Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes

Authors: O’Neill, Kieran ^{1, 9, 10}, Pleasance, Erin ^{1, 9}, Fan, Jeremy ^{1, 9}, Akbari, Vahid ^{1, 5, 9}, Chang, Glenn ^{1, 9}, Dixon, Katherine ^{1, 9}, Csizmok, Veronika ^{1, 9}, MacLennan, Signe ^{1, 5, 8, 9}, Porter, Vanessa ^{1, 5, 8}, Galbraith, Andrew ¹, Grisdale, Cameron J. ¹, Culibrk, Luka ¹, Dupuis, John H. ¹, Corbett, Richard ¹, Hopkins, James ¹, Bowlby, Reanne ¹, Pandoh, Pawan ¹, Smailus, Duane E. ¹, Cheng, Dean ¹, Wong, Tina ¹, Frey, Connor ², Shen, Yaoqing ¹, Lewis, Eleanor ¹, Paulin, Luis F. ³, Sedlazeck, Fritz J. ³, Nelson, Jessica M.T. ¹, Chuah, Eric ¹, Mungall, Karen L. ¹, Moore, Richard A. ¹, Coope, Robin ¹, Mungall, Andrew J. ¹, McConechy, Melissa K. ¹, Williamson, Laura M. ¹, Schrader, Kasmintan A. ^{4, 5}, Yip, Stephen ⁶, Marra, Marco A. ^{1, 5, 8}, Laskin, Janessa ⁷, Jones, Steven J.M. ^{1, 5, ∗}

Source: In Cell Genomics 13 November 2024 4(11)

An infant with congenital respiratory insufficiency and diaphragmatic paralysis: A novel BICD2 phenotype?

Authors: Chin, Hui‐Lin, Huynh, Stephanie, Ashkani, Jahanshah, Castaldo, Michael, Dixon, Katherine, Selby, Kathryn, Shen, Yaoqing, Wright, Marie, Boerkoel, Cornelius F., Hendson, Glenda, Jones, Steven J. M.

Source: American journal of medical genetics.Part A. 188(3):926-930

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100140903186.0x000001&indx=1&recIds=ETOCvdc_100140903186.0x000001

The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies

Authors: Tessier‐Cloutier, Basile, Grewal, Jasleen K, Jones, Martin R, Pleasance, Erin, Shen, Yaoqing, Cai, Ellen, Dunham, Chris, Hoang, Lynn, Horst, Basil, Huntsman, David G, Ionescu, Diana, Karnezis, Anthony N, Lee, Anna F, Lee, Cheng Han, Lee, Tae Hoon, Twa, David DW, Mungall, Andrew J, Mungall, Karen, Naso, Julia R, Ng, Tony, Schaeffer, David F, Sheffield, Brandon S, Skinnider, Brian, Smith, Tyler, Williamson, Laura, Zhong, Ellia, Regier, Dean A, Laskin, Janessa, Marra, Marco A, Gilks, C Blake, Jones, Steven JM, Yip, Stephen

Source: Journal of pathology.Clinical research. 8(4):395-407

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100151817136.0x000001&indx=1&recIds=ETOCvdc_100151817136.0x000001

Long‐read genome sequencing resolves a complex 13q structural variant associated with syndromic anophthalmia

Authors: Boerkoel, Pierre K., Dixon, Katherine, Fitzsimons, Carrie, Shen, Yaoqing, Huynh, Stephanie, Schlade‐Bartusiak, Kamilla, Culibrk, Luka, Chan, Simon, Boerkoel, Cornelius F., Jones, Steven J. M., Chin, Hui‐Lin

Source: American journal of medical genetics.Part A. 188(5):1589-1594

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100146659044.0x000001&indx=1&recIds=ETOCvdc_100146659044.0x000001

Long-read sequencing for detection and subtyping of Prader-Willi and Angelman syndromes

