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Connor AA, Adelman MW, Mobley CM, Moaddab M, Erhardt AJ, Hsu DE, Brombosz EW, Sanghvi M, Cheah YL, Simon CJ, Hobeika MJ, Saharia AS, Victor DW, Kodali S, Basra T, Graviss EA, Nguyen DT, Elsaiey A, Moore LW, Nigo M, Drews AL, Grimes KA, Arias CA, Li XC, Gaber AO, Ghobrial RM. Single-center Outcomes After Liver Transplantation With SARS-CoV-2-Positive Donors: An Argument for Increased Utilization. Transplant Direct 2024; 10:e1590. [PMID: 38464428 PMCID: PMC10923316 DOI: 10.1097/txd.0000000000001590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 03/12/2024] Open
Abstract
Background The COVID-19 pandemic has led to an increase in SARS-CoV-2-test positive potential organ donors. The benefits of life-saving liver transplantation (LT) must be balanced against the potential risk of donor-derived viral transmission. Although emerging evidence suggests that the use of COVID-19-positive donor organs may be safe, granular series thoroughly evaluating safety are still needed. Results of 29 consecutive LTs from COVID-19-positive donors at a single center are presented here. Methods A retrospective cohort study of LT recipients between April 2020 and December 2022 was conducted. Differences between recipients of COVID-19-positive (n = 29 total; 25 index, 4 redo) and COVID-19-negative (n = 472 total; 454 index, 18 redo) deceased donor liver grafts were compared. Results COVID-19-positive donors were significantly younger (P = 0.04) and had lower kidney donor profile indices (P = 0.04) than COVID-19-negative donors. Recipients of COVID-19-positive donor grafts were older (P = 0.04) but otherwise similar to recipients of negative donors. Donor SARS-CoV-2 infection status was not associated with a overall survival of recipients (hazard ratio, 1.11; 95% confidence interval, 0.24-5.04; P = 0.89). There were 3 deaths among recipients of liver grafts from COVID-19-positive donors. No death seemed virally mediated because there was no qualitative association with peri-LT antispike antibody titers, post-LT prophylaxis, or SARS-CoV-2 variants. Conclusions The utilization of liver grafts from COVID-19-positive donors was not associated with a decreased overall survival of recipients. There was no suggestion of viral transmission from donor to recipient. The results from this large single-center study suggest that COVID-19-positive donors may be used safely to expand the deceased donor pool.
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Affiliation(s)
- Ashton A. Connor
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Max W. Adelman
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, HMH, Houston TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Constance M. Mobley
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Mozhgon Moaddab
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX
| | - Alexandra J. Erhardt
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
| | - David E. Hsu
- Center for Health Data Science and Analytics, Houston Methodist Hospital, Houston, TX
| | | | - Mansi Sanghvi
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
| | - Yee Lee Cheah
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
| | - Caroline J. Simon
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
| | - Mark J. Hobeika
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Ashish S. Saharia
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - David W. Victor
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX
| | - Sudha Kodali
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX
| | - Tamneet Basra
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX
| | - Edward A. Graviss
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
| | - Duc T. Nguyen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Ahmed Elsaiey
- Department of Surgery, Houston Methodist Hospital, Houston, TX
| | - Linda W. Moore
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Masayuki Nigo
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Ashley L. Drews
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Kevin A. Grimes
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Cesar A. Arias
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Xian C. Li
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
- Immunobiology and Transplant Science Center, Houston Methodist Hospital, Houston, TX
| | - A. Osama Gaber
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - R. Mark Ghobrial
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX
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Kodali S, Connor AA, Thabet S, Brombosz EW, Ghobrial RM. Liver transplantation as an alternative for the treatment of intrahepatic cholangiocarcinoma: Past, present, and future directions. Hepatobiliary Pancreat Dis Int 2024; 23:129-138. [PMID: 37517983 DOI: 10.1016/j.hbpd.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a rare biliary tract cancer with high mortality rate. Complete resection of the iCCA lesion is the first choice of treatment, with good prognosis after margin-negative resection. Unfortunately, only 12%-40% of patients are eligible for resection at presentation due to cirrhosis, portal hypertension, or large tumor size. Liver transplantation (LT) offers margin-negative iCCA extirpation for patients with unresectable tumors. Initially, iCCA was a contraindication for LT until size-based selection criteria were introduced to identify patients with satisfied post-LT outcomes. Recent studies have shown that tumor biology-based selection can yield high post-LT survival in patients with locally advanced iCCA. Another selection criterion is the tumor response to neoadjuvant therapy. Patients with response to neoadjuvant therapy have better outcomes after LT compared with those without tumor response to neoadjuvant therapy. Another index that helps predict the treatment outcome is the biomarker. Improved survival outcomes have also opened the door for living donor LT for iCCA. Patients undergoing LT for iCCA now have statistically similar survival rates as patients undergoing resection. The combination of surgery and locoregional and systemic therapies improves the prognosis of iCCA patients.
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Affiliation(s)
- Sudha Kodali
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX 77030, USA; JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX 77030, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ashton A Connor
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX 77030, USA; JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX 77030, USA; Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA; Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | | | | | - R Mark Ghobrial
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston Methodist Hospital, Houston, TX 77030, USA; JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX 77030, USA; Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA; Department of Surgery, Weill Cornell Medical College, New York, NY, USA.
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Kodali S, Connor AA, Brombosz EW, Ghobrial RM. Update on the Screening, Diagnosis, and Management of Cholangiocarcinoma. Gastroenterol Hepatol (N Y) 2024; 20:151-158. [PMID: 38680168 PMCID: PMC11047158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Cholangiocarcinoma (CCA) is a neoplasm of the biliary tract that has become increasingly prevalent throughout the world. Common risk factors for developing CCA include cirrhosis, primary sclerosing cholangitis, and trematode fluke infestation, although there are no set screening guidelines in high-risk groups. Lesions are typically identified via cross-sectional imaging and/or elevated serum carbohydrate antigen 19-9 levels, often followed by cytology or brushings with fluorescence in situ hybridization for confirmation. Treatments can vary among CCA subtypes but frequently involve systemic therapies such as gemcitabine and cisplatin with durvalumab or pembrolizumab. Targeted therapies may also be effective (eg, ivosidenib, pemigatinib, infigratinib, futibatinib) depending on the molecular alterations present. Resection is the most common surgical treatment for CCA, although liver transplantation is also an option in highly selected patients with liver-limited unresectable disease. Radiotherapy may also be a treatment option, as well as transarterial radioembolization (eg, yttrium-90), which is often utilized in combination with systemic therapy. Although patients with CCA have traditionally had a poor prognosis, recent advances in treatment, including new systemic therapies and increased utilization of liver transplantation, have improved expected survival. This article reviews screening modalities, pros and cons of diagnostic techniques, and therapies that are currently available to treat patients with CCA.
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Affiliation(s)
- Sudha Kodali
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, J. C. Walter Jr Transplant Center, Houston Methodist Hospital, Houston, Texas
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ashton A. Connor
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, J. C. Walter Jr Transplant Center, Houston Methodist Hospital, Houston, Texas
- Department of Surgery, Houston Methodist Hospital, Houston, Texas
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | | | - R. Mark Ghobrial
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, J. C. Walter Jr Transplant Center, Houston Methodist Hospital, Houston, Texas
- Department of Surgery, Houston Methodist Hospital, Houston, Texas
- Department of Surgery, Weill Cornell Medical College, New York, New York
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Adelman MW, Connor AA, Hsu E, Saharia A, Mobley CM, Victor DW, Hobeika MJ, Lin J, Grimes KA, Ramos E, Pedroza C, Brombosz EW, Ghobrial RM, Arias CA. Bloodstream infections after solid organ transplantation: clinical epidemiology and antimicrobial resistance (2016-21). JAC Antimicrob Resist 2024; 6:dlad158. [PMID: 38213312 PMCID: PMC10783261 DOI: 10.1093/jacamr/dlad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024] Open
Abstract
Background Solid organ transplant (SOT) recipients are at risk of bloodstream infections (BSIs) with MDR organisms (MDROs). Objectives To describe the epidemiology of BSI in the year after several types of SOT, as well as the prevalence of MDRO infections in this population. Methods We conducted a single-centre, retrospective study of kidney, liver, heart, and multi-organ transplantation patients. We examined BSIs ≤1 year from SOT and classified MDRO phenotypes for Staphylococcus aureus, enterococci, Enterobacterales, Pseudomonas aeruginosa and Candida spp. We compared BSI characteristics between SOT types and determined risk factors for 90 day mortality. Results We included 2293 patients [1251 (54.6%) kidney, 663 (28.9%) liver, 219 (9.6%) heart and 160 (7.0%) multi-organ transplant]. Overall, 8.5% of patients developed a BSI. BSIs were most common after multi-organ (23.1%) and liver (11.3%) transplantation (P < 0.001). Among 196 patients with BSI, 323 unique isolates were recovered, 147 (45.5%) of which were MDROs. MDROs were most common after liver transplant (53.4%). The most frequent MDROs were VRE (69.8% of enterococci) and ESBL-producing and carbapenem-resistant Enterobacterales (29.2% and 27.2% of Enterobacterales, respectively). Mortality after BSI was 9.7%; VRE was independently associated with mortality (adjusted OR 6.0, 95% CI 1.7-21.3). Conclusions BSI incidence after SOT was 8.5%, with a high proportion of MDROs (45.5%), especially after liver transplantation. These data, in conjunction with local antimicrobial resistance patterns and prescribing practices, may help guide empirical antimicrobial selection and stewardship practices after SOT.
