Top

06-11-2017 | Liquid biopsy | Article

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

Journal: Nature Communications

Authors: Viktor A. Adalsteinsson, Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Gregory Gydush, Sarah C. Reed, Denisse Rotem, Justin Rhoades, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignaty Leshchiner, Jaegil Kim, Chip Stewart, Mara Rosenberg, Joshua M. Francis, Cheng-Zhong Zhang, Ofir Cohen, Coyin Oh, Huiming Ding, Paz Polak, Max Lloyd, Sairah Mahmud, Karla Helvie, Margaret S. Merrill, Rebecca A. Santiago, Edward P. O’Connor, Seong H. Jeong, Rachel Leeson, Rachel M. Barry, Joseph F. Kramkowski, Zhenwei Zhang, Laura Polacek, Jens G. Lohr, Molly Schleicher, Emily Lipscomb, Andrea Saltzman, Nelly M. Oliver, Lori Marini, Adrienne G. Waks, Lauren C. Harshman, Sara M. Tolaney, Eliezer M. Van Allen, Eric P. Winer, Nancy U. Lin, Mari Nakabayashi, Mary-Ellen Taplin, Cory M. Johannessen, Levi A. Garraway, Todd R. Golub, Jesse S. Boehm, Nikhil Wagle, Gad Getz, J. Christopher Love, Matthew Meyerson

Publisher: Nature Publishing Group UK

Abstract

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

Diehl, F. et al. Circulating mutant DNA to assess tumor dynamics. Nat. Med. 14, 985–990 (2008).CrossRefPubMed

Dawson, S.-J. et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N. Engl. J. Med. 368, 1199–1209 (2013).CrossRefPubMed

Newman, A. M. et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med. 20, 548–554 (2014).CrossRefPubMedPubMedCentral

Bettegowda, C. et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci. Transl. Med. 6, 224ra24 (2014).CrossRefPubMedPubMedCentral

Russo, M. et al. Tumor heterogeneity and lesion-specific response to targeted therapy in colorectal cancer. Cancer Discov. 6, 147–153 (2015).CrossRefPubMedPubMedCentral

Lanman, R. B. et al. Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA. PLoS ONE 10, e0140712 (2015).CrossRefPubMedPubMedCentral

Newman, A. M. et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat. Biotechnol. 34, 547–555 (2016).CrossRefPubMedPubMedCentral

Murtaza, M. et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497, 108–112 (2013).CrossRefPubMedADS

Murtaza, M. et al. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat. Commun. 6, 8760 (2015).CrossRefPubMedPubMedCentral

10.

Butler, T. M. et al. Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease. PLoS ONE 10, e0136407 (2015).CrossRefPubMedPubMedCentral

11.

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).CrossRefPubMedPubMedCentral

12.

Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).CrossRefPubMedPubMedCentralADS

13.

Heitzer, E. et al. Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. Genome Med. 5, 30 (2013).CrossRefPubMedPubMedCentral

14.

Leary, R. J. et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci. Transl. Med. 4, 162ra154 (2012).CrossRefPubMedPubMedCentral

15.

Chan, K. C. A. et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc. Natl Acad. Sci. USA 110, 18761–18768 (2013).CrossRefPubMedPubMedCentralADS

16.

Carter, S. L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).CrossRefPubMedPubMedCentral

17.

Ha, G. et al. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res. 24, 1881–1893 (2014).CrossRefPubMedPubMedCentral

18.

Snyder, M. W., Martin, K., Hill, A. J., Daza, R. M. & Shendure, J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164, 57–68 (2016).CrossRefPubMedPubMedCentral

19.

Szpechcinski, A. et al. Cell-free DNA levels in plasma of patients with non-small-cell lung cancer and inflammatory lung disease. Br. J. Cancer 113, 476–483 (2015).CrossRefPubMedPubMedCentral

20.

Robinson, D. et al. Integrative clinical genomics of advanced prostate cancer. Cell 161, 1215–1228 (2015).CrossRefPubMedPubMedCentral

21.

Grasso, C. S. et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 487, 239–243 (2012).CrossRefPubMedPubMedCentralADS

22.

Van Allen, E. M. et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat. Med. 20, 682–688 (2014).CrossRefPubMedPubMedCentral

23.

Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).CrossRefPubMedPubMedCentralADS

24.

Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2014).CrossRefPubMedPubMedCentralADS

25.

Ciriello, G. et al. Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163, 506–519 (2015).CrossRefPubMedPubMedCentral

26.

Cohen, O. et al. Whole Exome and Transcriptome Sequencing of Resistant ER+ Metastatic Breast Cancer. In Proc. 2016 San Antonio Breast Cancer Symposium Abstr. S1-01 (2016).

