The present invention provides a method for obtaining tumour nucleic acid for sequencing, comprising providing a medium containing tumour cells shed from a solid tumour sample into the medium ex vivo and/or released during mechanical disruption of a solid tumour sample and extracting nucleic acid from the shed and/or released tumour cells tumour cells.

Provided herein are methods and kits for detecting the presence of DNA and/or RNA mutations associated with cancer (e.g., lung cancer). The methods and kits employ microcarriers, each with a probe specific for a DNA or RNA mutation and an identifier unique to the probe sequence. Upon isolation and amplification of nucleic acids from a sample, hybridization of amplified DNA with a probe, specific for a DNA or RNA mutation, that is coupled to a microcarrier indicates the presence of the mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays are provided. Representative genes that can be screened for mutations include, e.g., KRAS, NRAS, PIK3CA, BRAF, EGFR, AKT1, MEK1, and HER2 for DNA mutations and/or ALK, ROS, RET, NTRK1, and cMET for RNA mutations.

Provided herein are methods and kits for detecting the presence of DNA and/or RNA mutations associated with cancer (e.g., lung cancer). The methods and kits employ microcarriers, each with a probe specific for a DNA or RNA mutation and an identifier unique to the probe sequence. Upon isolation and amplification of nucleic acids from a sample, hybridization of amplified DNA with a probe, specific for a DNA or RNA mutation, that is coupled to a microcarrier indicates the presence of the mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays are provided. Representative genes that can be screened for mutations include, e.g., KRAS, NRAS, PIK3CA, BRAF, EGFR, AKT1, MEK1, and HER2 for DNA mutations and/or ALK, ROS, RET, NTRK1, and cMET for RNA mutations.

Provided herein are methods and kits for detecting the presence of DNA and/or RNA mutations associated with cancer (e.g., lung cancer). The methods and kits employ microcarriers, each with a probe specific for a DNA or RNA mutation and an identifier unique to the probe sequence. Upon isolation and amplification of nucleic acids from a sample, hybridization of amplified DNA with a probe, specific for a DNA or RNA mutation, that is coupled to a microcarrier indicates the presence of the mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays are provided. Representative genes that can be screened for mutations include, e.g., KRAS, NRAS, PIK3CA, BRAF, EGFR, AKT1, MEK1, and HER2 for DNA mutations and/or ALK, ROS, RET, NTRK1, and cMET for RNA mutations.

Provided are methods of selecting a patient with cancer and/or treating a patient with cancer that comprises a deleterious alteration in FBXW7 and/or an amplification of CCNL1 for CDK11 inhibitor and/or ATR inhibitor treatment. For example, the method of selecting a patient afflicted with a cancer likely to benefit from a CDK11 inhibitor and/or ATR inhibitor treatment, the method comprising: obtaining a biological sample; testing the sample for i) loss of function FBXW7, optionally for a deleterious mutation in F box WD-repeat containing protein (FBXW7) substrate binding domain and/or ii) upregulated CCNL1, optionally a gain or amplification of CCNL1; and selecting the patient having i) loss of function FBXW7, optionally a deleterious mutation in the FBWX7 substrate-binding domain or ii) upregulated CCNL1, optionally a gain or amplification of CCNL1, as likely to benefit and/or for treatment with the CDK11 inhibitor and/or ATR inhibitor.

Provided are methods of selecting a patient with cancer and/or treating a patient with cancer that comprises a deleterious alteration in FBXW7 and/or an amplification of CCNL1 for CDK11 inhibitor and/or ATR inhibitor treatment. For example, the method of selecting a patient afflicted with a cancer likely to benefit from a CDK11 inhibitor and/or ATR inhibitor treatment, the method comprising: obtaining a biological sample; testing the sample for i) loss of function FBXW7, optionally for a deleterious mutation in F box WD-repeat containing protein (FBXW7) substrate binding domain and/or ii) upregulated CCNL1, optionally a gain or amplification of CCNL1; and selecting the patient having i) loss of function FBXW7, optionally a deleterious mutation in the FBWX7 substrate-binding domain or ii) upregulated CCNL1, optionally a gain or amplification of CCNL1, as likely to benefit and/or for treatment with the CDK11 inhibitor and/or ATR inhibitor.

Disclosed is a computer-implemented method for determining a measure correlated to the probability that two mutated sequence reads derive from the same sequence comprising mutations. The method comprises receiving mutated sequence reads each corresponding to a subsequence of a sequence comprising mutations compared to a sequence not comprising mutations, applying a common minimizer function to each mutated sequence read, to determining minimizers for each mutated sequence read, determining positions of the one or more minimizers in each mutated sequence read, determining positions of mutations in each mutated sequence read, and for at least two mutated sequence reads with a common minimizer, counting the number of mutations with matching position and/or mismatching position when the respective minimizers are aligned. Also disclosed is a corresponding method for determining at least a portion of a sequence of at least one target template nucleic acid molecule.

Disclosed is a computer-implemented method for determining a measure correlated to the probability that two mutated sequence reads derive from the same sequence comprising mutations. The method comprises receiving mutated sequence reads each corresponding to a subsequence of a sequence comprising mutations compared to a sequence not comprising mutations, applying a common minimizer function to each mutated sequence read, to determining minimizers for each mutated sequence read, determining positions of the one or more minimizers in each mutated sequence read, determining positions of mutations in each mutated sequence read, and for at least two mutated sequence reads with a common minimizer, counting the number of mutations with matching position and/or mismatching position when the respective minimizers are aligned. Also disclosed is a corresponding method for determining at least a portion of a sequence of at least one target template nucleic acid molecule.

The subject invention pertains to the detection and differentiation of genetic variations by nucleic acid amplification. The invention provides methods of detecting one or more genetic variations in a nucleic acid that are in close proximity simultaneously. The invention further provides primer and probe oligonucleotides and methods of using said primers and probes in assays to detect genetic variants of concern of SARS-CoV-2. The methods of the invention detect genetic variants of other pathogens, including influenza, or genetic variants involved in inheritable diseases or cancer.

The subject invention pertains to the detection and differentiation of genetic variations by nucleic acid amplification. The invention provides methods of detecting one or more genetic variations in a nucleic acid that are in close proximity simultaneously. The invention further provides primer and probe oligonucleotides and methods of using said primers and probes in assays to detect genetic variants of concern of SARS-CoV-2. The methods of the invention detect genetic variants of other pathogens, including influenza, or genetic variants involved in inheritable diseases or cancer.