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Affiliation(s)
- Max W Adelman
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, NewYork, NY, USA
| | - Ashton A Connor
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA
- J.C. Walter, Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - Enshuo Hsu
- Center for Health Data Science and Analytics, Houston Methodist Hospital, Houston, TX, USA
| | - Ashish Saharia
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA
- J.C. Walter, Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - Constance M Mobley
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA
- J.C. Walter, Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - David W Victor
- J.C. Walter, Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - Mark J Hobeika
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA
- J.C. Walter, Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - Jiejian Lin
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, NewYork, NY, USA
| | - Kevin A Grimes
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, NewYork, NY, USA
| | - Elizabeth Ramos
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - R Mark Ghobrial
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA
- J.C. Walter, Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - Cesar A Arias
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, NewYork, NY, USA
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Soliman N, Saharia A, Abdelrahim M, Connor AA. Molecular profiling in the management of hepatocellular carcinoma. Curr Opin Organ Transplant 2024; 29:10-22. [PMID: 38038621 DOI: 10.1097/mot.0000000000001124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to both summarize the current knowledge of hepatocellular carcinoma molecular biology and to suggest a framework in which to prospectively translate this knowledge into patient care. This is timely as recent guidelines recommend increased use of these technologies to advance personalized liver cancer care. RECENT FINDINGS The main themes covered here address germline and somatic genetic alterations recently discovered in hepatocellular carcinoma, largely owing to next generation sequencing technologies, and nascent efforts to translate these into contemporary practice. SUMMARY Early efforts of translating molecular profiling to hepatocellular carcinoma care demonstrate a growing number of potentially actionable alterations. Still lacking are a consensus on what biomarkers and technologies to adopt, at what scale and cost, and how to integrate them most effectively into care.
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Connor AA, Saharia A, Mobley CM, Hobeika MJ, Victor DW, Kodali S, Brombosz EW, Graviss EA, Nguyen DT, Moore LW, Gaber AO, Ghobrial RM. Modern Outcomes After Liver Retransplantation: A Single-center Experience. Transplantation 2023; 107:1513-1523. [PMID: 36706077 DOI: 10.1097/tp.0000000000004500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND The need for liver retransplantation (reLT) has increased proportionally with greater numbers of liver transplants (LTs) performed, use of marginal donors, degree of recipient preoperative liver dysfunction, and longer survival after LT. However, outcomes following reLT have been historically regarded as poor. METHODS To evaluate reLT in modern recipients, we retrospectively examined our single-center experience. Analysis included 1268 patients undergoing single LT and 68 patients undergoing reLT from January 2008 to December 2021. RESULTS Pre-LT mechanical ventilation, body mass index at LT, donor-recipient ABO incompatibility, early acute rejection, and length of hospitalization were associated with increased risk of needing reLT following index transplant. Overall and graft survival outcomes in the reLT cohort were equivalent to those after single LT. Mortality after reLT was associated with Kidney Donor Profile Index, national organ sharing at reLT, and LT donor death by anoxia and blood urea nitrogen levels. Survival after reLT was independent of the interval between initial LT and reLT, intraoperative packed red blood cell use, cold ischemia time, and preoperative mechanical ventilation, all previously linked to worse outcomes. CONCLUSIONS These data suggest that reLT is currently a safer option for patients with liver graft failure, with comparable outcomes to primary LT.
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Affiliation(s)
- Ashton A Connor
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
| | - Ashish Saharia
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Constance M Mobley
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Mark J Hobeika
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - David W Victor
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Sudha Kodali
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | | | - Edward A Graviss
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
| | - Duc T Nguyen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
| | - Linda W Moore
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - A Osama Gaber
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - R Mark Ghobrial
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Weill Cornell Medical College, New York, NY
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Connor AA, Huang HJ, Mobley CM, Graviss EA, Nguyen DT, Goodarzi A, Saharia A, Yau S, Hobeika MJ, Suarez EE, Moaddab M, Brombosz EW, Moore LW, Yi SG, Gaber AO, Ghobrial RM. Progress in Combined Liver-lung Transplantation at a Single Center. Transplant Direct 2023; 9:e1482. [PMID: 37096152 PMCID: PMC10121433 DOI: 10.1097/txd.0000000000001482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 04/26/2023] Open
Abstract
Combined liver-lung transplantation is an uncommon, although vital, procedure for patients with simultaneous end-stage lung and liver disease. The utility of lung-liver transplant has been questioned because of initial poor survival outcomes, particularly when compared with liver-alone transplant recipients. Methods A single-center, retrospective review of the medical records of 19 adult lung-liver transplant recipients was conducted, comparing early recipients (2009-2014) with a recent cohort (2015-2021). Patients were also compared with the center's single lung or liver transplant recipients. Results Recent lung-liver recipients were older (P = 0.004), had a higher body mass index (P = 0.03), and were less likely to have ascites (P = 0.02), reflecting changes in the etiologies of lung and liver disease. Liver cold ischemia time was longer in the modern cohort (P = 0.004), and patients had a longer posttransplant length of hospitalization (P = 0.048). Overall survival was not statistically different between the 2 eras studied (P = 0.61), although 1-y survival was higher in the more recent group (90.9% versus 62.5%). Overall survival after lung-liver transplant was equivalent to lung-alone recipients and was significantly lower than liver-alone recipients (5-y survival: 52%, 51%, and 75%, respectively). Lung-liver recipient mortality was primarily driven by deaths within 6 mo of transplant due to infection and sepsis. Graft failure was not significantly different (liver: P = 0.06; lung: P = 0.74). Conclusions The severity of illness in lung-liver recipients combined with the infrequency of the procedure supports its continued use. However, particular attention should be paid to patient selection, immunosuppression, and prophylaxis against infection to ensure proper utilization of scarce donor organs.
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Affiliation(s)
- Ashton A. Connor
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
| | - Howard J. Huang
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Constance M. Mobley
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Edward A. Graviss
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
| | - Duc T. Nguyen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
| | - Ahmad Goodarzi
- Department of Medicine, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Ashish Saharia
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Simon Yau
- Department of Medicine, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Mark J. Hobeika
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Erik E. Suarez
- Department of Medicine, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Mozhgon Moaddab
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX
| | | | - Linda W. Moore
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Stephanie G. Yi
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - A. Osama Gaber
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Rafik Mark Ghobrial
- JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX
- Department of Surgery, Houston Methodist Hospital, Houston, TX
- Department of Medicine, Weill Cornell Medical College, New York, NY
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Connor AA, Webster DR. Hydrodynamics of the fast-start caridoid escape response in Antarctic krill, Euphausia superba. Sci Rep 2023; 13:5376. [PMID: 37009788 PMCID: PMC10068603 DOI: 10.1038/s41598-023-31676-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2023] [Indexed: 04/04/2023] Open
Abstract
Krill are shrimp-like crustaceans with a high degree of mobility and variety of documented swimming behaviors. The caridoid escape response, a fast-start mechanism unique to crustaceans, occurs when the animal performs a series of rapid abdominal flexions and tail flipping that results in powerful backward strokes. The current results quantify the animal kinematics and three-dimensional flow field around a free-swimming Euphausia superba as it performs the caridoid escape maneuver. The specimen performs a single abdominal flexion-tail flip combination that leads to an acceleration over a 42 ms interval allowing it to reach a maximum speed of 57.0 cm/s (17.3 body lengths/s). The krill's tail flipping during the abdominal closure is a significant contributor to the thrust generation during the maneuver. The krill sheds a complex chain of vortex rings in its wake due to the viscous flow effects while the organism accelerates. The vortex ring structure reveals a strong suction flow in the wake, which suggests that the pressure distribution and form drag play a role in the force balance for this maneuver. Antarctic krill typically swim in a low to intermediate Reynolds number (Re) regime where viscous forces are significant, but as shown by this analysis, its high maneuverability allows it to quickly change its body angle and swimming speed.
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Affiliation(s)
- A A Connor
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0355, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0405, USA
| | - D R Webster
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0355, USA.
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Abboud K, Umoru G, Esmail A, Abudayyeh A, Murakami N, Al-Shamsi HO, Javle M, Saharia A, Connor AA, Kodali S, Ghobrial RM, Abdelrahim M. Immune Checkpoint Inhibitors for Solid Tumors in the Adjuvant Setting: Current Progress, Future Directions, and Role in Transplant Oncology. Cancers (Basel) 2023; 15:cancers15051433. [PMID: 36900226 PMCID: PMC10000896 DOI: 10.3390/cancers15051433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
The rationale for administering immune checkpoint inhibitors (ICIs) in the adjuvant setting is to eradicate micro-metastases and, ultimately, prolong survival. Thus far, clinical trials have demonstrated that 1-year adjuvant courses of ICIs reduce the risk of recurrence in melanoma, urothelial cancer, renal cell carcinoma, non-small cell lung cancer, and esophageal and gastroesophageal junction cancers. Overall survival benefit has been shown in melanoma while survival data are still not mature in other malignancies. Emerging data also show the feasibility of utilizing ICIs in the peri-transplant setting for hepatobiliary malignancies. While ICIs are generally well-tolerated, the development of chronic immune-related adverse events, typically endocrinopathies or neurotoxicities, as well as delayed immune-related adverse events, warrants further scrutiny regarding the optimal duration of adjuvant therapy and requires a thorough risk-benefit determination. The advent of blood-based, dynamic biomarkers such as circulating tumor DNA (ctDNA) can help detect minimal residual disease and identify the subset of patients who would likely benefit from adjuvant treatment. In addition, the characterization of tumor-infiltrating lymphocytes, neutrophil-to-lymphocyte ratio, and ctDNA-adjusted blood tumor mutation burden (bTMB) has also shown promise in predicting response to immunotherapy. Until additional, prospective studies delineate the magnitude of overall survival benefit and validate the use of predictive biomarkers, a tailored, patient-centered approach to adjuvant ICIs that includes extensive patient counseling on potentially irreversible adverse effects should be routinely incorporated into clinical practice.
