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Somatic DNA Copy-Number Alterations Detection for Esophageal Adenocarcinoma Using Digital Polymerase Chain Reaction

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Esophageal Adenocarcinoma

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1756))

Abstract

Somatic copy-number alterations are commonly found in cancer and play key roles in activating oncogenes and deactivating tumor suppressor genes. Digital polymerase chain reaction is an effective way to detect the changes in copy number. In esophageal adenocarcinoma, detection of somatic copy-number alterations could predict the prognosis of patients as well as the response to therapy. This chapter will review the methods involved in digital polymerase chain reaction for the research or potential clinical applications in esophageal adenocarcinoma.

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References

  1. Nones K, Waddell N, Wayte N, Patch AM, Bailey P, Newell F, Holmes O, Fink JL, Quinn MC, Tang YH, Lampe G, Quek K, Loffler KA, Manning S, Idrisoglu S, Miller D, Xu Q, Waddell N, Wilson PJ, Bruxner TJ, Christ AN, Harliwong I, Nourse C, Nourbakhsh E, Anderson M, Kazakoff S, Leonard C, Wood S, Simpson PT, Reid LE, Krause L, Hussey DJ, Watson DI, Lord RV, Nancarrow D, Phillips WA, Gotley D, Smithers BM, Whiteman DC, Hayward NK, Campbell PJ, Pearson JV, Grimmond SM, Barbour AP (2014) Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat Commun 5:5224. https://doi.org/10.1038/ncomms6224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R (2013) Pan-cancer patterns of somatic copy number alteration. Nat Genet 45:1134–1140. https://doi.org/10.1038/ng.2760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463:899–905. https://doi.org/10.1038/nature08822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Baudis M (2007) Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer 7:226. https://doi.org/10.1186/1471-2407-7-226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Cancer Genome Atlas Research N (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature 489:519–525. https://doi.org/10.1038/nature11404

    Article  CAS  Google Scholar 

  6. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerod A, Russnes HE, Foekens JA, Reis-Filho JS, van 't Veer L, Richardson AL, Borresen-Dale AL, Campbell PJ, Futreal PA, Stratton MR (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462:1005–1010. https://doi.org/10.1038/nature08645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao MS, Twomey D, Verhaak RG, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M (2007) Characterizing the cancer genome in lung adenocarcinoma. Nature 450:893–898. https://doi.org/10.1038/nature06358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Xue W, Kitzing T, Roessler S, Zuber J, Krasnitz A, Schultz N, Revill K, Weissmueller S, Rappaport AR, Simon J, Zhang J, Luo W, Hicks J, Zender L, Wang XW, Powers S, Wigler M, Lowe SW (2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc Natl Acad Sci U S A 109:8212–8217. https://doi.org/10.1073/pnas.1206062109

    Article  PubMed  PubMed Central  Google Scholar 

  9. Catenacci DV, Ang A, Liao WL, Shen J, O’Day E, Loberg RD, Cecchi F, Hembrough T, Ruzzo A, Graziano F (2016) MET tyrosine kinase receptor expression and amplification as prognostic biomarkers of survival in gastroesophageal adenocarcinoma. Cancer 123:1061–1070. https://doi.org/10.1002/cncr.30437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kim SY, Ahn T, Bang H, Ham JS, Kim J, Kim ST, Jang J, Shim M, Kang SY, Park SH, Min BH, Lee H, Kang WK, Kim KM, Park W, Lee J (2017) Acquired resistance to LY2874455 in FGFR2-amplified gastric cancer through an emergence of novel FGFR2-ACSL5 fusion. Oncotarget 8:15014–15022. https://doi.org/10.18632/oncotarget.14788

    Article  PubMed  PubMed Central  Google Scholar 

  11. Wiech T, Nikolopoulos E, Weis R, Langer R, Bartholome K, Timmer J, Walch AK, Hofler H, Werner M (2009) Genome-wide analysis of genetic alterations in Barrett’s adenocarcinoma using single nucleotide polymorphism arrays. Lab Investig 89:385–397. https://doi.org/10.1038/labinvest.2008.67

    Article  CAS  PubMed  Google Scholar 

  12. Miller CT, Moy JR, Lin L, Schipper M, Normolle D, Brenner DE, Iannettoni MD, Orringer MB, Beer DG (2003) Gene amplification in esophageal adenocarcinomas and Barrett's with high-grade dysplasia. Clin Cancer Res 9:4819–4825

