Emerging technologies for improved stratification of cancer patients: A review of opportunities, challenges, and tools

Cancer Journal

Volumn 17, Issue 6, 2011, Pages 451-464

  Lamlertthon, Wisut ^a   Hayward, Michele C ^a   Hayes, David Neil ^a,b  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Cancer biomarkers; next generation sequencing; stratification; technology

Indexed keywords

BIOLOGICAL MARKER; TUMOR MARKER;

CANCER PATIENT; CLINICAL DECISION MAKING; HUMAN; NUCLEIC ACID SEQUENCE BASED AMPLIFICATION; PATIENT CARE; PRIORITY JOURNAL; PROGNOSIS; REVIEW; TECHNOLOGY; TREATMENT RESPONSE;

BIOTECHNOLOGY; GENETIC PREDISPOSITION TO DISEASE; HUMANS; NEOPLASMS; TUMOR MARKERS, BIOLOGICAL;

EID: 83755174121     PISSN: 15289117     EISSN: 1540336X     Source Type: Journal    
DOI: 10.1097/PPO.0b013e31823bd1f8     Document Type: Review

References (134)

1. Kochanek KD, Xu JQ, Murphy SL, et al. Deaths: Preliminary data for 2009. Natl Vital Stat Rep. 2011;59:1-51.
2. Jemal A, Bray F, Center MM, et al. Global cancer statistics. CA Cancer J Clin. 2011;61:69-90.
3. Edge SBBD, Compton CC, Fritz AG, et al, eds. AJCC Cancer Staging Manual. 7th ed. New York, NY: Springer; 2010.
4. Collins FS, Barker AD. Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am. 2007;296:50-57.
5. Gail MH, Brinton LA, Byar DP, et al. Projecting individualized probabilities of developing breast cancer for white females who are being examined annually. J Natl Cancer Inst. 1989;81:1879-1886. (Pubitemid 20026073)
6. A predictive model for aggressive non-Hodgkin's lymphoma. The International Non-Hodgkin's Lymphoma Prognostic Factors Project. N Engl J Med. 1993;329:987-994.
7. HanashSM, Baik CS, Kallioniemi O. Emerging molecular biomarkersV blood-based strategies to detect and monitor cancer. Nat Rev Clin Oncol. 2011;8:142-150.
8. von Eyben FE. Laboratory markers and germ cell tumors. Crit Rev Clin Lab Sci. 2003;40:377-427. (Pubitemid 37204500)
9. Fan TW, Lane AN, Higashi RM, et al. Altered regulation of metabolic pathways in human lung cancer discerned by (13)C stable isotoperesolved metabolomics (SIRM). Mol Cancer. 2009;8:41.
10. Greipp PR, San Miguel J, Durie BG, et al. International staging system for multiple myeloma. J Clin Oncol. 2005;23:3412-3420.
11. Andersen JN, Sathyanarayanan S, Di Bacco A, et al. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med. 2010;2:43ra55.
12. Li H, Stampfer MJ, Hollis JBW, et al. A prospective study of plasma vitamin D metabolites, vitamin D receptor polymorphisms, and prostate cancer. PLoS medicine. 2007;4:e103.
13. Patz EF Jr, Campa MJ, Gottlin EB, et al. Panel of serum biomarkers for the diagnosis of lung cancer. J Clin Oncol. 2007;25:5578-5583.
14. Hansen HJ, Snyder JJ, Miller E, et al. Carcinoembryonic antigen (CEA) assay. A laboratory adjunct in the diagnosis and management of cancer. Hum Pathol. 1974;5:139-147.
15. Casciano I, Vinci AD, Banelli B, et al. Circulating tumor nucleic acids: perspective in breast cancer. Breast Care (Basel). 2010;5:75-80.
16. Lin K, Lipsitz R, Miller T, et al. Benefits and harms of prostatespecific antigen screening for prostate cancer: an evidence update for the U.S. Preventive Services Task Force. Ann Intern Med. 2008;149: 192-199.
