Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples von Zhang, Yifan, Blomquist, Thomas M, Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S, Mittal, Vinay K, Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L, Brock, Jay E, Farkas, Daniel H, Craig, Daniel J, Crawford, Erin L, Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E, Richmond, Todd A, Jones, Wendell, Johann, Jr, Donald J, Shi, Leming, Tong, Weida, Willey, James C, Xu, Joshua

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Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing von Gong, Binsheng, Li, Dan, Łabaj, Paweł P., Pan, Bohu, Novoradovskaya, Natalia, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Chen, Guangchun, Bergstrom Lucas, Anne, LoCoco, Jennifer S., Richmond, Todd A., Tseng, Elizabeth, Kusko, Rebecca, Happe, Scott, Mercer, Timothy R., Pabón-Peña, Carlos, Salmans, Michael, Tilgner, Hagen U., Xiao, Wenzhong, Johann, Donald J., Jones, Wendell, Tong, Weida, Mason, Christopher E., Kreil, David P., Xu, Joshua

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Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA von Willey, James C., Morrison, Tom B., Austermiller, Bradley, Crawford, Erin L., Craig, Daniel J., Blomquist, Thomas M., Jones, Wendell D., Wali, Aminah, Lococo, Jennifer S., Haseley, Nathan, Richmond, Todd A., Novoradovskaya, Natalia, Kusko, Rebecca, Chen, Guangchun, Li, Quan-Zhen, Johann, Donald J., Deveson, Ira W., Mercer, Timothy R., Wu, Leihong, Xu, Joshua

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Abstract 3607: An evaluation of NGS to identify gene fusions using RNA from FFPE solid tumor samples von Parks, Julianna Tdr, Byron, Luo, Crain, Brian, June, Snedecor, Chen, Zhao, Du, Tingting, Sica, Gabriel L., Owonikoko, Taofee K., Neill, Stewart G., Newman, Scott, Saxe, Debra F., LoCoco, Jennifer S., Chuang, Han-Yu, Lin, Charles, Stephens, Kathryn M., Rossi, Michael R., Friedenberg, Matthew C.

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Molecular profiling of ctDNA from NCI-MATCH patients enrolled for treatment with mTOR1/2 inhibitor sapanisertib (arm M) and the Hedgehog pathway inhibitor vismodegib (arm T) von LoCoco, Jennifer S., Das, Biswajit, Rahmanian, Sorena, Chang, Ting-Chia, Silhavy, Jennifer, Chen, Li, Harrington, Robin, Peach, Amanda, Fu, Yao, McShane, Lisa, Li, Jessica, Chen, Alice P., Takebe, Naoko, Harris, Lyndsay, Patton, David R., Pawlowski, Traci L., Febbo, Phillip G., Doroshow, James H., Williams, P. Mickey, Karlovich, Chris Alan

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Blood-based assessment of patients with mismatch repair-deficient tumors enrolled in NCI-MATCH Arm Z1D (nivolumab) von Karlovich, Chris Alan, Silhavy, Jennifer, LoCoco, Jennifer S., Das, Biswajit, Rahmanian, Sorena, Chang, Ting-Chia, Peach, Amanda, Harrington, Robin, Chen, Li, Harris, Lyndsay, Fu, Yao, Patton, David R., Li, Jessica, Chen, Alice P., Takebe, Naoko, Pawlowski, Traci L., McShane, Lisa, Febbo, Phillip G., Doroshow, James H., Williams, P. Mickey

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Blood-based detection of actionable alterations from NCI-MATCH patients with no tissue results von Harrington, Robin, Peach, Amanda, Howell, D'Andra, Das, Biswajit, Pauly, Rini, Chang, Ting-Chia, LoCoco, Jennifer S., Chen, Li, Jiwani, Shahanawaz, Lee, Jennifer, McShane, Lisa, Chen, Alice P., Febbo, Phillip G., Pawlowski, Traci L., Takebe, Naoko, Tricoli, James V., Doroshow, James H., Williams, Paul M., Karlovich, Chris Alan

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Development and analytical validation of a 523-gene clinical assay for cell-free DNA von Harrington, Robin, Das, Biswajit, Jiang, Tingting, LoCoco, Jennifer S., Patidar, Rajesh, Peach, Amanda, Zhao, Chen, Camalier, Corinne, Chang, Ting-Chia, Chen, Alice P., Chen, Li, Forbes, Thomas, Katz, Sigrid, Nair, Nikitha, Sims, David J., O'Sullivan Coyne, Geraldine Helen, Takebe, Naoko, Williams, Paul M., Karlovich, Chris Alan, Doroshow, James H.

