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Whole-Genome Sequencing of SARS-CoV-2 from Quarantine Hotel Outbreak.

Lex E X Leong, Julien Soubrier, Mark Turra, Emma Denehy, Luke Walters, Karin Kassahn, Geoff Higgins, Tom Dodd, Robert Hall, Katina D'Onise, Nicola Spurrier, Ivan Bastian, Chuan K Lim,

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same ... Read more >>

Emerg Infect Dis (Emerging infectious diseases)
[2021, 27(8):2219-2221]

Cited: 0 times

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Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, , , Gordon Saksena, Kyle Ellrott, Michael C Wendl, David A Wheeler, Gad Getz, Jared T Simpson, Mark B Gerstein, Li Ding, ,

Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w. ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):6232]

Cited: 0 times

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Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer.

Stephan B Dreyer, Rosie Upstill-Goddard, Viola Paulus-Hock, Clara Paris, Eirini-Maria Lampraki, Eloise Dray, Bryan Serrels, Giuseppina Caligiuri, Selma Rebus, Dennis Plenker, Zachary Galluzzo, Holly Brunton, Richard Cunningham, Mathias Tesson, Craig Nourse, Ulla-Maja Bailey, Marc Jones, Kim Moran-Jones, Derek W Wright, Fraser Duthie, Karin Oien, Lisa Evers, Colin J McKay, Grant A McGregor, Aditi Gulati, Rachel Brough, Ilirjana Bajrami, Stephan Pettitt, Michele L Dziubinski, Juliana Candido, Frances Balkwill, Simon T Barry, Robert Grützmann, Lola Rahib, , , Amber Johns, Marina Pajic, Fieke E M Froeling, Phillip Beer, Elizabeth A Musgrove, Gloria M Petersen, Alan Ashworth, Margaret C Frame, Howard C Crawford, Diane M Simeone, Chris Lord, Debabrata Mukhopadhyay, Christian Pilarsky, David A Tuveson, Susanna L Cooke, Nigel B Jamieson, Jennifer P Morton, Owen J Sansom, Peter J Bailey, Andrew V Biankin, David K Chang,

<h4>Background & aims</h4>Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in ... Read more >>

Gastroenterology (Gastroenterology)
[2021, 160(1):362-377.e13]

Cited: 5 times

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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, , , Gordon Saksena, Kyle Ellrott, Michael C Wendl, David A Wheeler, Gad Getz, Jared T Simpson, Mark B Gerstein, Li Ding, ,

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):4748]

Cited: 1 time

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Sex differences in oncogenic mutational processes.

Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, , Paul C Boutros, ,

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):4330]

Cited: 6 times

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HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer.

Holly Brunton, Giuseppina Caligiuri, Richard Cunningham, Rosie Upstill-Goddard, Ulla-Maja Bailey, Ian M Garner, Craig Nourse, Stephan Dreyer, Marc Jones, Kim Moran-Jones, Derek W Wright, Viola Paulus-Hock, Colin Nixon, Gemma Thomson, Nigel B Jamieson, Grant A McGregor, Lisa Evers, Colin J McKay, Aditi Gulati, Rachel Brough, Ilirjana Bajrami, Stephen J Pettitt, Michele L Dziubinski, Simon T Barry, Robert Grützmann, Robert Brown, Edward Curry, , , Marina Pajic, Elizabeth A Musgrove, Gloria M Petersen, Emma Shanks, Alan Ashworth, Howard C Crawford, Diane M Simeone, Fieke E M Froeling, Christopher J Lord, Debabrata Mukhopadhyay, Christian Pilarsky, Sean E Grimmond, Jennifer P Morton, Owen J Sansom, David K Chang, Peter J Bailey, Andrew V Biankin,

Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4A and GATA6, switch metabolic profiles from classical (pancreatic) ... Read more >>

Cell Rep (Cell reports)
[2020, 31(6):107625]

Cited: 10 times

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Pan-cancer analysis of whole genomes.

