A Review of Next-Generation Sequencing Technologies and Their Impact on Clinical Research: Assessing Clinical Efficacy and Cost-Effectiveness

Authors

  • Pratibha Neuome Technologies Private Limited, Helix Biotech Park, Bangalore Bioinnovation Centre, Electronics City Phase-I, Bengaluru, Karnataka 560100, India https://orcid.org/0009-0006-1444-2610
  • Saranya Kanukollu Neuome Technologies Private Limited, Helix Biotech Park, Bangalore Bioinnovation Centre, Electronics City Phase-I, Bengaluru, Karnataka 560100, India https://orcid.org/0000-0003-0614-3566
  • Anand Babu Vangala Neuome Technologies Private Limited, Helix Biotech Park, Bangalore Bioinnovation Centre, Electronics City Phase-I, Bengaluru, Karnataka 560100, India https://orcid.org/0000-0002-9075-1929
  • Rajani Kanth Vangala Neuome Technologies Private Limited, Helix Biotech Park, Bangalore Bioinnovation Centre, Electronics City Phase-I, Bengaluru, Karnataka 560100, India https://orcid.org/0000-0003-0173-3444
  • Pramod Nair Neuome Technologies Private Limited, Helix Biotech Park, Bangalore Bioinnovation Centre, Electronics City Phase-I, Bengaluru, Karnataka 560100, India https://orcid.org/0000-0002-2918-4929

DOI:

https://doi.org/10.14719/tcb.3569

Keywords:

Next Generation Sequencing, Hereditary neurological disorders, End-stage renal disease, Renal disorders, Heritable connective tissue disorders, Cost-effectiveness

Abstract

In contrast to microarray methods, sequence-based technologies directly determine the nucleic acid sequence. A number of modern sequencing technologies are referred to collectively as "next-generation sequencing" (NGS), often known as "high-throughput sequencing." Compared to conventional Sanger sequencing, NGS gives orders of magnitude more data at a much lower ongoing cost. These new technologies allow for much faster and more affordable sequencing of DNA and RNA, revolutionizing the study of genomics and molecular biology. Technical improvements in NGS sequencing methods have rapidly increased sequencing volume to several billion nucleotides within a short period and at a reasonable cost. Currently, NGS is developing into a molecular microscope that is permeating almost all areas of biological research. The last ten years have seen the development of NGS platforms and methodologies, and the quality of the sequences has increased to the point where NGS is now utilized in human clinical diagnosis. Due to significant cost reductions and greater community acceptance of NGS, the utilization of NGS techniques in studying clinical trials has significantly increased. NGS is a useful tool for detecting mutations in people with cancer and genetic abnormalities. To ascertain whether NGS can cost-effectively improve patient outcomes, more thorough cost-effectiveness studies of NGS applied to patient care management are required.

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References

Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A next-generation sequencing primer—how does it work and what can it do? Academic pathology. 2018. : https://doi.org/10.1177/2374289518766521

Levy SE, Myers RM. Advancements in next-generation sequencing. Annual review of genomics and human genetics. 2016. 17, 95-115. https://doi.org/10.1146/annurev-genom-083115-022413

Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of molecular biology. 1975. 94(3), 441-448. https://doi.org/10.1016/0022-2836(75)90213-2

Maxam AM, Gilbert W. A new method for sequencing DNA. Proceedings of the National Academy of Sciences. 1977. 74(2), 560-564. https://doi.org/10.1073/pnas.74.2.560

Venter JC, Adams MD, Myers EW, Li P. W, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Kalus F. The sequence of the human genome. Science. 2001. 291(5507), 1304-1351. https://doi.org/10.1126/science.1058040

Saiki RK, Gelfand DH, Stoffel S. Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich, HA. “Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase,” Science. 1988. Vol. 239, no. 4839, pp. 487–491. https://doi.org/10.1126/science.2448875

Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of ?-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 1985. 230(4732), 1350-1354. https://doi.org/10.1126/science.2999980

Nature Milestones – Genomic Sequencing. 2021. www.nature.com/collections/genomic-sequencing-milestones. 2021. https://www.nature.com/immersive/d42859-020 00099-0/pdf/d42859-020-00099-0.pdf

Immy M. A brief history of Next Generation Sequencing (NGS). 2021. https://frontlinegenomics.com/a-brief-history-of-next-generation-sequencing-ngs/