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Abstract 565: Analytical performance of TruSight® Tumor 170 in the detection of gene fusions and splice variants using RNA from formalin-fixed, paraffin-embedded (FFPE) solid tumor... von Du, Tingting, Snedecor, June, LoCoco, Jennifer S., Chen, Xiao, Ball, Laurel, Castaneda, Allan, Chou, Danny, Clark, Katie, Crain, Brian, Daulo, Anthony, Do, Manh, Dumm, Sarah, Han, Yonmee, Havern, Mike, Hsieh, Chia-Ling, Jiang, Tingting, Johansen, Suzanne, Lang, Scott, Liang, Rachel, McLean, Jaime, Nassiri, Yousef, Purdy, Austin, Rostron, Jason, Silhavy, Jennifer, Talago, Natasha, Teng, Li, Wu, Kevin, Zlatkov, Clare, Zhao, Chen, Kuraishy, Ali, Gutekunst, Karen, Rozieres, Sohela De, Friedenberg, Matthew, Jager, Anne C., Chuang, Han-Yu

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Abstract 3732: Analytical performance of TruSight® Tumor 170 on small nucleotide variations and gene amplifications using DNA from formalin-fixed, paraffin-embedded (FFPE) solid tu... von Chou, Danny, Chen, Xiao, Purdy, Austin, Teng, Li, Luo, Byron, Zhao, Chen, Ball, Laurel, Castaneda, Allan, Clark, Katie, Crain, Brian, Daulo, Anthony, Do, Manh, Du, Tingting, Dumm, Sarah, Han, Yonmee, Havern, Michael, Hsieh, Chia-Ling, Jiang, Tingting, Johansen, Suzanne, Lang, Scott, Liang, Rachel, LoCoco, Jennifer S., McLean, Jaime, Nassiri, Yousef, Rostron, Jason, Silhavy, Jennifer, Snedecor, June, Talago, Natasha, Wu, Kevin, Zlatkov, Clare, Kuraishy, Ali, Gutekunst, Karen, Rozieres, Sohela De, Friedenberg, Matthew, Chuang, Han-Yu, Jager, Anne C.

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Abstract 5354: Evaluation of quantity, quality and performance with the TruSight® Tumor 170 solid tumor profiling assay of nucleic acids extracted from formalin-fixed paraffin-embe... von LoCoco, Jennifer S., Teng, Li, Chou, Danny, Chen, Xiao, Luo, Byron, Sayne, Jennifer, Adams, Ashley, Ajili, Naseem, Chivers, Cody, Murthy, Beena, Ball, Laurel, Castaneda, Allan, Clark, Katie, Crain, Brian, Daulo, Anthony, Do, Manh, Du, Tingting, Dumm, Sarah, Han, Yonmee, Havern, Michael, Hsieh, Chia-Ling, Jiang, Tingting, Johansen, Suzanne, Lang, Scott, Liang, Rachel, McLean, Jaime, Nassiri, Yousef, Purdy, Austin, Rostron, Jason, Silhavy, Jennifer, Snedecor, June, Talago, Natasha, Wu, Kevin, Zhao, Chen, Zlatkov, Clare, Kuraishy, Ali, Gutekunst, Karen, Rozieres, Sohela De, Friedenberg, Matthew, Chuang, Han-Yu, Jager, Anne C.

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Additional file 2 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples von Zhang, Yifan, Blomquist, Thomas M., Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S., Mittal, Vinay K., Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L., Brock, Jay E., Farkas, Daniel H., Craig, Daniel J., Crawford, Erin L., Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E., Richmond, Todd A., Jones, Wendell, Johann, Donald J., Shi, Leming, Tong, Weida, Willey, James C., Xu, Joshua

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Additional file 3 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples von Zhang, Yifan, Blomquist, Thomas M., Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S., Mittal, Vinay K., Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L., Brock, Jay E., Farkas, Daniel H., Craig, Daniel J., Crawford, Erin L., Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E., Richmond, Todd A., Jones, Wendell, Johann, Donald J., Shi, Leming, Tong, Weida, Willey, James C., Xu, Joshua

