The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Anchored multiplex PCR for targeted next-generation sequencing
Open accessAbstract
We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5–100%) and 100% specificity (95% confidence limit: 99.3–100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Primer3—new capabilities and interfaces
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks596 · Cited by 9,461
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,905
Frohman, M. A., Dush, M. K., & Martin, G. R. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.23.8998 · Cited by 4,577
Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer
Kwak, E. L., Bang, Y.-J., Camidge, D. R., Shaw, A. T., Solomon, B., Maki, R. G., Ou, S.-H. I., Dezube, B. J., Jänne, P. A., Costa, D. B., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa1006448 · Cited by 4,446
Self-citationROS1 Rearrangements Define a Unique Molecular Class of Lung Cancers
Bergethon, K., Shaw, A. T., Ignatius Ou, S.-H., Katayama, R., Lovly, C. M., McDonald, N. T., Massion, P. P., Siwak-Tapp, C., Gonzalez, A., Fang, R., et al. (2012) · Journal of Clinical Oncology · doi:10.1200/jco.2011.35.6345 · Cited by 1,555
Self-citationRET, ROS1 and ALK fusions in lung cancer
Takeuchi, K., Soda, M., Togashi, Y., Suzuki, R., Sakata, S., Hatano, S., Asaka, R., Hamanaka, W., Ninomiya, H., Uehara, H., et al. (2012) · Nature Medicine · doi:10.1038/nm.2658 · Cited by 1,320
Target-enrichment strategies for next-generation sequencing
Mamanova, L., Coffey, A. J., Scott, C. E., Kozarewa, I., Turner, E. H., Kumar, A., Howard, E., Shendure, J., & Turner, D. J. (2010) · Nature Methods · doi:10.1038/nmeth.1419 · Cited by 1,219
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology · doi:10.1186/gb-2011-12-2-r18 · Cited by 1,174
Advances in understanding cancer genomes through second-generation sequencing
Meyerson, M., Gabriel, S., & Getz, G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2841 · Cited by 1,116
Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes
Oyola, S. O., Otto, T. D., Gu, Y., Maslen, G., Manske, M., Campino, S., Turner, D. J., MacInnis, B., Kwiatkowski, D. P., Swerdlow, H. P., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-1 · Cited by 653
Performance comparison of exome DNA sequencing technologies
Clark, M. J., Chen, R., Lam, H. Y. K., Karczewski, K. J., Chen, R., Euskirchen, G., Butte, A. J., & Snyder, M. (2011) · Nature Biotechnology · doi:10.1038/nbt.1975 · Cited by 511
Response to Cabozantinib in Patients with RET Fusion-Positive Lung Adenocarcinomas
Drilon, A., Wang, L., Hasanovic, A., Suehara, Y., Lipson, D., Stephens, P., Ross, J., Miller, V., Ginsberg, M., Zakowski, M. F., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0035 · Cited by 464
Microdroplet-based PCR enrichment for large-scale targeted sequencing
Tewhey, R., Warner, J. B., Nakano, M., Libby, B., Medkova, M., David, P. H., Kotsopoulos, S. K., Samuels, M. L., Hutchison, J. B., Larson, J. W., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1583 · Cited by 454
Beltran, H., Yelensky, R., Frampton, G. M., Park, K., Downing, S. R., MacDonald, T. Y., Jarosz, M., Lipson, D., Tagawa, S. T., Nanus, D. M., et al. (2013) · European Urology · doi:10.1016/j.eururo.2012.08.053 · Cited by 454
Dias‐Santagata, D., Akhavanfard, S., David, S. S., Vernovsky, K., Kuhlmann, G., Boisvert, S. L., Stubbs, H., McDermott, U., Settleman, J., Kwak, E. L., et al. (2010) · EMBO Molecular Medicine · doi:10.1002/emmm.201000070 · Cited by 396
Self-citationDifferential Protein Stability and ALK Inhibitor Sensitivity of EML4-ALK Fusion Variants