Pervez MT, Hasnain M.U, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. BioMed Research International. 2022 :3457806. https://doi.org/10.1155/2022/3457806

Qin D. Next-generation sequencing and its clinical application. Cancer Biology & Medicine. 2019 16(1):4-10. https://doi.org/10.20892%2Fj.issn.2095-3941.2018.0055

Jessica SB, Manuel ST, Ken IM, Mark AC. The impact of next generation sequencing technologies on haematological research – A review. Pathogenesis2 2015: 21-26, https://doi.org/10.1016/j.pathog.2015.05.004

Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science. 2013. 339, 1546–1558. https://doi.org/10.1126/science.1235122

Williams ES, Hegde M. Implementing genomic medicine in pathology. Advances in Anatomic Pathology. 2013; 20: 238–244. https://doi.org/10.1097/pap.0b013e3182977199

Choi BY, Kim BJ. Application of next generation sequencing upon the molecular genetic diagnosis of deafness. Korean Journal of Audiology. Korean Audiological Society; 2012.1 6: 1–5. https://doi.org/10.7874%2Fkja.2012.16.1.1

Di RC, Galbiati S, Carrera.P, Ferrari.M. Next-generation sequencing approach for the diagnosis of human diseases: open challenges and new opportunities. The electronic Journal of the International Federation of Clinical Chemistry and Laboratory Medicine. 2018. 29: 4–14. http://www.ncbi.nlm.nih.gov/pubmed/29765282

Lohmann K, Klein C. Next generation sequencing and the future of genetic diagnosis. Neurotherapeutics. 2014. 11(4) :699-707. https://doi.org/10.1007%2Fs13311-014-0288-8

Khan A, Tian S, Tariq M, Khan S, Safeer M, Ullah N, Akbar N, Javed I, Asif M, Ahmad I, Ullah S, Satti HS, Khan R, Naeem M, Ali M, Rendu J, Fauré J, Dieterich K, Latypova X, Baig SM, Malik NA, Zhang F, Khan TN, Liu C. NGS-driven molecular diagnosis of heterogeneous hereditary neurological disorders reveals novel and known variants in disease-causing genes. Molecular Genetics and Genomics. 2022. 97(6):1601-1613 https://doi.org/10.1007/s00438-022-01945-8

Liu Z, Zhu L, Roberts R, & Tong W. Toward clinical implementation of next-generation sequencing-based genetic testing in rare diseases: where are we? 2019. Trends in genetics, 35(11), 852-867. https://doi.org/10.1016/j.tig.2019.08.006

Ouellette AC, Mathew J, Manickaraj AK, Manase G, Zahavich L, Wilson J, George K, Benson L, Bowdin S, Mital S. Clinical genetic testing in pediatric cardiomyopathy: is bigger better? Clinical genetics, 2018. 93(1), 33-40. https://doi.org/10.1111/cge.13024

Niehaus A, Azzariti DR, Harrison SM, DiStefano MT, Hemphill SE, Senol-Cosar O, Rehm HL. A survey assessing adoption of the ACMG-AMP guidelines for interpreting sequence variants and identification of areas for continued improvement. 2019. Genetics in Medicine, 21(8), 1699-1701. https://doi.org/10.1038/s41436-018-0432-7

Ezquerra-Inchausti M, Anasagasti A, Barandika O, Garay-Aramburu G, Galdós M, López de Munain A, Irigoyen C, Ruiz-Ederra J. A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies. 2018. Scientific reports, 8(1), 1-12. https://doi.org/10.1038/s41598-018-33810-3

Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Alberti L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A new targeted CFTR mutation panel based on next-generation sequencing technology. 2017. The Journal of Molecular Diagnostics, 19(5), 788-800. https://doi.org/10.1016/j.jmoldx.2017.06.002

Komlosi K, Diederich S, Fend-Guella D. L, Bartsch O, Winter J, Zechner U, Beck M, Meyer P, Schweiger, S. Targeted next-generation sequencing analysis in couples at increased risk for autosomal recessive disorders. 2018. Orphanet journal of rare diseases, 13(1), 1-11. https://doi.org/10.1186/s13023-018-0763-0

Sun H, Shen X-R, Fang Z-B, Jiang Z-Z, Wei X-J, Wang Z-Y, Yu X-F. Next-Generation Sequencing Technologies and Neurogenetic Diseases. Life. 2021; 11(4):361. https://doi.org/10.3390/life11040361

