|
1
|
Renfro LA, An MW and Mandrekar SJ:
Precision oncology: A new era of cancer clinical trials. Cancer
Lett. S0304-3835(16)30163-X. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Arteaga CL and Baselga J: Impact of
genomics on personalized cancer medicine. Clin Cancer Res.
18:612–618. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
MacConaill LE, Van Hummelen P, Meyerson M
and Hahn WC: Clinical implementation of comprehensive strategies to
characterize cancer genomes: Opportunities and challenges. Cancer
Discov. 1:297–311. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Romano E, Schwartz GK, Chapman PB,
Wolchock JD and Carvajal RD: Treatment implications of the emerging
molecular classification system for melanoma. Lancet Oncol.
12:913–922. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Kwak EL, Bang YJ, Camidge DR, Shaw AT,
Solomon B, Maki RG, Ou SH, Dezube BJ, Jänne PA, Costa DB, et al:
Anaplastic lymphoma kinase inhibition in non-small-cell lung
cancer. N Engl J Med. 363:1693–1703. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Shaw AT, Kim DW, Nakagawa K, Seto T, Crinó
L, Ahn MJ, De Pas T, Besse B, Solomon BJ, Blackhall F, et al:
Crizotinib versus chemotherapy in advanced ALK-positive lung
cancer. N Engl J Med. 368:2385–2394. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Bollag G, Tsai J, Zhang J, Zhang C,
Ibrahim P, Nolop K and Hirth P: Vemurafenib: The first drug
approved for BRAF-mutant cancer. Nat Rev Drug Discov. 11:873–886.
2012. View
Article : Google Scholar : PubMed/NCBI
|
|
8
|
Garraway LA and Lander ES: Lessons from
the cancer genome. Cell. 153:17–37. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Pao W: New approaches to targeted therapy
in lung cancer. Proc Am Thorac Soc. 9:72–73. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Thomas RK, Baker AC, Debiasi RM, Winckler
W, Laframboise T, Lin WM, Wang M, Feng W, Zander T, MacConaill L,
et al: High-throughput oncogene mutation profiling in human cancer.
Nat Genet. 39:347–351. 2007. View
Article : Google Scholar : PubMed/NCBI
|
|
11
|
MacConaill LE, Campbell CD, Kehoe SM, Bass
AJ, Hatton C, Niu L, Davis M, Yao K, Hanna M, Mondal C, et al:
Profiling critical cancer gene mutations in clinical tumor samples.
PLoS One. 4:e78872009. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Tao YF, Wu D, Pang L, Zhao WL, Lu J, Wang
N, Wang J, Feng X, Li YH, Ni J, et al: Analyzing the gene
expression profile of pediatric acute myeloid leukemia with
real-time PCR arrays. Cancer Cell Int. 12:1946–1958. 2012.
|
|
13
|
McCourt CM, Boyle D, James J and
Salto-Tellez M: Immunohistochemistry in the era of personalised
medicine. J Clin Pathol. 66:58–61. 2013. View Article : Google Scholar
|
|
14
|
Forbes SA, Bindal N, Bamford S, Cole C,
Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al:
COSMIC: Mining complete cancer genomes in the Catalogue of Somatic
Mutations in Cancer. Nucleic Acids Res. 39(Database issue):
D945–D950. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Lawrence MS, Stojanov P, Mermel CH,
Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander
ES and Getz G: Discovery and saturation analysis of cancer genes
across 21 tumour types. Nature. 505:495–501. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Lawrence MS, Stojanov P, Polak P, Kryukov
GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH,
Roberts SA, et al: Mutational heterogeneity in cancer and the
search for new cancer-associated genes. Nature. 499:214–218. 2013.
View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Frampton GM, Fichtenholtz A, Otto GA, Wang
K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, et
al: Development and validation of a clinical cancer genomic
profiling test based on massively parallel DNA sequencing. Nat
Biotechnol. 31:1023–1031. 2013. View
Article : Google Scholar : PubMed/NCBI
|
|
18
|
Hovelson DH, McDaniel AS, Cani AK, Johnson
B, Rhodes K, Williams PD, Bandla S, Bien G, Choppa P, Hyland F, et
al: Development and validation of a scalable next-generation
sequencing system for assessing relevant somatic variants in solid
tumors. Neoplasia. 17:385–399. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
19
|
Choudhary A, Mambo E, Sanford T,
Boedigheimer M, Twomey B, Califano J, Hadd A, Oliner KS, Beaudenon
S, Latham GJ, et al: Evaluation of an integrated clinical workflow
for targeted next-generation sequencing of low-quality tumor DNA
using a 51-gene enrichment panel. BMC Med Genomics. 7:622014.