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Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions von Gong, Binsheng, Li, Dan, Kusko, Rebecca, Novoradovskaya, Natalia, Zhang, Yifan, Wang, Shangzi, Pabón-Peña, Carlos, Zhang, Zhihong, Lai, Kevin, Cai, Wanshi, LoCoco, Jennifer S, Lader, Eric, Richmond, Todd A, Mittal, Vinay K, Liu, Liang-Chun, Johann, Jr, Donald J, Willey, James C, Bushel, Pierre R, Yu, Ying, Xu, Chang, Chen, Guangchun, Burgess, Daniel, Cawley, Simon, Giorda, Kristina, Haseley, Nathan, Qiu, Fujun, Wilkins, Katherine, Arib, Hanane, Attwooll, Claire, Babson, Kevin, Bao, Longlong, Bao, Wenjun, Lucas, Anne Bergstrom, Best, Hunter, Bhandari, Ambica, Bisgin, Halil, Blackburn, James, Blomquist, Thomas M, Boardman, Lisa, Burgher, Blake, Butler, Daniel J, Chang, Chia-Jung, Chaubey, Alka, Chen, Tao, Chierici, Marco, Chin, Christopher R, Close, Devin, Conroy, Jeffrey, Cooley Coleman, Jessica, Craig, Daniel J, Crawford, Erin, Del Pozo, Angela, Deveson, Ira W, Duncan, Daniel, Eterovic, Agda Karina, Fan, Xiaohui, Foox, Jonathan, Furlanello, Cesare, Ghosal, Abhisek, Glenn, Sean, Guan, Meijian, Haag, Christine, Hang, Xinyi, Happe, Scott, Hennigan, Brittany, Hipp, Jennifer, Hong, Huixiao, Horvath, Kyle, Hu, Jianhong, Hung, Li-Yuan, Jarosz, Mirna, Kerkhof, Jennifer, Kipp, Benjamin, Kreil, David Philip, Łabaj, Paweł, Lapunzina, Pablo, Li, Peng, Li, Quan-Zhen, Li, Weihua, Li, Zhiguang, Liang, Yu, Liu, Shaoqing, Liu, Zhichao, Ma, Charles, Marella, Narasimha, Martín-Arenas, Rubén, Megherbi, Dalila B, Meng, Qingchang, Mieczkowski, Piotr A, Morrison, Tom, Muzny, Donna, Ning, Baitang, Parsons, Barbara L, Paweletz, Cloud P, Pirooznia, Mehdi, Qu, Wubin, Raymond, Amelia, Rindler, Paul, Ringler, Rebecca, Sadikovic, Bekim

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Abstract 529: SNAQ-SEQ™: Use of synthetic internal standards in conjunction with poisson exact test to call variants in contrived circulating tumor DNA specimens von Willey, James C., Crawford, Erin, Craig, Daniel J., Xu, Joshua, Haseley, Nathan, Lococo, Jennifer, Morrison, Tom

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Abstract 3624: Development of a comprehensive and highly sensitive next-generation sequencing assay for detection of copy number variations von Hsieh, Chia-Ling, Zlatkov, Clare, Luo, Byron, Zhao, Chen, Stephens, Kathryn, Chuang, Han-Yu, Kelly, Lisa, Chang, Katherine, Liang, Rachel, Cao, Jianli, Lang, Scott, Adams, Ashley, Ajili, Naseem, Ball, Laurel, Caves, Glorianna, Chou, Danny, Clark, Katie, Crain, Brian, Daulo, Anthony, Dumm, Sarah, Ekram, Ridwana, Han, Yonmee, Jager, Anne, Johansen, Suzanne, Teng, Li, Lococo, Jenn, McLean, Jaime, Parks, Juli, Rostron, Jason, Sayne, Jennifer, Silhavy, Jennifer, Snedecor, June, Toh, Mckenzi, Tong, Stephanie, Upsall, Elizabeth, Walichiewicz, Paulina, Chen, Xiao, Young, Amanda, Kuraishy, Ali, Gutekunst, Karen, Friedenberg, Matt, Lin, Charles

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Universal short adapters with variable length non-random unique molecular identifiers von CHUANG HAN-YU, SO ALEX, SINGER TATJANA, WU KEVIN, LOCOCO JENNIFER, BAKER DWIGHT, ZHAO CHEN

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NON-INVASIVE CANCER DETECTION METHODS von VIJAYARAGHAVAN, Raakhee, LIU, Li, SONG, Fan, GOLKARAM, Mahdi, PAPADOPOULOS, Frixos, LOCOCO, Jennifer, ZHAO, Chen

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UNIVERSAL SHORT ADAPTERS WITH VARIABLE LENGTH NON-RANDOM UNIQUE MOLECULAR IDENTIFIERS von Singer, Tatjana, Chuang, Han-Yu, Lococo, Jennifer, Wu, Kevin, Zhao, Chen, So, Alex, Baker, Dwight

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Universal short adapters with variable length non-random unique molecular identifiers von Singer, Tatjana, Chuang, Han-Yu, Lococo, Jennifer, Wu, Kevin, Zhao, Chen, So, Alex, Baker, Dwight

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