Sullivan R, Yau WY, O'Connor E, Houlden H. Spinocerebellar ataxia: an update. 2019. Journal of neurology, 266(2), 533-544. https://doi.org/10.1007%2Fs00415-018-9076-4

Ashley EA. The precision medicine initiative: a new national effort. (2015). JAMA, 313(21), 2119-2120. https://doi.org/10.1001/jama.2015.3595

Jiang T, Tan MS, Tan L, Yu JT. Application of next-generation sequencing technologies in Neurology. Annals of Translational Medicine. 2014. 2(12):125. https://doi.org/10.3978%2Fj.issn.2305-5839.2014.11.11

Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Frontiers in genetics. 2018. 9 (20) 1-11. https://doi.org/10.3389/fgene.2018.00020

Møller RS, Dahl HA, Helbig I. The contribution of next generation sequencing to epilepsy genetics. Expert review of molecular diagnostics. 2015. 15(12), 1531-1538. https://doi.org/10.1586/14737159.2015.1113132

Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen W.J, Bekheirnia MR, Stray-Pedersen A, Liu P, Wen S, Alcaraz W, Cui H, Walkiewicz M, Reid J, Bainbridge M, Patel A, Boerwinkle E, Beaudet A. L, Lupski JR, Plon SE, Gibbs RA, Eng CM. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014. 312(18), 1870-1879. https://doi.org/10.1001/jama.2014.14601

Valencia CA, Husami A, Holle J, Johnson JA, Qian Y, Mathur A, Wei C, Indugula SR, Zou F, Meng H, Wang L, Li X, Fisher R, Tan T, Hogart Begtrup A, Collins K, Wusik KA, Neilson D, Burrow T, Schorry E, Hopkin R, Keddache M, Harley JB, Kaufman KM, Zhang K. Clinical Impact and Cost-Effectiveness of Whole Exome Sequencing as a Diagnostic Tool: A Pediatric Center's Experience. Frontiers in pediatrics. 2015. 3(67). 1-15. https://doi.org/10.3389/fped.2015.00067

Abbasi MA, Chertow GM, & Hall YN. (2010). End-stage renal disease. British medical journal. Clinical evidence, 2010. 1-16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217820/pdf/2010-2002.pdf

Lepri FR, Scavelli R, Digilio MC, Gnazzo M, Grotta S, Dentici ML, Pisaneschi E, Sirleto P, Capolino R, Baban A, Russo S, Franchin T, Angioni A, Dallapiccola B. Diagnosis of Noonan syndrome and related disorders using target next generation sequencing. BMC Medical Genetics. 2014 2315:14. 1-11. https://doi.org/10.1186/1471-2350-15-14

Zhang J, Zhang C, Gao E, Zhou Q. Next-Generation Sequencing-Based Genetic Diagnostic Strategies of Inherited Kidney Diseases. Kidney Diseases. 2021.7(6). 425-437. https://doi.org/10.1159/000519095

Alizadeh R, Jamshidi S, Keramatipour M, Moeinian P, Hosseini R, Otukesh H, Talebi S. Whole Exome Sequencing Reveals a XPNPEP3 Novel Mutation Causing Nephronophthisis in a Pediatric Patient. Iranian Biomedical Journal. 2020 24(6):405-408. https://doi.org/10.29252/ibj.24.6.400

Chen F, Dai L, Zhang J, Li F, Cheng J, Zhao J, Zhang B. A case report of NPHP1 deletion in Chinese twins with nephronophthisis. BMC Medical Genetics 2020. 21:84 2-5. https://doi.org/10.1186%2Fs12881-020-01025-x

Braun DA, Schueler M, Halbritter J, Gee HY, Porath JD, Lawson JA, Airik R, Shril S, Allen SJ, Stein D, Al Kindy A, Beck BB, Cengiz N, Moorani KN, Ozaltin F, Hashmi S, Sayer JA, Bockenhauer D, Soliman NA, Otto EA, Lifton RP, Hildebrandt F. Whole exome sequencing identifies causative mutations in the majority of consanguineous or familial cases with childhood-onset increased renal echogenicity. Kidney International. 2016. 89(2):468-475. https://doi.org/10.1038/ki.2015.317

de Haan A, Eijgelsheim M, Vogt L, Knoers NVAM, de Borst M.H. Diagnostic Yield of Next-Generation Sequencing in Patients with Chronic Kidney Disease of Unknown Etiology. Frontiers in Genetics. 2019. https://doi.org/10.3389%2Ffgene.2019.01264