Heuckmann, J. M., Balke-Want, H., Malchers, F., Peifer, M., Sos, M. L., Koker, M., Meder, L., Lovly, C. M., Heukamp, L. C., Pao, W., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-3260 · Cited by 261
Self-citationMassively parallel exon capture and library-free resequencing across 16 genomes
Turner, E. H., Lee, C., Ng, S. B., Nickerson, D. A., & Shendure, J. (2009) · Nature Methods · doi:10.1038/nmeth.f.248 · Cited by 193
Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR
Chevet, É., e, G. L., & Katinka, M. D. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.16.3343 · Cited by 132
Donner, A. P., & Rotondi, M. A. (2010) · The International Journal of Biostatistics · doi:10.2202/1557-4679.1275 · Cited by 130
Do, H., Wong, S. Q., Li, J., & Dobrovic, A. (2013) · Clinical Chemistry · doi:10.1373/clinchem.2012.202390 · Cited by 115
Trk kinase inhibitors as new treatments for cancer and pain
Wang, T., Yu, D., & Lamb, M. L. (2009) · Expert Opinion on Therapeutic Patents · doi:10.1517/13543770902721261 · Cited by 102
Pulmonary Langerhans Cell Histiocytosis
Yousem, S. A., Đačić, S., Nikiforov, Y. E., & Nikiforova, M. N. (2013) · CHEST Journal · doi:10.1378/chest.12-1917 · Cited by 92
Targeted resequencing of candidate genes using selector probes
Johansson, H., Isaksson, M., Falk-Sörqvist, E., Roos, F., Stenberg, J., Sjöblom, T., Botling, J., Micke, P., Edlund, K., Fredriksson, S., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1005 · Cited by 76
Nested Patch PCR enables highly multiplexed mutation discovery in candidate genesPreprint
Varley, K. E., & Mitra, R. D. (2008) · Genome Research · doi:10.1101/gr.078204.108 · Cited by 59
Chmielecki, J., Peifer, M., Jia, P., Socci, N. D., Hutchinson, K. E., Viale, A. J., Zhao, Z., Thomas, R. K., & Pao, W. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq579 · Cited by 40
Self-citationNeiman, M., Sundling, S., Grönberg, H., Hall, P. N., Czene, K., Lindberg, J., & Klevebring, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048616 · Cited by 38
Cited by
Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., Srinivasan, P., Gao, J., Chakravarty, D., Devlin, S. M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4333 · Cited by 3,380
Puram, S. V., Tirosh, I., Parikh, A. S., Patel, A. P., Yizhak, K., Gillespie, S., Rodman, C., Luo, C. L., Mroz, E. A., Emerick, K. S., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.044 · Cited by 2,557
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268
Self-citationCrizotinib in ROS1-Rearranged Non–Small-Cell Lung Cancer
Shaw, A. T., Ou, S.-H. I., Bang, Y.-J., Camidge, D. R., Solomon, B. J., Salgia, R., Riely, G. J., Varella-Garcia, M., Shapiro, G. I., Costa, D. B., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1406766 · Cited by 1,964
Self-citationSTK11/LKB1 Mutations and PD-1 Inhibitor Resistance in KRAS -Mutant Lung Adenocarcinoma
Skoulidis, F., Goldberg, M. E., Greenawalt, D. M., Hellmann, M. D., Awad, M. M., Gainor, J. F., Schrock, A. B., Hartmaier, R. J., Trabucco, S. E., Gay, L., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0099 · Cited by 1,641
“55(0) 42(11) 20(32) 11(41) 6(44) 2(47) 0(49) 3(4) 0(6) 0(6) 0(6) 0(6) 0(6)”
Metadata
- Authors
- Zheng, Z., Liebers, M., Zhelyazkova, B., Cao, Y., Panditi, D., Lynch, K. D., Chen, J., Robinson, H. E., Shim, H. S., Chmielecki, J., Pao, W., Engelman, J. A., Iafrate, A. J., & Le, L. P.
- Venue
- Nature Medicine
- Published
- 2014-11-10
- Volume
- 20
- Issue
- 12
- Pages
- 1479-1484
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- OpenAlex
- W2062291041
- Cited by
- 915
- References
- 28
- FWCI
- 16.33
- Type
- journal article
- Language
- en
- Open access
- green
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