SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION
First Claim
1. A method, comprising:
- providing initial starting genetic material obtained from a bodily sample obtained from a subject;
converting double stranded polynucleotides from the initial starting genetic material into at least one set of non-uniquely tagged parent polynucleotides, wherein each polynucleotide in a set is mappable to a reference sequence; and
for each set of tagged parent polynucleotides;
i. amplifying the tagged parent polynucleotides in the set to produce a corresponding set of amplified progeny polynucleotides;
ii. sequencing the set of amplified progeny polynucleotides to produce a set of sequencing reads;
iii. collapsing the set of sequencing reads to generate a set of consensus sequences, wherein collapsing uses sequence information from a tag and at least one of;
sequence information at a beginning region of a sequence read, an end region of the sequence read and length of the sequence read, each consensus sequence corresponding to a unique polynucleotide among the set of tagged parent polynucleotides; and
ii. analyzing the set of consensus sequences for each set of tagged parent molecules separately or in combination.
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Abstract
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
86 Citations
30 Claims
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1. A method, comprising:
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providing initial starting genetic material obtained from a bodily sample obtained from a subject; converting double stranded polynucleotides from the initial starting genetic material into at least one set of non-uniquely tagged parent polynucleotides, wherein each polynucleotide in a set is mappable to a reference sequence; and for each set of tagged parent polynucleotides; i. amplifying the tagged parent polynucleotides in the set to produce a corresponding set of amplified progeny polynucleotides; ii. sequencing the set of amplified progeny polynucleotides to produce a set of sequencing reads; iii. collapsing the set of sequencing reads to generate a set of consensus sequences, wherein collapsing uses sequence information from a tag and at least one of;
sequence information at a beginning region of a sequence read, an end region of the sequence read and length of the sequence read, each consensus sequence corresponding to a unique polynucleotide among the set of tagged parent polynucleotides; andii. analyzing the set of consensus sequences for each set of tagged parent molecules separately or in combination. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30)
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Specification