Size-based analysis of tumor dna

Patent metadata

Field	Value
Publication number	US-2017235877-A1
Application number	US-201715587662-A
Country	US
Kind code	A1
Filing date	May 5, 2017
Priority date	Mar 8, 2012
Publication date	Aug 17, 2017
Grant date	—

Abstract

A classification of a level of cancer in an organism is determined by analyzing a biological sample of the organism. The biological sample comprises clinically-relevant DNA and other DNA. At least some of the DNA is cell-free in the biological sample. An amount of a first set of DNA fragments from the biological sample corresponding to each of a plurality of sizes is measured. A first value of a first parameter is calculated based on the amounts of DNA fragments at the plurality of sizes. The first value is compared to a reference value. A classification of a level of cancer in the organism is determined based on the comparison.

First claim

What is claimed is:

1 . A method for analyzing a biological sample of a subject to generate a classification of a level of cancer in the subject, the method comprising:
(a) obtaining the biological sample of the subject, the biological sample comprising a plurality of cell-free nucleic acid molecules; (b) sequencing the plurality of cell-free nucleic acid molecules to obtain sequence reads, wherein each sequence read of the sequence reads comprises at least one outermost nucleotide of a given cell-free nucleic acid molecule of the plurality of cell-free nucleic acid molecules; (c) aligning the sequence reads to a reference genome, thereby obtaining a set of genomic coordinates including a genomic coordinate of the at least one outermost nucleotide for each of the given cell-free nucleic acid molecules; (d) calculating a value based on a number of sequence reads of the sequence reads of (b) aligning to the set of genomic coordinates of (c); and (e) generating the classification of the level of cancer in the subject based on processing the value against a reference value.

2 . The method of claim 1 , wherein the biological sample is selected from the group consisting of blood, plasma, serum, urine and saliva.

3 . The method of claim 1 , wherein the set of genomic coordinates correspond to (i) the genomic coordinate of the at least one outermost nucleotide of the cell-free nucleic acid molecules or (ii) a region of the reference genome.

4 . The method of claim 3 , wherein the region of the reference genome is pre-determined.

5 . The method of claim 1 , wherein the sequencing comprises paired-end sequencing.

6 . The method of claim 1 , wherein each sequence read of the sequence reads comprises at least about 30 nucleotides from at least one end of the cell-free nucleic acid molecule.

7 . The method of claim 1 , wherein the value corresponds to a number of sequence reads having at least one end aligning to one or more genomic coordinates of the set of genomic coordinates.

8 . The method of claim 1 , wherein the value corresponds to a first number of sequence reads having at least one end aligning to a genomic coordinate of the set of genomic coordinates normalized by a second number of sequence reads spanning the genomic coordinate.

9 . The method of claim 1 , wherein the classification corresponds to a size or an existence of cancer, a stage of the cancer, or a size of a tumor.

10 . The method of claim 1 , wherein at least a portion of the plurality of cell-free nucleic acid molecules are derived from a tumor.

11 . A non-transitory computer-readable medium comprising machine executable code that, upon execution by one or more computer processors, cause the one or more computer processors to implement a method for analyzing a biological sample of a subject to generate a classification of a level of cancer in the subject, the method comprising:
(a) obtaining sequence reads from sequencing a plurality of cell-free nucleic acid molecules from the biological sample of the subject, wherein each sequence read of the sequence reads comprises at least one outermost nucleotide of a given cell-free nucleic acid molecule of the plurality of cell-free nucleic acid molecules; (b) aligning the sequence reads to a reference genome, thereby obtaining a set of genomic coordinates including a genomic coordinate of the at least one outermost nucleotide for each of the given cell-free nucleic acid molecules; (c) calculating a value based at least in part on a number of sequence reads of the sequence reads of (a) aligning to the set of genomic coordinates of (b); and (d) generating the classification of the level of cancer in the subject, which generating is based at least in part on processing the value against a reference value.

12 . The non-transitory computer-readable medium of claim 11 , wherein the biological sample is selected from the group consisting of blood, plasma, serum, urine and saliva.

13 . The non-transitory computer-readable medium of claim 11 , wherein the set of genomic coordinates correspond to (i) the at least one outermost nucleotide of the cell-free nucleic acid molecule or (ii) a region of the reference genome.

14 . The non-transitory computer-readable medium of claim 13 , wherein the region of the reference genome is pre-determined.

15 . The non-transitory computer-readable medium of claim 11 , wherein the plurality of cell-free nucleic acid molecules are sequenced by paired-end sequencing.

16 . The non-transitory computer-readable medium of claim 11 , wherein the sequence read comprises at least about 30 nucleotides from at least one end of the cell-free nucleic acid molecule.

17 . The non-transitory computer-readable medium of claim 11 , wherein the value corresponds to a number of sequence reads having at least one end aligning to one or more genomic coordinates of the set of genomic coordinates.

18 . The non-transitory computer-readable medium of claim 11 , wherein the value corresponds to a first number of sequence reads having at least one end aligning to a genomic coordinate of the set of genomic coordinates normalized by a second number of sequence reads spanning the genomic coordinate.

19 . The non-transitory computer-readable medium of claim 11 , wherein the classification corresponds to a size of an existence of cancer, a stage of the cancer, or a size of a tumor.

20 . The non-transitory computer-readable medium of claim 11 , wherein at least a portion of the plurality of cell-free nucleic acid molecules are derived from a tumor.

21 . A system for analyzing a biological sample of a subject to generate a classification of a level of cancer in the subject, the system comprising:
one or more computer processors that are individually or collectively programmed to:
(a) obtain sequence reads from sequencing a plurality of cell-free nucleic acid molecules from the biological sample of the subject, wherein each sequence read of the sequence reads comprises at least one outermost nucleotide of a given cell-free nucleic acid molecule of the plurality of cell-free nucleic acid molecules;
(b) align the sequence reads to a reference genome, thereby obtaining a set of genomic coordinates including a genomic coordinate of the at least one outermost nucleotide for each of the given cell-free nucleic acid molecules;
(c) calculate a value based at least in part on a number of sequence reads of the sequence reads of (a) aligning to the set of genomic coordinates of (b); and
(d) generate the classification of the level of cancer in the subject, which is based at least in part on processing the value against a reference value.

22 . The system of claim 21 , wherein the biological sample is selected from the group consisting of blood, plasma, serum, urine and saliva.

23 . The system of claim 21 , wherein the set of genomic coordinates correspond to (i) the at least one outermost nucleotide of the cell-free nucleic acid molecule or (ii) a region of the reference genome.

24 . The system of claim 23 , wherein the region of the reference genome is pre-determined.

25 . The system of claim 21 , wherein the plurality of cell-free nucleic acid molecules is sequenced by paired-end sequencing.

26 . The system of claim 21 , wherein the sequence read comprises at least about 30 nucleotides from at least one end of the cell-free nucleic acid molecule.

Assignees

• Univ Hong Kong Chinese

Inventors

• Lo Yuk Ming Dennis
• Chiu Wai Kwun Rossa
• Chan Kwan Chee
• Zheng Wenli
• Jiang Peiyong
• Liao Jiawei

Classifications

• G16H10/40

  for data related to laboratory analysis, e.g. patient specimen analysis · CPC title

• C12Q2600/112

  Disease subtyping, staging or classification · CPC title

• G16B20/00

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title