17. Miller MC, Doyle GV, Terstappen LW. Significance of circulating tumor cells detected by the CellSearch System in patients with metastatic breast colorectal and prostate cancer. J Oncol. 2010;2010: 617421.
18. Rankin W, Grill V, Martin TJ. Parathyroid hormone-related protein and hypercalcemia. Cancer. 1997;80:1564-1571. (Pubitemid 27444028)
19. Meijers-Heijboer H, Van Geel B, Van PuttenWL, et al. Breast cancer after prophylactic bilateral mastectomy in women with a BRCA1 or BRCA2 mutation. N Engl J Med. 2001;345:159-164. (Pubitemid 32662123)
20. Courjal F, Theillet C. Comparative genomic hybridization analysis of breast tumors with predetermined profiles of DNA amplification. Cancer Res. 1997;57:4368-4377. (Pubitemid 27413448)
21. Bastacky S, Ibrahim S, Wilczynski SP, et al. The accuracy of urinary cytology in daily practice. Cancer. 1999;87:118-128. (Pubitemid 29289245)
22. Ward DG, Nyangoma S, Joy H, et al. Proteomic profiling of urine for the detection of colon cancer. Proteome Sci. 2008;6:19.
23. Grondal S, Eriksson B, Hagenas L, et al. Steroid profile in urine: a useful tool in the diagnosis and follow up of adrenocortical carcinoma. Acta Endocrinol (Copenh). 1990;122:656-663. (Pubitemid 20183387)
24. Phe V, Cussenot O, Roupret M. Methylated genes as potential biomarkers in prostate cancer. BJU Int. 2010;105:1364-1370.
25. Kisiel JB, Ahlquist DA. Stool DNA screening for colorectal cancer: opportunities to improve value with next generation tests. J Clin Gastroenterol. 2011;45:301-308.
26. Kim MS, Lee J, Sidransky D. DNA methylation markers in colorectal cancer. Cancer Metastasis Rev. 2010;29:181-206.
27. Streckfus C, Bigler L, Dellinger T, et al. The presence of soluble cerbB- 2 in saliva and serum among women with breast carcinoma: a preliminary study. Clin Cancer Res. 2000;6:2363-2370. (Pubitemid 30399204)
28. Korostoff A, Reder L, Masood R, et al. The role of salivary cytokine biomarkers in tongue cancer invasion and mortality. Oral Oncol. 2011; 47:282-287.
29. Glantz MJ, Cole BF, Glantz LK, et al. Cerebrospinal fluid cytology in patients with cancer. Cancer. 1998;82:733-739.
30. Horvath I, Lazar Z, Gyulai N, et al. Exhaled biomarkers in lung cancer. Eur Respir J. 2009;34:261-275.
31. Ambinder RF, Bhatia K, Martinez-Maza O, et al. Cancer biomarkers in HIV patients. Curr Opin HIV AIDS. 2010;5:531-537.
32. Stolarek RA, Potargowicz E, Seklewska E, et al. Increased H2O2 level in exhaled breath condensate in primary breast cancer patients. J Cancer Res Clin Oncol. 2010;136:923-930.
33. Sugiura S, Ando Y, Minami H, et al. Prognostic value of pleural effusion in patients with non-small cell lung cancer. Clin Cancer Res. 1997;3:47-50. (Pubitemid 27079443)
34. Zheng PP, Luider TM, Pieters R, et al. Identification of tumor-related proteins by proteomic analysis of cerebrospinal fluid from patients with primary brain tumors. J Neuropathol Exp Neurol. 2003;62:855-862. (Pubitemid 37082779)
35. Porcel JM, Vives M, Esquerda A, et al. Use of a panel of tumor markers (carcinoembryonic antigen, cancer antigen 125, carbohydrate antigen 15-3, and cytokeratin 19 fragments) in pleural fluid for the differential diagnosis of benign and malignant effusions. Chest. 2004;126:1757-1763. (Pubitemid 39643976)
36. Miedouge M, Rouzaud P, Salama G, et al. Evaluation of seven tumour markers in pleural fluid for the diagnosis of malignant effusions. Br J Cancer. 1999;81:1059-1065. (Pubitemid 29516152)
37. Gueugnon F, Leclercq S, Blanquart C, et al. Identification of novel markers for the diagnosis of malignant pleural mesothelioma. Am J Pathol. 2011;178:1033-1042.
