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

• US 10,083,273 B2
• Filed: 07/23/2013
• Issued: 09/25/2018
• 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 MARIE
• Application Number:
  US13/949,212
• Publication Number:
  US 20140032128A1
• Time in Patent Office: 1,890 Days
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• 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
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16H 70/60 relating to pathologies

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 for measuring the amounts of fetal chromosome segments in a maternal blood sample, comprising:

obtaining fetal and maternal chromosome segments from cell-free DNA in a maternal blood sample;

ligating at least one adapter to the chromosome segments, wherein the at least one adapter comprises a universal amplification sequence;

performing universal amplification using universal primers that bind to the universal amplification sequence to generate amplified chromosome segments;

performing clonal amplification of the amplified chromosome segments to generate clonally amplified chromosome segments; and

measuring the amounts of clonally amplified fetal chromosome segments by performing next generation sequencing, wherein the measuring comprises quantitative allele measurements performed irrespective of allele value.

2. The method of claim 1, wherein the universal amplification is universal PCR.

3. The method of claim 1, wherein the fetal chromosome segments map to chromosomes 13, 18, and/or 21.

4. The method of claim 3, wherein the method further comprises detecting trisomy at chromosomes 13, 18, and/or 21.

5. The method of claim 1, wherein the method further comprises comparing the measured amounts of fetal chromosome segments for a target chromosome from the maternal blood sample with measured amounts of fetal chromosome segments for the target chromosome from reference maternal blood samples that are disomic for the target chromosome.

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

7. The method of claim 1, wherein the next generation sequencing is performed using sequencing-by-synthesis.

8. The method of claim 1, wherein the clonally amplified maternal chromosome segments are measured along with the clonally amplified fetal chromosome segments by performing next generation sequencing.