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Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale<sup>1-3</sup>. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) ... Read more >>

Nature (Nature)
[2020, 578(7793):82-93]

Cited: 227 times

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Identification and targeted management of a neurodegenerative disorder caused by biallelic mutations in SLC5A6.

Alicia B Byrne, Peer Arts, Steven W Polyak, Jinghua Feng, Andreas W Schreiber, Karin S Kassahn, Christopher N Hahn, Dylan A Mordaunt, Janice M Fletcher, Jillian Lipsett, Drago Bratkovic, Grant W Booker, Nicholas J Smith, Hamish S Scott,

We describe a sibling pair displaying an early infantile-onset, progressive neurodegenerative phenotype, with symptoms of developmental delay and epileptic encephalopathy developing from 12 to 14 months of age. Using whole exome sequencing, compound heterozygous variants were identified in <i>SLC5A6</i>, which encodes the sodium-dependent multivitamin transporter (SMVT) protein. SMVT is an ... Read more >>

NPJ Genom Med (NPJ genomic medicine)
[2019, 4:28]

Cited: 2 times

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Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies.

Hanyin Cheng, Avinash V Dharmadhikari, Sylvia Varland, Ning Ma, Deepti Domingo, Robert Kleyner, Alan F Rope, Margaret Yoon, Asbjørg Stray-Pedersen, Jennifer E Posey, Sarah R Crews, Mohammad K Eldomery, Zeynep Coban Akdemir, Andrea M Lewis, Vernon R Sutton, Jill A Rosenfeld, Erin Conboy, Katherine Agre, Fan Xia, Magdalena Walkiewicz, Mauro Longoni, Frances A High, Marjon A van Slegtenhorst, Grazia M S Mancini, Candice R Finnila, Arie van Haeringen, Nicolette den Hollander, Claudia Ruivenkamp, Sakkubai Naidu, Sonal Mahida, Elizabeth E Palmer, Lucinda Murray, Derek Lim, Parul Jayakar, Michael J Parker, Stefania Giusto, Emanuela Stracuzzi, Corrado Romano, Jennifer S Beighley, Raphael A Bernier, Sébastien Küry, Mathilde Nizon, Mark A Corbett, Marie Shaw, Alison Gardner, Christopher Barnett, Ruth Armstrong, Karin S Kassahn, Anke Van Dijck, Geert Vandeweyer, Tjitske Kleefstra, Jolanda Schieving, Marjolijn J Jongmans, Bert B A de Vries, Rolph Pfundt, Bronwyn Kerr, Samantha K Rojas, Kym M Boycott, Richard Person, Rebecca Willaert, Evan E Eichler, R Frank Kooy, Yaping Yang, Joseph C Wu, James R Lupski, Thomas Arnesen, Gregory M Cooper, Wendy K Chung, Jozef Gecz, Holly A F Stessman, Linyan Meng, Gholson J Lyon,

N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The ... Read more >>

Am J Hum Genet (American journal of human genetics)
[2018, 102(5):985-994]

Cited: 14 times

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Lost in translation: returning germline genetic results in genome-scale cancer research.

Amber L Johns, Skye H McKay, Jeremy L Humphris, Mark Pinese, Lorraine A Chantrill, R Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A High, Katia Nones, Ann-Marie Patch, Neil D Merrett, Nick Pavlakis, Karin S Kassahn, Jaswinder S Samra, David K Miller, David K Chang, Marina Pajic, , John V Pearson, Sean M Grimmond, Nicola Waddell, Nikolajs Zeps, Anthony J Gill, Andrew V Biankin,

<h4>Background</h4>The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer ... Read more >>

Genome Med (Genome medicine)
[2017, 9(1):41]

Cited: 15 times

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Case report of whole genome sequencing in the XY female: identification of a novel SRY mutation and revision of a misdiagnosis of androgen insensitivity syndrome.