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Affiliation(s)
- Karen Abboud
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Godsfavour Umoru
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Abdullah Esmail
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
- Correspondence: (A.E.); (M.A.)
| | - Ala Abudayyeh
- Section of Nephrology, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naoka Murakami
- Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Humaid O. Al-Shamsi
- Department of Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ashish Saharia
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Ashton A. Connor
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Sudha Kodali
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Rafik M. Ghobrial
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Maen Abdelrahim
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
- Cockrell Center of Advanced Therapeutics Phase I Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Internal Medicine, Weill Cornell Medical College, New York, NY 14853, USA
- Correspondence: (A.E.); (M.A.)
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, 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D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, 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Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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Connor AA, Kodali S, Abdelrahim M, Javle MM, Brombosz EW, Ghobrial RM. Intrahepatic cholangiocarcinoma: The role of liver transplantation, adjunctive treatments, and prognostic biomarkers. Front Oncol 2022; 12:996710. [PMID: 36479082 PMCID: PMC9719919 DOI: 10.3389/fonc.2022.996710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/31/2022] [Indexed: 08/01/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a primary epithelial cell malignancy of the liver with rising incidence rate globally. Its insidious presentation, heterogeneous and aggressive biology, and recalcitrance to current therapies results in unacceptably high morbidity and mortality. This has spurred research efforts in the last decade to better characterize it molecularly with translation to improved diagnostic tools and treatments. Much of this has been driven by patient advocacy. This has renewed interest in orthotopic liver transplantation (LT) with adjunctive therapies for iCCA, which was historically disparaged due to poor recipient outcomes and donor organ scarcity. However, the optimal use of LT as a treatment for iCCA care remains unclear. Here, we review the epidemiology of iCCA, the history of LT as a treatment modality, alternative approaches to iCCA local control, the evidence for peri-operative systemic therapies, and the potential roles of biomarkers and targeted agents. In doing so, we hope to prioritize areas for continued research and identify areas where multidisciplinary care can improve outcomes.
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Affiliation(s)
- Ashton A. Connor
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX, United States
- Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
| | - Sudha Kodali
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX, United States
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Maen Abdelrahim
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
- Section of Gastrointestinal Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX, United States
- Cockrell Center Phase 1 Unit, Cockrell Center for Advanced Therapeutics, Houston Methodist Hospital, Houston, TX, United States
| | - Milind M. Javle
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, United States
| | | | - R. Mark Ghobrial
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Transplant Center, Houston Methodist Hospital, Houston, TX, United States
- Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
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13
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Abstract
Pancreatic ductal adenocarcinoma (PDAC), already among the deadliest epithelial malignancies, is rising in both incidence and contribution to overall cancer deaths. Decades of research have improved our understanding of PDAC carcinogenesis, including characterizing germline predisposition, the cell of origin, precursor lesions, the sequence of genetic alterations, including simple and structural alterations, transcriptional changes and subtypes, tumour heterogeneity, metastatic progression and the tumour microenvironment. These fundamental advances inform contemporary translational efforts in primary prevention, screening and early detection, multidisciplinary management and survivorship, as prospective clinical trials begin to adopt molecular-based selection criteria to guide targeted therapies. Genomic and transcriptomic data on PDAC were also included in the international pan-cancer analysis of approximately 2,600 cancers, a milestone in cancer research that allows further insight through comparison with other tumour types. Thus, this is an ideal time to review our current knowledge of PDAC evolution and heterogeneity, gained from the study of preclinical models and patient biospecimens, and to propose a model of PDAC evolution that takes into consideration findings from varied sources, with a particular focus on the genomics of human PDAC.
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Affiliation(s)
- Ashton A Connor
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA
| | - Steven Gallinger
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada.
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada.
- Ontario Pancreas Cancer Study, Mount Sinai Hospital, Toronto, ON, Canada.
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14
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Mikhail A, Connor AA, Ahmed N. Impact of Research Training on Performance in General Surgery Residency. J Surg Educ 2022; 79:342-348. [PMID: 34824045 DOI: 10.1016/j.jsurg.2021.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/07/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION It is common for North American surgical trainees to interrupt clinical training to complete 2 or more years of research training. The impact of this practice on surgical aptitudes is unknown. The University of Toronto has large general surgery and surgeon scientist training programs. We compared the examination scores of general surgery residents in continuous clinical training with those of residents whose training was interrupted by research. METHODS We collected anonymized scores obtained at written and oral annual in-training examinations by general surgery residents at the University of Toronto from 2011 to 2016, inclusive. The written exam assessed knowledge, while the oral exam assessed judgment. Residents were dichotomized into continuous versus non-continuous clinical training streams. We compared performance prior to, during, and following divergence for research training both within and between the 2 groups. RESULTS At the junior resident level, future enrollment in research training was associated with higher examination performance (Pwritten = .003). Annual scores plateaued during research training, while scores of residents who continued in continuous clinical training improved year over year (Pwritten = .009). Non-continuous stream resident exam scores remained stagnant after 1 year then improved in the second year after return to clinical training (Pwritten = .00007). Scores obtained in the final year of residency training did not significantly differ between residents who underwent continuous versus non-continuous clinical training. Results from written and oral exams trended concordantly. CONCLUSIONS We demonstrate that interruption of clinical training for 2 or more years of research is associated with a stagnation of performance on annual in-training examinations assessing both knowledge and judgment. This phenomenon is followed by an eventual catching-up after at least 2 years return to full-time clinical training. This may inform residency program curriculum design.
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Affiliation(s)
| | - Ashton A Connor
- Department of Surgery, Houston Methodist Hospital, Houston, USA
| | - Najma Ahmed
- University of Toronto, Toronto, Ontario, Canada; St. Michael's Hospital, Toronto, Ontario, Canada.
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15
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Samoylova ML, Shaw BI, Irish W, McElroy LM, Connor AA, Barbas AS, Sanoff S, Ravindra KV. Decreased graft loss following implementation of the kidney allocation score (KAS). Am J Surg 2020; 220:1278-1283. [PMID: 32951852 DOI: 10.1016/j.amjsurg.2020.06.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/19/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND The Kidney Allocation System (KAS) was developed to improve equity and utility in organ allocation. We examine the effect of this change on kidney graft distribution and survival. METHODS UNOS data was used to identify first-time adult recipients of a deceased donor kidney-alone transplant pre-KAS (Jan 2012-Dec 2014, n = 26,612) and post-KAS (Jan 2015-Dec 2017, n = 30,701), as well as grafts recovered Jan 2012-Jun 2019. RESULTS Post-KAS, kidneys were more likely to experience cold ischemia time >24 h (20.0% vs. 18.8%, p < 0.001) and experienced more delayed graft function, though competing risks modeling demonstrated a lower hazard of graft loss post-KAS, HR 0.90 (95% CI 0.84-0.97, p = 0.007). Post-policy, KDPI >85% kidneys were more likely to be shared regionally (37% vs. 14%), and more likely to be discarded (60.6% vs. 54.9%) after the policy change. KDPI >85% graft and patient survival did not change. CONCLUSIONS Implementation of the KAS has increased sharing of high-KDPI kidneys and has decreased the hazard of graft loss without an impact on patient survival.
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Affiliation(s)
- Mariya L Samoylova
- Surgery, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
| | - Brian I Shaw
- Surgery, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
| | - William Irish
- School of Medicine, East Carolina University, Brody School of Medicine at East Carolina University, 600 Moye Boulevard, Greenville, NC, 27834, USA.
| | - Lisa M McElroy
- Surgery, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
| | - Ashton A Connor
- Surgery, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
| | - Andrew S Barbas
- Surgery, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
| | - Scott Sanoff
- Medicine, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
| | - Kadiyala V Ravindra
- Surgery, Duke University, 330 Trent Drive, DUMC 3512, Durham, NC, 27710, USA.
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16
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Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F. Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet 2020; 52:463. [PMID: 32051610 DOI: 10.1038/s41588-020-0588-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gavin W Wilson
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ashton A Connor
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert C Grant
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sheng-Ben Liang
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Sangeetha Kalimuthu
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul M Krzyzanowski
- Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vandana Sandhu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hervé Tiriac
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery, University of California San Diego, NCI-designated Comprehensive Cancer Center, La Jolla, CA, USA
| | - Fieke E M Froeling
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Runjan Chetty
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Bioinformatics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,The Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Fischer
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. .,Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. 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) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Dodd A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F. Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet 2020; 52:231-240. [PMID: 31932696 DOI: 10.1038/s41588-019-0566-9] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor tumor cellularity and extensive genomic instability. To address this, a dataset of whole genomes and transcriptomes was generated from purified epithelium of primary and metastatic tumors. Transcriptome analysis demonstrated that molecular subtypes are a product of a gene expression continuum driven by a mixture of intratumoral subpopulations, which was confirmed by single-cell analysis. Integrated whole-genome analysis uncovered that molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and GATA6. By mapping tumor genetic histories, tetraploidization emerged as a key mutational process behind these events. Taken together, these data support the premise that the constellation of genomic aberrations in the tumor gives rise to the molecular subtype, and that disease heterogeneity is due to ongoing genomic instability during progression.