    CAS  PubMed  Google Scholar 

  13. Albrecht B, Hausmann M, Zitzelsberger H, Stein H, Siewert JR, Hopt U, Langer R, Hofler H, Werner M, Walch A (2004) Array-based comparative genomic hybridization for the detection of DNA sequence copy number changes in Barrett’s adenocarcinoma. J Pathol 203:780–788. https://doi.org/10.1002/path.1576

    Article  CAS  PubMed  Google Scholar 

  14. Pasello G, Agata S, Bonaldi L, Corradin A, Montagna M, Zamarchi R, Parenti A, Cagol M, Zaninotto G, Ruol A, Ancona E, Amadori A, Saggioro D (2009) DNA copy number alterations correlate with survival of esophageal adenocarcinoma patients. Mod Pathol 22:58–65. https://doi.org/10.1038/modpathol.2008.150

    Article  CAS  PubMed  Google Scholar 

  15. Nancarrow DJ, Handoko HY, Smithers BM, Gotley DC, Drew PA, Watson DI, Clouston AD, Hayward NK, Whiteman DC (2008) Genome-wide copy number analysis in esophageal adenocarcinoma using high-density single-nucleotide polymorphism arrays. Cancer Res 68:4163–4172. https://doi.org/10.1158/0008-5472.can-07-6710

    Article  CAS  PubMed  Google Scholar 

  16. Choy B, Bandla S, Xia Y, Tan D, Pennathur A, Luketich JD, Godfrey TE, Peters JH, Sun J, Zhou Z (2012) Clinicopathologic characteristics of high expression of Bmi-1 in esophageal adenocarcinoma and squamous cell carcinoma. BMC Gastroenterol 12:146. https://doi.org/10.1186/1471-230x-12-146

    Article  PubMed  PubMed Central  Google Scholar 

  17. Davison JM, Yee M, Krill-Burger JM, Lyons-Weiler MA, Kelly LA, Sciulli CM, Nason KS, Luketich JD, Michalopoulos GK, LaFramboise WA (2014) The degree of segmental aneuploidy measured by total copy number abnormalities predicts survival and recurrence in superficial gastroesophageal adenocarcinoma. PLoS One 9:e79079. https://doi.org/10.1371/journal.pone.0079079

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lin L, Prescott MS, Zhu Z, Singh P, Chun SY, Kuick RD, Hanash SM, Orringer MB, Glover TW, Beer DG (2000) Identification and characterization of a 19q12 amplicon in esophageal adenocarcinomas reveals cyclin E as the best candidate gene for this amplicon. Cancer Res 60:7021–7027

    CAS  PubMed  Google Scholar 

  19. Frankel A, Armour N, Nancarrow D, Krause L, Hayward N, Lampe G, Smithers BM, Barbour A (2014) Genome-wide analysis of esophageal adenocarcinoma yields specific copy number aberrations that correlate with prognosis. Genes Chromosomes Cancer 53:324–338. https://doi.org/10.1002/gcc.22143

    Article  CAS  PubMed  Google Scholar 

  20. Rygiel AM, Milano F, Ten Kate FJ, Schaap A, Wang KK, Peppelenbosch MP, Bergman JJ, Krishnadath KK (2008) Gains and amplifications of c-myc, EGFR, and 20.q13 loci in the no dysplasia-dysplasia-adenocarcinoma sequence of Barrett’s esophagus. Cancer Epidemiol Biomark Prev 17:1380–1385. https://doi.org/10.1158/1055-9965.epi-07-2734

    Article  CAS  Google Scholar 

  21. Miller CT, Aggarwal S, Lin TK, Dagenais SL, Contreras JI, Orringer MB, Glover TW, Beer DG, Lin L (2003) Amplification and overexpression of the dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 (DYRK2) gene in esophageal and lung adenocarcinomas. Cancer Res 63:4136–4143

    CAS  PubMed  Google Scholar 

  22. Hasina R, Mollberg N, Kawada I, Mutreja K, Kanade G, Yala S, Surati M, Liu R, Li X, Zhou Y, Ferguson BD, Nallasura V, Cohen KS, Hyjek E, Mueller J, Kanteti R, El Hashani E, Kane D, Shimada Y, Lingen MW, Husain AN, Posner MC, Waxman I, Villaflor VM, Ferguson MK, Varticovski L, Vokes EE, Gill P, Salgia R (2013) Critical role for the receptor tyrosine kinase EPHB4 in esophageal cancers. Cancer Res 73:184–194. https://doi.org/10.1158/0008-5472.can-12-0915

