A newly developed capture-based sequencing panel for genomic assay of lung cancer

被引：5

作者：

Im, Sun-Wha ^{[1
]}

Chae, Jeesoo ^{[2
]}

Jang, Se Song ^{[2
]}

Choi, Jaeyong ^{[2
]}

Yun, Jihui ^{[2
]}

Cha, Soojin ^{[1
,8
]}

Kwon, Nak-Jung ^{[3
]}

Jeon, Yoon Kyung ^{[4
,5
]}

Hwang, Yoohwa ^{[6
,9
]}

Kim, Miso ^{[5
,7
]}

Kim, Tae Min ^{[5
,7
]}

Kim, Dong-Wan ^{[5
,7
]}

Kim, Jong-Il ^{[1
,2
,5
]}

Kim, Young Tae ^{[1
,5
,6
]}

机构：

[1] Seoul Natl Univ, Med Res Ctr, Genom Med Inst, 103 Daehak Ro, Seoul 03080, South Korea

[2] Seoul Natl Univ, Dept Biomed Sci, Grad Sch, Seoul, South Korea

[3] Macrogen Inc, Seoul, South Korea

[4] Seoul Natl Univ, Dept Pathol, Coll Med, Seoul, South Korea

[5] Seoul Natl Univ, Canc Res Inst, Seoul, South Korea

[6] Seoul Natl Univ Hosp, Dept Thorac & Cardiovasc Surg, 101 Daehak Ro, Seoul 03080, South Korea

[7] Seoul Natl Univ Hosp, Dept Internal Med, Seoul, South Korea

[8] Sungkyunkwan Univ, Samsung Med Ctr, Samsung Adv Inst Hlth Sci & Technol SAIHST, Seoul, South Korea

[9] Seoul Natl Univ, Dept Thorac & Cardiovasc Surg, Bundang Hosp, Seongnamsi, Gyeonggido, South Korea

来源：

GENES & GENOMICS | 2020年 / 42卷 / 07期

关键词：

Lung; Neoplasms; Cancer panel; Next-generation sequencing; COPY NUMBER VARIATION; VALIDATION; DISCOVERY; MUTATION;

D O I：

10.1007/s13258-020-00949-1

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Background The increase in genetic alterations targeted by specific chemotherapy in lung cancer has led to the need for universal use of more comprehensive genetic testing, which has highlighted the development of a lung cancer diagnostic panel using next-generation sequencing. Objective We developed a hybridization capture-based massively parallel sequencing assay named Friendly, Integrated, Research-based, Smart and Trustworthy (FIRST)-lung cancer panel (LCP), and evaluated its performance. Methods FIRST-LCP comprises 64 lung cancer-related genes to test for various kinds of genetic alterations including single nucleotide variations (SNVs), insertions and deletions (indels), copy number variations (CNVs), and structural variations. To assess the performance of FIRST-LCP, we compiled test sets using HapMap samples or tumor cell lines with disclosed genetic information, and also tested our clinical lung cancer samples whose genetic alterations were known by conventional methods. Results FIRST-LCP accomplished high sensitivity (99.4%) and specificity (100%) of the detection of SNVs. High precision was also achieved, with intra- or inter-run concordance rate of 0.99, respectively. FIRST-LCP detected indels and CNVs close to the expected allele frequency and magnitude, respectively. Tests with samples from lung cancer patients also identified all SNVs, indels and fusions. Conclusion Based on the current state of the art, continuous application of the panel design and analysis pipeline following up-to-date knowledge could ensure precision medicine for lung cancer patients.

引用

页码：751 / 759

页数：9

共 16 条

[1] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[2] 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].

Cheng, Donavan T. ;

Mitchell, Talia N. ;

Zehir, Ahmet ;

Shah, Ronak H. ;

Benayed, Ryma ;

Syed, Aijazuddin ;

Chandramohan, Raghu ;

Liu, Zhen Yu ;

Won, Helen H. ;

Scott, Sasinya N. ;

Brannon, A. Rose ;

O'Reilly, Catherine ;

Sadowska, Justyna ;

Casanova, Jacklyn ;

Yannes, Angela ;

Hechtman, Jaclyn F. ;

Yao, Jinjuan ;

Song, Wei ;

Ross, Dara S. ;

Oultache, Alifya ;

Dogan, Snjezana ;

Borsu, Laetitia ;

Hameed, Meera ;

Nafa, Khedoudja ;

Arcila, Maria E. ;

Ladanyi, Marc ;

Berger, Michael F. .

JOURNAL OF MOLECULAR DIAGNOSTICS, 2015, 17 (03) :251-264

[3] Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples [J].

Cibulskis, Kristian ;

Lawrence, Michael S. ;

Carter, Scott L. ;

Sivachenko, Andrey ;

Jaffe, David ;

Sougnez, Carrie ;

Gabriel, Stacey ;

Meyerson, Matthew ;

Lander, Eric S. ;

Getz, Gad .

NATURE BIOTECHNOLOGY, 2013, 31 (03) :213-219

[4] Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation [J].