27.

Alexandrov, L. B., Nik-Zainal, S., Siu, H. C., Leung, S. Y. & Stratton, M. R. A mutational signature in gastric cancer suggests therapeutic strategies. Nat. Commun. 6, 8683 (2015).CrossRefPubMedPubMedCentralADS

28.

Kasar, S. et al. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat. Commun. 6, 8866 (2015).CrossRefPubMedPubMedCentral

29.

Kim, J. et al. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat. Genet. 48, 600–606 (2016).CrossRefPubMedPubMedCentral

30.

Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).CrossRefPubMedPubMedCentral

31.

Mateo, J. et al. DNA-repair defects and olaparib in metastatic prostate cancer. N. Engl. J. Med. 373, 1697–1708 (2015).CrossRefPubMedPubMedCentral

32.

Rizvi, N. A. et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348, 124–128 (2015).CrossRefPubMedPubMedCentralADS

33.

Hoof, I. et al. NetMHCpan, a method for MHC class i binding prediction beyond humans. Immunogenetics 61, 1–13 (2009).CrossRefPubMed

34.

Shukla, S. A. et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol. 33, 1152–1158 (2015).CrossRefPubMedPubMedCentral

35.

Nielsen, M. et al. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2, e796 (2007).CrossRefPubMedPubMedCentralADS

36.

Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).PubMedPubMedCentral

37.

Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).CrossRefADS

38.

Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353–357 (2015).CrossRefPubMedPubMedCentral

39.

Brastianos, P. K. et al. Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. Cancer Discov. 5, 1164–1177 (2015).CrossRefPubMedPubMedCentral

40.

Sun, K. et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc. Natl Acad. Sci. USA 112, E5503–E5512 (2015).CrossRefPubMedPubMedCentral

41.

Lohr, J. G. et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat. Biotechnol. 32, 479–484 (2014).CrossRefPubMedPubMedCentral

42.

Oh, W. K. et al. Development of an integrated prostate cancer research information system. Clin. Genitourin. Cancer 5, 61–66 (2006).CrossRefPubMed

43.

Ha, G. et al. Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res. 22, 1995–2007 (2012).CrossRefPubMedPubMedCentral

44.

Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 1–6 (2010).CrossRef

45.

Yau, C. et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol. 11, R92 (2010).PubMedPubMedCentral

46.

Chapman, M. A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471, 467–472 (2011).CrossRefPubMedPubMedCentralADS

47.

DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).CrossRefPubMedPubMedCentral

48.

Berger, M. F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214–220 (2012).CrossRefADS

49.

Cibulskis, K. et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 27, 2601–2602 (2011).CrossRefPubMedPubMedCentral

50.

Costello, M. et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative dna damage during sample preparation. Nucleic Acids Res. 41, e67 (2013).CrossRefPubMedPubMedCentral

51.

Ramos, A. H. et al. Oncotator: cancer variant annotation tool. Hum. Mutat. 36, E2423–E2429 (2015).CrossRefPubMed

52.

Saunders, C. T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor- normal sample pairs. Bioinformatics 28, 1811–1817 (2012).CrossRefPubMed

53.

Olshen, A. B., Venkatraman, E. S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).CrossRefPubMedMATH

54.

Venkatraman, E. S. & Olshen, A. B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657–663 (2007).CrossRefPubMed

55.

McKenna, A. et al. The genome analysis toolkit: a mapreduce framework for analyzing next- generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).CrossRefPubMedPubMedCentral

56.

Landau, D. A. et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714–726 (2013).CrossRefPubMedPubMedCentral

57.

Harrow, J. et al. GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 22, 1760–1774 (2012).CrossRefPubMedPubMedCentral

58.

Stachler, M. D. et al. Paired exome analysis of Barrett’s esophagus and adenocarcinoma. Nat. Genet. 47, 1047–1055 (2015).CrossRefPubMedPubMedCentral

59.

60.

Tan, V. Y. F. & Fevotte, C. Automatic relevance determination in nonnegative matrix factorization with the beta-divergence. IEEE Trans. Pattern Anal. Mach. Intell. 35, 1592–1605 (2013).CrossRefPubMed

61.

Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J. & Stratton, M. R. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246–259 (2013).CrossRefPubMedPubMedCentral

62.

Shukla, S. A. et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol. 33, 1152–1158 (2015).CrossRefPubMedPubMedCentral

63.

Hoof, I. et al. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61, 1–13 (2009).CrossRefPubMed

Medicine Matters Oncology

Abstract