Systems and methods to detect rare mutations and copy number variation

• US 10,041,127 B2
• Filed: 09/04/2013
• Issued: 08/07/2018
• Est. Priority Date: 09/04/2012
• Status: Active Grant

• Current Assignee: Guardant Health Inc.
• Original Assignee: Guardant Health Inc.
• Inventors: Talasaz, AmirAli
• Primary Examiner(s): Horlick, Kenneth R
• Application Number:
  US14/425,189
• Publication Number:
  US 20150368708A1
• Time in Patent Office: 1,798 Days
• Field of Search: 435 612, 435 911, 435 912
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• 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 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• 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

The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Claims

1. A method, comprising:

a) non-uniquely tagging a population of extracellular polynucleotides obtained from a bodily sample from a subject to produce a population of non-uniquely tagged extracellular polynucleotides;

b) sequencing the population of non-uniquely tagged extracellular polynucleotides to produce a base call at a mappable position in the non-uniquely tagged extracellular polynucleotides; and

c) for the base call at the mappable position, measuring a frequency of unique molecules containing the base call in relation to the total number of unique molecules having a base call;

wherein a frequency of unique molecules containing the base call at the mappable position that is above a set measure of deviation from a plurality of reference sequences indicates a rare mutation at the mappable position.

2. The method of claim 1, further comprising isolating extracellular polynucleotides from the bodily sample.

3. The method of claim 1, further comprising amplifying the population of non-uniquely tagged extracellular polynucleotides prior to sequencing.

4. The method of claim 1, wherein non-uniquely tagging comprises attaching one or more barcodes to the population of extracellular polynucleotides prior to sequencing.

5. The method of claim 4, wherein a given barcode from the one or more barcodes comprises a fixed or semi-random oligonucleotide sequence that in combination with a diversity of molecules sequenced from a select region enables identification of unique molecules.

6. The method of claim 1, further comprising selectively enriching regions from a genome or transcriptome of the subject from the population of non-uniquely tagged extracellular polynucleotides prior to sequencing.

7. The method of claim 3, wherein the population of extracellular polynucleotides is non-uniquely tagged prior to amplifying.

8. The method of claim 1, wherein producing the base call comprises voting, averaging, maximum a posteriori or maximum likelihood detection, dynamic programming, Bayesian methods, hidden Markov methods, or support vector machine methods.

9. The method of claim 1, wherein sequencing comprises obtaining sequencing reads, which sequencing reads are used to generate a set of consensus sequences, wherein measuring the frequency comprises detecting a presence of a sequence variation in the set of consensus sequences compared with the plurality of reference sequences.

10. The method of claim 1, further comprising detecting a presence of sequence variations for a panel of oncogenes.

11. The method of claim 1, wherein sequencing comprises obtaining sequencing reads, which sequencing reads are mapped, wherein mapping the sequence reads comprises using information about a length of each of the sequence reads.

12. The method of claim 1, wherein the population of extracellular polynucleotides is tagged with from 10 to 100,000 different identifiers.

13. The method of claim 1, wherein the population of extracellular polynucleotides is tagged with n different unique identifiers, wherein n is no more than 100*z, wherein z is a mean of an expected number of duplicate molecules having the same start and stop positions in the bodily sample.

14. The method of claim 1, wherein the population of extracellular polynucleotides obtained from the bodily sample comprises no more than 100 nanograms of extracellular polynucleotides.

15. The method of claim 1, further comprising converting the population of extracellular polynucleotides into a population of non-uniquely tagged parent polynucleotides at a conversion efficiency of at least 30%.

16. The method of claim 1, further comprising converting the population of extracellular polynucleotides into a population of non-uniquely tagged parent polynucleotides at a conversion efficiency of at least 50%.

17. The method of claim 1, further comprising converting the population of extracellular polynucleotides into a population of non-uniquely tagged parent polynucleotides at a conversion efficiency of at least 80%.

18. The method of claim 1, further comprising selectively enriching regions from a genome or transcriptome from the population of extracellular polynucleotides prior to sequencing.

19. The method of claim 1, wherein sequencing comprises obtaining sequencing reads.

20. The method of claim 19, further comprising grouping the sequencing reads into families.

21. The method of claim 20, wherein a given family comprises duplicate sequencing reads.

22. The method of claim 21, wherein a given family comprises sequencing reads with the same start and stop positions and barcodes.

23. The method of claim 1, wherein the measure of deviation is a measure of variance.

24. The method of claim 1, wherein the population of extracellular polynucleotides is tagged with from 50 to 10,000 different identifiers.