38. Lee EJ, Kim SH, Kim YH, et al. Is CA-125 an additional help to radiologic findings for differentiation borderline ovarian tumor from stage I carcinoma? Acta Radiol. 2011;52:458-462.
39. Kuk C, Kulasingam V, Gunawardana CG, et al. Mining the ovarian cancer ascites proteome for potential ovarian cancer biomarkers.Mol Cell Proteomics. 2009;8:661-669.
40. Kisanga ER, Gjerde J, Guerrieri-Gonzaga A, et al. Tamoxifen and metabolite concentrations in serum and breast cancer tissue during three dose regimens in a randomized preoperative trial. Clin Cancer Res. 2004;10:2336-2343. (Pubitemid 38445691)
41. Sreekumar A, Poisson LM, Rajendiran TM, et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009;457:910-914.
42. Johansson L. Histopathologic classification of lung cancer: relevance of cytokeratin and TTF-1 immunophenotyping. Ann Diagn Pathol. 2004; 8:259-267. (Pubitemid 39370567)
43. Galvao ER, Martins LM, Ibiapina JO, et al. Breast cancer proteomics: a review for clinicians. J Cancer Res Clin Oncol. 2011;137:915-925.
44. Gown AM. Current issues in ER and HER2 testing by IHC in breast cancer. Mod Pathol. 2008;21(suppl 2):S8-S15. (Pubitemid 351592775)
45. Vogel CL, Cobleigh MA, Tripathy D, et al. Efficacy and safety of trastuzumab as a single agent in first-line treatment of HER2-overexpressing metastatic breast cancer. J Clin Oncol. 2002;20:719-726. (Pubitemid 34111379)
46. Slamon DJ, Clark GM, Wong SG, et al. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science. 1987;235:177.
47. Ross JS, Hatzis C, Symmans WF, et al. Commercialized multigene predictors of clinical outcome for breast cancer. Oncologist. 2008;13: 477-493. (Pubitemid 351872866)
48. Feng H, Shuda M, Chang Y, et al. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science. 2008;319:1096.
49. Pillai R, Deeter R, Rigl CT, et al. Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens. J Mol Diagn. 2011;13: 48-56.
50. Shaw AT, Yeap BY, Mino-Kenudson M, et al. Clinical features and outcome of patients with non-small-cell lung cancer who harbor EML4- ALK. J Clin Oncol. 2009;27:4247-4253.
51. Soda M, Choi YL, Enomoto M, et al. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature. 2007;448:561-566. (Pubitemid 47206930)
52. Han SW, Kim TY, Hwang PG, et al. Predictive and prognostic impact of epidermal growth factor receptor mutation in non-small-cell lung cancer patients treated with gefitinib. J ClinOncol. 2005;23:2493-2501.
53. Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364:2507-2516.
54. Zaravinos A, Mammas IN, Sourvinos G, et al. Molecular detection methods of human papillomavirus (HPV). Int J Biol Markers. 2009;24: 215-222.
55. Torigian DA, Huang SS, Houseni M, et al. Functional imaging of cancer with emphasis on molecular techniques. CA Cancer J Clin. 2007;57:206-224. (Pubitemid 47312081)
56. Somboonporn C, Simthamnimit P, Puttharak W, et al. Role of chest radiography in the diagnosis and follow-up of pulmonary metastasis in differentiated thyroid cancer. J Med Assoc Thai. 2010;93(suppl 3): S52-S60.