    Article  CAS  PubMed  Google Scholar 

  23. Hjortland GO, Meza-Zepeda LA, Beiske K, Ree AH, Tveito S, Hoifodt H, Bohler PJ, Hole KH, Myklebost O, Fodstad O, Smeland S, Hovig E (2011) Genome wide single cell analysis of chemotherapy resistant metastatic cells in a case of gastroesophageal adenocarcinoma. BMC Cancer 11:455. https://doi.org/10.1186/1471-2407-11-455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Tokunaga R, Imamura Y, Nakamura K, Ishimoto T, Nakagawa S, Miyake K, Nakaji Y, Tsuda Y, Iwatsuki M, Baba Y, Sakamoto Y, Miyamoto Y, Saeki H, Yoshida N, Oki E, Watanabe M, Oda Y, Bass AJ, Maehara Y, Baba H (2016) Fibroblast growth factor receptor 2 expression, but not its genetic amplification, is associated with tumor growth and worse survival in esophagogastric junction adenocarcinoma. Oncotarget 7:19748–19761. https://doi.org/10.18632/oncotarget.7782

    Article  PubMed  PubMed Central  Google Scholar 

  25. Walch A, Specht K, Braselmann H, Stein H, Siewert JR, Hopt U, Hofler H, Werner M (2004) Coamplification and coexpression of GRB7 and ERBB2 is found in high grade intraepithelial neoplasia and in invasive Barrett's carcinoma. Int J Cancer 112:747–753. https://doi.org/10.1002/ijc.20411

    Article  CAS  PubMed  Google Scholar 

  26. Kumarasinghe MP, de Boer WB, Khor TS, Ooi EM, Jene N, Jayasinghe S, Fox SB (2014) HER2 status in gastric/gastro-esophageal junctional cancers: should determination of gene amplification by SISH use HER2 copy number or HER2: CEP17 ratio? Pathology 46:184–187. https://doi.org/10.1097/pat.0000000000000075

    Article  CAS  PubMed  Google Scholar 

  27. Lange T, Nentwich MF, Luth M, Yekebas E, Schumacher U (2011) Trastuzumab has anti-metastatic and anti-angiogenic activity in a spontaneous metastasis xenograft model of esophageal adenocarcinoma. Cancer Lett 308(1):54–61. https://doi.org/10.1016/j.canlet.2011.04.013

    Article  CAS  PubMed  Google Scholar 

  28. Safran H, Dipetrillo T, Akerman P, Ng T, Evans D, Steinhoff M, Benton D, Purviance J, Goldstein L, Tantravahi U, Kennedy T (2007) Phase I/II study of trastuzumab, paclitaxel, cisplatin and radiation for locally advanced, HER2 overexpressing, esophageal adenocarcinoma. Int J Radiat Oncol Biol Phys 67:405–409. https://doi.org/10.1016/j.ijrobp.2006.08.076

    Article  CAS  PubMed  Google Scholar 

  29. Michalk M, Meinrath J, Kunstlinger H, Koitzsch U, Drebber U, Merkelbach-Bruse S, Bollschweiler E, Kloth M, Hartmann W, Holscher A, Quaas A, Grimminger PP, Odenthal M (2016) MDM2 gene amplification in esophageal carcinoma. Oncol Rep 35:2223–2227. https://doi.org/10.3892/or.2016.4578

    Article  CAS  PubMed  Google Scholar 

  30. Pal J, Bertheau R, Buon L, Qazi A, Batchu RB, Bandyopadhyay S, Ali-Fehmi R, Beer DG, Weaver DW, Shmookler Reis RJ, Goyal RK, Huang Q, Munshi NC, Shammas MA (2011) Genomic evolution in Barrett’s adenocarcinoma cells: critical roles of elevated hsRAD51, homologous recombination and Alu sequences in the genome. Oncogene 30:3585–3598. https://doi.org/10.1038/onc.2011.83

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Lockwood WW, Thu KL, Lin L, Pikor LA, Chari R, Lam WL, Beer DG (2012) Integrative genomics identified RFC3 as an amplified candidate oncogene in esophageal adenocarcinoma. Clin Cancer Res 18:1936–1946. https://doi.org/10.1158/1078-0432.ccr-11-1431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Akagi T, Ito T, Kato M, Jin Z, Cheng Y, Kan T, Yamamoto G, Olaru A, Kawamata N, Boult J, Soukiasian HJ, Miller CW, Ogawa S, Meltzer SJ, Koeffler HP (2009) Chromosomal abnormalities and novel disease-related regions in progression from Barrett’s esophagus to esophageal adenocarcinoma. Int J Cancer 125:2349–2359. https://doi.org/10.1002/ijc.24620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Pang C, LaLonde A, Godfrey TE, Que J, Sun J, Wu TT, Zhou Z (2017) Bile salt receptor TGR5 is highly expressed in esophageal adenocarcinoma and precancerous lesions with significantly worse overall survival and gender differences. Clin Exp Gastroenterol 10:29–37. https://doi.org/10.2147/ceg.s117842

