Methods and systems for detecting genetic variants
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
1. A method for treating a subject having a cancer associated with one or more genetic variants, comprising:
(a) selecting the subject having the cancer, comprising:
(i) providing a sample of cell-free deoxyribonucleic acid (cfDNA) molecules from the subject having the cancer;
(ii) ligating adapters to a plurality of the cfDNA molecules to produce tagged parent polynucleotides;
(iii) amplifying the tagged polynucleotides to produce tagged progeny polynucleotides;
(iv) enriching the tagged progeny polynucleotides with a sequencing panel to produce enriched polynucleotides, wherein the sequencing panel comprises oligonucleotide probes comprising genomic regions from each of the following genes:
ALK, APC, BRAF, CDKN2A, EGFR, ERBB2, FBXW7, KRAS, MYC, NOTCH1, NRAS, PIK3CA, PTEN, RB1, TP53, MET, AR, ABL1, AKT1, ATM, CDH1, CSF1R, CTNNB1, ERBB4, EZH2, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, MLH1, MPL, NPM1, PDGFRA, PTPN11, RET, SMAD4, SMARCB1, SMO, SRC, STK11, VHL, TERT, CCND1, CDK4, CDKN2B, RAF1, BRCA1, CCND2, CDK6, NF1, ARIDIA, BRCA2, CCNE1, ESR1, RIT1, GATA3, MAP2K1, RHEB, ROS1, ARAF, MAP2K2, NFE2L2, RHOA, and NTRK1;
(v) sequencing one or more genomic regions from each gene of the sequencing panel from a plurality of enriched polynucleotides to generate sequence reads;
(vi) determining, from a plurality of the sequence reads, a presence of one or more genetic variants from the one or more genomic regions; and
(b) treating the subject with a therapy based on determining the presence of the one or more genetic variants.
2. The method of claim 1 , wherein the sample comprises 1 nanogram (ng) to 100 ng of cfDNA molecules.
3. The method of claim 1 , wherein the adapters are ligated to the plurality of the cfDNA molecules using more than a 20× excess of adapters as compared to the cfDNA molecules from the sample to attach at least 20% of the cfDNA molecules with adapters.
4. The method of claim 3 , wherein the adapters are ligated to the plurality of the cfDNA molecules using more than a 50× excess of adapters as compared to the cfDNA molecules from the sample.
5. The method of claim 4 , wherein the adapters are ligated to the plurality of the cfDNA molecules using more than a 90× excess of adapters as compared to the cfDNA molecules from the sample.
6. The method of claim 4 , wherein at least 40% of the cfDNA molecules are attached with the adapters.
7. The method of claim 1 , wherein the adapters comprise molecular barcodes.
8. The method of claim 3 , wherein the adapters comprise molecular barcodes.
9. The method of claim 7 , wherein the plurality of the cfDNA molecules are tagged with n different combinations of molecular barcodes, wherein n is at least 2 and no more than 100,000*z, wherein z is a mean of an expected number of duplicate molecules in the sample of cfDNA molecules that map to identical start and stop positions on a reference sequence.
10. The method of claim 9 , wherein the plurality of the cfDNA molecules are tagged with n different combinations of molecular barcodes, wherein n is at least 2 and no more than 10,000*z, wherein z is a mean of an expected number of duplicate molecules in the sample of cfDNA molecules that map to identical start and stop positions on a reference sequence.
11. The method of claim 10 , wherein the plurality of the cfDNA molecules are tagged with n different combinations of molecular barcodes, wherein n is at least 2 and no more than 1,000*z, wherein z is a mean of an expected number of duplicate molecules in the sample of cfDNA molecules that map to identical start and stop positions on a reference sequence.
12. The method of claim 11 , wherein the plurality of the cfDNA molecules are tagged with n different combinations of molecular barcodes, wherein n is at least 2 and no more than 100*z, wherein z is a mean of an expected number of duplicate molecules in the sample of cfDNA molecules that map to identical start and stop positions on a reference sequence.
13. The method of claim 9 , wherein z is between 2 and 8.
14. The method of claim 11 , wherein z is between 2 and 8.
15. The method of claim 1 , further comprising amplifying a plurality of enriched polynucleotides prior to the sequencing.
16. The method of claim 7 , further comprising mapping a plurality of sequence reads to a reference sequence.
17. The method of claim 16 , further comprising grouping sequence reads into families based on (i) sequence information from the molecular barcodes, or (ii) a combination of sequence information from the molecular barcodes and a start base position of a given sequence read at which the given sequence read is determined to start mapping to the reference sequence and a stop base position of the given sequence read at which the given sequence read is determined to stop mapping to the reference sequence.
18. The method of claim 17 , wherein each family comprises at least 10 sequence reads.
19. The method of claim 17 , further comprising generating consensus sequences from (i) paired reads corresponding to sequence reads from a first strand and a second complementary strand from a cfDNA molecule in the plurality of tagged cfDNA molecules, and (ii) unpaired reads corresponding to sequence reads from a first tagged strand having no second tagged complementary strand from a cfDNA molecule from the tagged cfDNA molecules.
20. The method of claim 19 , wherein each base in a plurality of consensus sequences from among the consensus sequences generated is covered by at least 3,000 different families.
21. The method of claim 20 , further comprising determining with a programmed computer processor a quantitative measure of tagged parent polynucleotides that map to the genomic locus based on the quantitative measures of the paired reads and the unpaired reads.
22. The method of claim 21 , further comprising determining a quantitative measure of unseen sequence reads for which neither strand of the cfDNA molecule is detected from among the tagged parent polynucleotides, wherein the quantitative measure of unseen sequence reads is calculated based on the quantitative measure of the paired reads and the quantitative measure of the unpaired reads.
23. The method of claim 22 , further comprising determining with a programmed computer processor a total number of tagged parent polynucleotides that map to a locus of a reference sequence based on the quantitative measures of paired reads, unpaired reads, and unseen sequence reads.
24. The method of claim 1 , wherein the cancer is selected from one of non-small cell lung cancer, colorectal cancer, thyroid cancer, pancreatic cancer, breast cancer, squamous cell carcinoma, and melanoma.
25. The method of claim 24 , wherein the treatment comprises a chemotherapy.
26. The method of claim 1 , wherein:
the cancer is non-small cell lung cancer, thyroid cancer, or melanoma,
the one or more genetic variants is associated with a BRAF V600E mutation, and
the treatment comprises dabrafenib.
27. The method of claim 1 , wherein:
the cancer is non-small cell lung cancer,
the one or more genetic variants is associated with a EGFR L858R mutation, and
the treatment comprises erlotinib.
28. The method of claim 1 , wherein:
the cancer is non-small cell lung cancer,
the one or more genetic variants is associated with a EGFR T790M mutation, and
the treatment comprises administering a drug responsive to the EGFR T790M mutation.
29. The method of claim 28 , wherein the drug is ruxolitinib.
30. The method of claim 28 , wherein the method further comprises determining that a subject is resistant to erlotinib based on the determination of the presence of the one or more genetic variants associated with the EGFR T790M mutation.