57. Henderson E, Milosevic MF, Haider MA, et al. Functional CT imaging of prostate cancer. Phys Med Biol. 2003;48:3085-3100. (Pubitemid 37192922)
58. Costelloe CM, Rohren EM, Madewell JE, et al. Imaging bone metastases in breast cancer: techniques and recommendations for diagnosis. Lancet Oncol. 2009;10:606-614.
59. deSouza NM, Sala E. Imaging: standardizing the use of functional MRI in prostate cancer. Nat Rev Urol. 2011;8:127-129.
60. d'Assignies G, Couvelard A, Bahrami S, et al. Pancreatic endocrine tumors: tumor blood flow assessed with perfusion CT reflects angiogenesis and correlates with prognostic factors. Radiology. 2009;250: 407-416.
61. Aukema TS, Kappers I, Olmos RA, et al. Is 18F-FDG PET/CTuseful for the early prediction of histopathologic response to neoadjuvant erlotinib in patients with non-small cell lung cancer? J Nucl Med. 2010;51: 1344-1348.
62. Hirashima Y, Yamada Y, Tateishi U, et al. Pharmacokinetic parameters from 3-Tesla DCE-MRI as surrogate biomarkers of antitumor effects of bevacizumab plus FOLFIRI in colorectal cancer with liver metastasis. Int J Cancer. [published online ahead of print July 21, 2011] doi:10.1002/ijc.26282.
63. Cao Y, Sundgren PC, Tsien CI, et al. Physiologic and metabolic magnetic resonance imaging in gliomas. J Clin Oncol. 2006;24:1228-1235. (Pubitemid 46622025)
64. Scholl SM, Pallud C, Beuvon F, et al. AntiYcolony-stimulating factor-1 antibody staining in primary breast adenocarcinomas correlates with marked inflammatory cell infiltrates and prognosis. J Natl Cancer Inst. 1994;86:120-126. (Pubitemid 24040150)
65. Clarke LP, Sriram RD, Schilling LB. Imaging as a biomarker: Standards for Change Measurements in Therapy workshop summary. Acad Radiol. 2008;15:501-530.
66. Navin N, Kendall J, Troge J, et al. Tumour evolution inferred by singlecell sequencing. Nature. 2011;472:90-94.
67. Totoki Y, Tatsuno K, Yamamoto S, et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet. 2011;43: 464-469.
68. Kroneis T, Geigl JB, El-Heliebi A, et al. Combined molecular genetic and cytogenetic analysis from single cells after isothermalwhole-genome amplification. Clin Chem. 2011;57:1032-1041.
69. Wartman LD, Larson DE, Xiang Z, et al. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest. 2011;121:1445-1455.
70. Specht K, Richter T, Muller U, et al. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffinembedded tumor tissue. Am J Pathol. 2001;158:419-429. (Pubitemid 32158605)
71. Pathmanathan R, Prasad U, Sadler R, et al. Clonal proliferations of cells infected with Epstein-Barr virus in preinvasive lesions related to nasopharyngeal carcinoma. N Engl J Med. 1995;333:693-698.
72. zur Hausen H. Papillomaviruses and cancer: from basic studies to clinical application. Nat Rev Cancer. 2002;2:342-350. (Pubitemid 37328947)
73. Simon R. The use of genomics in clinical trial design. Clin Cancer Res. 2008;14:5984-5993.
74. National Cancer Institute Best Practices for Biospecimen Resources 2007. Available at: http://biospecimens.cancer.gov/bestpractices/. Accessed July 18, 2011.
75. Vaught JB, Caboux E, Hainaut P. International efforts to develop biospecimen best practices. Cancer Epidemiol Biomarkers Prev. 2010; 19:912-915.
76. Van Krieken JH, Jung A, Kirchner T, et al. KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for an European quality assurance program. Virchows Arch. 2008;453:417-431.
