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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<title font="Georgia">NGS Resources and Cancer </title>
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<meta name=”description” content=”Comprehensive Resources for Cancer NGS Data Analysis (CRCDA)”/>
<meta name=”keywords” content=”CRCDA, NGS, Cancer and NGS, NGS data analysis, CRCDA”/>
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<h1 ><font color="#5b1356">Comprehensive Resources for Cancer NGS Data Analysis</font> </h1>
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<li><a href="index.html">HOME</a></li>
<li><a href="ngstool.html">TOOLS</a>
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<li><a href="cancergenomics.html">Cancer Genomics</a></li>
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<li><a href="qualitycontrol.html">Quality Control</a></li>
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<p><h3 align="center"><b>CANCER NEXT GENERATION SEQUENCING </b></h3></p><p align="justify" ><font color="#3f3a01">
<div id="list"><h3 align="left" >Breast Cancer: </h3>
<ol type="0" >
<li align="left"><a href="http://breast-cancer-research.com/content/15/5/R97">Clinical application of high-throughput genomic technologies for treatment selection in breast cancer</a><br /> R Hansen and Philippe L Bedard, Breast Cancer Research 2013, 15:R97 </li>
<li align="left"><a href="http://breast-cancer-research.com/content/15/5/211">Nucleic acids as biomarkers in breast cancer </a><br />Heidi Schwarzenbach; Breast Cancer Research 2013, 15:211</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23014189">Next-generation sequencing in breast cancer: first take home messages </a><br />Desmedt C1, Voet T, Sotiriou C, Campbell PJ.Curr Opin Oncol. 2012 Nov;24(6):597-604</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/21965338">Insight into the heterogeneity of breast cancer through next-generation sequencing.</a><br /> Russnes HG, Navin N, Hicks J, Borresen-Dale AL.J Clin Invest 2011 Oct;121(10):3810-8.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/20975737">Trastuzumab and beyond: sequencing cancer genomes and predicting molecular networks.</a> <br /> Roukos DH . Pharmacogenomics J . 2011 Apr;11(2):81-92.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/22128823">The breast cancer genome--a key for better oncology.</a><br /> HK1, Caldas C. BMC Cancer. 2011 Nov 30 ; 11:501.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23973262">Significance of TP53 mutations determined by next-generation "deep" sequencing in prognosis of estrogen receptor-positive breast cancer.</a><br />Uji K, Naoi Y, Kagara N, Shimoda M, Shimomura A, Maruyama N, Shimazu K, Kim SJ, Noguchi S. Cancer Lett. 2014 Jan 1;342(1):19-26</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23879964">Next generation analysis of breast cancer genomes for precision medicine.</a><br />Previati M, Manfrini M, Galasso M, Zerbinati C, Palatini J, Gasparini P, Volinia S.Cancer Lett. 2013 Oct 1;339(1):1-7.</a><br /></li>
</ol>
<h3 align="left">Head and Neck Cancer</h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24440145">Next generation sequencing and its application in deciphering head and neck cancer.</a><br /> M, Farah CS.Oral Oncol. 2014 Apr;50(4):247-53.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24557572">Harnessing massively parallel sequencing in personalized head and neck oncology.</a><br />Jessri M, Farah CS.J Dent Res. 2014 May;93(5):437-44.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24725020">Defining the genomic landscape of head and neck cancers through next-generation sequencing.</a><br />Rizzo G, Black M, Mymryk J, Barrett J, Nichols A.Oral Dis. 2014 Apr 12</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/22911296">Frequent mutations in TP53 and CDKN2A found by next-generation sequencing of head and neck cancer cell lines.</a><br />Nichols AC1, Yoo J, Palma DA, Fung K, Franklin JH, Koropatnick J, Mymryk JS, Batada NN, Barrett JW.Arch Otolaryngol Head Neck Surg. 2012 Aug;138(8):732-9.</li>
</ol>
