Genotyping of polyploids
AssigneeKeygene N.V.
InventorsStefan John White, René Cornelis Josephus Hogers
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Abstract
The current invention pertains to a reliable method for determining the relative frequency of a sequence variant of interest in a nucleic acid sample derived from at least one polyploid cell, wherein the method uses a UMI to correct for any amplification biases. The invention further pertains to the use of a UMI for accurately determining the relative frequency of a sequence variant of interest in a nucleic acid sample derived from at least one polyploid cell.
Claims13
A method for determining the genotype of a polyploid cell by determining the relative frequency of an allelic variant of interest in a nucleic acid sample, wherein the nucleic acid sample comprises genomic DNA derived from the polyploid cell, wherein the method comprises:
- (a) providing polynucleotides derived from the nucleic acid sample, wherein the polynucleotides comprise the sequence of the allelic variant of interest or the reversed complement thereof, and wherein each polynucleotide comprises a unique molecular index (UMI),
- (b) amplifying the polynucleotides provided in (a);
- (c) determining the sequences of the amplified polynucleotides to obtain sequence reads;
- (d) grouping the sequence reads using at least the UMI and obtaining a consensus sequence of the grouped sequence reads;
- and
- (e) determining the genotype of the polyploid cell by calculating the number of times the allelic variant of interest occurs in the nucleic acid sample in relation to the total of the number of times all allelic variants thereof occur in the nucleic acid sample.
Dependencies are inferred from the claim text.