Diagnosing fetal chromosomal aneuploidy using massively parallel genomic sequencing

• US 8,972,202 B2
• Filed: 07/18/2014
• Issued: 03/03/2015
• Est. Priority Date: 07/23/2007
• Status: Active Grant

• Current Assignee: Chinese University of Hong Kong
• Original Assignee: Chinese University of Hong Kong
• Inventors: Lo, Yuk-Ming Dennis, Chiu, Rossa Wai Kwun, Chan, Kwan Chee
• Primary Examiner(s): SIMS, JASON M
• Application Number:
  US14/335,374
• Publication Number:
  US 20140329695A1
• Time in Patent Office: 228 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 2521/331 Methylation site specific nuclease
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2537/159 Reduction of complexity, e.g. amplification of subsets, removing duplicated genomic regions
• CPC Class Codes: C12Q 2537/16 Assays for determining copy number or wherein the copy number is of special importance
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 2800/387 Down syndrome; Trisomy 18; Trisomy 13
• 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 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.

Claims

1. A method for determining the presence or absence of fetal aneuploidy from a plasma or serum sample from a pregnant female subject, wherein the sample comprises cell-free nucleic acid molecules from the genome of both the female subject and a fetus, comprising:

(a) performing random massively parallel DNA sequencing on at least a portion of the cell-free nucleic acid molecules to generate random sequenced tags;

(b) aligning at least a portion of the sequenced tags obtained in step (a) to a reference genome;

(c) using alignment data obtained in step (b) to determine a first amount of sequenced tags originating from a first chromosome and a second amount of sequenced tags originating from at least one second chromosome;

(d) determining a parameter based on the first amount and second amount, wherein the parameter is a frequency of sequenced tags originating from the first chromosome that is normalized based on the relative size of the first chromosome; and

(e) comparing the parameter to a cutoff value to determine whether a fetal chromosomal aneuploidy exists for the first chromosome.

2. The method of claim 1, wherein the random massively parallel DNA sequencing is performed at less than 100% genomic coverage.

3. The method of claim 1, wherein the first chromosome is selected from the group consisting of chromosome 21, chromosome 18, chromosome 3, chromosome X, and chromosome Y.

4. The method of claim 1, wherein the at least one second chromosome consists of a single chromosome.

5. The method of claim 1, wherein the at least one second chromosome comprises two or more chromosomes.

6. The method of claim 1, wherein the sequenced cell-free nucleic acid molecules represent a portion of the human genome selected from the group consisting of at least about 0.1%, 0.5%, 1%, 5%, 10%, 20%, and 30% of the human genome.