Steinle J, Hossain WA, Veatch OJ, Strom SP, Butler MG. Next-generation sequencing and analysis of consecutive patients referred for connective tissue disorders. American Journal of Medical Genetics Part A. 2022 188(10):3016-3023. https://doi.org/10.1002/ajmg.a.62905

Cortini F, Villa C, Marinelli B, Combi R, Pesatori AC, Bassotti A. Understanding the basis of Ehlers-Danlos syndrome in the era of the next-generation sequencing. Archives of Dermatological Research 2019. 311(4):265-275. https://doi.org/10.1007/s00403-019-01894-0

VanderJagt K, Butler MG. Ehlers-Danlos syndrome and other heritable connective tissue disorders that impact pregnancies can be detected using next-generation DNA sequencing. Archives of Gynecology and Obstetrics. 2019. 300(3): 491-493. https://doi.org/10.1007/s00404-019-05226-5

Kärkkäinen S, Peuhkurinen K. Genetics of dilated cardiomyopathy. Annals of medicine, 2007. 39(2), 91-107. https://doi.org/10.1080/07853890601145821

Parikh VN, Ashley EA. Next-Generation Sequencing in Cardiovascular Disease: Present Clinical Applications and the Horizon of Precision Medicine. Circulation. 2017.135(5), 406-409 https://doi.org/10.1161/CIRCULATIONAHA.116.024258

Sturm AC, Hershberger RE. Genetic testing in cardiovascular medicine: current landscape and future horizons. Current opinion in cardiology. 2013. 28(3), 317-325. https://doi.org/10.1097/hco.0b013e32835fb728

Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, Homer N, Huentelman MJ. Identification of genetic variants using bar-coded multiplexed sequencing. Nature methods. 2008. 5(10), 887-893. https://doi.org/10.1038%2Fnmeth.1251

Nigro V, Savarese M. Next-generation sequencing approaches for the diagnosis of skeletal muscle disorders. Current Opinion in Neurology. 2016 29(5):621-7. https://doi.org/10.1097/wco.0000000000000371

Brugnoni R, Maggi L, Canioni E, Verde F, Gallone A, Ariatti A, Filosto M, Petrelli C, Logullo FO, Esposito M, Ruggiero L, Tonin P, Riguzzi P, Pegoraro E, Torri F, Ricci G, Siciliano G, Silani V, Merlini L, De Pasqua S, Liguori R, Pini A, Mariotti C, Moroni I, Imbrici P, Desaphy JF, Mantegazza R, Bernasconi P. Next-generation sequencing application to investigate skeletal muscle channelopathies in a large cohort of Italian patients. Neuromuscular Disorders. 2021. 31(4), 336-347. https://doi.org/10.1016/j.nmd.2020.12.003

Tangye SG, Al-Herz W, Bousfiha A, Chatila T, Cunningham-Rundles C, Etzioni A, Franco JL, Holland SM, Klein C, Morio T, Ochs HD, Oksenhendler E, Picard C, Puck J, Torgerson TR, Casanova JL, Sullivan KE. Human inborn errors of immunity: 2019 update on the Classification from the International Union of Immunological Societies Expert Committee. Journal of Clinical Immunology 2020. 40:24–64. https://doi.org/10.1007%2Fs10875-022-01289-3

Vorsteveld EE, Hoischen A, van der Made C.I. Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives. Clinical Reviews in Allergy & Immunology 2021 61(2):212-225. https://doi.org/10.1007/s12016-021-08838-5

Gallo V, Dotta L, Giardino G, Cirillo E, Lougaris V, D'Assante R, Prandini A, Consolini R, Farrow EG, Thiffault I, Saunders CJ, Leonardi A, Plebani A, Badolato R, Pignata C. Diagnostics of primary immunodeficiencies through next-generation sequencing. Frontiers in immunology, V7:466. https://doi.org/10.3389/fimmu.2016.00466

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church D.M, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nature Biotechnology. 2015. 3(7):689-93. https://doi.org/10.1038/nbt.3237

Elsink K, Huibers MMH, Hollink IHIM, van der Veken LT, Ernst RF, Simons A, Zonneveld-Huijssoon E, van der Hout AH, Abbott KM, Hoischen A, Pieterse M, Kuijpers TW, van Montfrans JM, van Gijn ME. National external quality assessment for next-generation sequencing-based diagnostics of primary immunodeficiencies. European Journal of Human Genetics 2021. 29(1):20-28. https://doi.org/10.1038/s41431-020-0702-0