<h3 align="left">Ovarian Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/22155315">Isolation of single, intact chromosomes from single, selected ovarian cancer cells for in situ hybridization and sequencing.</a><br />Malecki M, Szybalski W. ;Gene. 2012 Feb 1;493(1):132-9</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/22216282">Global analysis of DNA methylation by Methyl-Capture sequencing reveals epigenetic control of cisplatin resistance in ovarian cancer cell.</a><br />Yu W, Jin C, Lou X, Han X, Li L, He Y, Zhang H, Ma K, Zhu J, Cheng L, Lin B.PLoS One. 2011;6(12):e29450.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24549055">Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes.</a><br />Castéra L, Krieger S, Rousselin A, Legros A, Baumann JJ, Bruet O, Brault B, Fouillet R, Goardon N, Letac O, Baert-Desurmont S, Tinat J, Bera O, Dugast C, Berthet P, Polycarpe F, Layet V, Hardouin A, Frébourg T, Vaur D.Eur J Hum Genet. 2014 Feb 19.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24504028">Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status.</a><br />Cunningham JM, Cicek MS, Larson NB, Davila J, Wang C, Larson MC, Song H, Dicks EM, Harrington P, Wick M, Winterhoff BJ, Hamidi H, Konecny GE, Chien J, Bibikova M, Fan JB, Kalli KR, Lindor NM, Fridley BL, Pharoah PP, Goode EL.Sci Rep. 2014 Feb 7;4:4026.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23791828">Comprehensive genomic profiling of epithelial ovarian cancer by next generation sequencing-based diagnostic assay reveals new routes to targeted therapies.</a><br />Ross JS, Ali SM, Wang K, Palmer G, Yelensky R, Lipson D, Miller VA, Zajchowski D, Shawver LK, Stephens PJ.Gynecol Oncol. 2013 Sep;130(3):554-9</li>
</ol>
<h3 align="left">Lung Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23980680">Next-generation sequencing for lung cancer.</a><br />Wu K, Huang RS, House L, Cho WC.Future Oncol. 2013 Sep;9(9):1323-36</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23362162">Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS.</a><br />Tuononen K, Mäki-Nevala S, Sarhadi VK, Wirtanen A, Ronty M, Salmenkivi K, Andrews JM, Telaranta-Keerie AI, Hannula S, Lagstrom S, Ellonen P, Knuuttila A, Knuutila S.Genes Chromosomes Cancer. 2013 May;52(5):503-11.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24227699">Targeted next-generation sequencing using fine-needle aspirates from adenocarcinomas of the lung.</a><br />Karnes HE, Duncavage EJ, Bernadt CT.Cancer Cytopathol. 2014 Feb;122(2):104-13.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24868222">KRAS Mutation Detection in Non-small Cell Lung Cancer Using a Peptide Nucleic Acid-Mediated Polymerase Chain Reaction Clamping Method and Comparative Validation with Next-Generation Sequencing.</a><br />Lee B, Lee B, Han G, Kwon MJ, Han J, Choi YL.Korean J Pathol. 2014 Apr;48(2):100-7.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24857785">Comparison of targeted next-generation sequencing with conventional sequencing for predicting the responsiveness to epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) therapy in never-smokers with lung adenocarcinoma.</a><br />Han JY, Kim SH, Lee YS, Lee SY, Hwang JA, Kim JY, Yoon SJ, Lee GK.Lung Cancer. 2014 Apr 29. pii: S0169-5002(14)00180-9</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24130455">Identification of candidate genes for lung cancer somatic mutation test kits.</a><br />Chen Y, Shi JX, Pan XF, Feng J, Zhao H.Genet Mol Biol. 2013 Sep;36(3):455-64</li>
</ol>
<h3 align="left">Liver Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23750322">Next-generation sequencing: application in liver cancer-past, present and future</a><br />Marquardt JU, Andersen JB.Biology (Basel). 2012 Aug 31;1(2):383-94</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24878701">Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue.</a><br />Hedegaard J, Thorsen K, Lund MK, Hein AM, Hamilton-Dutoit SJ, Vang S, Nordentoft I, Birkenkamp-Demtroder K, Kruhøffer M, Hager H, Knudsen B, Andersen CL, Sørensen KD, Pedersen JS, Orntoft TF, Dyrskjøt L.PLoS One. 2014 May 30;9(5):e98187.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/21499249">
High-resolution characterization of a hepatocellular carcinoma genome.
</a><br />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.;Nat Genet 2011, 43:464–469.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23063663">Next generation sequencing reveals genetic landscape of hepatocellular carcinomas.</a><br />Li S, Mao M.Cancer Lett. 2013 Nov 1;340(2):247-53. doi: 10.1016/j.canlet.2012.09.027.
</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/2412070">Characterization of translocations in mesenchymal hamartoma and undifferentiated embryonal sarcoma of the liver.</a><br />Mathews J, Duncavage EJ, Pfeifer JD.Exp Mol Pathol. 2013 Dec;95(3):319-24.</li>
</ol>
<h3 align="left">Renal Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23841900">Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis.</a><br />Chen J, Zhang D, Zhang W, Tang Y, Yan W, Guo L, Shen B.