Authors: Akbari, Vahid, Dada, Sarah, Shen, Yaoqing, Dixon, Katherine, Hejla, Duha, Galbraith, Andrew, Choufani, Sanaa, Weksberg, Rosanna, Boerkoel, Cornelius F, Stewart, Laura, Gibson, William T, Jones, Steven J M

Source: Journal of Medical Genetics (JMG); 2025, Vol. 62 Issue: 1 p32-36, 5p

NTRK2 Fusion driven pediatric glioblastoma: Identification of oncogenic Drivers via integrative Genome and transcriptome profiling

Authors: Britton, Heidi M., Levine, Adrian B., Shen, Yaoqing, Mungall, Karen, Serrano, Jonathan, Snuderl, Matija, Pleasance, Erin, Jones, Steven J. M., Laskin, Janessa, Marra, Marco A., Rassekh, Shahrad R., Deyell, Rebecca, Yip, Stephen, Cheng, Sylvia, Dunham, Chris

Source: Clinical case reports. 9(3):1472-1477

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100116922079.0x000001&indx=1&recIds=ETOCvdc_100116922079.0x000001

Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing

Authors: Thibodeau, My Linh, O’Neill, Kieran, Dixon, Katherine, Reisle, Caralyn, Mungall, Karen L., Krzywinski, Martin, Shen, Yaoqing, Lim, Howard J., Cheng, Dean, Tse, Kane, Wong, Tina, Chuah, Eric, Fok, Alexandra, Sun, Sophie, Renouf, Daniel, Schaeffer, David F., Cremin, Carol, Chia, Stephen, Young, Sean, Pandoh, Pawan, Pleasance, Stephen, Pleasance, Erin, Mungall, Andrew J., Moore, Richard, Yip, Stephen, Karsan, Aly, Laskin, Janessa, Marra, Marco A., Schrader, Kasmintan A., Jones, Steven J.M.

Source: In Genetics in Medicine November 2020 22(11):1892-1897

Whole genome transcriptome analysis in a case of a neonatal soft tissue sarcoma with YWHAE:NUTM2B fusion

Authors: Locke, Arielle, Terry, Jefferson, Shen, Yaoqing, Courtemanche, Douglas, Rosenbaum, Daniel G., Rassekh, S. Rod, Deyell, Rebecca J., Cheng, Sylvia

Source: Pediatric blood & cancer. 70(7)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183854729.0x000001&indx=1&recIds=ETOCvdc_100183854729.0x000001

Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments

Authors: Shen, Yaoqing, Grisdale, Cameron J., Islam, Sumaiya A., Bose, Pinaki, Lever, Jake, Zhao, Eric Y., Grinshtein, Natalie, Ma, Yussanne, Mungall, Andrew J., Moore, Richard A., Lun, Xueqing, Senger, Donna L., Robbins, Stephen M., Wang, Alice Yijun, MacIsaac, Julia L., Kobor, Michael S., Luchman, H. Artee, Weiss, Samuel, Chan, Jennifer A., Blough, Michael D., Kaplan, David R., Cairncross, J. Gregory, Marra, Marco A., Jones, Steven J. M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Sep . 116(38), 19098-19108.

Access URL: https://www.jstor.org/stable/26851673

Mutations in ILK, encoding integrin-linked kinase, are associated with arrhythmogenic cardiomyopathy

Authors: Brodehl, Andreas, Rezazadeh, Saman, Williams, Tatjana, Munsie, Nicole M., Liedtke, Daniel, Oh, Tracey, Ferrier, Raechel, Shen, Yaoqing, Jones, Steven J.M., Stiegler, Amy L., Boggon, Titus J., Duff, Henry J., Friedman, Jan M., Gibson, William T., Childs, Sarah J., Gerull, Brenda