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Affiliation(s)
- Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gavin W Wilson
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ashton A Connor
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert C Grant
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anna Dodd
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sheng-Ben Liang
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Sangeetha Kalimuthu
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul M Krzyzanowski
- Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vandana Sandhu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hervé Tiriac
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery, University of California San Diego, NCI-designated Comprehensive Cancer Center, La Jolla, CA, USA
| | - Fieke E M Froeling
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Runjan Chetty
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Bioinformatics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,The Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Fischer
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. .,Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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19
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Connor AA, Denroche RE, Jang GH, Lemire M, Zhang A, Chan-Seng-Yue M, Wilson G, Grant RC, Merico D, Lungu I, Bartlett JMS, Chadwick D, Liang SB, Eagles J, Mbabaali F, Miller JK, Krzyzanowski P, Armstrong H, Luo X, Jorgensen LGT, Romero JM, Bavi P, Fischer SE, Serra S, Hafezi-Bakhtiari S, Caglar D, Roehrl MHA, Cleary S, Hollingsworth MA, Petersen GM, Thayer S, Law CHL, Nanji S, Golan T, Smith AL, Borgida A, Dodd A, Hedley D, Wouters BG, O'Kane GM, Wilson JM, Zogopoulos G, Notta F, Knox JJ, Gallinger S. Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases. Cancer Cell 2019; 35:267-282.e7. [PMID: 30686769 PMCID: PMC6398439 DOI: 10.1016/j.ccell.2018.12.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/14/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022]
Abstract
We integrated clinical, genomic, and transcriptomic data from 224 primaries and 95 metastases from 289 patients to characterize progression of pancreatic ductal adenocarcinoma (PDAC). Driver gene alterations and mutational and expression-based signatures were preserved, with truncations, inversions, and translocations most conserved. Cell cycle progression (CCP) increased with sequential inactivation of tumor suppressors, yet remained higher in metastases, perhaps driven by cell cycle regulatory gene variants. Half of the cases were hypoxic by expression markers, overlapping with molecular subtypes. Paired tumor heterogeneity showed cancer cell migration by Halstedian progression. Multiple PDACs arising synchronously and metachronously in the same pancreas were actually intra-parenchymal metastases, not independent primary tumors. Established clinical co-variates dominated survival analyses, although CCP and hypoxia may inform clinical practice.
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Affiliation(s)
- Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Michelle Chan-Seng-Yue
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Gavin Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Robert C Grant
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Daniele Merico
- Deep Genomics, Inc., Toronto, ON M5G 1L7, Canada; The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ilinca Lungu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Dianne Chadwick
- UHN Biobank, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Sheng-Ben Liang
- UHN Biobank, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Jenna Eagles
- Genomics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Faridah Mbabaali
- Genomics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Jessica K Miller
- Genomics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Paul Krzyzanowski
- Genomics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Heather Armstrong
- Genome Sequence Informatics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Xuemei Luo
- Genome Sequence Informatics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Lars G T Jorgensen
- Genome Sequence Informatics, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Joan M Romero
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Prashant Bavi
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Sandra E Fischer
- Department of Pathology, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Stefano Serra
- Department of Pathology, University Health Network, Toronto, ON M5G 2M9, Canada
| | | | - Derin Caglar
- Department of Pathology, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michael H A Roehrl
- UHN Biobank, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Pathology, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Department of Pathology, Memorial Sloan Kettering Cancer Centre, New York, NY 10065, USA
| | - Sean Cleary
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Sarah Thayer
- University of Nebraska Medical Centre, Omaha, NE 68198, USA; Massachusetts General Hospital, Boston, MA 02114, USA
| | - Calvin H L Law
- Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Sulaiman Nanji
- Department of Surgery, Kingston General Hospital, Kingston, ON K7L 2V7, Canada
| | - Talia Golan
- Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alyssa L Smith
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Ayelet Borgida
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Anna Dodd
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - David Hedley
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Bradly G Wouters
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Goodman Cancer Research Centre, Montreal, QC H3A 1A3, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON M5G 2M9, Canada; Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
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20
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Smith AL, Wong C, Cuggia A, Borgida A, Holter S, Hall A, Connor AA, Bascuñana C, Asselah J, Bouganim N, Poulin V, Jolivet J, Vafiadis P, Le P, Martel G, Lemay F, Beaudoin A, Rafatzand K, Chaudhury P, Barkun J, Metrakos P, Marcus V, Omeroglu A, Chong G, Akbari MR, Foulkes WD, Gallinger S, Zogopoulos G. Reflex Testing for Germline BRCA1, BRCA2, PALB2, and ATM Mutations in Pancreatic Cancer: Mutation Prevalence and Clinical Outcomes From Two Canadian Research Registries. JCO Precis Oncol 2018; 2:1-16. [DOI: 10.1200/po.17.00098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose We investigated the translational value of reflex testing for germline mutations in four homology-directed DNA repair predisposition genes ( BRCA1, BRCA2, PALB2, and ATM) in consecutive patients with pancreatic adenocarcinoma. Methods One hundred fifty patients with French-Canadian (FC) ancestry were evaluated for founder mutations, and 114 patients were subsequently assessed by full gene sequencing and multiplex ligation-dependent probe amplification for nonfounder mutations. Two hundred thirty-six patients unselected for ancestry were also assessed for mutations by full gene sequencing. Results The FC founder mutation prevalence among the 150 patients was 5.3% (95% CI, 2.6% to 10.3%), and the nonfounder mutation prevalence across the four genes among the 114 patients tested was 2.6% (95% CI, 0.6% to 7.8%). In the case series unselected for ancestry, 10.0% (95% CI, 2.7% to 26.4%) of patients reporting Ashkenazi Jewish (AJ) ancestry carried an AJ founder mutation, with no nonfounder mutations identified. The mutation prevalence among patients without FC/AJ ancestry was 4.9% (95% CI, 2.6% to 8.8%). Mutations were more frequent in patients diagnosed at ≤ 50 years of age ( P = .03) and in patients with either two or more first- or second-degree relatives with pancreas, breast, ovarian or prostate cancer, or one such relative and a second primary of one of these cancer types ( P < .001). BRCA1, BRCA2, and PALB2 carriers with late-stage (III or IV) disease had an overall survival advantage ( P = .049), particularly if treated with platinum-based chemotherapies ( P = .030). Conclusion Considering these results, we recommend reflex founder mutation testing of patients with FC/AJ ancestry and full gene sequencing of patients who are ≤ 50 years or meet the identified family history criteria. Reflex testing of all incident patients for these four genes may become justified as full gene sequencing costs decline.
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Affiliation(s)
- Alyssa L. Smith
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Cavin Wong
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Adeline Cuggia
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Ayelet Borgida
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Spring Holter
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Anita Hall
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Ashton A. Connor
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Claire Bascuñana
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Jamil Asselah
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Nathaniel Bouganim
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Véronique Poulin
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Jacques Jolivet
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Petro Vafiadis
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Philippe Le
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Guillaume Martel
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Frédéric Lemay
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Annie Beaudoin
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Khashayar Rafatzand
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Prosanto Chaudhury
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Jeffrey Barkun
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Peter Metrakos
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Victoria Marcus
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Atilla Omeroglu
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - George Chong
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Mohammad R. Akbari
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - William D. Foulkes
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - Steven Gallinger
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
| | - George Zogopoulos
- Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, and George Zogopoulos, Goodman Cancer Research Centre, McGill University; Alyssa L. Smith, Cavin Wong, Adeline Cuggia, Anita Hall, Claire Bascuñana, Peter Metrakos, William D. Foulkes, and George Zogopoulos, Research Institute of the McGill University Health Centre; Jamil Asselah, Nathaniel Bouganim, Khashayar Rafatzand, Prosanto Chaudhury, Jeffrey Barkun, Peter Metrakos, Victoria Marcus, Atilla Omeroglu, William D. Foulkes, and
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Hopkins JF, Denroche RE, Aguiar JA, Notta F, Connor AA, Wilson JM, Stein LD, Gallinger S, Boutros PC. Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress. Gastroenterology 2018; 154:1620-1624.e5. [PMID: 29378198 DOI: 10.1053/j.gastro.2018.01.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/27/2017] [Accepted: 01/07/2018] [Indexed: 01/17/2023]
Abstract
Somatic mutations have been found in the mitochondria in different types of cancer cells, but it is not clear whether these affect tumorigenesis or tumor progression. We analyzed mitochondrial genomes of 268 early-stage, resected pancreatic ductal adenocarcinoma tissues and paired non-tumor tissues. We defined a mitochondrial somatic mutation (mtSNV) as a position where the difference in heteroplasmy fraction between tumor and normal sample was ≥0.2. Our analysis identified 304 mtSNVs, with at least 1 mtSNV in 61% (164 of 268) of tumor samples. The noncoding control region had the greatest proportion of mtSNVs (60 of 304 mutations); this region contains sites that regulate mitochondrial DNA transcription and replication. Frequently mutated genes included ND5, RNR2, and CO1, plus 29 mutations in transfer RNA genes. mtSNVs in 2 separate mitochondrial genes (ND4 and ND6) were associated with shorter overall survival time. This association appeared to depend on the level of mtSNV heteroplasmy. Non-random co-occurrence between mtSNVs and mutations in nuclear genes indicates interactions between nuclear and mitochondrial DNA. In an analysis of primary tumors and metastases from 6 patients, we found tumors to accumulate mitochondrial mutational mutations as they progress.