    Article  PubMed  PubMed Central  Google Scholar 

  34. Leicht DT, Kausar T, Wang Z, Ferrer-Torres D, Wang TD, Thomas DG, Lin J, Chang AC, Lin L, Beer DG (2014) TGM2: a cell surface marker in esophageal adenocarcinomas. J Thorac Oncol 9:872–881. https://doi.org/10.1097/jto.0000000000000229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Zhou Z, Xia Y, Bandla S, Zakharov V, Wu S, Peters J, Godfrey TE, Sun J (2014) Vitamin D receptor is highly expressed in precancerous lesions and esophageal adenocarcinoma with significant sex difference. Human Pathol 45:1744–1751. https://doi.org/10.1016/j.humpath.2014.02.029

    Article  CAS  Google Scholar 

  36. Boonstra JJ, van Marion R, Douben HJ, Lanchbury JS, Timms KM, Abkevich V, Tilanus HW, de Klein A, Dinjens WN (2012) Mapping of homozygous deletions in verified esophageal adenocarcinoma cell lines and xenografts. Genes Chromosomes Cancer 51:272–282. https://doi.org/10.1002/gcc.20952

    Article  CAS  PubMed  Google Scholar 

  37. Soutto M, Peng D, Razvi M, Ruemmele P, Hartmann A, Roessner A, Schneider-Stock R, El-Rifai W (2010) Epigenetic and genetic silencing of CHFR in esophageal adenocarcinomas. Cancer 116:4033–4042. https://doi.org/10.1002/cncr.25151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bandla S, Peters JH, Ruff D, Chen SM, Li CY, Song K, Thoms K, Litle VR, Watson T, Chapurin N, Lada M, Pennathur A, Luketich JD, Peterson D, Dulak A, Lin L, Bass A, Beer DG, Godfrey TE, Zhou Z (2014) Comparison of cancer-associated genetic abnormalities in columnar-lined esophagus tissues with and without goblet cells. Ann Surg 260:72–80. https://doi.org/10.1097/SLA.0000000000000424

    Article  PubMed  PubMed Central  Google Scholar 

  39. Zhang K, Wu X, Wang J, Lopez J, Zhou W, Yang L, Wang SE, Raz DJ, Kim JY (2016) Circulating miRNA profile in esophageal adenocarcinoma. Am J Cancer Res 6:2713–2721

    PubMed  PubMed Central  Google Scholar 

  40. Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O’Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC (2011) Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in esophageal adenocarcinoma. Gut 60:1317–1326. https://doi.org/10.1136/gut.2010.234179

    Article  CAS  PubMed  Google Scholar 

  41. Silvers AL, Lin L, Bass AJ, Chen G, Wang Z, Thomas DG, Lin J, Giordano TJ, Orringer MB, Beer DG, Chang AC (2010) Decreased selenium-binding protein 1 in esophageal adenocarcinoma results from posttranscriptional and epigenetic regulation and affects chemosensitivity. Clin Cancer Res 16:2009–2021. https://doi.org/10.1158/1078-0432.ccr-09-2801

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Obulkasim A, Ylstra B, van Essen HF, Benner C, Stenning S, Langley R, Allum W, Cunningham D, Inam I, Hewitt LC, West NP, Meijer GA, van de Wiel MA, Grabsch HI (2016) Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma. Oncotarget 7:44084–44095. https://doi.org/10.18632/oncotarget.9857

    Article  PubMed  PubMed Central  Google Scholar 

  43. Aichler M, Motschmann M, Jutting U, Luber B, Becker K, Ott K, Lordick F, Langer R, Feith M, Siewert JR, Walch A (2014) Epidermal growth factor receptor (EGFR) is an independent adverse prognostic factor in esophageal adenocarcinoma patients treated with cisplatin-based neoadjuvant chemotherapy. Oncotarget 5:6620–6632. https://doi.org/10.18632/oncotarget.2268