Source: In Translational Research June 2019 208:15-29

Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes

Authors: Pleasance, Erin, Titmuss, Emma, Williamson, Laura, Kwan, Harwood, Culibrk, Luka, Zhao, Eric Y., Dixon, Katherine, Fan, Kevin, Bowlby, Reanne, Jones, Martin R., Shen, Yaoqing, Grewal, Jasleen K., Ashkani, Jahanshah, Wee, Kathleen, Grisdale, Cameron J., Thibodeau, My Linh, Bozoky, Zoltan, Pearson, Hillary, Majounie, Elisa, Vira, Tariq, Shenwai, Reva, Mungall, Karen L., Chuah, Eric, Davies, Anna, Warren, Mya, Reisle, Caralyn, Bonakdar, Melika, Taylor, Gregory A., Csizmok, Veronika, Chan, Simon K., Zong, Zusheng, Bilobram, Steve, Muhammadzadeh, Amir, D'Souza, Darryl, Corbett, Richard D., MacMillan, Daniel, Carreira, Marcus, Choo, Caleb, Bleile, Dustin, Sadeghi, Sara, Zhang, Wei, Wong, Tina, Cheng, Dean, Brown, Scott D., Holt, Robert A., Moore, Richard A., Mungall, Andrew J., Zhao, Yongjun, Nelson, Jessica, Fok, Alexandra, Ma, Yussanne, Lee, Michael K. C., Lavoie, Jean-Michel, Mendis, Shehara, Karasinska, Joanna M., Deol, Balvir, Fisic, Ana, Schaeffer, David F., Yip, Stephen, Schrader, Kasmintan, Regier, Dean A., Weymann, Deirdre, Chia, Stephen, Gelmon, Karen, Tinker, Anna, Sun, Sophie, Lim, Howard, Renouf, Daniel J., Laskin, Janessa, Jones, Steven J. M., Marra, Marco A.

Source: Nature cancer. 1(4):452-468

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100172463393.0x000001&indx=1&recIds=ETOCvdc_100172463393.0x000001

Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1

Authors: Mazor, Tali, Chesnelong, Charles, Pankov, Aleksandr, Jalbert, Llewellyn E., Hong, Chibo, Hayes, Josie, Smirnov, Ivan V., Marshall, Roxanne, Souza, Camila F., Shen, Yaoqing, Viswanath, Pavithra, Noushmehr, Houtan, Ronen, Sabrina M., Jones, Steven J. M., Marra, Marco A., Cairncross, J. Gregory, Perry, Arie, Nelson, Sarah J., Chang, Susan M., Bollen, Andrew W., Molinaro, Annette M., Bengtsson, Henrik, Olshen, Adam B., Weiss, Samuel, Phillips, Joanna J., Luchman, H. Artee, Costello, Joseph F.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Oct 01. 114(40), 10743-10748.

Access URL: https://www.jstor.org/stable/26488127

Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers.

Authors: Deyell, Rebecca J., Shen, Yaoqing, Titmuss, Emma, Dixon, Katherine, Williamson, Laura M., Pleasance, Erin, Nelson, Jessica M. T., Abbasi, Sanna, Krzywinski, Martin, Armstrong, Linlea, Bonakdar, Melika, Ch'ng, Carolyn, Chuah, Eric, Dunham, Chris, Fok, Alexandra, Jones, Martin, Lee, Anna F., Ma, Yussanne, Moore, Richard A., Mungall, Andrew J.

Source: Nature Communications; 5/16/2024, Vol. 15 Issue 1, p1-15, 15p

Subject Terms: NUCLEOTIDE sequencing, CLINICAL medicine, CANCER prognosis, PEDIATRIC therapy, DNA copy number variations, SOMATIC mutation

P658: Detection of variant parent-of-origin in diverse hereditary cancer syndromes using only the proband’s blood sample

Authors: Schrader, Kasmintan, Akbari, Vahid, Hanlon, Vincent, Leung, Tiffany, Dixon, Katherine, O’Neill, Kieran, Roston, Alexandra, Cordova, Lilian, Wong, Karen, Sharma, Alshanee, Shen, Yaoqing, Senz, Janine, Wang, Yanni, Chan, Daniel, Fok, Alexandra, Hong, Quan, Nuk, Jennifer, Coope, Robin, Chuah, Eric, Chan, Simon, Lee, Hyun-Wu, Bilobram, Steve, Zhao, Yongjun, Bala, Miruna, Mungall, Karen, Mungall, Andy, Moore, Richard, Regier, Dean, Virani, Alice, Lefebvre, Louis, Feldman, Fabio, Marra, Marco, Sun, Sophie, Yip, Stephen, Lansdorp, Peter, Jones, Steven

