System and method for cleaning noisy genetic data and determining chromosome copy number

• US 20080243398A1
• Filed: 03/17/2008
• Published: 10/02/2008
• Est. Priority Date: 12/06/2005
• Status: Active Grant

• Current Assignee: Natera Incorporated (Natera)
• Original Assignee: Natera Incorporated (Natera)
• Inventors: Demko, Zachary, Rabinowitz, Matthew, Banjevic, Milena, Xu, Jing, Petrov, Dimitri, Kijacic, Dusan, Sweetkind-Singer, Josh, Scott Johnson, David
• Granted Patent: US 8,515,679 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G06Q 50/22 Social work or social welfare, e.g. community support activities or counselling services
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

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. Genetic material from the target individual is acquired, amplified and the genetic data is measured using known methods. 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 of the invention, 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 of the invention, the chromosome copy number can be determined from the measured genetic data of a single or small number of cells, with or without genetic information from one or both parents. In another embodiment of the invention, these determinations are made for the purpose of embryo selection in the context of in-vitro fertilization. In another embodiment of the invention, the genetic data can be reconstructed for the purposes of making phenotypic predictions.

Claims

1. A method for determining the number of copies of a segment of a chromosome in the genome of a target individual, the method comprising:

(i) creating a set of copy number hypotheses about how many copies of the chromosome segment are present in the genome of a target individual, and

(ii) incorporating genetic information from the target individual and genetic information from one or more related individuals into a data set, and

(iii) estimating the characteristics of the platform response associated with the data set, where the platform response may vary from one experiment to another, and

(iv) computing the conditional probabilities of each copy number hypothesis, given the data set and the platform response characteristics, and

(v) determining the copy number of the chromosome segment based on the most probable copy number hypothesis.

2. The method of claim 1, the method comprising:

(i) creating a set of copy number hypotheses about how many copies of the chromosome segment are present in the genome of a target individual, and

(ii) measuring the genetic data for some or all of the possible alleles at a plurality of loci on the given segment of both the target individual and one or more individuals related to the target,

(iii) determining the relative probability of each of the hypotheses given the measurements of the target individual'"'"'s genetic data and also the genetic data of the individuals related to the target, and

(iv) using the relative probabilities associated with each hypothesis to determine the most likely state of the actual genetic material of the target individual.

3. The method of claim 1, the method comprising:

(i) creating a set of hypotheses about the number and identity of chromosome segments that were contributed to the target individual by each of the related individuals in a way that makes use of imperfect genetic measurements of both the target individual and genetic measurements of one or more individuals related to the target individual, and

(ii) determining the probability of the genetic measurements of the target individual given the hypothesis on the target individual'"'"'s genetic data, and given the genetic measurements of the related individual(s) at a plurality of loci, and given a plurality of parameters that may differ from one experiment to another, and

(iii) integrating the probabilities over the possible set of parameters that vary across measurement experiment, and

(iv) selecting those hypotheses that have the highest probabilities.

4. The method of claim 1 where the determination of the number of instances of chromosomes or chromosome segments that are present in the target'"'"'s genome is done in the context of screening for a chromosomal condition, that condition taken from a list comprising euploidy, nullsomy, monosomy, uniparental disomy, trisomy, tetrasomy, other aneuploidy, unbalanced translocation, deletions, insertions, mosaicism, and combinations thereof.

5. The method of claim 1 where the genetic measurements are made using qualitative techniques that make use of allele calls.

6. The method of claim 1 where the genetic measurements make use of known alleles of reference sequences and quantitative allele measurements.

7. The method of claim 1, wherein the target individual'"'"'s genetic material has been amplified using techniques taken from the group comprising Polymerase Chain Reaction (PCR), ligand mediated PCR, Whole Genome Amplification, degenerative oligonucleotide primer PCR, Multiple Displacement Amplification, allele-specific amplification and combinations thereof.

8. The method of claim 1, wherein the target individual'"'"'s genetic data have been measured using tools and or techniques taken from the group comprising Molecular Inversion Probes (MIP), Genotyping Microarrays, the TaqMan SNP Genotyping Assay, the Illumina Genotyping System, other genotyping assays, fluorescent in-situ hybridization (FISH), sequencing, other high through-put genotyping platforms, and combinations thereof.

9. The method of claim 1, wherein the target individual'"'"'s genetic data have been measured by analyzing substances taken from the group comprising one or more diploid cells from the target individual, one or more haploid cells from the target individual, one or more blastomeres from the target individual, extra-cellular genetic material found on the target individual, extra-cellular genetic material from the target individual found in maternal blood, cells from the target individual found in maternal blood, genetic material known to have originated from the target individual, and combinations thereof.

10. The method of claim 1, wherein the related individual'"'"'s genetic data have been measured by analyzing substances taken from the group comprising the related individual'"'"'s bulk diploid tissue, one or more diploid cells from the related individual, one or more haploid cells taken from the related individual, one or more embryos created from (a) gamete(s) from the related individual, one or more blastomeres taken from such an embryo, extra-cellular genetic material found on the related individual, genetic material known to have originated from the related individual, and combinations thereof.

11. The method of claim 1, wherein the determination of the number of chromosome segments in the genome of the target is used for the purpose of embryo selection in the context of in-vitro fertilization.

12. The method of claim 1, wherein the determination of the number of chromosome segments in the genome of the target is used for the purpose of prenatal genetic diagnosis.