Sunita M C De Sousa, Karin S Kassahn, Liam C McIntyre, Chan-Eng Chong, Hamish S Scott, David J Torpy,

<h4>Background</h4>The 46,XY female is characterised by a male karyotype and female phenotype arising due to any interruption in the sexual development pathways in utero. The cause is usually genetic and various genes are implicated.<h4>Case presentation</h4>Herein we describe a 46,XY woman who was first diagnosed with androgen insensitivity syndrome (testicular feminisation) ... Read more >>

BMC Endocr Disord (BMC endocrine disorders)
[2016, 16(1):58]

Cited: 2 times

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Hypermutation In Pancreatic Cancer.

Jeremy L Humphris, Ann-Marie Patch, Katia Nones, Peter J Bailey, Amber L Johns, Skye McKay, David K Chang, David K Miller, Marina Pajic, Karin S Kassahn, Michael C J Quinn, Timothy J C Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Craig Nourse, Ehsan Nourbakhsh, Andrew Stone, Peter J Wilson, Matthew Anderson, J Lynn Fink, Oliver Holmes, Stephen Kazakoff, Conrad Leonard, Felicity Newell, Nick Waddell, Scott Wood, Ronald S Mead, Qinying Xu, Jianmin Wu, Mark Pinese, Mark J Cowley, Marc D Jones, Adnan M Nagrial, Venessa T Chin, Lorraine A Chantrill, Amanda Mawson, Angela Chou, Christopher J Scarlett, Andreia V Pinho, Ilse Rooman, Marc Giry-Laterriere, Jaswinder S Samra, James G Kench, Neil D Merrett, Christopher W Toon, Krishna Epari, Nam Q Nguyen, Andrew Barbour, Nikolajs Zeps, Nigel B Jamieson, Colin J McKay, C Ross Carter, Euan J Dickson, Janet S Graham, Fraser Duthie, Karin Oien, Jane Hair, Jennifer P Morton, Owen J Sansom, Robert Grützmann, Ralph H Hruban, Anirban Maitra, Christine A Iacobuzio-Donahue, Richard D Schulick, Christopher L Wolfgang, Richard A Morgan, Rita T Lawlor, Borislav Rusev, Vincenzo Corbo, Roberto Salvia, Ivana Cataldo, Giampaolo Tortora, Margaret A Tempero, , Oliver Hofmann, James R Eshleman, Christian Pilarsky, Aldo Scarpa, Elizabeth A Musgrove, Anthony J Gill, John V Pearson, Sean M Grimmond, Nicola Waddell, Andrew V Biankin,

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched ... Read more >>

Gastroenterology (Gastroenterology)
[2017, 152(1):68-74.e2]

Cited: 68 times

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Genomic analyses identify molecular subtypes of pancreatic cancer.

Peter Bailey, David K Chang, Katia Nones, Amber L Johns, Ann-Marie Patch, Marie-Claude Gingras, David K Miller, Angelika N Christ, Tim J C Bruxner, Michael C Quinn, Craig Nourse, L Charles Murtaugh, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Ehsan Nourbakhsh, Shivangi Wani, Lynn Fink, Oliver Holmes, Venessa Chin, Matthew J Anderson, Stephen Kazakoff, Conrad Leonard, Felicity Newell, Nick Waddell, Scott Wood, Qinying Xu, Peter J Wilson, Nicole Cloonan, Karin S Kassahn, Darrin Taylor, Kelly Quek, Alan Robertson, Lorena Pantano, Laura Mincarelli, Luis N Sanchez, Lisa Evers, Jianmin Wu, Mark Pinese, Mark J Cowley, Marc D Jones, Emily K Colvin, Adnan M Nagrial, Emily S Humphrey, Lorraine A Chantrill, Amanda Mawson, Jeremy Humphris, Angela Chou, Marina Pajic, Christopher J Scarlett, Andreia V Pinho, Marc Giry-Laterriere, Ilse Rooman, Jaswinder S Samra, James G Kench, Jessica A Lovell, Neil D Merrett, Christopher W Toon, Krishna Epari, Nam Q Nguyen, Andrew Barbour, Nikolajs Zeps, Kim Moran-Jones, Nigel B Jamieson, Janet S Graham, Fraser Duthie, Karin Oien, Jane Hair, Robert Grützmann, Anirban Maitra, Christine A Iacobuzio-Donahue, Christopher L Wolfgang, Richard A Morgan, Rita T Lawlor, Vincenzo Corbo, Claudio Bassi, Borislav Rusev, Paola Capelli, Roberto Salvia, Giampaolo Tortora, Debabrata Mukhopadhyay, Gloria M Petersen, , Donna M Munzy, William E Fisher, Saadia A Karim, James R Eshleman, Ralph H Hruban, Christian Pilarsky, Jennifer P Morton, Owen J Sansom, Aldo Scarpa, Elizabeth A Musgrove, Ulla-Maja Hagbo Bailey, Oliver Hofmann, Robert L Sutherland, David A Wheeler, Anthony J Gill, Richard A Gibbs, John V Pearson, Nicola Waddell, Andrew V Biankin, Sean M Grimmond,