Costello, Maura ;

Pugh, Trevor J. ;

Fennell, Timothy J. ;

Stewart, Chip ;

Lichtenstein, Lee ;

Meldrim, James C. ;

Fostel, Jennifer L. ;

Friedrich, Dennis C. ;

Perrin, Danielle ;

Dionne, Danielle ;

Kim, Sharon ;

Gabriel, Stacey B. ;

Lander, Eric S. ;

Fisher, Sheila ;

Getz, Gad .

NUCLEIC ACIDS RESEARCH, 2013, 41 (06) :e67

[5] A framework for variation discovery and genotyping using next-generation DNA sequencing data [J].

DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

[6] Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors [J].

Frampton, Garrett M. ;

Ali, Siraj M. ;

Rosenzweig, Mark ;

Chmielecki, Juliann ;

Lu, Xinyuan ;

Bauer, Todd M. ;

Akimov, Mikhail ;

Bufill, Jose A. ;

Lee, Carrie ;

Jentz, David ;

Hoover, Rick ;

Ou, Sai-Hong Ignatius ;

Salgia, Ravi ;

Brennan, Tim ;

Chalmers, Zachary R. ;

Jaeger, Savina ;

Huang, Alan ;

Elvin, Julia A. ;

Erlich, Rachel ;

Fichtenholtz, Alex ;

Gowen, Kyle A. ;

Greenbowe, Joel ;

Johnson, Adrienne ;

Khaira, Depinder ;

McMahon, Caitlin ;

Sanford, Eric M. ;

Roels, Steven ;

White, Jared ;

Greshock, Joel ;

Schlegel, Robert ;

Lipson, Doron ;

Yelensky, Roman ;

Morosini, Deborah ;

Ross, Jeffrey S. ;

Collisson, Eric ;

Peters, Malte ;

Stephens, Philip J. ;

Miller, Vincent A. .

CANCER DISCOVERY, 2015, 5 (08) :850-859

[7] Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing [J].

Frampton, Garrett M. ;

Fichtenholtz, Alex ;

Otto, Geoff A. ;

Wang, Kai ;

Downing, Sean R. ;

He, Jie ;

Schnall-Levin, Michael ;

White, Jared ;

Sanford, Eric M. ;

An, Peter ;

Sun, James ;

Juhn, Frank ;

Brennan, Kristina ;

Iwanik, Kiel ;

Maillet, Ashley ;

Buell, Jamie ;

White, Emily ;

Zhao, Mandy ;

Balasubramanian, Sohail ;

Terzic, Selmira ;

Richards, Tina ;

Banning, Vera ;

Garcia, Lazaro ;

Mahoney, Kristen ;

Zwirko, Zac ;

Donahue, Amy ;

Beltran, Himisha ;

Mosquera, Juan Miguel ;

Rubin, Mark A. ;

Dogan, Snjezana ;

Hedvat, Cyrus V. ;

Berger, Michael F. ;

Pusztai, Lajos ;

Lechner, Matthias ;

Boshoff, Chris ;

Jarosz, Mirna ;

Vietz, Christine ;

Parker, Alex ;

Miller, Vincent A. ;

Ross, Jeffrey S. ;

Curran, John ;

Cronin, Maureen T. ;

Stephens, Philip J. ;

Lipson, Doron ;

Yelensky, Roman .

NATURE BIOTECHNOLOGY, 2013, 31 (11) :1023-+

[8] Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies [J].

Jordan, Emmet J. ;

Kim, Hyunjae R. ;

Arcila, Maria E. ;

Barron, David ;

Chakravarty, Debyani ;

Gao, JianJiong ;

Chang, Matthew T. ;

Ni, Andy ;

Kundra, Ritika ;

Jonsson, Philip ;

Jayakumaran, Gowtham ;

Gao, Sizhi Paul ;

Johnsen, Hannah C. ;

Hanrahan, Aphrothiti J. ;

Zehir, Ahmet ;

Rekhtman, Natasha ;

Ginsberg, Michelle S. ;

Li, Bob T. ;

Yu, Helena A. ;

Paik, Paul K. ;

Drilon, Alexander ;

Hellmann, Matthew D. ;

Reales, Dalicia N. ;

Benayed, Ryma ;

Rusch, Valerie W. ;

Kris, Mark G. ;

Chaft, Jamie E. ;

Baselga, Jose ;

Taylor, Barry S. ;

Schultz, Nikolaus ;

Rudin, Charles M. ;

Hyman, David M. ;

Berger, Michael F. ;

Solit, David B. ;

Ladanyi, Marc ;

Riely, Gregory J. .

CANCER DISCOVERY, 2017, 7 (06) :596-609

[9] Copy number variation detection and genotyping from exome sequence data [J].

Krumm, Niklas ;

Sudmant, Peter H. ;

Ko, Arthur ;

O'Roak, Brian J. ;

Malig, Maika ;

Coe, Bradley P. ;

Quinlan, Aaron R. ;

Nickerson, Deborah A. ;

Eichler, Evan E. .

GENOME RESEARCH, 2012, 22 (08) :1525-1532

[10] Axl Receptor Axis: A New Therapeutic Target in Lung Cancer [J].

Levin, Pavel A. ;

Brekken, Rolf A. ;

Byers, Lauren Averett ;

Heymach, John V. ;

Gerber, David E. .

JOURNAL OF THORACIC ONCOLOGY, 2016, 11 (08) :1357-1362

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