Sequencing controls
AssigneeGarvan Institute of Medical Research
InventorTimothy Mercer
Life of this patent
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Abstract
The present disclosure generally relates to artificial controls for genetic sequencing and quantitation assays, which can be used to calibrate a wide variety of genetic sequencing and quantitation methods. For example, the controls disclosed herein can be used to calibrate a wide variety of high throughput sequencing methods (for example, those referred to as next generation sequencing methods). The present disclosure also generally relates to the use of the sequencing controls in a wide variety of applications including, for example, in the calibration of a wide variety of sequencing methods.
Claims21
1-19. (canceled)
A DNA polynucleotide, comprising an artificial portion of at least 100 contiguous nucleotides, wherein the at least 100 contiguous nucleotides in the artificial portion:
- (a) have a same relative order as in a 5′ to 3′ portion of a polynucleotide comprising a human gene locus;
- and
- (b) are connected in the 3′ to 5′ direction in the artificial portion,
- wherein:
- the human gene locus is in human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19;
- or
- the 5′ to 3′ portion of the polynucleotide comprising the human gene locus comprises a genetic variation of the human gene locus relative to human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19.
A composition comprising a first amount of a target DNA polynucleotide comprising a human gene locus and a predetermined amount of a DNA polynucleotide comprising an artificial portion of at least 1000 contiguous nucleotides, wherein the at least 1000 contiguous nucleotides in the artificial portion:
- (a) have a same relative order as in a 5′ to 3′ portion of the target DNA polynucleotide comprising the human gene locus;
- and
- (b) are connected in the 3′ to 5′ direction in the artificial portion,
- wherein:
- the human gene locus is in human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19;
- or
- the 5′ to 3′ portion of the polynucleotide comprising the human gene locus comprises a genetic variation of the human gene locus relative to human genome NA12878, GRCh38.p13, or hg19.
A method of synthesizing one or more polynucleotides, the method comprising:
- (i) obtaining a first nucleotide sequence comprising at least 1000 contiguous nucleotides having a same relative order as in a 5′ to 3′ portion of a target polynucleotide comprising a human gene locus, wherein:
- the human gene locus is in human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19;
- or
- the 5′ to 3′ portion of the polynucleotide comprising the human gene locus comprises a genetic variation of the human gene locus relative to human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19;
- (ii) reversing the first nucleotide sequence to obtain a second nucleotide sequence;
- (iii) synthesizing a polynucleotide using the second nucleotide sequence to obtain a synthesized polynucleotide containing an artificial portion consisting of at least 100 contiguous nucleotides that:
- (a) have a same relative order as in the 5′ to 3′ portion of the target polynucleotide;
- and
- (b) are connected in the 3′ to 5′ direction in the artificial portion.
A method of synthetizing a polynucleotide, the method comprising:
- (i) obtaining a sequence to use for synthesizing the polynucleotide, wherein the sequence comprises at least 1000 contiguous nucleotide that:
- (a) have a same relative order as in a 5′ to 3′ portion of a target polynucleotide comprising a human gene locus;
- and
- (b) are connected in the 3′ to 5′ direction,
- wherein:
- the human gene locus is in human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19;
- or
- the 5′ to 3′ portion of the polynucleotide comprising the human gene locus comprises a genetic variation of the human gene locus relative to human genome human genome NA12878, human reference genome GRCh38.p13, or human reference genome hg19;
- and
- (ii) synthesizing the polynucleotide using the sequence to obtain a synthesized polynucleotide.
Dependencies are inferred from the claim text.