Ann Lab Med.  2021 Jan;41(1):25-43. 10.3343/alm.2021.41.1.25.

Application of Next Generation Sequencing in Laboratory Medicine

Affiliations
  • 1Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
  • 2Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
  • 3Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

Abstract

The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.

Keyword

Next-generation sequencing; Oncology; Constitutional disorders; Infectious diseases

Figure

  • Fig. 1 Representations of genomic alterations identified by the Children’s Hospital of Philadelphia Division of Genomic Diagnostics NGS tests. (A) A KIAA1549-BRAF fusion detected in the Fusion panel. Red and blue represent forward and reverse sequencing reads. (B) FLT3-ITD identified in the NGS solid tumor panel. (C) CNVs identified by the NGS solid tumor panel. (C-1) CNV analysis based on reading depth. (C-2) B allele frequency analysis demonstrating SNV separation. Red arrows indicate one copy of 11q; green arrows indicate three copies of the 17q genomic region. Abbreviations: NGS, next-generation sequencing; CNV, copy number variation; SNV, single-nucleotide variation.


Cited by  8 articles

The First Korean Case of NUP98-NSD1 and a Novel SNRK-ETV6 Fusion in a Pediatric Therapy-related Acute Myeloid Leukemia Patient Detected by Targeted RNA Sequencing
Ha Jin Lim, Jun Hyung Lee, Young Eun Lee, Hee-Jo Baek, Hoon Kook, Ju Heon Park, Seung Yeob Lee, Hyun-Woo Choi, Hyun-Jung Choi, Seung-Jung Kee, Jong Hee Shin, Myung Geun Shin
Ann Lab Med. 2021;41(4):443-446.    doi: 10.3343/alm.2021.41.4.443.

Concurrent Nanopore Next-Generation Sequencing of Hepatitis B and Delta Virus Genomes Directly From Patient Plasma
Philippe Colson, Céline Boschi, Jessica Grace Bengone-Abogourin, Ludivine Brechard, Anne Motte, Isabelle Allemand
Ann Lab Med. 2021;41(6):608-611.    doi: 10.3343/alm.2021.41.6.608.

Clinical Utility of Next-Generation Flow-Based Minimal Residual Disease Assessment in Patients with Multiple Myeloma
Hyun-Young Kim, In Young Yoo, Dae Jin Lim, Hee-Jin Kim, Sun-Hee Kim, Sang Eun Yoon, Seok Jin Kim, Duck Cho, Kihyun Kim
Ann Lab Med. 2022;42(5):558-565.    doi: 10.3343/alm.2022.42.5.558.

Clinical, Mutational, and Transcriptomic Characteristics in Elderly Korean Individuals With Clonal Hematopoiesis Driver Mutations
Inki Moon, Min Gyu Kong, Young Sok Ji, Se Hyung Kim, Seong Kyu Park, Jon Suh, Mi-Ae Jang
Ann Lab Med. 2023;43(2):145-152.    doi: 10.3343/alm.2023.43.2.145.

Rapid Targeted Genomic Testing: A Powerful Tool for Diagnostic Evaluation of Critically Ill Neonates and Infants With Suspected Genetic Diseases
Mi-Ae Jang
Ann Lab Med. 2023;43(3):223-224.    doi: 10.3343/alm.2023.43.3.223.

Development of a Next-generation Sequencing-based Gene Panel Test to Detect Measurable Residual Disease in Acute Myeloid Leukemia
Jin Ju Kim, Ji Eun Jang, Hyeon Ah Lee, Mi Ri Park, Hye Won Kook, Seung-Tae Lee, Jong Rak Choi, Yoo Hong Min, Saeam Shin, June-Won Cheong
Ann Lab Med. 2023;43(4):328-336.    doi: 10.3343/alm.2023.43.4.328.

Measurable Residual Disease Testing Using Next-Generation Sequencing in Acute Myeloid Leukemia
Seon Young Kim, Hee Jin Huh
Ann Lab Med. 2023;43(4):323-324.    doi: 10.3343/alm.2023.43.4.323.

Next-Generation Sequencing-Based Molecular Profiling Using Cell-Free DNA: A Valuable Tool for the Diagnostic and Prognostic Evaluation of Patients With Gastric Cancer
Mi-Ae Jang
Ann Lab Med. 2024;44(2):119-121.    doi: 10.3343/alm.2023.0391.


