ten Bosch, J.R. & Grody, W.W. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J. Mol. Diagn. 10, 484–492 (2008).
Fox, E.J., Reid-Bayliss, K.S., Emond, M.J. & Loeb, L.A. Accuracy of next generation sequencing platforms. Next Gener. Seq. Appl. 1 (2014).
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K.W. & Vogelstein, B. Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. USA 108, 9530–9535 (2011).
Schmitt, M.W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. USA 109, 14508–14513 (2012).
Flaherty, P. et al. Ultrasensitive detection of rare mutations using next-generation targeted resequencing. Nucleic Acids Res. 40, e2 (2012).
Newman, A.M. et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med. 20, 548–554 (2014).
Kennedy, S.R. et al. Detecting ultralow-frequency mutations by duplex sequencing. Nat. Protoc. 9, 2586–2606 (2014).
Lou, D.I. et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl. Acad. Sci. USA 110, 19872–19877 (2013).
Stahlberg, A. et al. Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing. Nucleic Acids Res. 44, e105 (2016).
Murtaza, M. et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497, 108–112 (2013).
Wu, H.H. et al. Utilization of cell-transferred cytologic smears in detection of EGFR and KRAS mutation on adenocarcinoma of lung. Mod. Pathol. 27, 930–935 (2013).
Boadas, J. et al. Clinical usefulness of K-ras gene mutation detection and cytology in pancreatic juice in the diagnosis and screening of pancreatic cancer. Eur. J. Gastroenterol. Hepatol. 13, 1153–1159 (2001).
Ohori, N.P. et al. BRAF mutation detection in indeterminate thyroid cytology specimens: underlying cytologic, molecular, and pathologic characteristics of papillary thyroid carcinoma. Cancer Cytopathol. 121, 197–205 (2013).
Malapelle, U. et al. EGFR mutations detected on cytology samples by a centralized laboratory reliably predict response to gefitinib in non-small cell lung carcinoma patients. Cancer Cytopathol. 121, 552–560 (2013).
Hoque, M.O. et al. High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array. Cancer Res. 63, 5723–5726 (2003).
Thunnissen, F.B. Sputum examination for early detection of lung cancer. J. Clin. Pathol. 56, 805–810 (2003).
Diehl, F. et al. Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology 135, 489–498 (2008).
Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 4, 136ra68 (2012).
Lo, Y.M. & Chiu, R.W. Genomic analysis of fetal nucleic acids in maternal blood. Annu. Rev. Genomics Hum. Genet. 13, 285–306 (2012).
New, M.I. et al. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J. Clin. Endocrinol. Metab. 99, E1022–E1030 (2014).
Chitty, L.S. & Lo, Y.M. Noninvasive prenatal screening for genetic diseases using massively parallel sequencing of maternal plasma DNA. Cold Spring Harb. Perspect. Med. 5, a023085 (2015).
Tsui, N.B. et al. Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood 117, 3684–3691 (2011).
Li, M. et al. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am. J. Hum. Genet. 87, 237–249 (2010).
He, Y. et al. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature 464, 610–614 (2010).
Eastman, P.S. et al. Maternal viral genotypic zidovudine resistance and infrequent failure of zidovudine therapy to prevent perinatal transmission of human immunodeficiency virus type 1 in pediatric AIDS Clinical Trials Group Protocol 076. J. Infect. Dis. 177, 557–564 (1998).
McMahon, M.A. et al. The HBV drug entecavir - effects on HIV-1 replication and resistance. N. Engl. J. Med. 356, 2614–2621 (2007).
Snyder, T.M., Khush, K.K., Valantine, H.A. & Quake, S.R. Universal noninvasive detection of solid organ transplant rejection. Proc. Natl. Acad. Sci. USA 108, 6229–6234 (2011).
Kukita, Y. et al. High-fidelity target sequencing of individual molecules identified using barcode sequences: de novo detection and absolute quantitation of mutations in plasma cell-free DNA from cancer patients. DNA Res. 22, 269–277 (2015).
Gregory, M.T. et al. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res. 44, e22 (2016).
Bettegowda, C. et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci. Transl. Med. 6, 224ra24 (2014).
Shugay, M. et al. Towards error-free profiling of immune repertoires. Nat. Methods 11, 653–655 (2014).
Mouliere, F. et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS One 6, e23418 (2011).