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated ... Read more >>

Nature (Nature)
[2016, 531(7592):47-52]

Cited: 948 times

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Corrigendum: Whole-genome characterization of chemoresistant ovarian cancer.

Ann-Marie Patch, Elizabeth L Christie, Dariush Etemadmoghadam, Dale W Garsed, Joshy George, Sian Fereday, Katia Nones, Prue Cowin, Kathryn Alsop, Peter J Bailey, Karin S Kassahn, Felicity Newell, Michael C J Quinn, Stephen Kazakoff, Kelly Quek, Charlotte Wilhelm-Benartzi, Ed Curry, Huei San Leong, , Anne Hamilton, Linda Mileshkin, George Au-Yeung, Catherine Kennedy, Jillian Hung, Yoke-Eng Chiew, Paul Harnett, Michael Friedlander, Michael Quinn, Jan Pyman, Stephen Cordner, Patricia O'Brien, Jodie Leditschke, Greg Young, Kate Strachan, Paul Waring, Walid Azar, Chris Mitchell, Nadia Traficante, Joy Hendley, Heather Thorne, Mark Shackleton, David K Miller, Gisela Mir Arnau, Richard W Tothill, Timothy P Holloway, Timothy Semple, Ivon Harliwong, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Senel Idrisoglu, Timothy J C Bruxner, Angelika N Christ, Barsha Poudel, Oliver Holmes, Matthew Anderson, Conrad Leonard, Andrew Lonie, Nathan Hall, Scott Wood, Darrin F Taylor, Qinying Xu, J Lynn Fink, Nick Waddell, Ronny Drapkin, Euan Stronach, Hani Gabra, Robert Brown, Andrea Jewell, Shivashankar H Nagaraj, Emma Markham, Peter J Wilson, Jason Ellul, Orla McNally, Maria A Doyle, Ravikiran Vedururu, Collin Stewart, Ernst Lengyel, John V Pearson, Nicola Waddell, Anna deFazio, Sean M Grimmond, David D L Bowtell,

Nature (Nature)
[2015, 527(7578):398]

Cited: 4 times

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Presentation of m.3243A>G (MT-TL1; tRNALeu) variant with focal neurology in infancy.

Dylan A Mordaunt, Liam C McIntyre, Hayley Salvemini, Afdal Ibrahim, Drago Bratkovic, David Ketteridge, Hamish S Scott, Karin S Kassahn, Nicholas Smith,

The Mitochondrial tRNALeu (MT-TL1) mutation, m.3243A>G constitutes the commonest identified mitochondrial genome mutation. Characteristically, giving rise to MELAS (mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes), a phenotypic spectrum associated with this genetic variant is now apparent. We report on the first patient with infantile hemiparesis, without comorbid encephalopathy, attributed to ... Read more >>

Am J Med Genet A (American journal of medical genetics. Part A)
[2015, 167A(11):2697-2701]

Cited: 2 times

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Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance.