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Affiliation(s)
- Julia F Hopkins
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Robert E Denroche
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jennifer A Aguiar
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.
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22
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Grant RC, Denroche RE, Borgida A, Virtanen C, Cook N, Smith AL, Connor AA, Wilson JM, Peterson G, Roberts NJ, Klein AP, Grimmond SM, Biankin A, Cleary S, Moore M, Lemire M, Zogopoulos G, Stein L, Gallinger S. Exome-Wide Association Study of Pancreatic Cancer Risk. Gastroenterology 2018; 154:719-722.e3. [PMID: 29074453 PMCID: PMC5811358 DOI: 10.1053/j.gastro.2017.10.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
We conducted a case-control exome-wide association study to discover germline variants in coding regions that affect risk for pancreatic cancer, combining data from 5 studies. We analyzed exome and genome sequencing data from 437 patients with pancreatic cancer (cases) and 1922 individuals not known to have cancer (controls). In the primary analysis, BRCA2 had the strongest enrichment for rare inactivating variants (17/437 cases vs 3/1922 controls) (P = 3.27x10-6; exome-wide statistical significance threshold P < 2.5x10-6). Cases had more rare inactivating variants in DNA repair genes than controls, even after excluding 13 genes known to predispose to pancreatic cancer (adjusted odds ratio, 1.35; P = .045). At the suggestive threshold (P < .001), 6 genes were enriched for rare damaging variants (UHMK1, AP1G2, DNTA, CHST6, FGFR3, and EPHA1) and 7 genes had associations with pancreatic cancer risk, based on the sequence-kernel association test. We confirmed variants in BRCA2 as the most common high-penetrant genetic factor associated with pancreatic cancer and we also identified candidate pancreatic cancer genes. Large collaborations and novel approaches are needed to overcome the genetic heterogeneity of pancreatic cancer predisposition.
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Affiliation(s)
| | | | | | | | - Natalie Cook
- Princess Margaret Genomics Centre, Toronto, Canada
| | - Alyssa L Smith
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | | | | | - Gloria Peterson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Nicholas J Roberts
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Alison P Klein
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Australia
| | - Andrew Biankin
- Wohl Cancer Research Centre, Institute of, Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, Australia
| | - Sean Cleary
- Ontario Institute for Cancer Research, Toronto, Canada; Ontario Pancreas Cancer Study, Toronto, Canada
| | | | | | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Canada; Ontario Pancreas Cancer Study, Toronto, Canada.
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23
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Aung KL, Fischer SE, Denroche RE, Jang GH, Dodd A, Creighton S, Southwood B, Liang SB, Chadwick D, Zhang A, O'Kane GM, Albaba H, Moura S, Grant RC, Miller JK, Mbabaali F, Pasternack D, Lungu IM, Bartlett JMS, Ghai S, Lemire M, Holter S, Connor AA, Moffitt RA, Yeh JJ, Timms L, Krzyzanowski PM, Dhani N, Hedley D, Notta F, Wilson JM, Moore MJ, Gallinger S, Knox JJ. Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial. Clin Cancer Res 2017; 24:1344-1354. [PMID: 29288237 DOI: 10.1158/1078-0432.ccr-17-2994] [Citation(s) in RCA: 341] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/04/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022]
Abstract
Purpose: To perform real-time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for better treatment selection.Experimental Design: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image-guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases. Primary endpoint was feasibility to report WGS results prior to first disease assessment CT scan at 8 weeks. The main secondary endpoint was discovery of patient subsets with predictive mutational and transcriptional signatures.Results: Sixty-three patients underwent a tumor biopsy between December 2015 and June 2017. WGS and RNASeq were successful in 62 (98%) and 60 (95%), respectively. Genomic results were reported at a median of 35 days (range, 19-52 days) from biopsy, meeting the primary feasibility endpoint. Objective responses to first-line chemotherapy were significantly better in patients with the classical PDAC RNA subtype compared with those with the basal-like subtype (P = 0.004). The best progression-free survival was observed in those with classical subtype treated with m-FOLFIRINOX. GATA6 expression in tumor measured by RNA in situ hybridization was found to be a robust surrogate biomarker for differentiating classical and basal-like PDAC subtypes. Potentially actionable genetic alterations were found in 30% of patients.Conclusions: Prospective genomic profiling of advanced PDAC is feasible, and our early data indicate that chemotherapy response differs among patients with different genomic/transcriptomic subtypes. Clin Cancer Res; 24(6); 1344-54. ©2017 AACR.
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Affiliation(s)
- Kyaw L Aung
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Fischer
- Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun-Ho Jang
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anna Dodd
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sean Creighton
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Bernadette Southwood
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sheng-Ben Liang
- UHN Biobank, University Health Network, Toronto, Ontario, Canada
| | - Dianne Chadwick
- UHN Biobank, University Health Network, Toronto, Ontario, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Hamzeh Albaba
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Shari Moura
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Robert C Grant
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jessica K Miller
- Genomics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faridah Mbabaali
- Genomics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Ilinca M Lungu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sangeet Ghai
- Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Richard A Moffitt
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Jen Jen Yeh
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Surgery, University of North Carolina, Chapel Hill, North Carolina
| | - Lee Timms
- Genomics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Neesha Dhani
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - David Hedley
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada
| | - Malcolm J Moore
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven Gallinger
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Jennifer J Knox
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.
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24
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O’Kane GM, Connor AA, Gallinger S. Characterization, Detection, and Treatment Approaches for Homologous Recombination Deficiency in Cancer. Trends Mol Med 2017; 23:1121-1137. [DOI: 10.1016/j.molmed.2017.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
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Abstract
Pancreatic ductal adenocarcinoma (PDAC) has the highest mortality rate of all epithelial malignancies and a paradoxically rising incidence rate. Clinical translation of next generation sequencing (NGS) of tumour and germline samples may ameliorate outcomes by identifying prognostic and predictive genomic and transcriptomic features in appreciable fractions of patients, facilitating enrolment in biomarker-matched trials. Areas covered: The literature on precision oncology is reviewed. It is found that outcomes may be improved across various malignancies, and it is suggested that current issues of adequate tissue acquisition, turnaround times, analytic expertise and clinical trial accessibility may lessen as experience accrues. Also reviewed are PDAC genomic and transcriptomic NGS studies, emphasizing discoveries of promising biomarkers, though these require validation, and the fraction of patients that will benefit from these outside of the research setting is currently unknown. Expert commentary: Clinical use of NGS with PDAC should be used in investigational contexts in centers with multidisciplinary expertise in cancer sequencing and pancreatic cancer management. Biomarker directed studies will improve our understanding of actionable genomic variation in PDAC, and improve outcomes for this challenging disease.
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Affiliation(s)
- Ashton A Connor
- a PanCuRx Translational Research Initiative , Ontario Institute for Cancer Research , Toronto , Ontario , Canada.,b Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , Ontario , Canada.,c Hepatobiliary/Pancreatic Surgical Oncology Program , University Health Network , Toronto , Ontario , Canada
| | - Steven Gallinger
- a PanCuRx Translational Research Initiative , Ontario Institute for Cancer Research , Toronto , Ontario , Canada.,b Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , Ontario , Canada.,c Hepatobiliary/Pancreatic Surgical Oncology Program , University Health Network , Toronto , Ontario , Canada
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26
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Connor AA, Denroche RE, Jang GH, Timms L, Kalimuthu SN, Selander I, McPherson T, Wilson GW, Chan-Seng-Yue MA, Borozan I, Ferretti V, Grant RC, Lungu IM, Costello E, Greenhalf W, Palmer D, Ghaneh P, Neoptolemos JP, Buchler M, Petersen G, Thayer S, Hollingsworth MA, Sherker A, Durocher D, Dhani N, Hedley D, Serra S, Pollett A, Roehrl MHA, Bavi P, Bartlett JMS, Cleary S, Wilson JM, Alexandrov LB, Moore M, Wouters BG, McPherson JD, Notta F, Stein LD, Gallinger S. Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma. JAMA Oncol 2017; 3:774-783. [PMID: 27768182 PMCID: PMC5824324 DOI: 10.1001/jamaoncol.2016.3916] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/18/2016] [Indexed: 12/20/2022]
Abstract
IMPORTANCE Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease. OBJECTIVE To classify PDAC according to distinct mutational processes, and explore their clinical significance. DESIGN, SETTING, AND PARTICIPANTS We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium. The discovery cohort comprised 160 PDAC cases from 154 patients (148 primary; 12 metastases) that underwent tumor enrichment prior to whole-genome and RNA sequencing. The replication cohort comprised 95 primary PDAC cases that underwent whole-genome sequencing and expression microarray on bulk biospecimens. MAIN OUTCOMES AND MEASURES Somatic mutations accumulate from sequence-specific processes creating signatures detectable by DNA sequencing. Using nonnegative matrix factorization, we measured the contribution of each signature to carcinogenesis, and used hierarchical clustering to subtype each cohort. We examined expression of antitumor immunity genes across subtypes to uncover biomarkers predictive of response to systemic therapies. RESULTS The discovery cohort was 53% male (n = 79) and had a median age of 67 (interquartile range, 58-74) years. The replication cohort was 50% male (n = 48) and had a median age of 68 (interquartile range, 60-75) years. Five predominant mutational subtypes were identified that clustered PDAC into 4 major subtypes: age related, double-strand break repair, mismatch repair, and 1 with unknown etiology (signature 8). These were replicated and validated. Signatures were faithfully propagated from primaries to matched metastases, implying their stability during carcinogenesis. Twelve of 27 (45%) double-strand break repair cases lacked germline or somatic events in canonical homologous recombination genes-BRCA1, BRCA2, or PALB2. Double-strand break repair and mismatch repair subtypes were associated with increased expression of antitumor immunity, including activation of CD8-positive T lymphocytes (GZMA and PRF1) and overexpression of regulatory molecules (cytotoxic T-lymphocyte antigen 4, programmed cell death 1, and indolamine 2,3-dioxygenase 1), corresponding to higher frequency of somatic mutations and tumor-specific neoantigens. CONCLUSIONS AND RELEVANCE Signature-based subtyping may guide personalized therapy of PDAC in the context of biomarker-driven prospective trials.