13. The method of claim 1, wherein measured genetic data from sperm from the father of the individual are used to enhance the accuracy of the determination of the number of copies of the chromosome segment.

14. The method of claim 1, wherein the maternal haplotypic genetic data are determined by inference using diploid genetic data measured from one or more blastomeres, diploid genetic data from one or more parents, and haploid genetic data from the father.

15. The method of claim 1, wherein the maternal haplotypic genetic data that are used in the method have been determined without the use of genetic data from a born child, and without the use of genetic data from a parent of the mother, and without making use of a haplotypic tissue sample from the mother.

16. The method of claim 1, where the target individual is an embryo, and where the determination is done for the purpose of selecting embryos for transfer in the context of IVF, and where the related individuals are taken from the group consisting of the father, the mother, one or more embryos that are from the same parents, one or more sperm from the father, and combinations thereof.

17. The method of claim 1, wherein the method is run alongside or in conjunction with a method that makes allele calls at multiple loci of the target individual, and where both methods use the same cell, or group of cells, from the target individual as a source of genetic material.

18. A method to call one or more alleles of a target individual, the method comprising:

(i) incorporating into a dataset measured genetic data, at a plurality of loci, of a target individual and of at least one related individual, and

(ii) estimating the characteristics of the platform response associated with the data set, where the platform response may vary from one experiment to another, and

(iii) calculating the most likely correct allele calls of the target individual given the genetic data and the platform response characteristics.

19. The method of claim 18, the method comprising:

(i) creating a set of one or more hypotheses concerning the true state of the genetic material of a target individual,

(ii) determining the probability of each of the hypotheses given the measurements of the target individual'"'"'s genetic data and of the related individual'"'"'s genetic data, and

(iii) using the probabilities associated with each hypothesis to determine the most likely state of the actual genetic material of the target individual.

20. The method of claim 18, the method comprising:

(i) measuring the genetic data at a plurality of loci of both the target individual and the related individual(s), referred to collectively as the “

genetic measurements,” and

(ii) creating a set of one or more hypotheses concerning which segments of which chromosomes from the related individual(s) correspond to those segments found in the target individual'"'"'s genome, and

(iii) creating a set of one or more hypothesis about the underlying genetic states of the target individual and related individuals at a given locus, and

(iv) determining the joint probability of these hypotheses and the genetic measurements at a given locus, for each locus and for each hypothesis, and

(v) combining the above probabilities to calculate the probability of each possible genetic state of the target individual at the locus of interest, given the genetic measurements, and

(vi) selecting that genetic state of the target individual that has maximum probability.

21. The method of claim 18, wherein the increase in fidelity of the allele calls in the genetic data of the target individual is used for the purpose of embryo selection in the context of in-vitro fertilization.

22. The method of claim 18, wherein the increase in fidelity of the allele calls in the genetic data of the target individual is done in the context of prenatal genetic diagnosis.

23. The method of claim 18, wherein the target individual'"'"'s genetic data have been measured by analyzing substances taken from the group comprising one or more diploid cells from the target individual, one or more haploid cells from the target individual, one or more blastomeres from the target individual, extra-cellular genetic material found on the target individual, extra-cellular genetic material from the target individual found in maternal blood, cells from the target individual found in maternal blood, genetic material known to have originated from the target individual, and combinations thereof.

24. The method of claim 18, wherein the related individual'"'"'s genetic data have been measured by analyzing substances taken from the group comprising the related individual'"'"'s bulk diploid tissue, one or more diploid cells from the related individual, one or more haploid cells taken from the related individual, one or more embryos created from a gamete(s) from the related individual, one or more blastomeres taken from such an embryo, extra-cellular genetic material found on the related individual, genetic material known to have originated from the related individual, and combinations thereof.

25. The method of claim 18, wherein the target individual'"'"'s genetic data have been measured using techniques taken from the group comprising Molecular Inversion Probes (MIP), Genotyping Microarrays, the TaqMan SNP Genotyping Assay, the Illumina Genotyping System, other genotyping assays, sequencing, fluorescent in-situ hybridization (FISH), other high through-put genotyping platforms, and combinations thereof.

26. The method of claim 18, wherein the method does not make use of short tandem repeats.

27. The method of claim 18, wherein the method takes into account the possibility of DNA crossovers that may occur during meiosis.

28. The method of claim 18, wherein the maternal haplotypic genetic data are determined by inference using diploid genetic data measured from one or more blastomeres, diploid genetic data from one or more parents, and haploid genetic data from the father.

29. The method of claim 18, wherein the maternal haplotypic genetic data that are used in the method have been determined without the use of genetic data from a born child, and without the use of genetic data from a parent of the mother, and without making use of a haplotypic tissue sample from the mother.

30. The method of claim 18, wherein the increase in fidelity of the allele calls in the genetic data of the target individual is done in the context of preimplantation or prenatal genetic diagnosis for a genetic disease, and where the genetic data of only one related individual who is a carrier of the disease is used.

31. The method of claim 18, where the target individual is an embryo, and where the determination is done for the purpose of selecting embryos for transfer in the context of IVF, and where the related individuals are taken from the group consisting of the father, the mother, one or more embryos that are from the same parents, one or more sperm from the father, and combinations thereof.

32. The method of claim 18, where the target individual is a fetus, and where the determination is done in the context of prenatal diagnosis.

33. The method of claim 18, wherein the method is run alongside or in conjunction with a method that determines the number of copies of a given chromosome segment present in the target individual, and where both methods use the same cell, or group of cells, from the target individual as a source of genetic material.