View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Cheng DT, Mitchell TN, Zehir A, Shah RH,
Benayed R, Syed A, Chandramohan R, Liu ZY, Won HH, Scott SN, et al:
Memorial Sloan Kettering-Integrated Mutation Profiling of
Actionable Cancer Targets (MSK-IMPACT): A hybridization
capture-based next-generation sequencing clinical assay for solid
tumor molecular oncology. J Mol Diagn. 17:251–264. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Cibulskis K, McKenna A, Fennell T, Banks
E, DePristo M and Getz G: ContEst: Estimating cross-contamination
of human samples in next-generation sequencing data.
Bioinformatics. 27:2601–2602. 2011.PubMed/NCBI
|
|
22
|
Gerlinger M, Rowan AJ, Horswell S, Larkin
J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A,
Tarpey P, et al: Intratumor heterogeneity and branched evolution
revealed by multiregion sequencing. N Engl J Med. 366:883–892.
2012. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Kinz E, Leiherer A, Lang AH, Drexel H and
Muendlein A: Accurate quantitation of JAK2 V617F allele burden by
array-based digital PCR. Int J Lab Hematol. 37:217–224. 2015.
View Article : Google Scholar
|
|
24
|
Shao D1, Lin Y, Liu J, Wan L, Liu Z, Cheng
S, Fei L, Deng R, Wang J, Chen X, et al: A targeted next-generation
sequencing method for identifying clinically relevant mutation
profiles in lung adenocarcinoma. Sci Rep. 6:223382016. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Forbes SA1, Tang G, Bindal N, Bamford S,
Dawson E, Cole C, Kok CY, Jia M, Ewing R, Menzies A, et al: COSMIC
(the Catalogue of Somatic Mutations in Cancer): A resource to
investigate acquired mutations in human cancer. Nucleic Acids Res.
8(Database issue): D652–D657. 2009.
|
|
26
|
Abecasis GR, Altshuler D, Auton A, Brooks
LD, Durbin RM, Gibbs RA, Hurles ME and McVean GA; 1000 Genomes
Project Consortium. A map of human genome variation from
population-scale sequencing. Nature. 467:1061–1073. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Warrick JI, Hovelson DH, Amin A, Liu CJ,
Cani AK, McDaniel AS, Yadati V, Quist MJ, Weizer AZ, Brenner JC, et
al: Tumor evolution and progression in multifocal and paired
non-invasive/invasive urothelial carcinoma. Virchows Arch.
466:297–311. 2015. View Article : Google Scholar
|
|
28
|
Li H and Durbin R: Fast and accurate
long-read alignment with Burrows-Wheeler transform. Bioinformatics.
26:589–595. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
McKenna A, Hanna M, Banks E, Sivachenko A,
Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly
M, et al: The Genome Analysis Toolkit: A MapReduce framework for
analyzing next-generation DNA sequencing data. Genome Res.
20:1297–1303. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
DePristo MA, Banks E, Poplin R, Garimella
KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA,
Hanna M, et al: A framework for variation discovery and genotyping
using next-generation DNA sequencing data. Nat Genet. 43:491–498.
2011. View
Article : Google Scholar : PubMed/NCBI
|
|
31
|
Li H, Handsaker B, Wysoker A, Fennell T,
Ruan J, Homer N, Marth G, Abecasis G and Durbin R; 1000 Genome
Project Data Processing Subgroup. The sequence alignment/map format
and SAMtools. Bioinformatics. 25:2078–2079. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Arsenic R, Treue D, Lehmann A, Hummel M,
Dietel M, Denkert C and Budczies J: Comparison of targeted
next-generation sequencing and Sanger sequencing for the detection
of PIK3CA mutations in breast cancer. BMC Clin Pathol. 15:202015.
View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Borad MJ, Champion MD, Egan JB, Liang WS,
Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD,
et al: Integrated genomic characterization reveals novel,
therapeutically relevant drug targets in FGFR and EGFR pathways in
sporadic intrahepatic cholangiocarcinoma. PLoS Genet.