    Article  PubMed  PubMed Central  Google Scholar 

  44. Xu E, Sun W, Gu J, Chow WH, Ajani JA, Wu X (2013) Association of mitochondrial DNA copy number in peripheral blood leukocytes with risk of esophageal adenocarcinoma. Carcinogenesis 34:2521–2524. https://doi.org/10.1093/carcin/bgt230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lee S, Han MJ, Lee KS, Back SC, Hwang D, Kim HY, Shin JH, Suh SP, Ryang DW, Kim HR, Shin MG (2012) Frequent occurrence of mitochondrial DNA mutations in Barrett’s metaplasia without the presence of dysplasia. PLoS One 7:e37571. https://doi.org/10.1371/journal.pone.0037571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Geppert CI, Rummele P, Sarbia M, Langer R, Feith M, Morrison L, Pestova E, Schneider-Stock R, Hartmann A, Rau TT (2014) Multi-colour FISH in esophageal adenocarcinoma-predictors of prognosis independent of stage and grade. Br J Cancer 110:2985–2995. https://doi.org/10.1038/bjc.2014.238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Ismail A, Bandla S, Reveiller M, Toia L, Zhou Z, Gooding WE, Kalatskaya I, Stein L, D’Souza M, Litle VR, Peters JH, Pennathur A, Luketich JD, Godfrey TE (2011) Early G(1) cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma. Clin Cancer Res 17:4513–4522. https://doi.org/10.1158/1078-0432.ccr-11-0244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Bang YJ, Van Cutsem E, Feyereislova A, Chung HC, Shen L, Sawaki A, Lordick F, Ohtsu A, Omuro Y, Satoh T, Aprile G, Kulikov E, Hill J, Lehle M, Ruschoff J, Kang YK, To GATI (2010) Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-esophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial. Lancet 376:687–697. https://doi.org/10.1016/S0140-6736(10)61121-X

    Article  CAS  PubMed  Google Scholar 

  49. Almhanna K, Meredith KL, Hoffe SE, Shridhar R, Coppola D (2013) Targeting the human epidermal growth factor receptor 2 in esophageal cancer. Cancer Control 20:111–116

    Article  Google Scholar 

  50. Li X, Galipeau PC, Paulson TG, Sanchez CA, Arnaudo J, Liu K, Sather CL, Kostadinov RL, Odze RD, Kuhner MK, Maley CC, Self SG, Vaughan TL, Blount PL, Reid BJ (2014) Temporal and spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett’s esophagus. Cancer Prev Res (Phila) 7:114–127. https://doi.org/10.1158/1940-6207.CAPR-13-0289

    Article  Google Scholar 

  51. Sykes PJ, Neoh SH, Brisco MJ, Hughes E, Condon J, Morley AA (1992) Quantitation of targets for PCR by use of limiting dilution. Biotechniques 13:444–449

    CAS  PubMed  Google Scholar 

  52. Vogelstein B, Kinzler KW (1999) Digital PCR. Proc Natl Acad Sci U S A 96:9236–9241

    Article  CAS  Google Scholar 

  53. Fan HC, Quake SR (2007) Detection of aneuploidy with digital polymerase chain reaction. Anal Chem 79:7576–7579. https://doi.org/10.1021/ac0709394

    Article  CAS  PubMed  Google Scholar 

  54. Baker M (2012) Digital PCR hits its stride. Nat Methods 9:541–544

    Article  CAS  Google Scholar 

  55. McDermott GP, Do D, Litterst CM, Maar D, Hindson CM, Steenblock ER, Legler TC, Jouvenot Y, Marrs SH, Bemis A, Shah P, Wong J, Wang S, Sally D, Javier L, Dinio T, Han C, Brackbill TP, Hodges SP, Ling Y, Klitgord N, Carman GJ, Berman JR, Koehler RT, Hiddessen AL, Walse P, Bousse L, Tzonev S, Hefner E, Hindson BJ, Cauly TH 3rd, Hamby K, Patel VP, Regan JF, Wyatt PW, Karlin-Neumann GA, Stumbo DP, Lowe AJ (2013) Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR. Anal Chem 85:11619–11627. https://doi.org/10.1021/ac403061n

    Article  CAS  PubMed  Google Scholar 

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  1. Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia

    Katherine T. W. Lee, Vinod Gopalan & Alfred K. Lam

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  1. Katherine T. W. Lee
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  2. Vinod Gopalan
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    Alfred K. Lam

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Lee, K.T.W., Gopalan, V., Lam, A.K. (2018). Somatic DNA Copy-Number Alterations Detection for Esophageal Adenocarcinoma Using Digital Polymerase Chain Reaction. In: Lam, A. (eds) Esophageal Adenocarcinoma. Methods in Molecular Biology, vol 1756. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7734-5_18

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