DETECTING MUTATIONS AND PLOIDY IN CHROMOSOMAL SEGMENTS
The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.
1 . A method for preparing a plasma sample of a subject having cancer or suspected of having cancer useful for detecting one or more genetic variants in the plasma sample, the method comprising:
performing whole exome sequencing or whole genome sequencing on a tumor sample of the subject to identify a plurality of tumor-specific genomic variants;
performing targeted multiplex amplification to amplify a plurality of target loci from cell-free DNA isolated from a plasma sample of the subject or DNA derived therefrom to obtain amplicons, wherein the target loci each encompasses one of the tumor-specific genetic variants identified in the tumor sample of the subject; and
identifying one or more of the tumor-specific genomic variants present in the cell-free DNA from the amplicons.
2 . The method of claim 1 , wherein the targeted multiplex amplification comprises emulsion PCR.
3 . The method of claim 1 , wherein the targeted multiplex amplification comprises digital PCR.
4 . The method of claim 1 , wherein the cell-free DNA comprises circulating tumor DNA.
5 . The method of claim 1 , wherein the genomic variants comprise one or more insertion, deletion, duplication, or translocation.
6 . The method of claim 1 , wherein the tumor sample of the subject is a tumor tissue sample.
7 . The method of claim 1 , wherein the targeted multiplex amplification amplifies 10 to 50 target loci each encompassing a different tumor-specific genetic variants.
8 . The method of claim 1 , wherein the method further comprises designing PCR primers targeting the plurality of genomic variants identified in the tumor sample.
9 . The method of claim 1 , wherein the method further comprises detecting recurrence and/or metastases of the cancer from the genomic variants detected in the cell-free DNA.
10 . The method of claim 1 , wherein the cancer is colorectal cancer, lung cancer, bladder cancer, or breast cancer.
11 . The method of claim 1 , wherein the method identifies a tumor-specific genomic variant present in the cell-free DNA at a limit of detection of less than or equal to 0.015%.