J Transl Med. 2013 Jul 10;11:169.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/2415512">Targeted next-generation sequencing and non-coding RNA expression analysis of clear cell papillary renal cell carcinoma suggests distinct pathological mechanisms from other renal tumour subtypes.</a><br />Lawrie CH, Larrea E, Larrinaga G, Goicoechea I, Arestin M, Fernandez-Mercado M, Hes O, Caceres F, Manterola L, Lopez JI.J Pathol. 2014 Jan;232(1):32-42.</li>
</ol>
<h3 align="left">Cervical Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24838323">Development and validation of a new HPV genotyping assay based on next-generation sequencing.</a><br />Yi X, Zou J, Xu J, Liu T, Liu T, Hua S, Xi F, Nie X, Ye L, Luo Y, Xu L, Du H, Wu R, Yang L, Liu R, Yang B, Wang J, Belinson JL.Am J Clin Pathol. 2014 Jun;141(6):796-804. </li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23573945">Accurate human papillomavirus genotyping by 454 pyrosequencing.</a><br />Militello V, Lavezzo E, Costanzi G, Franchin E, Di Camillo B, Toppo S, Palu G, Barzon L.Clin Microbiol Infect. 2013 Oct;19(10):E428-34.</li>
</ol>
<h3 align="left">Melanoma </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/22248438">Reviewing the somatic genetics of melanoma: from current to future analytical approaches.</a><br /> Dutton-Regester K, Hayward NK. Pigment Cell Melanoma Res. 2012 Mar;25(2):144-54.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24023765">In-depth characterization of microRNA transcriptome in melanoma. </a><br />Kozubek J, Ma Z, Fleming E, Duggan T, Wu R, Shin DG, Dadras SS. PLoS One. 2013 Sep 4;8(9):e72699.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24345920">BRAF fusions define a distinct molecular subset of melanomas with potential sensitivity to MEK inhibition.</a><br />Hutchinson KE, Lipson D, Stephens PJ, Otto G, Lehmann BD, Lyle PL, Vnencak-Jones CL, Ross JS, Pietenpol JA, Sosman JA, Puzanov I, Miller VA, Pao W.Clin Cancer Res. 2013 Dec 15;19(24):6696-702.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24410877">Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations.</a><br /> Ihle MA, Fassunke J, König K, Grünewald I, Schlaak M, Kreuzberg N, Tietze L, Schildhaus HU, Büttner R, Merkelbach-Bruse S.BMC Cancer. 2014 Jan 10;14:13. </li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24755198">A Meta-analysis of Somatic Mutations from Next Generation Sequencing of 241 Melanomas: A Road Map for the Study of Genes with Potential Clinical Relevance. </a><br /> Xia J, Jia P, Hutchinson KE, Dahlman KB, Johnson D, Sosman J, Pao W, Zhao Z.Mol Cancer Ther. 2014 Apr 22.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24797823">Enabling a genetically informed approach to cancer medicine: a retrospective evaluation of the impact of comprehensive tumor profiling using a targeted next-generation sequencing panel.
</a><br />Johnson DB, Dahlman KH, Knol J, Gilbert J, Puzanov I, Means-Powell J, Balko JM, Lovly CM, Murphy BA, Goff LW, Abramson VG, Crispens MA, Mayer IA, Berlin JD, Horn L, Keedy VL, Reddy NM, Arteaga CL, Sosman JA, Pao W. Oncologist. 2014 Jun;19(6):616-22.</li>
</ol>
<h3 align="left">Leukemia </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24342950">Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders.</a><br />Ladetto M, Brüggemann M, Monitillo L, Ferrero S, Pepin F, Drandi D, Barbero D, Palumbo A, Passera R, Boccadoro M, Ritgen M, Gökbuget N, Zheng J, Carlton V, Trautmann H, Faham M, Pott C. Leukemia. 2014 Jun;28(6):1299-307. doi: 10.1038/leu.2013.375.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23167608">Exploring the genetic landscape in chronic lymphocytic leukemia using high-resolution technologies.</a><br />Gunnarsson R1, Mansouri L, Rosenquist R.Leuk Lymphoma. 2013 Aug;54(8):1583-90.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24949228">Childhood B-acute lymphoblastic leukemia: a genetic update.</a><br />Woo JS, Alberti MO, Tirado CA.Exp Hematol Oncol. 2014 Jun 13;3:16.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24817963">Applicability of next-generation sequencing to decalcified formalin-fixed and paraffin-embedded chronic myelomonocytic leukaemia samples.