Reference

1. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016; 17:333–51.
Article
2. Schwarze K, Buchanan J, Fermont JM, Dreau H, Tilley MW, Taylor JM, et al. The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom. Genet Med. 2020; 22:85–94.
Article
3. Lalonde E, Wertheim G, Li MM. Clinical impact of genomic information in pediatric leukemia. Front Pediatr. 2017; 5:263.
Article
4. Gutowska-Ding MW, Deans ZC, Roos C, Matilainen J, Khawaja F, Brugger K, et al. One byte at a time: evidencing the quality of clinical service next-generation sequencing for germline and somatic variants. Eur J Hum Genet. 2020; 28:202–12.
Article
5. Gwinn M, MacCannell D, Armstrong GL. Next-generation sequencing of infectious pathogens. JAMA. 2019; 321:893–4.
Article
6. Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell. 2018; 173:291–304.e6.
7. Luh F, Yen Y. FDA guidance for next generation sequencing-based testing: balancing regulation and innovation in precision medicine. NPJ Genom Med. 2018; 3:28.
Article
8. Allegretti M, Fabi A, Buglioni S, Martayan A, Conti L, Pescarmona E, et al. Tearing down the walls: FDA approves next generation sequencing (NGS) assays for actionable cancer genomic aberrations. J Exp Clin Cancer Res. 2018; 37:47.
Article
9. Yuan M, Huang LL, Chen JH, Wu J, Xu Q. The emerging treatment landscape of targeted therapy in non-small-cell lung cancer. Signal Transduct Target Ther. 2019; 4:61.
Article
10. Mardis ER. A decade’s perspective on DNA sequencing technology. Nature. 2011; 470:198.
Article
11. Mardis ER. DNA sequencing technologies: 2006–2016. Nature Protoc. 2017; 12:213.
Article
12. Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnol. 2008; 26:1135.
Article
13. Glenn TC. Field guide to next-generation DNA sequencers. Molecular Ecol Resour. 2011; 11:759–69.
Article
14. Sanger F, Donelson J, Coulson A, Kössel H, Fischer D. Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage f1 DNA. Proc Natl Acad Sci U S A. 1973; 70:1209–13.
Article
15. Sanger F, Donelson J, Coulson A, Kössel H, Fischer D. Determination of a nucleotide sequence in bacteriophage f1 DNA by primed synthesis with DNA polymerase. J Mol Biol. 1974; 90:315–33.
Article
16. Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975; 94:441–8.
Article
17. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001; 409:860–901.
18. Archer J, Weber J, Henry K, Winner D, Gibson R, Lee L, et al. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS One. 2012; 7:e49602.
Article
19. Burghel GJ, Hurst CD, Watson CM, Chambers PA, Dickinson H, Roberts P, et al. Towards a next-generation sequencing diagnostic service for tumour genotyping: A comparison of panels and platforms. Biomed Res Int. 2015; 2015:478017.
Article
20. Mardis ER. New strategies and emerging technologies for massively parallel sequencing: applications in medical research. Genome Med. 2009; 1:40.
Article
21. Chang F, Li MM. Clinical application of amplicon-based next-generation sequencing in cancer. Cancer Genet. 2013; 206:413–9.
Article
22. Mardis ER. Sequencing the AML genome, transcriptome, and epigenome. Sem Hematol. 2014; 51:250–8.
Article
23. Misyura M, Zhang T, Sukhai MA, Thomas M, Garg S, Kamel-Reid S, et al. Comparison of next-generation sequencing panels and platforms for detection and verification of somatic tumor variants for clinical diagnostics. J Mol Diagn. 2016; 18:842–50.
Article
24. Fernandez-Cuesta L, Sun R, Menon R, George J, Lorenz S, Meza-Zepeda LA, et al. Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biol. 2015; 16:7.
Article
25. Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda). 2013; 3:387–97.
Article
26. Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE. Landscape of next-generation sequencing technologies. Anal Chem. 2011; 83:4327–41.
Article
27. Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sc USA. 2003; 100:8817–22.
Article
28. Ansorge WJ. Next-generation DNA sequencing techniques. N Biotechnol. 2009; 25:195–203.
Article
29. Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet. 2010; 11:31.
30. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437:376.
31. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007; 8:R143.
Article
32. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011; 475:348.
33. Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012; 2012:251364.
Article
34. Mason CE, Elemento O. Faster sequencers, larger datasets, new challenges. Genome Biol. 2012; 13:314.
Article
35. Boland JF, Chung CC, Roberson D, Mitchell J, Zhang X, Im KM, et al. The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Human Genet. 2013; 132:1153–63.
Article
36. Mehrotra M, Duose DY, Singh RR, Barkoh BA, Manekia J, Harmon MA, et al. Versatile ion S5XL sequencer for targeted next generation sequencing of solid tumors in a clinical laboratory. PLoS One. 2017; 12:e0181968.
Article
37. Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, et al. Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol. 2015; 13:360–72.
Article
38. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009; 10:57–63.
Article
39. Wilhelm BT, Landry JR. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods. 2009; 48:249–57.
Article
40. Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One. 2014; 9:e78644.
Article
41. Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio. 2015; 6:e02288–14.
Article
42. Chen G, Chakravarti N, Aardalen K, Lazar AJ, Tetzlaff MT, Wubbenhorst B, et al. Molecular profiling of patient-matched brain and extracranial melanoma metastases implicates the PI3K pathway as a therapeutic target. Clin Cancer Res. 2014; 20:5537–46.