77. Pollack A. FDA faults companies on unapproved genetic tests. The New York Times; June 11, 2010:B2.
78. Gulley ML, Braziel RM, Halling KC, et al. Clinical laboratory reports in molecular pathology. Arch Pathol Lab Med. 2007;131:852-863. (Pubitemid 46906376)
79. Schmidt C. Personal genetic tests facing scrutiny. J Natl Cancer Inst. 2008;100:382-383, 6.
80. Levenson D. The trouble with Ovasure. Am J Med Genet A. 2009;149A:viiiYix.
81. Jin L, Lloyd RV. In situ hybridization: methods and applications. J Clin Lab Anal. 1997;11:2-9. (Pubitemid 27053382)
82. Rudkin GT, Stollar BD. High resolution detection of DNA-RNA hybrids in situ by indirect immunofluorescence. Nature. 1977;265: 472-473. (Pubitemid 8023617)
83. Wolff AC, Hammond ME, Schwartz JN, et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. J Clin Oncol. 2007;25:118-145. (Pubitemid 350003059)
84. Tkachuk DC, Westbrook CA, Andreeff M, et al. Detection of BCRABL fusion in chronic myelogeneous leukemia by in situ hybridization. Science. 1990;250:559-562. (Pubitemid 120031786)
85. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A. 1977;74:5463-5467.
86. Di Fiore F, Blanchard F, Charbonnier F, et al. Clinical relevance of KRAS mutation detection in metastatic colorectal cancer treated by cetuximab plus chemotherapy. Br J Cancer. 2007;96:1166-1169. (Pubitemid 46625066)
87. Zinsky R, Bolukbas S, Bartsch H, et al. Analysis of KRAS mutations of exon 2 codons 12 and 13 by SNaPshot analysis in comparison to common DNA sequencing. Gastroenterol Res Pract. 2010;2010:789363.
88. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001;11:3-11. (Pubitemid 32117949)
89. Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011; 475:348-352.
90. Pennisi E. Genomics. Semiconductors inspire new sequencing technologies. Science. 2010;327:1190.
91. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on realtime pyrophosphate. Science. 1998;281:363, 5.
92. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402.
93. Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133-138.
94. Single Molecule Real Time (SMRTi) DNA sequencing: long reads, fast results, and more informative data at lower overall cost. 2011. Available at: www.pacificbiosciences.com/assets/files/pacbio-technology- backgrounder.pdf. Accessed June 27, 2011.
95. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31-46.
96. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour. 2011;11:759-769.
97. Zhou X, Ren L, Meng Q, et al. The next-generation sequencing technology and application. Protein Cell. 2010;1:520-536.
98. Herman JG, Graff JR, Myohanen S, et al. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A. 1996;93:9821-9826. (Pubitemid 26296693)
99. Hegi ME, Diserens AC, Godard S, et al. Clinical trial substantiates the predictive value of O-6-methylguanine-DNA methyltransferase promoter methylation in glioblastoma patients treated with temozolomide. Clin Cancer Res. 2004;10:1871-1874. (Pubitemid 38375541)
100. Paz MF, Yaya-Tur R, Rojas-Marcos I, et al. CpG island hypermethylation of the DNA repair enzyme methyltransferase predicts response to temozolomide in primary gliomas. Clin Cancer Res. 2004;10: 4933-4938. (Pubitemid 39099766)
101. Hegi ME, Liu L, Herman JG, et al. Correlation of O6-methylguanine methyltransferase (MGMT) promoter methylation with clinical outcomes in glioblastoma and clinical strategies to modulate MGMT activity. J Clin Oncol. 2008;26:4189-4199.
102. Yanaihara N, Caplen N, Bowman E, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 2006; 9:189-198. (Pubitemid 43357945)
103. Schumacher A, Kapranov P, Kaminsky Z, et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res. 2006;34:528-542. (Pubitemid 43240241)
104. Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 2004;83:349-360. (Pubitemid 38220840)
105. Monzon FA, Lyons-Weiler M, Buturovic LJ, et al. Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin. J Clin Oncol. 2009;27:2503-2508.
