Method and apparatus for pattern identification in diploid DNA sequence data
AssigneeIllumigen Biosciences, Inc.
InventorsCharles Lee Magness, Dake Sun
Life of this patent
Estimating the term…
Abstract
This invention provides methods for identifying mutations and methylation patterns in diploid DNA sequence signal data. In particular, the invention provides methods for (1) obtaining two parental allele sequences from diploid DNA sequence signal data, (2) identifying the mutation and haplotype patterns in the two parental allele sequences, (3) assigning likelihood scores for the mutations thus identified, and (4) identifying patterns of methylation.
Claims67
A method for deriving two haploid DNA sequences from a diploid DNA sequence signal comprising:
- obtaining two initial base sequences from the diploid DNA sequence signal;
- determining alignments of each of the two initial base sequences with a reference DNA sequence;
- and
- deriving two haploid DNA sequences from the alignments.
A method for identifying the methylation patterns in a chemically-treated diploid DNA sequence signal relative to two reference haploid DNA sequences, comprising:
- deriving two chemically-treated haploid DNA sequences from the chemically-treated DNA sequence signal;
- comparing the two reference haploid DNA sequences at nucleotide positions consisting of 5′-CpG-3′ bases with the two chemically-treated haploid DNA sequences at the corresponding positions;
- and
- identifying the methylation pattern based on the comparison of the two reference haploid DNA sequences with the two chemically-treated haploid DNA sequences.
A method of assigning a likelihood score to each genetic mutation identified on DNA sequences, comprising:
- calculating quality scores for each base in the DNA sequences;
- and
- assigning likelihood scores to each of the genetic mutations by calculating a weighted average of the quality scores in the neighborhood of the mutation.
A computer-readable media that causes a computer to derive two haploid DNA sequences from a diploid DNA sequence signal, by performing the steps of:
- obtaining two initial base sequences from the diploid DNA sequence signal;
- determining alignments of each of the two initial base sequences with a reference DNA sequence;
- and
- deriving two haploid DNA sequences from the alignments.
A computer-readable media that causes a computer to identify methylation patterns in a chemically-treated diploid DNA sequence signal relative to two reference haploid DNA sequences, by performing the steps of:
- deriving two chemically-treated haploid DNA sequences from the chemically-treated DNA sequence signal;
- comparing the two reference haploid DNA sequences at nucleotide positions consisting of 5′-CpG-3′ bases with the two chemically-treated haploid DNA sequences at the corresponding positions;
- and
- identifying the methylation pattern based on the comparison of the two reference haploid DNA sequences with the two chemically-treated haploid DNA sequences.
An apparatus to derive two haploid DNA sequences comprising:
- in input interface coupled to a sequencing device to receive a diploid DNA sequence signal;
- and
- a processor configured to:
- determine two initial base sequences from the diploid DNA sequence signal;
- to determine alignments of each of the two initial base sequences with a reference DNA sequence;
- and
- to derive two haploid DNA sequences from the alignments.
An apparatus to identify the methylation patterns in a chemically-treated diploid DNA sequence signal relative to two reference haploid DNA sequences, comprising:
- in input interface coupled to a sequencing device to receive the chemically-treated diploid DNA sequence signal;
- and
- a processor configured to:
- derive two chemically-treated haploid DNA sequences from the chemically-treated DNA sequence signal;
- compare the two reference haploid DNA sequences at nucleotide positions consisting of 5′-CpG-3′ bases with the two chemically-treated haploid DNA sequences at the corresponding positions;
- and
- identify the methylation pattern based on the comparison of the two reference haploid DNA sequences with the two chemically-treated haploid DNA sequences.
An apparatus for assigning a likelihood score to each genetic mutation identified on DNA sequences, comprising:
- an input device to receive data indicative of DNA sequences;
- and
- a processor configured to:
- calculate quality scores for each base in the DNA sequences;
- and
- assign likelihood scores to each of the genetic mutations by calculating a weighted average of the quality scores in the neighborhood of the mutation.
Dependencies are inferred from the claim text.