Article
43. Hamid O, Robert C, Daud A, Hodi FS, Hwu WJ, Kefford R, et al. Safety and tumor responses with lambrolizumab (anti-PD-1) in melanoma. N Engl J Med. 2013; 369:134–44.
Article
44. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008; 456:53–9.
45. Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014; 30:418–26.
Article
46. Ravi RK, Walton K, Khosroheidari M. MiSeq: A next generation sequencing platform for genomic analysis. Methods Mol Biol. 2018; 1706:223–32.
Article
47. Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnol. 2015; 33:623–30.
48. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009; 323:133–8.
49. Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, et al. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics. 2013; 14:670.
Article
50. van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The third revolution in sequencing technology. Trends Genetics. 2018; 34:666–81.
Article
51. Travers KJ, Chin C-S, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res. 2010; 38:e159-e.
Article
52. Coupland P, Chandra T, Quail M, Reik W, Swerdlow H. Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation. Biotechniques. 2012; 53:365–72.
Article
53. Baker EAG, Goodwin S, McCombie WR, Ramos OM. SiLiCO: a simulator of long read sequencing in PacBio and Oxford Nanopore. BioRxiv. 2016; 076901.
Article
54. Korlach J, Marks PJ, Cicero RL, Gray JJ, Murphy DL, Roitman DB, et al. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc Natl Acad Sci U S A. 2008; 105:1176–81.
Article
55. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012; 13:341.
Article
56. Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, et al. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnol Biofuels. 2014; 7:40.
Article
57. Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, et al. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing. Nucleic Acids Res. 2015; 43:e116.
Article
58. Bashir A, Klammer AA, Robins WP, Chin C-S, Webster D, Paxinos E, et al. A hybrid approach for the automated finishing of bacterial genomes. Nature Biotechnol. 2012; 30:701.
Article
59. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnol. 2012; 30:693.
Article
60. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010; 86:749–64.
Article
61. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013; 369:1502–11.
Article
62. Jacob HJ, Abrams K, Bick DP, Brodie K, Dimmock DP, Farrell M, et al. Genomics in clinical practice: lessons from the front lines. Sci Transl Med. 2013; 5:194cm5.
Article
63. Jones MA, Rhodenizer D, da Silva C, Huff IJ, Keong L, Bean LJ, et al. Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing. Mol Genet Metab. 2013; 110:78–85.
Article
64. Vincent LM, Dugan EK, Funari T, Richard G, Meck J. 78: Multi-gene NGS panel yields high diagnostic rate of skeletal dysplasias detected by fetal ultrasound. Am J Obstet Gynecol. 2018; 218:S57–S8.
Article
65. Takahashi JS, Pinto LH, Vitaterna MH. Forward and reverse genetic approaches to behavior in the mouse. Science. 1994; 264:1724–33.
Article
66. Schulze TG, McMahon FJ. Defining the phenotype in human genetic studies: forward genetics and reverse phenotyping. Hum Hered. 2004; 58:131–8.
Article
67. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet. 2013; 14:681–91.
Article
68. Arif B, Kumar KR, Seibler P, Vulinovic F, Fatima A, Winkler S, et al. A novel OPA3 mutation revealed by exome sequencing: an example of reverse phenotyping. JAMA Neurol. 2013; 70:783–7.
69. Urreizti R, Cueto-Gonzalez AM, Franco-Valls H, Mort-Farre S, Roca-Ayats N, Ponomarenko J, et al. A de novo nonsense mutation in MAGEL2 in a patient initially diagnosed as Opitz-C: similarities between Schaaf-Yang and Opitz-C syndromes. Sci Rep. 2017; 7:44138.
Article
70. Graziano C, Wischmeijer A, Pippucci T, Fusco C, Diquigiovanni C, Noukas M, et al. Syndromic intellectual disability: a new phenotype caused by an aromatic amino acid decarboxylase gene (DDC) variant. Gene. 2015; 559:144–8.
Article
71. Liu H, Sawyer SL, Gos M, Grynspan D, Issa K, Ramphal R, et al. Atypical fibrodysplasia ossificans progressiva diagnosed by whole-exome sequencing. Am J Med Genet A. 2015; 167:1337–41.
Article
72. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011; 13:255–62.
Article
73. Dillon OJ, Lunke S, Stark Z, Yeung A, Thorne N, et al. Melbourne Genomics Health Alliance. Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders. Eur J Hum Genet. 2018; 26:644–51.
Article
74. Consugar MB, Navarro-Gomez D, Place EM, Bujakowska KM, Sousa ME, Fonseca-Kelly ZD, et al. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet Med. 2015; 17:253–61.
Article
75. Guan Q, Balciuniene J, Cao K, Fan Z, Biswas S, Wilkens A, et al. AUDIOME: a tiered exome sequencing-based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss. Genet Med. 2018; 20:1600–8.
Article
76. Shashi V, McConkie-Rosell A, Rosell B, Schoch K, Vellore K, McDonald M, et al. The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders. Genet Med. 2014; 16:176–82.
Article
77. Kalia SS, Adelman K, Bale SJ, Chung WK, Eng C, Evans JP, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017; 19:249–55.
Article
78. Retterer K, Juusola J, Cho MT, Vitazka P, Millan F, Gibellini F, et al. Clinical application of whole-exome sequencing across clinical indications. Genet Med. 2016; 18:696–704.
Article
79. Tan TY, Dillon OJ, Stark Z, Schofield D, Alam K, Shrestha R, et al. Diagnostic impact and cost-effectiveness of whole-exome sequencing for ambulant children with suspected monogenic conditions. JAMA Pediatr. 2017; 171:855–62.