Birtel J, Gliem M, Mangold E, Müller PL, Holz FG, Neuhaus C, Lenzner S, Zahnleiter D, Betz C, Eisenberger T, Bolz HJ, Charbel Issa P. Next-generation sequencing identifies unexpected genotype-phenotype correlations in patients with retinitis pigmentosa. PLoS One. 2018.13(12). 1-18 https://doi.org/10.1371/journal.pone.0207958

Charif M, Bris C, Goudenège D, Desquiret-Dumas V, Colin E, Ziegler A, Procaccio V, Reynier P, Bonneau D, Lenaers G, Amati-Bonneau P. Use of Next-Generation Sequencing for the Molecular Diagnosis of 1,102 Patients With a Autosomal Optic Neuropathy. Frontiers in Neurology. 2021. 12, Article No. 602979. https://doi.org/10.3389%2Ffneur.2021.602979

Tiwari A, Bahr A, Bähr L, Fleischhauer J, Zinkernagel MS, Winkler N, Barthelmes D, Berger L, Gerth-Kahlert C, Neidhardt J, Berger W. Next generation sequencing based identification of disease-associated mutations in Swiss patients with retinal dystrophies. Scientific reports. 2016. 6(1). 1-11. https://doi.org/10.1038/srep28755

Neuillé M, Malaichamy S, Vadalà M, Michiels C, Condroyer C, Sachidanandam R, Srilekha S, Arokiasamy T, Letexier M, Démontant V, Sahel JA, Sen P, Audo I, Soumittra N, Zeitz C. Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness. Clinical Genetics. 2016. 89(6):690-699. https://doi.org/10.1111/cge.12746 .

Gao X, Dai P. Impact of next-generation sequencing on molecular diagnosis of inherited non-syndromic hearing loss. 2014. Journal of Otology, 9(3), 122-125. https://doi.org/10.1016/j.joto.2014.11.003

Levenson, D. (2014). New testing guidelines for hearing loss support next?generation sequencing: Testing method may help determine genetic causes of hearing loss among patients whose phenotypes are not easily distinguished clinically. American Journal of Medical Genetics Part A, 164(7), vii-viii. https://doi.org/10.1002/ajmg.a.36643

Vona B, Müller T, Nanda I, Neuner C, Hofrichter MA, Schröder J, Bartsch O, Läßig A, Keilmann A, Schraven S, Kraus F, Shehata-Dieler W, Haaf T. Targeted next-generation sequencing of deafness genes in hearing-impaired individuals uncovers informative mutations. Genetics in Medicine. 2014. 16. 945–953. https://doi.org/10.1038/gim.2014.65

Shang H, Yan D, Tayebi N, Saeidi K, Sahebalzamani A, Feng Y, Blanton S, Liu X. Targeted Next-Generation Sequencing of a Deafness Gene Panel (MiamiOtoGenes) Analysis in Families Unsuitable for Linkage Analysis. 2018. BioMed Research international. Volume 2018, Article ID 3103986. https://doi.org/10.1155/2018/3103986

An J, Yang J, Wang Y, Wang Y, Xu B, Xie G, Chai S, Liu X, Xu S, Wen X, He Q, Liu H, Li C, Dey SK, Ni Y, Banerjee S. Targeted Next Generation Sequencing Revealed a Novel Homozygous Loss-of-Function Mutation in ILDR1 Gene Causes Autosomal Recessive Nonsyndromic Sensorineural Hearing Loss in a Chinese Family. Frontiers in genetics. 2019. 10(1).1-7. https://doi.org/10.3389/fgene.2019.00001

Ewalt MD, West H, Aisner DL. Next Generation Sequencing-Testing Multiple Genetic Markers at Once. JAMA oncology. 2019. 5(7), 1076-1076. https://doi.org/10.1001/jamaoncol.2019.0453

Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA. Jr, Kinzler KW. Cancer genome landscapes. Science. 2013. 339(6127), 1546-1558. https://doi.org/10.1126/science.1235122

Kinzler KW, Vogelstein B. Lessons from hereditary colorectal cancer. Cell. 1996. 87(2):159-170. https://doi.org/10.1016/s0092-8674(00)81333-1