Jodi M Saunus, Michael C J Quinn, Ann-Marie Patch, John V Pearson, Peter J Bailey, Katia Nones, Amy E McCart Reed, David Miller, Peter J Wilson, Fares Al-Ejeh, Mythily Mariasegaram, Queenie Lau, Teresa Withers, Rosalind L Jeffree, Lynne E Reid, Leonard Da Silva, Admire Matsika, Colleen M Niland, Margaret C Cummings, Timothy J C Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Craig Nourse, Ehsan Nourbakhsh, Shivangi Wani, Matthew J Anderson, J Lynn Fink, Oliver Holmes, Stephen Kazakoff, Conrad Leonard, Felicity Newell, Darrin Taylor, Nick Waddell, Scott Wood, Qinying Xu, Karin S Kassahn, Vairavan Narayanan, Nur Aishah Taib, Soo-Hwang Teo, Yock Ping Chow, kConFab, Parmjit S Jat, Sebastian Brandner, Adrienne M Flanagan, Kum Kum Khanna, Georgia Chenevix-Trench, Sean M Grimmond, Peter T Simpson, Nicola Waddell, Sunil R Lakhani,

Treatment options for patients with brain metastases (BMs) have limited efficacy and the mortality rate is virtually 100%. Targeted therapy is critically under-utilized, and our understanding of mechanisms underpinning metastatic outgrowth in the brain is limited. To address these deficiencies, we investigated the genomic and transcriptomic landscapes of 36 BMs ... Read more >>

J Pathol (The Journal of pathology)
[2015, 237(3):363-378]

Cited: 48 times

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Whole-genome characterization of chemoresistant ovarian cancer.

Ann-Marie Patch, Elizabeth L Christie, Dariush Etemadmoghadam, Dale W Garsed, Joshy George, Sian Fereday, Katia Nones, Prue Cowin, Kathryn Alsop, Peter J Bailey, Karin S Kassahn, Felicity Newell, Michael C J Quinn, Stephen Kazakoff, Kelly Quek, Charlotte Wilhelm-Benartzi, Ed Curry, Huei San Leong, , Anne Hamilton, Linda Mileshkin, George Au-Yeung, Catherine Kennedy, Jillian Hung, Yoke-Eng Chiew, Paul Harnett, Michael Friedlander, Michael Quinn, Jan Pyman, Stephen Cordner, Patricia O'Brien, Jodie Leditschke, Greg Young, Kate Strachan, Paul Waring, Walid Azar, Chris Mitchell, Nadia Traficante, Joy Hendley, Heather Thorne, Mark Shackleton, David K Miller, Gisela Mir Arnau, Richard W Tothill, Timothy P Holloway, Timothy Semple, Ivon Harliwong, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Senel Idrisoglu, Timothy J C Bruxner, Angelika N Christ, Barsha Poudel, Oliver Holmes, Matthew Anderson, Conrad Leonard, Andrew Lonie, Nathan Hall, Scott Wood, Darrin F Taylor, Qinying Xu, J Lynn Fink, Nick Waddell, Ronny Drapkin, Euan Stronach, Hani Gabra, Robert Brown, Andrea Jewell, Shivashankar H Nagaraj, Emma Markham, Peter J Wilson, Jason Ellul, Orla McNally, Maria A Doyle, Ravikiran Vedururu, Collin Stewart, Ernst Lengyel, John V Pearson, Nicola Waddell, Anna deFazio, Sean M Grimmond, David D L Bowtell,

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 ... Read more >>

Nature (Nature)
[2015, 521(7553):489-494]

Cited: 530 times

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Whole genomes redefine the mutational landscape of pancreatic cancer.