Article
80. Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014; 312:1870–9.
Article
81. Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Tippin Davis B, et al. Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med. 2015; 17:578–86.
Article
82. Xiao B, Qiu W, Ji X, Liu X, Huang Z, Liu H, et al. Marked yield of re-evaluating phenotype and exome/target sequencing data in 33 individuals with intellectual disabilities. Am J Med Genet A. 2018; 176:107–15.
Article
83. Belkadi A, Bolze A, Itan Y, Cobat A, Vincent QB, Antipenko A, et al. Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proc Natl Acad Sci U S A. 2015; 112:5473–8.
Article
84. Stavropoulos DJ, Merico D, Jobling R, Bowdin S, Monfared N, Thiruvahindrapuram B, et al. Whole genome sequencing expands diagnostic utility and improves clinical management in pediatric medicine. NPJ Genom Med. 2016; 1:15012.
85. Ellingford JM, Barton S, Bhaskar S, Williams SG, Sergouniotis PI, O’Sullivan J, et al. Whole genome sequencing increases molecular diagnostic yield compared with current diagnostic testing for inherited retinal disease. Ophthalmology. 2016; 123:1143–50.
Article
86. Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S, et al. Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization. NPJ Genom Med. 2018; 3:10.
Article
87. Petrikin JE, Willig LK, Smith LD, Kingsmore SF. Rapid whole genome sequencing and precision neonatology. Semin Perinatol. 2015; 39:623–31.
Article
88. Schwarze K, Buchanan J, Taylor JC, Wordsworth S. Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature. Genet Med. 2018; 20:1122–30.
Article
89. Ghemlas I, Li H, Zlateska B, Klaassen R, Fernandez CV, Yanofsky RA, et al. Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes. J Med Genet. 2015; 52:575–84.
Article
90. Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi AR, Vetrini F, et al. Use of exome sequencing for infants in intensive care units: ascertainment of severe single-gene disorders and effect on medical management. JAMA Pediatr. 2017; 171:e173438.
91. Surrey LF, MacFarland SP, Chang F, Cao K, Rathi KS, Akgumus GT, et al. Clinical utility of custom-designed NGS panel testing in pediatric tumors. Genome Med. 2019; 11:32.
Article
92. Miller TE, Yang M, Bajor D, Friedman JD, Chang RYC, Dowlati A, et al. Clinical utility of reflex testing using focused next-generation sequencing for management of patients with advanced lung adenocarcinoma. J Clin Pathol. 2018; 71:1108–15.
Article
93. Kim H, Yun JW, Lee ST, Kim HJ, Kim SH, Kim JW, et al. Korean society for genetic diagnostics guidelines for validation of next-generation sequencing-based somatic variant detection in hematologic malignancies. Ann Lab Med. 2019; 39:515–23.
Article
94. Chang F, Lin F, Cao K, Surrey LF, Aplenc R, Bagatell R, et al. Development and clinical validation of a large fusion gene panel for pediatric cancers. J Mol Diagn. 2019; 21:873–83.
Article
95. Hutchins RJ, Phan KL, Saboor A, Miller JD, Muehlenbachs A. CDC NGS Quality Workgroup. Practical guidance to implementing quality management systems in public health laboratories performing next-generation sequencing: personnel, equipment, and process management (Phase 1). J Clin Microbiol. 2019; 57:e00261–19.
Article
96. Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, et al. Guidelines for validation of next-generation sequencing-based oncology panels: a joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn. 2017; 19:341–65.
97. Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, et al. Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017; 19:4–23.
98. Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, et al. Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn. 2018; 20:4–27.
99. Luthra R, Patel KP, Routbort MJ, Broaddus RR, Yau J, Simien C, et al. A targeted high-throughput next-generation sequencing panel for clinical screening of mutations, gene amplifications, and fusions in solid tumors. J Mol Diagn. 2017; 19:255–64.
Article
100. Sakai K, Ohira T, Matsubayashi J, Yoneshige A, Ito A, Mitsudomi T, et al. Performance of Oncomine Fusion Transcript kit for formalin-fixed, paraffin-embedded lung cancer specimens. Cancer Sci. 2019; 110:2044–9.
Article
101. Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017; 23:703–13.
102. Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol. 2013; 31:1023–31.
Article
103. Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, et al. Memorial Sloan Kettering-integrated mutation profiling of actionable cancer targets (MSK-IMPACT): a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. J Mol Diagn. 2015; 17:251–64.
104. Hodgson DR, Dougherty BA, Lai Z, Fielding A, Grinsted L, Spencer S, et al. Candidate biomarkers of PARP inhibitor sensitivity in ovarian cancer beyond the BRCA genes. Br J Cancer. 2018; 119:1401–9.
Article
105. Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-generation sequencing in acute lymphoblastic leukemia. Int J Mol Sci. 2019; 20:2929.
Article
106. Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, et al. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med. 2016; 374:2209–21.
Article
107. Dufour A, Schneider F, Metzeler KH, Hoster E, Schneider S, Zellmeier E, et al. Acute myeloid leukemia with biallelic CEBPA gene mutations and normal karyotype represents a distinct genetic entity associated with a favorable clinical outcome. J Clin Oncol. 2010; 28:570–7.
Article
108. Sood R, Kamikubo Y, Liu P. Role of RUNX1 in hematological malignancies. Blood. 2017; 129:2070–82.