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Affiliation(s)
- Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada2Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada3Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada4Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada4Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada5Department of Statistical Science, University of Toronto, Toronto, Ontario, Canada
| | - Lee Timms
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada6Genome Technologies Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sangeetha N Kalimuthu
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Iris Selander
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Treasa McPherson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gavin W Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada4Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michelle A Chan-Seng-Yue
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ivan Borozan
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vincent Ferretti
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert C Grant
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada2Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ilinca M Lungu
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | - Sarah Thayer
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Alana Sherker
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada13Molecular Genetics Department, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada13Molecular Genetics Department, University of Toronto, Toronto, Ontario, Canada
| | - Neesha Dhani
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David Hedley
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Stefano Serra
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Aaron Pollett
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada15Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Michael H A Roehrl
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada15Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada16Department of Pathology, University Health Network, Toronto, Ontario, Canada17Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada18BioSpecimen Sciences Program, University Health Network, Toronto, Ontario, Canada
| | - Prashant Bavi
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sean Cleary
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada3Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico20Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Malcolm Moore
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Bradly G Wouters
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - John D McPherson
- Genome Technologies Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada17Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada13Molecular Genetics Department, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada2Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada3Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
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27
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Oldfield LE, Connor AA, Gallinger S. Molecular Events in the Natural History of Pancreatic Cancer. Trends Cancer 2017; 3:336-346. [PMID: 28718411 DOI: 10.1016/j.trecan.2017.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 12/12/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest epithelial malignancies. Improvements in our understanding of PDAC carcinogenesis will hopefully improve its detection, management, and outcomes, as has been achieved with other malignancies. Here we review the literature on the natural history of PDAC, including its cell of origin, the initiating somatic mutational events, pathways deranged in the mature tumor, its biological heterogeneity, and the relationship of the primary tumor with metastases. We also suggest areas for further research and highlight translatable findings that are beginning to make clinical inroads.
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Affiliation(s)
- Leslie E Oldfield
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Canada.
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28
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Connor AA, Lerner-Ellis J, Akbari MR, Cybulski C, Lubinski J, Badouel C, McNeill H, Dowty JG, Clendenning M, Buchanan DD. Abstract A23: Rare variants in the FAT1 gene may predispose to familial colorectal cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.crc16-a23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Population- and family-based studies suggest germline predisposition in up to 35% of colorectal cancer (CRC) cases. Known genetic factors, including three highly penetrant Mendelian cancer syndromes and approximately 45 low penetrant alleles, account for less than 15% of all CRC and only a small proportion of early onset CRC. Identifying the genes responsible for the “missing” CRC predisposition will inform prevention and management.
Methods: Our discovery cohort were selected to enrich for likely heritable susceptibility and consisted of 127 CRC cases from 86 pedigrees selected from Canadian and Australian CRC Family Registries (CCFRs) that met the Familial Colorectal Cancer Type X definition (satisfy Amsterdam I Criteria and lack other features of known cancer syndromes). Germline DNA from multiple CRC–affected individuals per pedigree underwent whole exome sequencing. The two replication cohorts were composed of pedigrees with multiple generations affected by CRC, one an Australian cohort of 166 families from which multiple affected and unaffected members were genotyped for rare (<0.01 MAF) germline likely deleterious variants in FAT1, the other a Polish cohort of 496 probands that underwent targeted next generation sequencing of FAT1. Alignment and variant calling followed the Genome Analysis Tool Kit “best practices”, and ANNOVAR was used for functional effect, allele frequency and intolerance score annotations. Variant filtering and statistical analysis were done in R (version 3.0). A hemizygous transgenic mouse model of our top genetic candidate was developed and exposed to intra-peritoneal azoxymethane (AOM) to induce colonic dysplasia. Necropsies were performed at 6 months of age, and the colons underwent gross and histologic inspection. This work was supported by grant UM1 CA167551 from the National Cancer Institute (NCI) to the Colon Cancer Family Registry.
Outcomes: Using filter-based approaches in our discovery cohort, we identified rare, non-silent variants in FAT1 that co-segregated with CRC in Ontario (Canadian), Newfoundland (Canadian) and Australian pedigrees, including one stopgain variant that was found in all 4 affected of one Ontario pedigree and in 2 of 6 unaffected. Somatic loss of heterozygosity of FAT1 was seen in available FFPE tumors from 3 Ontario and 4 Australian pedigrees by either Sanger sequencing or microarray. Modified segregation analysis of genotyped multi-case families from the Australian CCFR demonstrated an overall increased risk for CRC in FAT1 carriers (HR 1.44, 95%CI 1.05-1.97), with greater hazard ratios (>2.5) for individual FAT1 variants identified in sufficient numbers of families. Deep sequencing in 496 Polish probands identified 4 additional rare truncating FAT1 variants. Using the ExAC database as controls, variant-level association analyses of the Polish cohort cases revealed two strongly predisposing FAT1 rare missense variants, namely c.T9440G (OR 7.53, 95%CI 4.1-12.8, Fisher's exact test, q < 0.05 by false discovery rates) and c.G3067A (OR 10.8, 95%CI 3.3-26.8, q < 0.05). Gene-level association testing was also significant for increased CRC risk when considering all rare, non-silent FAT1 variants (OR 2.2, 95%CI 1.8-2.6, q < 0.05). 30 FAT1 hemizygous and 28 wild type mice on a CD1 background, balanced for sex and weight, did not show differences in number or greatest size of aberrant crypts, adenoma or adenocarcinoma.
Conclusions: We have shown that rare germline variants in FAT1 may predispose to CRC. Discovery of such causal genes and associated pathways will improve our understanding of early onset CRC for both familial and sporadic cases. Stratifying CRC risk by familial susceptibility genes should foster tailored, cost-effective primary and secondary prevention strategies.
Citation Format: Ashton A. Connor, Jordan Lerner-Ellis, Mohammad R. Akbari, Cezary Cybulski, J Lubinski, Caroline Badouel, Helen McNeill, James G. Dowty, Mark Clendenning, Daniel D. Buchanan. Rare variants in the FAT1 gene may predispose to familial colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A23.