Rahman N, Seal S, Thompson D, Kelly P, Renwick A, Elliott A, Reid S, Spanova K, Barfoot R, Chagtai T, Jayatilake H, McGuffog L, Hanks S, Evans D. G, Eccles D. PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nature Genetics. 2007. 39:165–167. https://doi.org/10.1038/ng1959

Study C, Houlston RS, Webb E, Broderick P, Pittman AM, Di Bernardo MC, Lubbe S, Chandler I, Vijayakrishnan J, Sullivan K, Penegar S; Colorectal Cancer Association Study Consortium; Carvajal-Carmona L, Howarth K, Jaeger E, Spain SL, Walther A, Barclay E, Martin L, Gorman M, Domingo E, Teixeira AS; CoRGI Consortium; Kerr D, Cazier JB, Niittymäki I, Tuupanen S, Karhu A, Aaltonen LA, Tomlinson IP, Farrington SM, Tenesa A, Prendergast JG, Barnetson RA, Cetnarskyj R, Porteous ME, Pharoah PD, Koessler T, Hampe J, Buch S, Schafmayer C, Tepel J, Schreiber S, Völzke H, Chang-Claude J, Hoffmeister M, Brenner H, Zanke BW, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG. Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nature Genetics. 2008. 40:1426–1435. https://doi.org/10.1038%2Fng.262

Jóri B, Kamps R, Xanthoulea S, Delvoux B, Blok MJ, Van de Vijver KK, de Koning B, Oei FT, Tops CM, Speel EJ, Kruitwagen RF, Gomez-Garcia EB, Romano A. Germ-line variants identified by next generation sequencing in a panel of estrogen and cancer associated genes correlate with poor clinical outcome in Lynch syndrome patients. Oncotarget. 2015. 6 (38) :41108–41122. https://doi.org/10.18632/oncotarget.5694

Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature. 2009. 461(7265):747-53. https://doi.org/10.1038/nature08494

Zhang B, Beeghly-Fadiel A, Long J, Zheng W. Genetic variants associated with breast-cancer risk: comprehensive research synopsis, meta-analysis, and epidemiological evidence. The Lancet Oncology; 2011. 12(5): 477–488. https://doi.org/10.1016%2FS1470-2045(11)70076-6

Kamps R, Brandão RD, Bosch BJ, Paulussen AD, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. International Journal of Molecular Sciences - MDPI 2017. 18(2):308. https://doi.org/10.3390%2Fijms18020308

Hermsen MA, Riobello C, García-Marín R, Cabal VN, Suárez-Fernández L, López F, Llorente JL. Translational genomics of sinonasal cancers. In Seminars in Cancer Biology 2020.V61,101-109. AcademicPress. https://doi.org/10.1016/j.semcancer.2019.09.016

Sánchez-Fernández P, Riobello C, Costales M, Vivanco B, Cabal VN, García-Marín R, Suárez-Fernández L, López F, Cabanillas R, Hermsen MA, Llorente JL. Next-generation sequencing for identification of actionable gene mutations in intestinal-type sinonasal adenocarcinoma. Scientific reports, 2021. 11(1), 1-10. https://doi.org/10.1038/s41598-020-80242-z

Chen M, Zhao H. Next-generation sequencing in liquid biopsy: cancer screening and early detection. Human genomics. 2019. 13(1), 1-10. https://doi.org/10.1186/s40246-019-0220-8

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network; Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske E.P, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer cell. 2014. 26(3), 319-330. https://doi.org/10.1016%2Fj.ccr.2014.07.014

Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012. 490(7418), 61-70. https://doi.org/10.1038%2Fnature11412

Calapre L, Giardina T, Beasley AB, Reid AL, Stewart C, Amanuel B, Meniawy TM, Gray ES. Identification of TP53 mutations in circulating tumour DNA in high grade serous ovarian carcinoma using next generation sequencing technologies. Scientific Reports 2023. 13:278. https://doi.org/10.1038/s41598-023-27445-2

Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature, 2012. 487(7407), 330. http://www.nature.com/nature/journal/v487/n7407/full/nature11252

Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature, 2012. 489(7417), 519. https://doi.org/10.1038%2Fnature11404

Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011 333(6046),1154-1157. https://doi.org/10.1126/science.1206923

Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, Shibata T. High-resolution characterization of a hepatocellular carcinoma genome. Nature genetics, 2011. 43(5), 464-469. https://doi.org/10.1038/ng.804

Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature, 2012. 485(7399), 502-506. Available https://doi.org/10.1038%2Fnature11071

Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini VJ, Cook L, McGrath SD, Vickery TL, Wendl MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis ER, Wilson RK, DiPersio JF. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature, 2012. 481(7382), 506-510. https://doi.org/10.1038/nature10738

Taylor BS, Ladanyi M. Clinical cancer genomics: how soon is now? The Journal of pathology, 2012. 23(2), 319-327. https://doi.org/10.1002/path.2794

Shyr D, Liu Q. Next generation sequencing in cancer research and clinical application. Biological procedures online, 2013. 15(1), 1-11. https://doi.org/10.1186/1480-9222-15-4

Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics, 2011. 13(1), 36-46. https://doi.org/10.1038/nrg3117

Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics, 2011. 12(9), 628-640. https://doi.org/10.1038/nrg3046

Pervez MT, Hasnain MJU, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. 2022. BioMed Research International. 2022, Article ID 3457806. https://doi.org/10.1155/2022/3457806

Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A next-generation sequencing primer—how does it work and what can it do? Academic pathology, 2018. V5-1–11. https://doi.org/10.1177%2F2374289518766521

Rabbani B, Nakaoka H, Akhondzadeh S, Tekin M, Mahdieh N. Next generation sequencing: implications in personalized medicine and pharmacogenomics. Molecular biosystems. 2016. 12(6):1818-1830. https://doi.org/10.1039/c6mb00115g

DNA Sequencing Costs: 2021. National Human Genome Research Institute (NHGRI): Last updated: November 1, 2021 Data https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data

Pennell NA, Zhou J. Hobbs B. A model comparing the value of broad next-gen sequencing (NGS)-based testing to single gene testing (SGT) in patients with nonsquamous non-small cell lung cancer (NSCLC) in the United States. 2020. Journal of Clinical Oncology V38(15) 9529-9529 https://doi.org/10.1200/JCO.2020.38.15_suppl.9529

Zou D, Ye W, Hess LM, Bhandari NR, Ale-Ali A, Foster J, Quon P, Harris M. Diagnostic Value and Cost-Effectiveness of Next-Generation Sequencing-Based Testing for Treatment of Patients with Advanced/Metastatic Non-Squamous Non-Small-Cell Lung Cancer in the United States. The Journal of Molecular Diagnostics. 2022. 24(8):901-914. https://doi.org/10.1016/j.jmoldx.2022.04.010

Tan O, Shrestha R, Cunich M, Schofield DJ. Application of next-generation sequencing to improve cancer management: A review of the clinical effectiveness and cost-effectiveness. Clinical Genetics. 93(3):533-544. https://doi.org/10.1111/cge.13199

Vanderpoel J, Stevens AL, Emond B, Lafeuille MH, Hilts A, Lefebvre P, Morrison L. Total cost of testing for genomic alterations associated with next-generation sequencing versus polymerase chain reaction testing strategies among patients with metastatic non-small cell lung cancer. 2022. Journal of medical economics, 25(1), 457-468. https://doi.org/10.1080/13696998.2022.2053403

Pruneri G, De Braud F, Sapino A, Aglietta M, Vecchione A, Giusti R, Marchiò C, Scarpino S, Baggi A, Bonetti G, Franzini JM, Volpe M, Jommi C. Next-Generation Sequencing in Clinical Practice: Is It a Cost-Saving Alternative to a Single-Gene Testing Approach? 2021. PharmacoEconomics-open, 5(2).285-298. https://doi.org/10.1007/s41669-020-00249-0

van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. 2014 Trends in genetics, 30(9)418-426. https://doi.org/10.1016/j.tig.2014.07.001

Weymann D, Pataky R, Regier DA. Economic Evaluations of Next-Generation Precision Oncology: A Critical Review. 2018. JCO Precision Oncology (2) 1-23. https://doi.org/10.1200/po.17.00311

Hatz MH, Schremser K, Rogowski WH. Is individualized medicine more cost-effective? A systematic review. 2014. Pharmacoeconomics32(5) 443-455. https://doi.org/10.1007/s40273-014-0143-0

Frank M, Prenzler A, Eils R, Graf von der Schulenburg J. Genome sequencing: a systematic review of health economic evidence. 2013. Health economics review, 3(1)1-8. https://doi.org/10.1186/2191-1991-3-29

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02-07-2024

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