Article
109. Daver N, Schlenk RF, Russell NH, Levis MJ. Targeting FLT3 mutations in AML: review of current knowledge and evidence. Leukemia. 2019; 33:299–312.
Article
110. Medeiros BC, Fathi AT, DiNardo CD, Pollyea DA, Chan SM, Swords R. Isocitrate dehydrogenase mutations in myeloid malignancies. Leukemia. 2017; 31:272–81.
Article
111. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010; 363:2424–33.
112. Delhommeau F, Dupont S, Della Valle V, James C, Trannoy S, Masse A, et al. Mutation in TET2 in myeloid cancers. N Engl J Med. 2009; 360:2289–301.
113. Weissmann S, Alpermann T, Grossmann V, Kowarsch A, Nadarajah N, Eder C, et al. Landscape of TET2 mutations in acute myeloid leukemia. Leukemia. 2012; 26:934–42.
Article
114. Chou WC, Chou SC, Liu CY, Chen CY, Hou HA, Kuo YY, et al. TET2 mutation is an unfavorable prognostic factor in acute myeloid leukemia patients with intermediate-risk cytogenetics. Blood. 2011; 118:3803–10.
Article
115. Itzykson R, Kosmider O, Cluzeau T, Mansat-De Mas V, Dreyfus F, Beyne-Rauzy O, et al. Impact of TET2 mutations on response rate to azacitidine in myelodysplastic syndromes and low blast count acute myeloid leukemias. Leukemia. 2011; 25:1147–52.
Article
116. Metzeler KH, Herold T, Rothenberg-Thurley M, Amler S, Sauerland MC, Gorlich D, et al. Spectrum and prognostic relevance of driver gene mutations in acute myeloid leukemia. Blood. 2016; 128:686–98.
Article
117. Campo E, Harris NL, Pileri SA, Jaffe ES, Stein H, Thiele J. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. Lyon, France: IARC;2017.
118. Rosell R, Moran T, Queralt C, Porta R, Cardenal F, Camps C, et al. Screening for epidermal growth factor receptor mutations in lung cancer. N Engl J Med. 2009; 361:958–67.
119. Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014; 511:543–50.
120. D’Angelo SP, Pietanza MC, Johnson ML, Riely GJ, Miller VA, Sima CS, et al. Incidence of EGFR exon 19 deletions and L858R in tumor specimens from men and cigarette smokers with lung adenocarcinomas. J Clin Oncol. 2011; 29:2066–70.
121. Shaw AT, Engelman JA. ALK in lung cancer: past, present, and future. J Clin Oncol. 2013; 31:1105–11.
122. Shaw AT, Ou SH, Bang YJ, Camidge DR, Solomon BJ, Salgia R, et al. Crizotinib in ROS1-rearranged non-small-cell lung cancer. N Engl J Med. 2014; 371:1963–71.
Article
123. Shaw AT, Riely GJ, Bang YJ, Kim DW, Camidge DR, Solomon BJ, et al. Crizotinib in ROS1-rearranged advanced non-small-cell lung cancer (NSCLC): updated results, including overall survival, from PROFILE 1001. Ann Oncol. 2019; 30:1121–6.
Article
124. Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, et al. Updated molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors: guideline from the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med. 2018; 142:p321–46.
Article
125. Yamamoto H, Imai K. An updated review of microsatellite instability in the era of next-generation sequencing and precision medicine. Semin Oncol. 2019; 46:261–70.
Article
126. Zhao P, Li L, Jiang X, Li Q. Mismatch repair deficiency/microsatellite instability-high as a predictor for anti-PD-1/PD-L1 immunotherapy efficacy. J Hematol Oncol. 2019; 12:54.
Article
127. Marcus L, Lemery SJ, Keegan P, Pazdur R. FDA approval summary: pembrolizumab for the treatment of microsatellite instability-high solid tumors. Clin Cancer Res. 2019; 25:3753–8.
Article
128. Mehrvarz Sarshekeh A, Overman MJ, Kopetz S. Nivolumab in the treatment of microsatellite instability high metastatic colorectal cancer. Future Oncol. 2018; 14:1869–74.
129. Overman MJ, Lonardi S, Wong KYM, Lenz HJ, Gelsomino F, Aglietta M, et al. Durable clinical benefit with nivolumab plus ipilimumab in DNA mismatch repair-deficient/microsatellite instability-high metastatic colorectal cancer. J Clin Oncol. 2018; 36:773–9.
Article
130. Cocco E, Scaltriti M, Drilon A. NTRK fusion-positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol. 2018; 15:731–47.
Article
131. Hsiao SJ, Zehir A, Sireci AN, Aisner DL. Detection of tumor NTRK gene fusions to identify patients who may benefit from tyrosine kinase (TRK) inhibitor therapy. J Mol Diagn. 2019; 21:553–71.
Article
132. Ricciuti B, Genova C, Crino L, Libra M, Leonardi GC. Antitumor activity of larotrectinib in tumors harboring NTRK gene fusions: a short review on the current evidence. Onco Targets Ther. 2019; 12:3171–9.
133. Drilon A, Laetsch TW, Kummar S, DuBois SG, Lassen UN, Demetri GD, et al. Efficacy of larotrectinib in TRK fusion-positive cancers in adults and children. N Engl J Med. 2018; 378:731–9.
134. Doebele RC, Drilon A, Paz-Ares L, Siena S, Shaw AT, Farago AF, et al. Entrectinib in patients with advanced or metastatic NTRK fusion-positive solid tumours: integrated analysis of three phase 1–2 trials. Lancet Oncol. 2020; 21:271–82.
135. Drilon A, Siena S, Dziadziuszko R, Barlesi F, Krebs MG, Shaw AT, et al. Entrectinib in ROS1 fusion-positive non-small-cell lung cancer: integrated analysis of three phase 1–2 trials. Lancet Oncol. 2020; 21:261–70.
136. Chan TA, Yarchoan M, Jaffee E, Swanton C, Quezada SA, Stenzinger A, et al. Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic. Ann Oncol. 2019; 30:44–56.
Article
137. Steuer CE, Ramalingam SS. Tumor mutation burden: leading immunotherapy to the era of precision medicine? J Clin Oncol. 2018; 36:631–2.
Article
138. Cunanan KM, Iasonos A, Shen R, Begg CB, Gonen M. An efficient basket trial design. Stat Med. 2017; 36:1568–79.
Article
139. Strzebonska K, Waligora M. Umbrella and basket trials in oncology: ethical challenges. BMC Med Ethics. 2019; 20:58.
