Methods for screening biological samples for contamination
AssigneeInguran, LLC
InventorsWalid Korani, Nader Deeb, Alan Mileham, Charles Michael Cowan
Life of this patent
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Abstract
The invention includes a method of screening a biological sample for contamination by sequencing a first biological sample at a first depth to generate a first nucleotide sequence; determining map coordinates for one or more homozygous loci in the first nucleotide sequence; sequencing a second biological sample at a second depth to generate a second nucleotide sequence, wherein the second depth is lower than the first depth; determining loci in the second nucleotide sequence at the determined map coordinates; and comparing the one or more homozygous loci in the first nucleotide sequence with the determined loci in the second nucleotide sequence.
Claims18
A method of screening a biological sample for contamination comprising:
- sequencing a first biological sample at a first depth to generate a first nucleotide sequence;
- determining map coordinates for one or more high confidence homozygous loci (HCHL) in the first nucleotide sequence;
- sequencing a second biological sample at a second depth to generate a second nucleotide sequence, wherein the second depth is lower than the first depth;
- identifying a nucleotide in the second nucleotide sequence at the determined map coordinates;
- and
- comparing a nucleotide in the one or more HCHL in the first nucleotide sequence with the identified nucleotide in the second nucleotide sequence.
A method of screening a biological sample for contamination comprising:
- sequencing a first biological sample at a first depth to generate a first nucleotide sequence;
- determining map coordinates for one or more high confidence homozygous loci (HCHL) in the first nucleotide sequence;
- sequencing a second biological sample at a second depth to generate a second nucleotide sequence, wherein the second depth is lower than the first depth;
- sequencing at least one replicate of the first biological sample at the second depth to generate a third nucleotide sequence;
- identifying a nucleotide in the second nucleotide sequence at the determined map coordinates and a nucleotide in the third nucleotide sequence at the determined map coordinates;
- and
- comparing a nucleotide in the one or more HCHL in the first nucleotide sequence with i) the identified nucleotide in the second nucleotide sequence and ii) the identified nucleotide in the third nucleotide sequence.
A method of screening a biological sample for contamination comprising:
- determining or imputing a first nucleotide sequence for a first biological sample and a second nucleotide sequence for a second biological sample, the first biological sample and the second biological sample being from the same individual of a species;
- identifying matched and mismatched high confidence homozygous loci (HCHL) between the first nucleotide sequence and the second nucleotide sequence;
- determining a matched HCHL count and a mismatched HCHL count from the identified matched and mismatched HCHL, wherein a sum of the matched HCHL count and the mismatched HCHL count constitutes a total HCHL count;
- calculating a ratio of the matched HCHL count to the total HCHL count or a ratio of the mismatched HCHL count to the total HCHL count.
Dependencies are inferred from the claim text.