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

• US 10,392,664 B2
• Filed: 01/26/2018
• Issued: 08/27/2019
• Est. Priority Date: 07/29/2005
• Status: Active Grant

• Current Assignee: Natera Incorporated (Natera)
• Original Assignee: Natera Incorporated (Natera)
• Inventors: Rabinowitz, Matthew, Banjevic, Milena, Demko, Zachary, Johnson, David, Kijacic, Dusan, Petrov, Dimitri, Sweetkind-Singer, Joshua, Xu, Jing
• Primary Examiner(s): Bertagna, Angela M.
• Application Number:
  US15/881,488
• Publication Number:
  US 20180155792A1
• Time in Patent Office: 578 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2537/16 Assays for determining copy number or wherein the copy number is of special importance
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G06N 7/01 Probabilistic graphical models, e.g. probabilistic networks
• 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. 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.

Claims

1. A method of detecting aneuploidy of one or more chromosomes of interest in a fetus, the method comprising:

obtaining fetal and maternal chromosome segments from cell-free DNA in a maternal blood sample comprising chromosome segments from the one or more chromosomes of interest and chromosome segments from one or more reference chromosomes;

ligating at least one adapter comprising a universal amplification sequence to the chromosome segments to obtain adapter-ligated chromosome segments;

performing universal amplification of the adapter-ligated chromosome segments to generate amplified chromosome segments;

measuring the amounts of the amplified chromosome segments; and

detecting aneuploidy of the one or more chromosomes of interest using the amounts of amplified chromosome segments from the one or more chromosomes of interest and the amounts of amplified chromosome segments from the one or more reference chromosomes.

2. The method of claim 1, wherein a statistical difference is detected by computing a standard deviation and a mean value for the measured amounts for each of the one or more chromosomes of interest and for each of the one or more reference chromosomes, and comparing the mean value for each of the chromosomes of interest to the mean value of the reference chromosome in terms of the standard deviations.

3. The method of claim 1, wherein the method further comprises comparing the measured amounts of chromosome segments for the one or more chromosomes of interest from the maternal blood sample with measured amounts of chromosome segments for the one or more chromosomes of interest from maternal blood samples that are disomic for the one or more chromosomes of interest.

4. The method of claim 1, wherein the measuring is performed irrespective of allele value.

5. The method of claim 1, wherein the measuring comprises measurement of alleles having 100% penetrance.

6. The method of claim 1, wherein the measured amounts for different alleles are combined.

7. The method of claim 1, wherein the amounts of amplified chromosome segments are measured using sequencing.

8. The method of claim 1, wherein the chromosome segments from the one or more chromosomes of interest map to chromosomes 13, 18, and/or 21, and the method is used to detect trisomy at chromosomes 13, 18, and/or 21.

9. The method of claim 1, wherein the measuring comprises quantitative allele measurements.

10. The method of claim 1, wherein the measured amounts of amplified chromosome segments from each chromosome are combined into a single measurement for each chromosome.

11. The method of claim 1, wherein aneuploidy of the one or more chromosomes of interest is detected by comparing the amount of amplified chromosome segments from the one or more chromosomes of interest in the maternal blood sample to a threshold determined from normal samples.