Nicola Waddell, Marina Pajic, Ann-Marie Patch, David K Chang, Karin S Kassahn, Peter Bailey, Amber L Johns, David Miller, Katia Nones, Kelly Quek, Michael C J Quinn, Alan J Robertson, Muhammad Z H Fadlullah, Tim J C Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Craig Nourse, Ehsan Nourbakhsh, Shivangi Wani, Peter J Wilson, Emma Markham, Nicole Cloonan, Matthew J Anderson, J Lynn Fink, Oliver Holmes, Stephen H Kazakoff, Conrad Leonard, Felicity Newell, Barsha Poudel, Sarah Song, Darrin Taylor, Nick Waddell, Scott Wood, Qinying Xu, Jianmin Wu, Mark Pinese, Mark J Cowley, Hong C Lee, Marc D Jones, Adnan M Nagrial, Jeremy Humphris, Lorraine A Chantrill, Venessa Chin, Angela M Steinmann, Amanda Mawson, Emily S Humphrey, Emily K Colvin, Angela Chou, Christopher J Scarlett, Andreia V Pinho, Marc Giry-Laterriere, Ilse Rooman, Jaswinder S Samra, James G Kench, Jessica A Pettitt, Neil D Merrett, Christopher Toon, Krishna Epari, Nam Q Nguyen, Andrew Barbour, Nikolajs Zeps, Nigel B Jamieson, Janet S Graham, Simone P Niclou, Rolf Bjerkvig, Robert Grützmann, Daniela Aust, Ralph H Hruban, Anirban Maitra, Christine A Iacobuzio-Donahue, Christopher L Wolfgang, Richard A Morgan, Rita T Lawlor, Vincenzo Corbo, Claudio Bassi, Massimo Falconi, Giuseppe Zamboni, Giampaolo Tortora, Margaret A Tempero, , Anthony J Gill, James R Eshleman, Christian Pilarsky, Aldo Scarpa, Elizabeth A Musgrove, John V Pearson, Andrew V Biankin, Sean M Grimmond,

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, ... Read more >>

Nature (Nature)
[2015, 518(7540):495-501]

Cited: 950 times

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Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling.

Katia Nones, Nic Waddell, Sarah Song, Ann-Marie Patch, David Miller, Amber Johns, Jianmin Wu, Karin S Kassahn, David Wood, Peter Bailey, Lynn Fink, Suzanne Manning, Angelika N Christ, Craig Nourse, Stephen Kazakoff, Darrin Taylor, Conrad Leonard, David K Chang, Marc D Jones, Michelle Thomas, Clare Watson, Mark Pinese, Mark Cowley, Ilse Rooman, Marina Pajic, , Giovanni Butturini, Anna Malpaga, Vincenzo Corbo, Stefano Crippa, Massimo Falconi, Giuseppe Zamboni, Paola Castelli, Rita T Lawlor, Anthony J Gill, Aldo Scarpa, John V Pearson, Andrew V Biankin, Sean M Grimmond,

The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using ... Read more >>

Int J Cancer (International journal of cancer)
[2014, 135(5):1110-1118]

Cited: 92 times

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A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing.

Kelly Quek, Katia Nones, Ann-Marie Patch, J Lynn Fink, Felicity Newell, Nicole Cloonan, David Miller, Muhammad Z H Fadlullah, Karin Kassahn, Angelika N Christ, Timothy J C Bruxner, Suzanne Manning, Ivon Harliwong, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Shivangi Wani, Anita Steptoe, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, , Peter Wilson, Andrew V Biankin, John V Pearson, Nic Waddell, Sean M Grimmond,

Somatic rearrangements, which are commonly found in human cancer genomes, contribute to the progression and maintenance of cancers. Conventionally, the verification of somatic rearrangements comprises many manual steps and Sanger sequencing. This is labor intensive when verifying a large number of rearrangements in a large cohort. To increase the verification ... Read more >>

Biotechniques (BioTechniques)
[2014, 57(1):31-38]

Cited: 0 times

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Returning individual research results for genome sequences of pancreatic cancer.

