Systems and methods for detection of genomic copy number changes
First Claim
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1. A method of detecting chromosomal copy number changes or altered expression of a nucleic acid region of interest, comprising:
- a) amplifying nucleic acid from said region of interest and at least one control region on the same chromosome as said region of interest and at least one control region on a different chromosome than said region of interest to generate a library of one or more target and one or more control amplicons;
b) sequencing said target and control amplicons to generate sequencing reads wherein said sequencing is selected from the group consisting of pyrosequencing, sequencing-by-ligation, single molecule sequencing, sequence-by-synthesis (SBS), massive parallel clonal sequencing, massive parallel single molecule SBS, massive parallel single molecule real-time sequencing, and massive parallel single molecule real-time nanopore sequencing;
c) using said sequencing reads to compare the level of target amplicon to the level of control amplicon; and
d) detecting chromosomal copy number changes or altered expression of said nucleic acid region of interest when the level of target amplicon is different than the level of at least one said control amplicon generated from said nucleic acid from said at least one control region on the same chromosome as said region of interest.
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Abstract
The present invention relates to systems and methods for detecting genomic copy number changes. In particular, the present invention relates to next generation sequencing methods for detection of copy number changes.
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12 Claims
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1. A method of detecting chromosomal copy number changes or altered expression of a nucleic acid region of interest, comprising:
- a) amplifying nucleic acid from said region of interest and at least one control region on the same chromosome as said region of interest and at least one control region on a different chromosome than said region of interest to generate a library of one or more target and one or more control amplicons;
b) sequencing said target and control amplicons to generate sequencing reads wherein said sequencing is selected from the group consisting of pyrosequencing, sequencing-by-ligation, single molecule sequencing, sequence-by-synthesis (SBS), massive parallel clonal sequencing, massive parallel single molecule SBS, massive parallel single molecule real-time sequencing, and massive parallel single molecule real-time nanopore sequencing;
c) using said sequencing reads to compare the level of target amplicon to the level of control amplicon; and
d) detecting chromosomal copy number changes or altered expression of said nucleic acid region of interest when the level of target amplicon is different than the level of at least one said control amplicon generated from said nucleic acid from said at least one control region on the same chromosome as said region of interest. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
- a) amplifying nucleic acid from said region of interest and at least one control region on the same chromosome as said region of interest and at least one control region on a different chromosome than said region of interest to generate a library of one or more target and one or more control amplicons;
Specification