System and method for cleaning noisy genetic data and determining chromosome copy number
Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
1. A method for determining genetic data for DNA from a first individual in a biological sample of a second individual, the method comprising:
amplifying a plurality of target loci on cell-free DNA extracted from the biological sample to generate amplified products;
sequencing the amplified products by sequencing-by-synthesis to obtain genetic data of the plurality of target loci;
determining the most likely genetic data for DNA from the first individual based on allele frequencies in the genetic data at the plurality of target loci.
2. The method of claim 1 , wherein the biological sample is a blood sample.
3. The method of claim 1 , wherein the target loci are SNP loci.
4. The method of claim 1 , wherein the target loci are on a plurality of chromosomes.
5. The method of claim 1 , wherein the amplifying comprises targeted PCR.
6. The method of claim 1 , wherein the amplifying comprises targeted PCR and universal PCR.
7. The method of claim 1 , wherein the sequencing-by-synthesis comprises clonal amplification of the amplified products and measurement of sequences of the clonally amplified DNA.
8. The method of claim 1 , wherein the genetic data produced by sequencing is noisy and comprises allele drop out errors.
9. The method of claim 1 , wherein the genetic data produced by sequencing is noisy and comprises measurement bias.
10. The method of claim 1 , wherein the genetic data produced by sequencing is noisy and comprises incorrect measurements.
11. The method of claim 1 , further comprising normalizing the genetic data for differences in amplification and/or sequencing efficiency between the target loci.
12. The method of claim 3 , wherein the confidence that each SNP is correctly called is at least 95%.
13. The method of claim 3 , wherein the confidence that each SNP is correctly called is at least 99%.
14. The method of claim 1 , wherein the target loci comprises at least 70 SNPs.
15. The method of claim 1 , wherein the target loci comprises at least 131 SNPs.
16. The method of claim 1 , wherein the target loci comprises at least 384 SNPs.
17. The method of claim 1 , wherein the target loci comprises at least 500 SNPs.
18. A method for determining genetic data for DNA from a first individual in a blood sample of a second individual, the method comprising:
performing targeted PCR to amplify a plurality of SNP loci on cell-free DNA extracted from the blood sample to generate amplified products, wherein the SNP loci are on a plurality of chromosomes;
sequencing the amplified products by sequencing-by-synthesis to obtain genetic data of the plurality of SNP loci, wherein the sequencing-by-synthesis comprises clonal amplification of the amplified products and measurement of sequences of the clonally amplified DNA;
determining the most likely genetic data for DNA from the first individual based on allele frequencies in the genetic data at the plurality of SNP loci.
19. The method of claim 18 , wherein the confidence that each SNP is correctly called is at least 95%.
20. The method of claim 18 , wherein the confidence that each SNP is correctly called is at least 99%.
21. A method for preparing a preparation of amplified DNA derived from a biological sample of a second individual useful for determining genetic data for DNA from a first individual in the biological sample, the method comprising:
extracting cell-free DNA from the biological sample;
preparing a preparation of amplified DNA by amplifying a plurality of target loci on the cell-free DNA extracted from the biological sample to generate amplified DNA;
analyzing the preparation of amplified DNA by sequencing the amplified DNA using sequencing-by-synthesis to obtain genetic data of the plurality of target loci, and determining the most likely genetic data for DNA from the first individual based on allele frequencies in the genetic data at the plurality of target loci.
22. The method of claim 21 , wherein the biological sample is a blood sample.
23. The method of claim 21 , wherein the target loci are SNP loci.
24. The method of claim 21 , wherein the target loci are on a plurality of chromosomes.
25. The method of claim 21 , wherein the amplifying comprises targeted PCR.
26. The method of claim 21 , wherein the amplifying comprises targeted PCR and universal PCR.
27. The method of claim 21 , wherein the sequencing-by-synthesis comprises clonal amplification of the amplified DNA and measurement of sequences of the clonally amplified DNA.
28. The method of claim 21 , wherein the genetic data produced by sequencing is noisy and comprises allele drop out errors.
29. The method of claim 21 , wherein the genetic data produced by sequencing is noisy and comprises measurement bias.
30. The method of claim 21 , wherein the genetic data produced by sequencing is noisy and comprises incorrect measurements.
31. The method of claim 21 , further comprising normalizing the genetic data for differences in amplification and/or sequencing efficiency between the target loci.
32. The method of claim 23 , wherein the confidence that each SNP is correctly called is at least 95%.
33. The method of claim 23 , wherein the confidence that each SNP is correctly called is at least 99%.
34. The method of claim 21 , wherein the target loci comprises at least 70 SNPs.
35. The method of claim 21 , wherein the target loci comprises at least 131 SNPs.
36. The method of claim 21 , wherein the target loci comprises at least 384 SNPs.
37. The method of claim 21 , wherein the target loci comprises at least 500 SNPs.
38. A method for preparing a preparation of amplified DNA derived from a biological sample of a second individual useful for determining genetic data for DNA from a first individual in the blood sample, the method comprising:
extracting cell-free DNA from the biological sample;
preparing a preparation of amplified DNA by performing targeted PCR to amplify a plurality of SNP loci on the cell-free DNA extracted from the blood sample to generate amplified DNA, wherein the SNP loci are on a plurality of chromosomes;
analyzing the preparation of amplified DNA by sequencing the amplified DNA using sequencing-by-synthesis to obtain genetic data of the plurality of SNP loci, wherein the sequencing-by-synthesis comprises clonal amplification of the amplified DNA and measurement of sequences of the clonally amplified DNA, and determining the most likely genetic data for DNA from the first individual based on allele frequencies in the genetic data at the plurality of SNP loci.
39. The method of claim 38 , wherein the confidence that each SNP is correctly called is at least 95%.
40. The method of claim 38 , wherein the confidence that each SNP is correctly called is at least 99%.