Diagnosing cancer using genomic sequencing

• US 9,121,069 B2
• Filed: 07/08/2013
• Issued: 09/01/2015
• Est. Priority Date: 07/23/2007
• Status: Active Grant

• Current Assignee: Chinese University of Hong Kong
• Original Assignee: Chinese University of Hong Kong
• Inventors: Chiu, Rossa Wai Kwun, Lo, Yuk-Ming Dennis, Chan, Kwan Chee
• Primary Examiner(s): SIMS, JASON M
• Application Number:
  US13/937,162
• Publication Number:
  US 20130310263A1
• Time in Patent Office: 785 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• 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: 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: G16B 30/10 Sequence alignment; Homology search

Abstract

Methods, systems, and apparatus determine whether a first chromosomal region exhibits a deletion or an amplification associated with cancer in a sample from a subject (e.g., where the sample includes a mixture of cell-free DNA from tumor cells and non-malignant cells. Nucleic acid molecules of the biological sample are sequenced. Respective amounts of a clinically-relevant chromosomal region and of background chromosomal region(s) 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 first chromosomal region exhibits a deletion or an amplification associated with cancer.

Claims

1. A method of analyzing a biological sample of a human for deletions or amplifications in one or more chromosomal regions associated with cancer, the biological sample including cell-free nucleic acid molecules originating from non-malignant cells and potentially from tumor cells associated with cancer, the method comprising:

performing a random sequencing of nucleic acid molecules from biological sample by;

attaching adaptors to at least one end of the nucleic acid molecules; and

sequencing, using the adaptors, the nucleic acid molecules to obtain sequences, including at least 120,000 sequences;

receiving, at a computer system, the sequences obtained from the random sequencing of nucleic acid molecules contained in the biological sample;

aligning, by the computer system, at least a portion of the sequences to a human genome;

determining, by the computer system, a first amount of sequences identified as aligning to a first chromosomal region that is part of a first chromosome, wherein a deletion or an amplification in the first chromosomal region is associated with cancer;

determining, by the computer system, a second amount of sequences identified as aligning to one or more second chromosomal regions;

determining a first parameter from the first amount and the second amount, wherein the first parameter represents a relative amount between the first and second amounts; and

comparing the first parameter to one or more cutoff values to determine a classification of whether the first chromosomal region exhibits a deletion or an amplification associated with cancer in the human.

2. The method of claim 1, wherein the classification includes whether the first chromosomal region is amplified, and wherein a classification of amplification is made when the first parameter is greater than a first cutoff value of the one or more cutoff values.

3. The method of claim 1, wherein the classification includes whether the first chromosomal region has a deletion, and wherein a classification of deletion is made when the first parameter is less than a first cutoff value of the one or more cutoff values.

4. The method of claim 1, further comprising:

determining a third amount of sequences identified as aligning to a third chromosomal region, wherein an aberration in the third chromosomal region is associated with cancer;

determining a second parameter for the third chromosomal region, wherein the second parameter represents a relative amount between the third and second amounts;

comparing the second parameter to one or more cutoff values to determine a classification of whether the third chromosomal region exhibits a deletion and/or an amplification associated with cancer; and

using the classifications of the first and third chromosomal regions to determine whether the human has cancer.

5. The method of claim 1, wherein the biological sample is blood, plasma, serum, urine or saliva.

6. The method of claim 1, wherein the first parameter is calculated from a ratio that includes the first amount.

7. The method of claim 6, wherein the ratio provides a percentage of the sequences identified as aligning to the first chromosomal region among the sequences.

8. The method of claim 6, wherein the ratio is obtained from any one or more of a fractional count of the number of sequenced tags, a fractional number of sequenced nucleotides, and a fractional length of accumulated sequences.

9. The method of claim 6, wherein the sequences that are used to determine the first amount are selected to be less than a specified number of bases.

10. The method of claim 9, wherein the specified number of bases is 300 bases, 200 bases, or 100 bases.

11. The method of claim 1, wherein the nucleic acid molecules of the biological sample have been enriched for sequences originating from the first chromosomal region.

12. The method of claim 1, wherein the nucleic acid molecules of the biological sample have been enriched for sequences less than 300 bases or enriched for sequences less than 200 bases.

13. The method of claim 1, wherein the nucleic acid molecules of the biological sample have been amplified using a polymerase chain reaction.

14. The method of claim 1, wherein the aligned portion represents at least a pre-determined fraction of the human genome.

15. The method of claim 1, wherein the fraction represents at least 0.1% of the human genome or represents at least 0.5% of the human genome.

16. The method of claim 1, wherein at least one of the cutoff values is derived from a percentage of tumor cells in the biological sample.

17. The method of claim 1, wherein at least one of the cutoff values is a reference value established in a normal biological sample.

18. The method of claim 17, wherein the at least one cutoff value is determined from a mean of the value of the first parameter in a plurality of normal biological samples.

19. The method of claim 1, further comprising:

identifying an amount of tumor DNA in the biological sample; and

calculating a number N of sequences to be analyzed based on a desired accuracy.

20. The method of claim 1, wherein the sequences identified as aligning to the first chromosomal region uniquely align to the first chromosomal region.

21. The method of claim 1, wherein the sequences identified as aligning to the one or more of the second chromosomal regions uniquely align to only one of the second chromosomal regions.

22. The method of claim 1, wherein the human genome is repeat-masked.

23. The method of claim 1, wherein the first amount is determined based on a pool of sequenced tags that align to a plurality of positions of the first chromosomal region.

24. The method of claim 23, wherein which part of the human genome that the sequenced tags are aligned is not pre-determined.

25. The method of claim 24, wherein the part of the human genome corresponding to the sequenced tags aligned to the first chromosomal region is not pre-determined.

26. The method of claim 6, wherein the first parameter is a fractional representation of sequences identified as aligning to the first chromosomal region, the fractional representation being a measure of a proportion of nucleic acid molecules in the biological sample that are from the first chromosomal region.

27. The method of claim 26, wherein the one or more cutoff values take into account a size of the first chromosomal region relative to a size of the one or more second chromosomal regions.

28. The method of claim 1, wherein the sequencing includes paired-end sequencing, and wherein aligning each sequence includes aligning paired-end sequences.

29. The method of claim 1, wherein the cell-free nucleic acid molecules are DNA fragments.