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Affiliation(s)
| | | | | | - Cezary Cybulski
- 2Pomeranian Medical University, Szczecin, West Pomeranian, Poland,
| | - J Lubinski
- 2Pomeranian Medical University, Szczecin, West Pomeranian, Poland,
| | | | | | - James G. Dowty
- 3University of Melbourne, Melbourne, Victoria, Australia
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Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AMK, Kim JC, Wang T, Simpson JT, Beck T, Borgida A, Buchner N, Chadwick D, Hafezi-Bakhtiari S, Dick JE, Heisler L, Hollingsworth MA, Ibrahimov E, Jang GH, Johns J, Jorgensen LGT, Law C, Ludkovski O, Lungu I, Ng K, Pasternack D, Petersen GM, Shlush LI, Timms L, Tsao MS, Wilson JM, Yung CK, Zogopoulos G, Bartlett JMS, Alexandrov LB, Real FX, Cleary SP, Roehrl MH, McPherson JD, Stein LD, Hudson TJ, Campbell PJ, Gallinger S. Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature 2016; 542:124. [PMID: 27851734 DOI: 10.1038/nature20164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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30
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Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AMK, Kim JC, Wang T, Simpson JT, Beck T, Borgida A, Buchner N, Chadwick D, Hafezi-Bakhtiari S, Dick JE, Heisler L, Hollingsworth MA, Ibrahimov E, Jang GH, Johns J, Jorgensen LGT, Law C, Ludkovski O, Lungu I, Ng K, Pasternack D, Petersen GM, Shlush LI, Timms L, Tsao MS, Wilson JM, Yung CK, Zogopoulos G, Bartlett JMS, Alexandrov LB, Real FX, Cleary SP, Roehrl MH, McPherson JD, Stein LD, Hudson TJ, Campbell PJ, Gallinger S. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature 2016; 538:378-382. [PMID: 27732578 DOI: 10.1038/nature19823] [Citation(s) in RCA: 355] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 09/02/2016] [Indexed: 12/11/2022]
Abstract
Pancreatic cancer, a highly aggressive tumour type with uniformly poor prognosis, exemplifies the classically held view of stepwise cancer development. The current model of tumorigenesis, based on analyses of precursor lesions, termed pancreatic intraepithelial neoplasm (PanINs) lesions, makes two predictions: first, that pancreatic cancer develops through a particular sequence of genetic alterations (KRAS, followed by CDKN2A, then TP53 and SMAD4); and second, that the evolutionary trajectory of pancreatic cancer progression is gradual because each alteration is acquired independently. A shortcoming of this model is that clonally expanded precursor lesions do not always belong to the tumour lineage, indicating that the evolutionary trajectory of the tumour lineage and precursor lesions can be divergent. This prevailing model of tumorigenesis has contributed to the clinical notion that pancreatic cancer evolves slowly and presents at a late stage. However, the propensity for this disease to rapidly metastasize and the inability to improve patient outcomes, despite efforts aimed at early detection, suggest that pancreatic cancer progression is not gradual. Here, using newly developed informatics tools, we tracked changes in DNA copy number and their associated rearrangements in tumour-enriched genomes and found that pancreatic cancer tumorigenesis is neither gradual nor follows the accepted mutation order. Two-thirds of tumours harbour complex rearrangement patterns associated with mitotic errors, consistent with punctuated equilibrium as the principal evolutionary trajectory. In a subset of cases, the consequence of such errors is the simultaneous, rather than sequential, knockout of canonical preneoplastic genetic drivers that are likely to set-off invasive cancer growth. These findings challenge the current progression model of pancreatic cancer and provide insights into the mutational processes that give rise to these aggressive tumours.
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Affiliation(s)
- Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Gavin W Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ashton A Connor
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Robert E Denroche
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Sheng-Ben Liang
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Andrew M K Brown
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Jaeseung C Kim
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Tao Wang
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Timothy Beck
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ayelet Borgida
- Eppley Institute for Research in Cancer, Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Nicholas Buchner
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Sara Hafezi-Bakhtiari
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - John E Dick
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Lawrence Heisler
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer, Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Emin Ibrahimov
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Jeremy Johns
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Calvin Law
- Division of Surgical Oncology, Sunnybrook Health Sciences Centre, Odette Cancer Centre, Toronto, Ontario M4N 3M5, Canada
| | - Olga Ludkovski
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Ilinca Lungu
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karen Ng
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Liran I Shlush
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ming-Sound Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Christina K Yung
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Québec, Canada, H3H 2L9
| | - John M S Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6) and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, 87545
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sean P Cleary
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Surgery, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Michael H Roehrl
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada.,Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - John D McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Surgery, University Health Network, Toronto, Ontario M5G 2C4, Canada
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Wang M, Aldubayan S, Connor AA, Wong B, Mcnamara K, Khan T, Semotiuk K, Khalouei S, Holter S, Aronson M, Cohen Z, Gallinger S, Charames G, Pollett A, Lerner-Ellis J. Genetic testing for Lynch syndrome in the province of Ontario. Cancer 2016; 122:1672-9. [PMID: 27019099 DOI: 10.1002/cncr.29950] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/10/2015] [Accepted: 01/07/2016] [Indexed: 01/13/2023]
Abstract
BACKGROUND In November 2001, genetic testing for Lynch syndrome (LS) was introduced by the Ministry of Health and Long-Term Care (MOH) in Ontario for individuals at high risk for LS cancers according to either tumor immunohistochemistry staining or their family history. This article describes the outcomes of the program and makes recommendations for improving it and informing other public health care programs. METHODS Subjects were referred for molecular testing of the mismatch repair (MMR) genes MutL homolog 1, MutS homolog 2, and MutS homolog 6 if they met 1 of 7 MOH criteria. Testing was conducted from January 2001 to March 2015 at the Molecular Diagnostic Laboratory of Mount Sinai Hospital in Toronto. RESULTS A total of 1452 subjects were tested. Of the 662 subjects referred for testing because their tumor was immunodeficient for 1 or more of the MMR genes, 251 (37.9%) carried a germline mutation. In addition, 597 subjects were tested for a known family mutation, and 298 (49.9%) were positive; 189 of these 298 subjects (63.4%) were affected with cancer at the time of testing. An additional 193 subjects were referred because of a family history of LS, and 34 of these (17.6%) had a mutation identified. CONCLUSIONS These results indicate that the provincial criteria are useful in identifying LS carriers after an MMR-deficient tumor is identified. Placing greater emphasis on testing unaffected relatives in families with a known mutation may identify more unaffected carriers and facilitate primary prevention in those individuals. Cancer 2016;122:1672-9. © 2016 American Cancer Society.
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Affiliation(s)
- Marina Wang
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Saud Aldubayan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Ashton A Connor
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Beatrix Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Kate Mcnamara
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Tahsin Khan
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Kara Semotiuk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - Sam Khalouei
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - Melyssa Aronson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - Zane Cohen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - George Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Aaron Pollett
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
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Connor AA, McNamara K, Al-Sukhni E, Diskin J, Chan D, Ash C, Lowes LE, Allan AL, Zogopoulos G, Moulton CA, Gallinger S. Central, But Not Peripheral, Circulating Tumor Cells are Prognostic in Patients Undergoing Resection of Colorectal Cancer Liver Metastases. Ann Surg Oncol 2015; 23:2168-75. [PMID: 26714949 DOI: 10.1245/s10434-015-5038-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Colorectal cancer liver metastases (CRLMs) are potentially curable with resection, but most patients recur and succumb to their disease. Clinical covariates do not account for all outcomes. Circulating tumor cells (CTCs) are prognostic in the primary and metastatic settings of breast, prostate and colorectal cancer (CRC), and evolving evidence supports their role in CRLMs. Our objective was to determine whether CTCs in peripheral (PV) and hepatic venous (HV) compartments are associated with disease-free survival (DFS) and overall survival (OS) post-CRLM resection. METHODS CTCs were measured by CellSearch assay from intraoperative HV and PV samples from 63 patients who underwent CRLM resection from June 2007 to August 2012 at a single center. DFS and OS were primary endpoints. RESULTS HV CTCs > 3 were associated with shorter DFS and OS, but not PV CTCs, although no significant difference was found between CTC measurements in the two compartments. By univariate analysis, CRC stage and site, CRLM recurrence, and hepatic capsule invasion were also associated with OS, but only HV CTCs and CRC site were significant by multivariate Cox. Only HV CTCs were associated with DFS by multivariate analysis. Cases with elevated HV CTCs had hepatic vein invasion and lymph node metastases, and were younger with larger tumors. CONCLUSIONS Elevated HV CTCs are prognostic for DFS and OS following CRLM resection. Clinicopathologic features associated with HV CTCs are identifiable preoperatively and should be considered in CRLM surgical decision making. We found no evidence that PV CTCs are prognostic in this setting.
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Affiliation(s)
- Ashton A Connor
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada.,The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Kate McNamara
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Eisar Al-Sukhni
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Jacob Diskin
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - David Chan
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada
| | - Colleen Ash
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Lori E Lowes
- Departments of Oncology, and Anatomy and Cell Biology, Western University, London, ON, Canada.,London Regional Cancer Program, London Health Sciences Centre, London, ON, Canada
| | - Alison L Allan
- Departments of Oncology, and Anatomy and Cell Biology, Western University, London, ON, Canada.,London Regional Cancer Program, London Health Sciences Centre, London, ON, Canada
| | - George Zogopoulos
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Carol-Anne Moulton
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada
| | - Steven Gallinger
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada. .,The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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Connor AA, Chan-Seng-Yue M, Denroche RE, Borgida A, Liang SB, Notta F, Stein L, Roehrl MH, McPherson J, Gallinger S. Abstract A1-17: Genomic analysis of metachronous pancreatic ductal adenocarcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-a1-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Improving outcomes for pancreatic ductal adenocarcinoma (PDAC) requires more complete understanding of pancreatic carcinogenesis, including tumor heterogeneity and mutational evolution. Such studies in PDAC are hampered by presentation at advanced stages and rarely operable recurrences. We present a case of metachronous PDAC managed by serial resections and interrogated by whole genome sequencing of all three lesions.
Methods: Tumors underwent either laser capture microscopy or flow cytometry of fresh frozen tissue. Germline DNA was obtained from normal tissue. Genomic DNA was isolated, and sequencing libraries were prepared. Whole genome sequencing was performed on the Illumina HiSeq2500 system. Pipeline analysis included quality control, alignment to the reference genome (hg19), variant calling and annotation. Structural variants were called by the union of two tools, DELLY and CREST. Copy number variants were called using an in-house tool. Single nucleotide polymorphisms and short insertions and deletions were identified by the intersection of two tools, Strelka and MuTect, and annotated using ANNOVAR. All structural, copy number and non-silent variants were manually reviewed in the Integrated Genome Viewer. Secondary analyses were done in R. Representative sections of the three tumors also underwent formalin fixation, paraffin embedding, sectioning at five micron thickness and hematoxylin and eosin staining for microscopic analysis.
