Methods and materials for assessing allelic imbalance
Inventors
Gutin, Alexander • Timms, Kirsten • Lanchbury, Jerry
Assignees
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Publication Number
US-11225685-B2
Publication Date
2022-01-18
Expiration Date
Abstract
Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.
Core Innovation
The invention relates to in vitro detecting loss of heterozygosity (LOH) status in a plurality of single nucleotide polymorphism (SNP) genomic loci in a formalin-fixed paraffin-embedded tissue sample from a patient. Genomic DNA is enriched so that test DNA molecules each comprise a SNP locus of interest located on average every 5 Mb within each examined chromosome, and the enriched DNA molecules are sequenced to determine the genotype at each SNP locus.
For each homozygous SNP locus, the method determines whether the homozygosity is due to LOH. Quantitative signals produced for the SNP loci are analyzed to determine genotype and to determine LOH status for homozygous SNP loci in formalin-fixed paraffin-embedded tissue samples.
The disclosed approaches also address selecting and arranging SNP loci for analysis, including constraints on locus spacing and quantitative scaling of signals for determining genotype and LOH. The described system uses a sample analyzer configured to enrich, a sequencing step producing quantitative signals, and computer program analysis configured to determine genotype and LOH from the quantitative signals.
Claims Coverage
The document includes two independent claims, an in vitro method and a system, covering LOH detection at multiple SNP genomic loci in formalin-fixed paraffin-embedded tissue. Across the independent claims, the core inventive features are enrichment of SNP-locus DNA molecules from FFPE samples, sequencing-based genotype determination using quantitative signals, and determining whether homozygous loci are homozygous due to LOH.
LOH detection in FFPE SNP loci by enrichment, sequencing, and LOH calling
An in vitro method of detecting loss of heterozygosity (LOH) status in a plurality of single nucleotide polymorphism (SNP) genomic loci in a formalin-fixed paraffin-embedded tissue sample from a patient by enriching a genomic DNA sample for DNA molecules each comprising a SNP locus of interest with at least one SNP locus located on average every 5 Mb within each chromosome that is examined, sequencing the DNA molecules to determine the genotype at each such SNP locus, and determining for each homozygous SNP locus whether it is homozygous due to LOH.
System for determining LOH status in FFPE SNP loci using a sample analyzer and computer program analysis
A system for determining LOH status in a plurality of SNP genomic loci in a formalin-fixed paraffin-embedded tissue sample comprising a sample analyzer configured to enrich a genomic DNA sample for DNA molecules each test DNA molecule comprising a SNP locus of interest and wherein there is at least one SNP locus located on average every 5 Mb within each chromosome that is examined, sequencing the DNA molecules to produce a plurality of quantitative signals for each such SNP locus, and computer program configured to analyze the plurality of quantitative signals to determine the genotype of each such SNP locus and to determine, for each homozygous SNP locus, whether the locus is homozygous due to LOH.
Both independent claims are directed to determining LOH status at multiple SNP genomic loci from formalin-fixed paraffin-embedded tissue by enriching SNP-locus-containing DNA molecules, sequencing to obtain genotype and quantitative signals, and calling LOH by determining whether each homozygous SNP locus is homozygous due to LOH, with SNP locus density constrained to at least one SNP locus on average every 5 Mb within examined chromosomes.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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