</a><br />Bernard V, Gebauer N, Dinh T, Stegemann J, Feller AC, Merz H. Int J Clin Exp Pathol. 2014 Mar 15;7(4):1667-76.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24746875">Expression profiling of leukemia patients: Key lessons and future directions. </a><br />Shivarov V, Bullinger L. Exp Hematol. 2014 Apr 15. pii: S0301-472X(14)00145-3.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24501221">Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.</a><br />Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Fama R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foà R, Rabadan R, Gaidano G. Blood. 2014 Apr 3;123(14):2139-47.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24498620">Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases.</a><br />Spinelli R, Pirola A, Redaelli S, Sharma N, Raman H, Valletta S, Magistroni V, Piazza R, Gambacorti-Passerini C.Mol Genet Genomic Med. 2013 Nov;1(4):246-59. </li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24515762">A comparison of deep sequencing of TCRG rearrangements vs traditional capillary electrophoresis for assessment of clonality in T-Cell lymphoproliferative disorders.</a><br /> Schumacher JA, Duncavage EJ, Mosbruger TL, Szankasi PM, Kelley TW. Am J Clin Pathol. 2014 Mar;141(3):348-59.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24474533">Genomic tools in acute myeloid leukemia: From the bench to the bedside.</a><br />White BS, DiPersio JF. Cancer. 2014 Apr 15;120(8):1134-44.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24415659">TP53 mutation analysis in clinical practice: lessons from chronic lymphocytic leukemia.</a><br />Malcikova J, Pavlova S, Kozubik KS, Pospisilova S. Hum Mutat. 2014 Jun;35(6):663-71.</li>
</ol>
<h3 align="left">Oral Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24668645">A surprising cross-species conservation in the genomic landscape of mouse and human oral cancer identifies a transcriptional signature predicting metastatic disease.</a><br />Onken MD, Winkler AE, Kanchi KL, Chalivendra V, Law JH, Rickert CG, Kallogjeri D, Judd NP, Dunn GP, Piccirillo JF, Lewis JS Jr, Mardis ER, Uppaluri R. Clin Cancer Res. 2014 Jun 1;20(11):2873-84. </li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24422024">Animal models to study the mutational landscape for oral cavity and oropharyngeal cancers. </a><br />Spiotto MT, Pytynia M, Liu GF, Ranck MC, Widau R. J Oral Maxillofac Res. 2013 Apr 1;4(1):e1.</li>
</ol>
<h3 align="left">ColoRectal Cancer </h3> <div id="top"><a href='#top1' > Back to Top</a></div>
<ol>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/21203531">Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.</a><br />
Timmermann B, Kerick M, Roehr C, Fischer A, Isau M, Boerno ST, Wunderlich A, Barmeyer C, Seemann P, Koenig J, Lappe M, Kuss AW, Garshasbi M, Bertram L, Trappe K, Werber M, Herrmann BG, Zatloukal K, Lehrach H, Schweiger MR.;PLoS One. 2010 Dec 22;5(12):e15661.
</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24943349">Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.</a><br />Shanmugam V, Ramanathan RK, Lavender NA, Sinari S, Chadha M, Liang WS, Kurdoglu A, Izatt T, Christoforides A, Benson H, Phillips L, Baker A, Murray C, Hostetter G, Von Hoff DD, Craig DW, Carpten JD. BMC Med Genomics. 2014 Jun 18;7(1):36.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24937453">Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors.</a><br />Kim HK, Park WC, Lee KM, Hwang HL, Park SY, Sorn S, Chandra V, Kim KG, Yoon WB, Bae JS, Shin HD, Shin JY, Seoh JY, Kim JI, Hong KM.PLoS One. 2014 Jun 17;9(6):e100089.</li>
<li align="left"><a href="http://www.ncbi.nlm.nih.gov/pubmed/24942275">Clinical activity of FOLFIRI plus cetuximab according to extended gene mutation status by next generation sequencing: findings from the CAPRI-GOIM trial.</a><br />Ciardiello F, Normanno N, Maiello E, Martinelli E, Troiani T, Pisconti S, Giuliani F, Barone C, Cartenì G, Rachiglio AM, Montesarchio V, Tonini G, Rizzi D, Cinieri S, Bordonaro R, Febbraro A, De Vita F, Orditura M, Fenizia F, Lambiase M, Rinaldi A, Tatangelo F, Botti G, Colucci G. Ann Oncol. 2014 Jun 18. pii: mdu230.</li>
</ol>
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