Granted Patent B2

US 12,612,655 · App. 17/384,390 · Granted Apr 28, 2026

Inventors: Walid Korani (Madison, AL); Nader Deeb (Navasota, TX); Alan Mileham (Middleton, WI); Charles Michael Cowan (Middleton, WI)

Assignee: Inguran, LLC

C12Q1/6816C12Q1/6806C12Q1/6827G16B30/10

Abstract

Claims (39)

1 . 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.

2 . The method of claim 1 , further comprising the step of detecting a mismatch between the nucleotide in the one or more HCHL in the first nucleotide sequence and the identified nucleotide in the second nucleotide sequence.

3 . The method of claim 2 , further comprising the step of discarding the second biological sample based on the mismatch.

4 . The method of claim 1 , further comprising the steps of

detecting a match between the nucleotide in the one or more HCHL in the first nucleotide sequence and the identified nucleotide in the second nucleotide sequence; and

further processing the second biological sample based on the match.

5 . The method of claim 4 , wherein the second biological sample comprises a sperm cell sample and wherein the step of further processing the second biological sample comprises sex-sorting the second biological sample, ablating sperm cells bearing an undesired sex chromosome in the second biological sample or cryopreserving sperm cells in the second biological sample.

6 . The method of claim 1 , wherein the first biological sample comprises a pure biological sample.

7 . The method of claim 6 , wherein the second biological sample comprises a test biological sample.

8 . 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.

9 . The method of claim 8 , wherein the step of 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 comprises

generating read data from the second nucleotide sequence and read data from the third nucleotide sequence; and

mapping the read data from the second nucleotide sequence and the read data from the third nucleotide sequence.

10 . The method of claim 8 , further comprising the step of detecting a mismatch between the nucleotide in the one or more HCHL in the first nucleotide sequence and i) the identified nucleotide in the second nucleotide sequence or ii) the identified nucleotide in the third nucleotide sequence.

11 . The method of claim 10 , further comprising the step of discarding the second biological sample based on the mismatch.

12 . The method of claim 8 , further comprising the steps of

detecting a match between the nucleotide in the one or more HCHL in the first nucleotide sequence and i) the identified nucleotide in the second nucleotide sequence or ii) the identified nucleotide in the third nucleotide sequence; and

further processing the second biological sample based on the match.

13 . The method of claim 12 , wherein the second biological sample comprises a sperm cell sample and wherein the step of further processing the second biological sample comprises sex-sorting the second biological sample, ablating sperm cells bearing an undesired sex chromosome in the second biological sample or cryopreserving sperm cells in the second biological sample.

14 . The method of claim 8 , wherein the first biological sample comprises a pure biological sample.

15 . The method of claim 14 , wherein the second biological sample comprises a test biological sample.

16 . The method of claim 8 , wherein the at least one replicate comprises a biological replicate.

17 . The method of claim 16 , wherein the biological replicate comprises a portion of a pure biological sample.

18 . 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.

Assignments (4)

Continuity (2)

References Cited (17)