10:e10041352014. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Hadd AG, Houghton J, Choudhary A, Sah S,
Chen L, Marko AC, Sanford T, Buddavarapu K, Krosting J, Garmire L,
et al: Targeted, high-depth, next-generation sequencing of cancer
genes in formalin-fixed, paraffin-embedded and fine-needle
aspiration tumor specimens. J Mol Diagn. 15:234–247. 2013.
View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Roychowdhury S, Iyer MK, Robinson DR,
Lonigro RJ, Wu YM, Cao X, Kalyana-Sundaram S, Sam L, Balbin OA,
Quist MJ, et al: Personalized oncology through integrative
high-throughput sequencing: A pilot study. Sci Transl Med.
3:111ra1212011. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Kerick M, Isau M, Timmermann B, Sültmann
H, Herwig R, Krobitsch S, Schaefer G, Verdorfer I, Bartsch G,
Klocker H, et al: Targeted high throughput sequencing in clinical
cancer settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor
tissues, input amount and tumor heterogeneity. BMC Med Genomics.
4:682011. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Schweiger MR, Kerick M, Timmermann B,
Albrecht MW, Borodina T, Parkhomchuk D, Zatloukal K and Lehrach H:
Genome-wide massively parallel sequencing of formaldehyde
fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and
mutation-analysis. PLoS One. 4:e55482009. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Chevrier S, Arnould L, Ghiringhelli F,
Coudert B, Fumoleau P and Boidot R: Next-generation sequencing
analysis of lung and colon carcinomas reveals a variety of genetic
alterations. Int J Oncol. 45:1167–1174. 2014.PubMed/NCBI
|
|
39
|
Cottrell CE, Al-Kateb H, Bredemeyer AJ,
Duncavage EJ, Spencer DH, Abel HJ, Lockwood CM, Hagemann IS, O'Guin
SM, Burcea LC, et al: Validation of a next-generation sequencing
assay for clinical molecular oncology. J Mol Diagn. 16:89–105.
2014. View Article : Google Scholar
|
|
40
|
Haber DA and Velculescu VE: Blood-based
analyses of cancer: Circulating tumor cells and circulating tumor
DNA. Cancer Discov. 4:650–661. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Arnedos M, Vicier C, Loi S, Lefebvre C,
Michiels S, Bonnefoi H and Andre F: Precision medicine for
metastatic breast cancer--limitations and solutions. Nat Rev Clin
Oncol. 12:693–704. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Newman AM, Bratman SV, To J, Wynne JF,
Eclov NC, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, et
al: An ultrasensitive method for quantitating circulating tumor DNA
with broad patient coverage. Nat Med. 20:548–554. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Ignatiadis M and Dawson SJ: Circulating
tumor cells and circulating tumor DNA for precision medicine: Dream
or reality? Ann Oncol. 25:2304–2313. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Lipson EJ, Velculescu VE, Pritchard TS,
Sausen M, Pardoll DM, Topalian SL and Diaz LA Jr: Circulating tumor
DNA analysis as a real-time method for monitoring tumor burden in
melanoma patients undergoing treatment with immune checkpoint
blockade. J Immunother Cancer. 2:422014. View Article : Google Scholar : PubMed/NCBI
|
|
45
|
Schmitt MW, Kennedy SR, Salk JJ, Fox EJ,
Hiatt JB and Loeb LA: Detection of ultra-rare mutations by
next-generation sequencing. Proc Natl Acad Sci USA.
109:14508–14513. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
46
|
Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF,
Salk JJ, Ahn EH, Prindle MJ, Kuong KJ, Shen JC, Risques RA, et al:
Detecting ultralow-frequency mutations by Duplex Sequencing. Nat
Protoc. 9:2586–2606. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Newman AM, Lovejoy AF, Klass DM, Kurtz DM,
Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, et al:
Integrated digital error suppression for improved detection of
circulating tumor DNA. Nat Biotechnol. 34:547–555. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Luo H, Li H, Hu Z, Wu H, Liu C, Li Y,
Zhang X, Lin P, Hou Q, Ding G, et al: Noninvasive diagnosis and
monitoring of mutations by deep sequencing of circulating tumor DNA
in esophageal squamous cell carcinoma. Biochem Biophys Res Commun.
471:596–602. 2016. View Article : Google Scholar : PubMed/NCBI
|
