNA as the first class or the second class based on the first prediction and the second prediction.

Abstract: The present disclosure provides a method for enrichment of at least one target nucleic acid in a library of nucleic acids. A first oligonucleotide is hybridized to a target nucleic acid in library of nucleic acids having first and second adapters. The hybridized first oligonucleotide is extended with a first polymerase, thereby producing a first primer extension complex including the target nucleic acid and the extended first oligonucleotide. The first primer extension complex is captured, enriched relative to the library of nucleic acids, and a second oligonucleotide is hybridized to the target nucleic acid. The hybridized second oligonucleotide is extended with a second polymerase, thereby producing a second primer extension complex including the target nucleic acid and the extended second oligonucleotide, and further liberating the extended first oligonucleotide from the first primer extension complex.

Abstract: The present disclosure provides a kit for preparing a library of nucleic acids. The kit includes first and second oligonucleotide, each having a tail sequence, a common sequence, and at least one of a unique identifier sequence, and a variable length punctuation mark. The kit further includes a first primer having a first sample identifier sequence and a first priming sequence at a 3? end of the first primer. The first priming sequence includes the tail sequence of the first oligonucleotide. The kit further includes a second primer having a second sample identifier sequence and a second priming sequence at a 3? end of the second primer. The second priming sequence is complimentary to the second tail sequence of the second oligonucleotide.

Abstract: Present disclosure provides a method including isolating DNA from a source, thereby providing a composition including the isolated DNA. The isolated DNA has at least first and second target regions, where the length of the second target region is greater than the length of the first target region. The method further includes quantifying a total mass of the isolated DNA, quantifying a first quantification cycle (Cq) of the first target region and a second Cq of the second target region, and calculating a Q-ratio for the isolated DNA by dividing the second Cq by the first Cq. The method further includes determining a value for a quality-mass constant (kQm), estimating a required input mass by dividing kQm by the Q-ratio, and preparing the isolated DNA for sequencing if the total mass of the isolated DNA in the composition is equal or greater than the required input mass.

Abstract: The present disclosure provides a method for enrichment of at least one target nucleic acid in a library of nucleic acids. A first oligonucleotide is hybridized to a target nucleic acid in library of nucleic acids having first and second adapters. The hybridized first oligonucleotide is extended with a first polymerase, thereby producing a first primer extension complex including the target nucleic acid and the extended first oligonucleotide. The first primer extension complex is captured, enriched relative to the library of nucleic acids, and a second oligonucleotide is hybridized to the target nucleic acid. The hybridized second oligonucleotide is extended with a second polymerase, thereby producing a second primer extension complex including the target nucleic acid and the extended second oligonucleotide, and further liberating the extended first oligonucleotide from the first primer extension complex.

Abstract: The invention comprises novel methods and compositions for detecting whether a patient will be responsive to ALK inhibitors and methods of treating the patient.