Amber L Johns, David K Miller, Skye H Simpson, Anthony J Gill, Karin S Kassahn, Jeremy L Humphris, Jaswinder S Samra, Katherine Tucker, Lesley Andrews, David K Chang, Nicola Waddell, Marina Pajic, John V Pearson, Sean M Grimmond, Andrew V Biankin, Nikolajs Zeps,

<h4>Background</h4>Disclosure of individual results to participants in genomic research is a complex and contentious issue. There are many existing commentaries and opinion pieces on the topic, but little empirical data concerning actual cases describing how individual results have been returned. Thus, the real life risks and benefits of disclosing individual ... Read more >>

Genome Med (Genome medicine)
[2014, 6(5):42]

Cited: 16 times

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Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge.

Karin S Kassahn, Hamish S Scott, Melody C Caramins,

Massively parallel sequencing has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in ... Read more >>

Hum Mutat (Human mutation)
[2014, 35(4):413-423]

Cited: 13 times

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Somatic point mutation calling in low cellularity tumors.

Karin S Kassahn, Oliver Holmes, Katia Nones, Ann-Marie Patch, David K Miller, Angelika N Christ, Ivon Harliwong, Timothy J Bruxner, Qinying Xu, Matthew Anderson, Scott Wood, Conrad Leonard, Darrin Taylor, Felicity Newell, Sarah Song, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Shivangi Wani, Anita Steptoe, Marina Pajic, Mark J Cowley, Mark Pinese, David K Chang, Anthony J Gill, Amber L Johns, Jianmin Wu, Peter J Wilson, Lynn Fink, Andrew V Biankin, Nicola Waddell, Sean M Grimmond, John V Pearson,

Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline ... Read more >>

PLoS One (PloS one)
[2013, 8(11):e74380]

Cited: 34 times

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Clinical and molecular characterization of HER2 amplified-pancreatic cancer.

Angela Chou, Nicola Waddell, Mark J Cowley, Anthony J Gill, David K Chang, Ann-Marie Patch, Katia Nones, Jianmin Wu, Mark Pinese, Amber L Johns, David K Miller, Karin S Kassahn, Adnan M Nagrial, Harpreet Wasan, David Goldstein, Christopher W Toon, Venessa Chin, Lorraine Chantrill, Jeremy Humphris, R Scott Mead, Ilse Rooman, Jaswinder S Samra, Marina Pajic, Elizabeth A Musgrove, John V Pearson, Adrienne L Morey, Sean M Grimmond, Andrew V Biankin,

<h4>Background</h4>Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Repurposing of therapeutics that target specific molecular mechanisms in different disease types offers potential for rapid improvements in outcome. Although HER2 amplification occurs in pancreatic cancer, it is inadequately characterized to exploit the potential of anti-HER2 therapies.<h4>Methods</h4>HER2 amplification ... Read more >>

Genome Med (Genome medicine)
[2013, 5(8):78]

Cited: 53 times

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Computational approaches to identify functional genetic variants in cancer genomes.

Abel Gonzalez-Perez, Ville Mustonen, Boris Reva, Graham R S Ritchie, Pau Creixell, Rachel Karchin, Miguel Vazquez, J Lynn Fink, Karin S Kassahn, John V Pearson, Gary D Bader, Paul C Boutros, Lakshmi Muthuswamy, B F Francis Ouellette, Jüri Reimand, Rune Linding, Tatsuhiro Shibata, Alfonso Valencia, Adam Butler, Serge Dronov, Paul Flicek, Nick B Shannon, Hannah Carter, Li Ding, Chris Sander, Josh M Stuart, Lincoln D Stein, Nuria Lopez-Bigas, ,

The International Cancer Genome Consortium (ICGC) aims to catalog genomic abnormalities in tumors from 50 different cancer types. Genome sequencing reveals hundreds to thousands of somatic mutations in each tumor but only a minority of these drive tumor progression. We present the result of discussions within the ICGC on how ... Read more >>

Nat Methods (Nature methods)
[2013, 10(8):723-729]

Cited: 98 times

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