106. Monzon FA, Dumur CI. Diagnosis of uncertain primary tumors with the pathwork tissue-of-origin test. Expert Rev Mol Diagn. 2010;10: 17-25.
107. Ruiz C, Lenkiewicz E, Evers L, et al. Advancing a clinically relevant perspective of the clonal nature of cancer. Proc Natl Acad Sci U S A. 2011;108:12054-12059.
108. Teruya-Feldstein J. The immunohistochemistry laboratory: looking at molecules and preparing for tomorrow. Arch Pathol Lab Med. 2010;134:1659-1665.
109. Ang MK, Hayes DN. Imaging: mass spectrometry in HNSCCVa peek at response prediction? Nat Rev Clin Oncol. 2010;7:193-195.
110. Bravo HC, Irizarry RA. Model-based quality assessment and basecalling for second-generation sequencing data. Biometrics. 2010;66: 665-674.
111. MacConaill LE, Campbell CD, Kehoe SM, et al. Profiling critical cancer gene mutations in clinical tumor samples. PLoS One. 2009;4:e7887.
112. Grewal RK, Tuttle RM, Fox J, et al. The effect of posttherapy 131I SPECT/CT on risk classification and management of patients with differentiated thyroid cancer. J Nucl Med. 2010;51:1361-1367.
113. Zhao J, Qiao W, Wang C, et al. Therapeutic evaluation and prognostic value of interim hybrid PET/CT with (18)F-FDG after three to four cycles of chemotherapy in non-Hodgkin's lymphoma. Hematology. 2007;12:423-430.
114. Cerci JJ, Pracchia LF, Linardi CC, et al. 18F-FDG PET after 2 cycles of ABVD predicts event-free survival in early and advanced Hodgkin lymphoma. J Nucl Med. 2010;51:1337-1343.
115. Mikhaeel NG, Hutchings M, Fields PA, et al. FDG-PET after two to three cycles of chemotherapy predicts progression-free and overall survival in high-grade non-Hodgkin lymphoma. Ann Oncol. 2005;16: 1514-1523. (Pubitemid 41222425)
116. Lee DH, Kim SK, Lee HY, et al. Early prediction of response to firstline therapy using integrated 18F-FDG PET/CT for patients with advanced/ metastatic non-small cell lung cancer. J Thorac Oncol. 2009;4:816-821.
117. Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet. 2011;52:413-435.
118. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26:1135-1145.
119. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010;11:685-696.
120. Voelkerding KV, Dames SA, Durtschi JD. Next-generation sequencing: from basic research to diagnostics. Clin Chem. 2009;55:641-658.
121. Li R, Li Y, Kristiansen K, et al. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713-714. (Pubitemid 351321217)
122. Lin H, Zhang Z, Zhang MQ, et al. ZOOM! Zillions of oligos mapped. Bioinformatics. 2008;24:2431-2437.
123. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008;18: 1851-1858.
124. Smith DR, Quinlan AR, Peckham HE, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 2008;18:1638-1642.
125. Wang K, Singh D, Zeng Z, et al. MapSplice: accurate mapping of RNAseq reads for splice junction discovery. Nucleic Acids Res. 2010; 38:e178.
126. Warren RL, Sutton GG, Jones SJ, et al. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007;23:500-501. (Pubitemid 46323134)
127. Dohm JC, Lottaz C, Borodina T, et al. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 2007;17:1697-1706. (Pubitemid 350074864)
128. Simpson JT, Wong K, Jackman SD, et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19:1117-1123.
129. Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics. 2010;Chapter 11: Unit 11, 5.
130. Kaminker JS, Zhang Y,Watanabe C, et al. CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res. 2007;35:W595-W598.
131. Carter H, Chen S, Isik L, et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 2009;69:6660-6667.
132. Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7: 248-249.
133. Hayes DN, Monti S, Parmigiani G, et al. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol. 2006;24:5079-5090. (Pubitemid 46631412)
134. Wilkerson MD, Yin X, Hoadley KA, et al. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clin Cancer Res. 2010;16: 4864-4875.