Article
140. McNeil C. NCI-MATCH launch highlights new trial design in precision-medicine era. J Natl Cancer Inst. 2015; 107:djv193.
Article
141. Luskin MR, Murakami MA, Manalis SR, Weinstock DM. Targeting minimal residual disease: a path to cure? Nat Rev Cancer. 2018; 18:255–63.
Article
142. Cilloni D, Petiti J, Rosso V, Andreani G, Dragani M, Fava C, et al. Digital PCR in myeloid malignancies: ready to replace quantitative PCR? Int J Mol Sci. 2019; 20:2249.
Article
143. Romano A, Palumbo GA, Parrinello NL, Conticello C, Martello M, Terragna C. Minimal residual disease assessment within the bone marrow of multiple myeloma: a review of caveats, clinical significance and future perspectives. Front Oncol. 2019; 9:699.
Article
144. Wu D, Emerson RO, Sherwood A, Loh ML, Angiolillo A, Howie B, et al. Detection of minimal residual disease in B lymphoblastic leukemia by high-throughput sequencing of IGH. Clin Cancer Res. 2014; 20:4540–8.
Article
145. Wood B, Wu D, Crossley B, Dai Y, Williamson D, Gawad C, et al. Measurable residual disease detection by high-throughput sequencing improves risk stratification for pediatric B-ALL. Blood. 2018; 131:1350–9.
Article
146. Berger MF, Mardis ER. The emerging clinical relevance of genomics in cancer medicine. Nat Rev Clin Oncol. 2018; 15:353–65.
Article
147. Chin RI, Chen K, Usmani A, Chua C, Harris PK, Binkley MS, et al. Detection of solid tumor molecular residual disease (MRD) using circulating tumor DNA (ctDNA). Mol Diagn Ther. 2019; 23:311–31.
148. Rossi G, Ignatiadis M. Promises and pitfalls of using liquid biopsy for precision medicine. Cancer Res. 2019; 79:2798–804.
Article
149. Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet. 2019; 20:71–88.
150. Ulrich BC, Paweletz CP. Cell-Free DNA in oncology: gearing up for clinic. Ann Lab Med. 2018; 38:1–8.
Article
151. Brown P. The Cobas EGFR Mutation Test v2 assay. Future Oncol. 2016; 12:451–2.
Article
152. Clark TA, Chung JH, Kennedy M, Hughes JD, Chennagiri N, Lieber DS, et al. Analytical validation of a hybrid capture-based next-generation sequencing clinical assay for genomic profiling of cell-free circulating tumor DNA. J Mol Diagn. 2018; 20:686–702.
Article
153. Aravanis AM, Lee M, Klausner RD. Next-generation sequencing of circulating tumor DNA for early cancer detection. Cell. 2017; 168:571–4.
Article
154. Wang Y, Li L, Douville C, Cohen JD, Yen TT, Kinde I, et al. Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers. Sci Transl Med. 2018; 10:eaap8793.
Article
155. Cohen JD, Li L, Wang Y, Thoburn C, Afsari B, Danilova L, et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science. 2018; 359:926–30.
Article
156. Merker JD, Oxnard GR, Compton C, Diehn M, Hurley P, Lazar AJ, et al. Circulating tumor DNA analysis in patients with cancer: American Society of Clinical Oncology and College of American Pathologists joint review. J Clin Oncol. 2018; 36:1631–41.
Article
157. Razavi P, Li BT, Brown DN, Jung B, Hubbell E, Shen R, et al. High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants. Nat Med. 2019; 25:1928–37.
Article
158. Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K, Aboyans V, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012; 380:2095–128.
159. Ewig S, Torres A, Angeles Marcos M, Angrill J, Rano A, de Roux A, et al. Factors associated with unknown aetiology in patients with community-acquired pneumonia. Eur Respir J. 2002; 20:1254–62.
Article
160. Bleeker-Rovers CP, Vos FJ, de Kleijn EM, Mudde AH, Dofferhoff TS, Richter C, et al. A prospective multicenter study on fever of unknown origin: the yield of a structured diagnostic protocol. Medicine (Baltimore). 2007; 86:26–38.
161. Karkhane M, Pourhosiengholi MA, Akbariyan Torkabad MR, Kimiia Z, Mortazavi SM, Hossieni Aghdam SK, et al. Annual antibiotic related economic burden of healthcare associated infections; a cross-sectional population based study. Iran J Pharm Res. 2016; 15:605–10.
162. Weng QY, Raff AB, Cohen JM, Gunasekera N, Okhovat JP, Vedak P, et al. Costs and consequences associated with misdiagnosed lower extremity cellulitis. JAMA Dermatol. 2017; 153:141–6.
Article
163. Amexo M, Tolhurst R, Barnish G, Bates I. Malaria misdiagnosis: effects on the poor and vulnerable. Lancet. 2004; 364:1896–8.
Article
164. Kapur V, Li LL, Hamrick MR, Plikaytis BB, Shinnick TM, Telenti A, et al. Rapid Mycobacterium species assignment and unambiguous identification of mutations associated with antimicrobial resistance in Mycobacterium tuberculosis by automated DNA sequencing. Arch Pathol Lab Med. 1995; 119:131–8.
165. Tang YW, Ellis NM, Hopkins MK, Smith DH, Dodge DE, Persing DH. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol. 1998; 36:3674–9.
Article
166. Allicock OM, Guo C, Uhlemann AC, Whittier S, Chauhan LV, Garcia J, et al. BacCapSeq: a platform for diagnosis and characterization of bacterial infections. mBio. 2018; 9:e02007–18.
Article
167. Briese T, Kapoor A, Mishra N, Jain K, Kumar A, Jabado OJ, et al. Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio. 2015; 6:e01491–15.
Article
168. Buss SN, Leber A, Chapin K, Fey PD, Bankowski MJ, Jones MK, et al. Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis. J Clin Microbiol. 2015; 53:915–25.
Article
169. Babady NE. The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens. Expert Rev Mol Diagn. 2013; 13:779–88.
Article
170. Leber AL, Everhart K, Balada-Llasat JM, Cullison J, Daly J, Holt S, et al. Multicenter evaluation of biofire filmarray meningitis/encephalitis panel for detection of bacteria, viruses, and yeast in cerebrospinal fluid specimens. J Clin Microbiol. 2016; 54:2251–61.
