Computer software for genotyping analysis using pattern recognition
View Patent ↗Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.
1. A computer implemented method for determining the genotype of a sample comprising:
obtaining a plurality of sample probe intensities;
determining a tentative genotype based upon the sample probe intensities;
calculating linear correlation coefficient between the sample probe intensities and reference probe intensities; and accepting the tentative genotype as the genotype of the sample if the linear correlation coefficient is greater than a threshold value.
2. The method of claim 1 wherein the threshold value is at least 0.8.
3. The method of claim 2 wherein the threshold value is at least 0.9.
4. The method of claim 3 wherein the threshold value is at least 0.95.
5. The method of claim 1 wherein the tentative genotype is determined based upon relative allele signal.
6. The method of claim 5 wherein the probes are immobilized on a substrate at a density of at least 400 probes per cm 2 .
7. The method of claim 6 wherein the probes are immobilized on a substrate at a density of at least 1000 probes per cm 2 .
8. The method of claim 7 wherein the reference genotype is a homozygous genotype.
9. The method of claim 7 wherein the reference genotype is a heterozygous genotype.
10. The method of claim 7 wherein the probes contain probes designed to be perfect match for a first genotype and a second genotype.
11. The method of claim 10 wherein the probes contain probes designed to be mismatch for a first genotype and a second genotype.
12. A computer implemented method for determining the genotype of a sample comprising:
obtaining a plurality of sample probe intensities; and
determining whether the pattern of the sample probe intensities is similar to that of reference probe intensities, wherein the reference probe intensities reflect hybridization between the plurality of probes and a reference sample having a reference genotype, wherein the determining comprising calculating correlation coefficient between the sample probe intensities and reference probe intensities; and indicating that the genotype of the sample is the same as the reference genotype, if the correlation coefficient is greater than a threshold value.
13. The method of claim 12 wherein the threshold value is at least 0.8.
14. The method of claim 13 wherein the threshold value is at least 0.9.
15. The method of claim 14 wherein the threshold value is at least 0.95.
16. A system for determining the genotype of a sample comprising:
a processor; and
a memory coupled with the least one processor, the memory storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps include:
obtaining a plurality of sample probe intensities;
determining a tentative genotype based upon the sample probe intensities; and
calculating linear correlation coefficient between the sample probe intensities and reference probe intensities; and accepting the tentative genotype as the genotype of the sample if the linear correlation coefficient is greater than a threshold value.
17. The system of claim 16 wherein the threshold value is at least 0.8.
18. The system of claim 17 wherein the threshold value is at least 0.9.
19. The system of claim 18 wherein the threshold value is at least 0.95.
20. The system of claim 19 wherein the tentative genotype is determined based upon relative allele signal.
21. The system of claim 20 wherein the probes are immobilized on a substrate at a density of at least 400 probes per cm 2 .
22. The system of claim 21 wherein the probes are immobilized on a substrate at a density of at least 1000 probes per cm 2 .
23. The system of claim 22 wherein the reference genotype is a homozygous genotype.
24. The system of claim 23 wherein the reference genotype is a heterozygous genotype.
25. The system of claim 24 wherein the probes contain probes designed to be perfect match for a first genotype and a second genotype.
26. The method of claim 25 wherein the probes contain probes designed to be mismatch for a first genotype and a second genotype.
27. A system for determining the genotype of sample comprising:
a processor; and
a memory coupled with the least one processor, the memory storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps include:
obtaining a plurality of sample probe intensities; and
determining whether the pattern of the sample probe intensities is similar to that of reference probe intensities, wherein the reference probe intensities reflect hybridization between the plurality of probes and a reference sample having a reference genotype, wherein the determining comprising calculating correlation coefficient between the sample probe intensities and reference probe intensities; and indicating that the genotype of the sample is the same as the reference genotype, if the correlation coefficient is greater than a threshold value.
28. The system of claim 27 wherein the threshold value is at least 0.8.
29. The system of claim 28 wherein the threshold value is at least 0.9.
30. The system of claim 29 wherein the threshold value is at least 0.95.
31. A computer readable medium comprising computer-executable instructions for performing the method for determining the genotype of a sample comprising:
obtaining a plurality of sample probe intensities;
determining a tentative genotype based upon the sample probe intensities; and
calculating linear correlation coefficient between the sample probe intensities and reference probe intensities; and accepting the tentative genotype as the genotype of the sample if the linear correlation coefficient is greater than a threshold value.
32. The computer readable medium of claim 31 wherein the threshold value is at least 0.8.
33. The computer readable medium of claim 32 wherein the threshold value is at least 0.9.
34. The computer readable medium of claim 33 wherein the threshold value is at least 0.95.
35. The computer readable medium of claim 34 wherein the tentative genotype is determined based upon relative allele signal.
36. The computer readable medium of claim 35 wherein the probes are immobilized on a substrate at a density of at least 400 probes per cm 2 .
37. The computer readable medium of claim 36 wherein the probes are immobilized on a substrate at a density of at least 1000 probes per cm 2 .
38. The computer readable medium of claim 37 wherein the reference genotype is a homozygous genotype.
39. The computer readable medium of claim 38 wherein the reference genotype is a heterozygous genotype.
40. The computer readable medium of claim 37 wherein the probes contain probes designed to be perfect match for a first genotype and a second genotype.
41. The computer readable medium of claim 40 wherein the probes contain probes designed to be mismatch for a first genotype and a second genotype.
42. A computer readable medium comprising computer-executable instructions for performing the methods comprising:
obtaining a plurality of sample probe intensities; and
determining whether the pattern of the sample probe intensities is similar to that of reference probe intensities, wherein the reference probe intensities reflect the hybridization between the plurality of probes and a reference sample having a reference genotype, wherein the determining comprising calculating correlation coefficient between the sample probe intensities and reference probe intensities; and indicating that the genotype of the sample is the same as the reference genotype, if the correlation coefficient is greater than a threshold value.
43. The computer readable medium of claim 42 wherein the threshold value is at least 0.8.
44. The computer readable medium of claim 43 wherein the threshold value is at least 0.9.
45. The computer readable medium of claim 44 wherein the threshold value is at least 0.95.