Source: In Genetics in Medicine Open 2024 2 Supplement 1

Hypermutation signature reveals a slippage and realignment model of translesion synthesis by Rev3 polymerase in cisplatin-treated yeast

Authors: Segovia, Romulo, Shen, Yaoqing, Lujan, Scott A., Jones, Steven J. M., Stirling, Peter C.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Mar 01. 114(10), 2663-2668.

Access URL: https://www.jstor.org/stable/26480086

RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability

Authors: Chang, Emily Yun-Chia, Novoa, Carolina A., Aristizabal, Maria J., Coulombe, Yan, Segovia, Romulo, Chaturvedi, Richa, Shen, Yaoqing, Keong, Christelle, Tam, Annie S., Jones, Steven J. M.

Source: Journal of cell biology. 216(12):3991-4006

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN613991851&indx=1&recIds=ETOCRN613991851

O35: Parent-of-origin-aware genomic analysis infers segregation of pathogenic variants in SDHD without parental data*

Authors: Schrader, Kasmintan, Akbari, Vahid, Hanlon, Vincent, Dixon, Katherine, O’Neill, Kieran, Shen, Yaoqing, Sharma, Alshanee, Senz, Janine, Wang, Yanni, Chan, Daniel, Fok, Alexandra, Hong, Quan, Nuk, Jennifer, Regier, Dean, Virani, Alice, Lefebvre, Louis, Feldman, Fabio, Marra, Marco, Sun, Sophie, Yip, Stephen, Lansdorp, Peter, Jones, Steven

Source: In Genetics in Medicine Open 2023 1(1) Supplement

Exome Sequencing Identifies a Novel Variant in ACTC1 Associated With Familial Atrial Septal Defect

Authors: Greenway, Steven C., McLeod, Ross, Hume, Stacey, Roslin, Nicole M., Alvarez, Nanette, Giuffre, Michael, Zhan, Shing H., Shen, Yaoqing, Preuss, Christoph, Andelfinger, Gregor, Jones, Steven J.M., Gerull, Brenda

Source: In Canadian Journal of Cardiology February 2014 30(2):181-187

ETV6-NTRK3 Is Expressed in a Subset of ALK-Negative Inflammatory Myofibroblastic Tumors

Authors: Alassiri, Ali H., Ali, Rola H., Shen, Yaoqing, Lum, Amy, Strahlendorf, Caron, Deyell, Rebecca, Rassekh, Rod, Sorensen, Poul H., Laskin, Janessa, Marra, Marco, Yip, Stephen, Lee, Cheng-Han, Ng, Tony L.

Source: American journal of surgical pathology. 40(8):1051-1061

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100033890518.0x000001&indx=1&recIds=ETOCvdc_100033890518.0x000001

Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression

Authors: De Boeck, Astrid, Ahn, Bo Young, D'Mello, Charlotte, Lun, Xueqing, Menon, Shyam V., Alshehri, Mana M., Szulzewsky, Frank, Shen, Yaoqing, Khan, Lubaba, Dang, Ngoc Ha, Reichardt, Elliott, Goring, Kimberly-Ann, King, Jennifer, Grisdale, Cameron J., Grinshtein, Natalie, Hambardzumyan, Dolores, Reilly, Karlyne M., Blough, Michael D., Cairncross, J. Gregory, Yong, V. Wee, Marra, Marco A., Jones, Steven J. M., Kaplan, David R., McCoy, Kathy D., Holland, Eric C., Bose, Pinaki, Chan, Jennifer A., Robbins, Stephen M., Senger, Donna L.

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174505060.0x000001&indx=1&recIds=ETOCvdc_100174505060.0x000001