Article
171. CRyPTIC Consortium and the 100,000 Genomes Project. Allix-Beguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, et al. Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing. N Engl J Med. 2018; 379:1403–15.
Article
172. Nimmo C, Doyle R, Burgess C, Williams R, Gorton R, McHugh TD, et al. Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum. Int J Infect Dis. 2017; 62:44–6.
Article
173. Quan TP, Bawa Z, Foster D, Walker T, Del Ojo Elias C, Rathod P, et al. Evaluation of whole-genome sequencing for mycobacterial species identification and drug susceptibility testing in a clinical setting: a large-scale prospective assessment of performance against line probe assays and phenotyping. J Clin Microbiol. 2018; 56:e01480–17.
Article
174. Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect. 2017; 23:2–22.
Article
175. Burnham P, Dadhania D, Heyang M, Chen F, Westblade LF, Suthanthiran M, et al. Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. Nat Commun. 2018; 9:2412.
Article
176. Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, et al. Metagenomic DNA sequencing for the diagnosis of intraocular infections. Ophthalmology. 2017; 124:1247–8.
Article
177. Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, et al. Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. J Clin Microbiol. 2016; 54:1000–7.
Article
178. Mongkolrattanothai K, Naccache SN, Bender JM, Samayoa E, Pham E, Yu G, et al. Neurobrucellosis: unexpected answer from metagenomic next-generation sequencing. J Pediatric Infect Dis Soc. 2017; 6:393–8.
Article
179. Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, et al. Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics. J Clin Microbiol. 2018; 56:e00472–18.
Article
180. Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G, et al. Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med. 2017; 141:776–86.
Article
181. Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 2019; 29:831–42.
Article
182. Hasan MR, Rawat A, Tang P, Jithesh PV, Thomas E, Tan R, et al. Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J Clin Microbiol. 2016; 54:919–27.
Article
183. Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019; 4:663–74.
Article
184. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, et al. Impact of contaminating DNA in whole-genome amplification kits used for metagenomic shotgun sequencing for infection diagnosis. J Clin Microbiol. 2017; 55:1789–801.
Article
185. Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, Rein-Weston A, et al. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J Virol. 2013; 87:11966–77.
Article
186. de Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A, Charnock-Jones DS, et al. Recognizing the reagent microbiome. Nat Microbiol. 2018; 3:851–3.
Article
187. Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016; 530:228–32.
188. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579:270–3.
189. Sammons JS, Graf EH, Townsend S, Hoegg CL, Smathers SA, Coffin SE, et al. Outbreak of adenovirus in a neonatal intensive care unit: critical importance of equipment cleaning during inpatient ophthalmologic examinations. Ophthalmology. 2019; 126:137–43.
190. Etienne KA, Roe CC, Smith RM, Vallabhaneni S, Duarte C, Escadon P, et al. Whole-genome sequencing to determine origin of multinational outbreak of Sarocladium kiliense bloodstream infections. Emerg Infect Dis. 2016; 22:476–81.
191. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Group NCSP, Henderson DK, et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012; 4:148ra116.
Article
192. Paterson GK, Harrison EM, Murray GGR, Welch JJ, Warland JH, Holden MTG, et al. Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat Commun. 2015; 6:6560.
Article
193. Lockhart SR, Etienne KA, Vallabhaneni S, Farooqi J, Chowdhary A, Govender NP, et al. Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis. 2017; 64:134–40.
194. Hoffmann M, Luo Y, Monday SR, Gonzalez-Escalona N, Ottesen AR, Muruvanda T, et al. Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States. J Infect Dis. 2016; 213:502–8.
195. Jackson BR, Tarr C, Strain E, Jackson KA, Conrad A, Carleton H, et al. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin Infect Dis. 2016; 63:380–6.
Article
196. Moura A, Tourdjman M, Leclercq A, Hamelin E, Laurent E, Fredriksen N, et al. Real-time whole-genome sequencing for surveillance of Listeria monocytogenes, France. Emerg Infect Dis. 2017; 23:1462–70.
197. Shepard SS, Meno S, Bahl J, Wilson MM, Barnes J, Neuhaus E. Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics. 2016; 17:708.
Article
198. Gwinn M, MacCannell DR, Khabbaz RF. Integrating advanced molecular technologies into public health. J Clin Microbiol. 2017; 55:703–14.
Article
199. Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, et al. Identification of prosthetic joint infection pathogens using a shotgun metagenomics approach. Clin Infect Dis. 2018; 67:1333–8.
Article
200. Ivy MI, Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Hanssen AD, Abdel MP, et al. Direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic shotgun sequencing. J Clin Microbiol. 2018; 56:e00402–18.
Article
201. Zhou Y, Wylie KM, El Feghaly RE, Mihindukulasuriya KA, Elward A, Haslam DB, et al. Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens. J Clin Microbiol. 2016; 54:368–75.
Article
202. Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, et al. Identifying corneal infections in formalin-fixed specimens using next generation sequencing. Invest Ophthalmol Vis Sci. 2018; 59:280–8.
