Methods and materials for assessing allelic imbalance
Inventors
Gutin, Alexander • Timms, Kirsten • Lanchbury, Jerry
Assignees
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Publication Number
US-10626449-B2
Publication Date
2020-04-21
Expiration Date
Abstract
Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.
Core Innovation
The invention describes nucleic-acid sequencing methods and systems for detecting copy number at a plurality of single nucleotide polymorphism loci using test DNA molecules enriched from a formalin-fixed paraffin-embedded sample comprising at least one tumor cell obtained from a patient. The plurality of single nucleotide polymorphism loci includes at least 1,000 single nucleotide polymorphism loci, and there is at least one single nucleotide polymorphism locus located on average every 5 Mb within each chromosome. Quantitative signals representing the alleles for each locus are produced by sequencing the test DNA molecules.
A computer program determines, based on the plurality of quantitative signals, the copy number at each locus in the plurality of single nucleotide polymorphism loci. The described processing is associated with quantitative allele signals and locus-level outputs for the plurality of single nucleotide polymorphism loci present in the test DNA molecules, including computation of copy number across the loci set.
The description further characterizes the locus set selection in terms of dense and evenly spaced SNP panels, including selecting single nucleotide polymorphism loci distributed on average every 1 Mb or every 100 kb along each chromosome, and selecting genomic spacing constrained by a percentage threshold. The described approach supports deriving tumor-related genomic measurements from FFPE-derived DNA and emphasizes likelihood-based computation in the reconstruction of allelic imbalance and copy number signals.
Claims Coverage
The independent claim covers a system that combines enrichment of test DNA from a formalin-fixed paraffin-embedded tumor sample at a plurality of single nucleotide polymorphism loci with defined locus count and genomic spacing, sequencing to produce quantitative allele signals for each locus, and a computer program that determines copy number at each locus from those quantitative signals. The claim set includes refinements specifying minimum SNP counts and denser, evenly spaced genomic panels via numeric spacing constraints.
Enriching and sequencing tumor FFPE DNA at densely spaced SNP loci
Enrich test DNA molecules from a formalin-fixed paraffin-embedded sample comprising at least one tumor cell, where each test DNA molecule comprises at least one locus from a plurality of single nucleotide polymorphism loci having at least 1,000 single nucleotide polymorphism loci, with at least one single nucleotide polymorphism locus located on average every 5 Mb within each chromosome, and sequence the test DNA molecules to produce quantitative signals representing alleles for each locus present.
Copy number determination from quantitative allele signals
Determine, based on the plurality of quantitative signals, the copy number at each locus in the plurality of single nucleotide polymorphism loci using a computer program configured for the determination.
High-density SNP panel specification
Configure the plurality of single nucleotide polymorphism loci to include at least 10,000 single nucleotide polymorphism loci and/or require at least one single nucleotide polymorphism locus on average every 1 Mb across each chromosome, and/or include SNP loci distributed on average every 100 kb along each chromosome, and/or ensure genomic spacing among the plurality of single nucleotide polymorphism loci is less than or equal to 10%.
Overall claim coverage centers on a system that enriches and sequences FFPE tumor-derived DNA at a specified plurality of evenly spaced SNP loci to generate quantitative allele signals, followed by computer-based determination of copy number at each locus. Dependent refinements narrow the SNP locus set by enforcing larger SNP counts and tighter genomic spacing constraints.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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