Article
203. Wilson MR, O’Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, et al. Chronic meningitis investigated via metagenomic next-generation sequencing. JAMA Neurol. 2018; 75:947–55.
Article
204. Grumaz S, Stevens P, Grumaz C, Decker SO, Weigand MA, Hofer S, et al. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med. 2016; 8:73.
Article
205. Long Y, Zhang Y, Gong Y, Sun R, Su L, Lin X, et al. Diagnosis of sepsis with ell-free DNA by next-generation sequencing technology in ICU patients. Arch Med Res. 2016; 47:365–71.
206. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. Sequence analysis of the human virome in febrile and afebrile children. PLoS One. 2012; 7:e27735.
Article
207. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014; 370:2408–17.
Article
208. Hoffmann B, Tappe D, Hoper D, Herden C, Boldt A, Mawrin C, et al. A variegated squirrel bornavirus associated with fatal human encephalitis. N Engl J Med. 2015; 373:154–62.
Article
209. Greninger AL, Messacar K, Dunnebacke T, Naccache SN, Federman S, Bouquet J, et al. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med. 2015; 7:113.
Article
210. Wilson MR, Shanbhag NM, Reid MJ, Singhal NS, Gelfand JM, Sample HA, et al. Diagnosing Balamuthia mandrillaris encephalitis with metagenomic deep sequencing. Ann Neurol. 2015; 78:722–30.
211. Schmidt K, Mwaigwisya S, Crossman LC, Doumith M, Munroe D, Pires C, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother. 2017; 72:104–14.
Article
212. Lemon JK, Khil PP, Frank KM, Dekker JP. Rapid nanopore sequencing of plasmids and resistance gene detection in clinical isolates. J Clin Microbiol. 2017; 55:3530–43.
Article
213. Tamma PD, Fan Y, Bergman Y, Pertea G, Kazmi AQ, Lewis S, et al. Applying rapid whole-genome sequencing to predict phenotypic antimicrobial susceptibility testing results among carbapenem-resistant Klebsiella pneumoniae clinical isolates. Antimicrob Agents Chemother. 2019; 63:e01923–18.
Article
214. Tzou PL, Ariyaratne P, Varghese V, Lee C, Rakhmanaliev E, Villy C, et al. Comparison of an in vitro diagnostic next-generation sequencing assay with Sanger sequencing for HIV-1 genotypic resistance testing. J Clin Microbiol. 2018; 56:e00105–18.
Article
215. Tyson GH, McDermott PF, Li C, Chen Y, Tadesse DA, Mukherjee S, et al. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother. 2015; 70:2763–9.
216. Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, et al. Comprehensive whole-genome sequencing and reporting of drug resistance profiles on clinical cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol. 2017; 55:1871–82.
Article
217. Jaillard M, van Belkum A, Cady KC, Creely D, Shortridge D, Blanc B, et al. Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa. Int J Antimicrob Agents. 2017; 50:210–8.
218. Sabat AJ, van Zanten E, Akkerboom V, Wisselink G, van Slochteren K, de Boer RF, et al. Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species. Sci Rep. 2017; 7:3434.
Article
219. Salipante SJ, Hoogestraat DR, Abbott AN, SenGupta DJ, Cummings LA, Butler-Wu SM, et al. Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing. J Clin Microbiol. 2014; 52:1789–92.
Article
220. Sardi SI, Somasekar S, Naccache SN, Bandeira AC, Tauro LB, Campos GS, et al. Coinfections of Zika and chikungunya viruses in Bahia, Brazil, identified by metagenomic next-generation sequencing. J Clin Microbiol. 2016; 54:2348–53.
Article
221. Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 2018; 67(S2):S231–S40.
Article
222. Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A. 2018; 115:E12353–E62.
Article
223. Bal A, Sarkozy C, Josset L, Cheynet V, Oriol G, Becker J, et al. Metagenomic next-generation sequencing reveals individual composition and dynamics of anelloviruses during autologous stem cell transplant recipient management. Viruses. 2018; 10:633.
Article
224. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, et al. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell. 2013; 155:1178–87.
Article
225. De Vlaminck I, Martin L, Kertesz M, Patel K, Kowarsky M, Strehl C, et al. Noninvasive monitoring of infection and rejection after lung transplantation. Proc Natl Acad Sci U S A. 2015; 112:13336–41.
Article
226. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A. 2012; 109:5809–14.
Article
227. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012; 13:R79.
Article
228. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013; 368:407–15.
229. Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A. Opportunities and challenges of whole-genome and -exome sequencing. BMC Genet. 2017; 18:14.
Article
230. Kim YE, Ki CS, Jang MA. Challenges and considerations in sequence variant interpretation for Mendelian disorders. Ann Lab Med. 2019; 39:421–9.
Article
231. Chen G, Ning B, Shi T. Single-cell RNA-seq technologies and related computational data analysis. Front Genet. 2019; 10:317.
Article
232. Schrader KA, Cheng DT, Joseph V, Prasad M, Walsh M, Zehir A, et al. Germline variants in targeted tumor sequencing using matched normal DNA. JAMA Oncol. 2016; 2:104–11.
Article
233. Akkari Y, Smith T, Westfall J, Lupo S. Implementation of cancer next-generation sequencing testing in a community hospital. Cold Spring Harb Mol Case Stud. 2019; 5:a003707.
Article
Full Text Links
  • ALM
Actions
Cited
CITED
export Copy
Close
Share
  • Twitter
  • Facebook
Similar articles
Copyright © 2024 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: koreamed@kamje.or.kr