Results: The first tumor was located in the head of the pancreas and resected by Whipple operation, the second and third in the body and tail, respectively, and resected by completion pancreatectomy 14 months later. The patient received chemotherapy in the interim.
Histologically, all 3 tumors were moderately differentiated adenocarcinomas with focal mucinous areas and extensive lymphovascular and perineural invasion. There were no distinguishing morphological features.
For the 3 lesions, we achieved average sequence coverage of 52.3x, 54.3x, and 70.7x, respectively.
A total of 69 structural variants and 62 copy number variants were identified, with concordance of 75% and 92% in all three lesions.
A total of 61 non-silent exonic variants were identified, with concordance of 33% in all three lesions. A KRAS (NM_004985) c.G34C missense and TP53 (NM_001126115) c.G418A missense were present in all three, whereas a SMAD4 (NM_005359) c.118delC frameshift was present in only the second and third tumors.
Hierarchical clustering by non-silent variants, copy number variants, and an intersect of all variants showed the tumors in the head and tail to be more closely related to one another than to the body lesion, whereas clustering by structural variants showed little difference between the three.
Conclusions: The highly similar structural and copy number profiles across the three lesions suggests that these tumors arose from a common precursor, and that large chromosomal changes occurred early in its mutational evolution.
The poor concordance of simple somatic mutations imply that these evolved gradually and are responsible for tumor heterogeneity and possibly acquired phenotypes, include therapeutic resistance.
This study also demonstrates that isolated, intra-parenchymal metastases (as opposed to de novo tumors within a “field defect”) are possible with PDAC, which has been suggested in case reports but never definitively proven, further implying that these patients may benefit from re-operation despite disease relapse.
Further analysis will include mathematical modeling of mutation rates and validation in three additional metachronous cases identified in our biospecimen repository and in specimens obtained by our rapid autopsy program.
Citation Format: Ashton A. Connor, Michelle Chan-Seng-Yue, Robert E. Denroche, Ayelet Borgida, Sheng-Ben Liang, Faiyaz Notta, Lincoln Stein, Michael H. Roehrl, John McPherson, Steven Gallinger. Genomic analysis of metachronous pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-17.
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Affiliation(s)
| | | | | | | | | | - Faiyaz Notta
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Lincoln Stein
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - John McPherson
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
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Connor AA, Chan-Seng-Yue M, Denroche RE, Borgida A, Liang SB, Notta F, Stein L, Roehrl MH, McPherson J, Gallinger S. Abstract B2-57: Genomic analysis of metachronous pancreatic ductal adenocarcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Improving outcomes for pancreatic ductal adenocarcinoma (PDAC) requires more complete understanding of pancreatic carcinogenesis, including tumor heterogeneity and mutational evolution. Such studies in PDAC are hampered by presentation at advanced stages and rarely operable recurrences. We present a case of metachronous PDAC managed by serial resections and interrogated by whole genome sequencing of all three lesions.
Methods: Tumors underwent either laser capture microscopy or flow cytometry of fresh frozen tissue. Germline DNA was obtained from normal tissue. Genomic DNA was isolated, and sequencing libraries were prepared. Whole genome sequencing was performed on the Illumina HiSeq2500 system. Pipeline analysis included quality control, alignment to the reference genome (hg19), variant calling and annotation. Structural variants were called by the union of two tools, DELLY and CREST. Copy number variants were called using an in-house tool. Single nucleotide polymorphisms and short insertions and deletions were identified by the intersection of two tools, Strelka and MuTect, and annotated using ANNOVAR. All structural, copy number and non-silent variants were manually reviewed in the Integrated Genome Viewer. Secondary analyses were done in R. Representative sections of the three tumors also underwent formalin fixation, paraffin embedding, sectioning at five micron thickness and hematoxylin and eosin staining for microscopic analysis.
Results: The first tumor was located in the head of the pancreas and resected by Whipple operation, the second and third in the body and tail, respectively, and resected by completion pancreatectomy 14 months later. The patient received chemotherapy in the interim.
Histologically, all 3 tumors were moderately differentiated adenocarcinomas with focal mucinous areas and extensive lymphovascular and perineural invasion. There were no distinguishing morphological features.
For the 3 lesions, we achieved average sequence coverage of 52.3x, 54.3x, and 70.7x, respectively.
A total of 69 structural variants and 62 copy number variants were identified, with concordance of 75% and 92% in all three lesions.
A total of 61 non-silent exonic variants were identified, with concordance of 33% in all three lesions. A KRAS (NM_004985) c.G34C missense and TP53 (NM_001126115) c.G418A missense were present in all three, whereas a SMAD4 (NM_005359) c.118delC frameshift was present in only the second and third tumors.
Hierarchical clustering by non-silent variants, copy number variants, and an intersect of all variants showed the tumors in the head and tail to be more closely related to one another than to the body lesion, whereas clustering by structural variants showed little difference between the three.
Conclusions: The highly similar structural and copy number profiles across the three lesions suggests that these tumors arose from a common precursor, and that large chromosomal changes occurred early in its mutational evolution.
The poor concordance of simple somatic mutations imply that these evolved gradually and are responsible for tumor heterogeneity and possibly acquired phenotypes, include therapeutic resistance.
This study also demonstrates that isolated, intra-parenchymal metastases (as opposed to de novo tumors within a “field defect”) are possible with PDAC, which has been suggested in case reports but never definitively proven, further implying that these patients may benefit from re-operation despite disease relapse.
Further analysis will include mathematical modeling of mutation rates and validation in three additional metachronous cases identified in our biospecimen repository and in specimens obtained by our rapid autopsy program.
Citation Format: Ashton A. Connor, Michelle Chan-Seng-Yue, Robert E. Denroche, Ayelet Borgida, Sheng-Ben Liang, Faiyaz Notta, Lincoln Stein, Michael H. Roehrl, John McPherson, Steven Gallinger. Genomic analysis of metachronous pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-57.
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Affiliation(s)
| | | | | | | | | | - Faiyaz Notta
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Lincoln Stein
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - John McPherson
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
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Abstract
Despite decades of scientific and clinical research, pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy. The clinical and pathologic features of PDAC, specifically the known environmental and genetic risk factors, are reviewed here with special emphasis on the hereditary pancreatic cancer (HPC) syndromes. For these latter conditions, strategies are described for their identification, for primary and secondary prevention in unaffected carriers, and for disease management in affected carriers. Nascent steps have been made toward personalized medicine based on the rational use of screening, tumor subtyping, and targeted therapies; these have been guided by growing knowledge of HPC syndromes in PDAC.
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Affiliation(s)
- Ashton A Connor
- Division of General Surgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Division of General Surgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Grant RC, Selander I, Connor AA, Selvarajah S, Borgida A, Briollais L, Petersen GM, Lerner-Ellis J, Holter S, Gallinger S. Prevalence of germline mutations in cancer predisposition genes in patients with pancreatic cancer. Gastroenterology 2015; 148:556-64. [PMID: 25479140 PMCID: PMC4339623 DOI: 10.1053/j.gastro.2014.11.042] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/20/2014] [Accepted: 11/23/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS We investigated the prevalence of germline mutations in APC, ATM, BRCA1, BRCA2, CDKN2A, MLH1, MSH2, MSH6, PALB2, PMS2, PRSS1, STK11, and TP53 in patients with pancreatic cancer. METHODS The Ontario Pancreas Cancer Study enrolls consenting participants with pancreatic cancer from a province-wide electronic pathology database; 708 probands were enrolled from April 2003 through August 2012. To improve the precision of BRCA2 prevalence estimates, 290 probands were selected from 3 strata, based on family history of breast and/or ovarian cancer, pancreatic cancer, or neither. Germline DNA was analyzed by next-generation sequencing using a custom multiple-gene panel. Mutation prevalence estimates were calculated from the sample for the entire cohort. RESULTS Eleven pathogenic mutations were identified: 3 in ATM, 1 in BRCA1, 2 in BRCA2, 1 in MLH1, 2 in MSH2, 1 in MSH6, and 1 in TP53. The prevalence of mutations in all 13 genes was 3.8% (95% confidence interval, 2.1%-5.6%). Carrier status was associated significantly with breast cancer in the proband or first-degree relative (P < .01), and with colorectal cancer in the proband or first-degree relative (P < .01), but not family history of pancreatic cancer, age at diagnosis, or stage at diagnosis. Of patients with a personal or family history of breast and colorectal cancer, 10.7% (95% confidence interval, 4.4%-17.0%) and 11.1% (95% confidence interval, 3.0%-19.1%) carried pathogenic mutations, respectively. CONCLUSIONS A small but clinically important proportion of pancreatic cancer is associated with mutations in known predisposition genes. The heterogeneity of mutations identified in this study shows the value of using a multiple-gene panel in pancreatic cancer.
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Affiliation(s)
- Robert C Grant
- Ontario Institute for Cancer Research, Canada; Department of Medicine, University of Toronto, Canada
| | - Iris Selander
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Canada
| | - Ashton A Connor
- Division of General Surgery, Department of Surgery, University Health Network, University of Toronto, Canada
| | | | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Canada
| | - Laurent Briollais
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Canada
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jordan Lerner-Ellis
- Ontario Institute for Cancer Research, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Canada
| | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Canada; Division of General Surgery, Department of Surgery, University Health Network, University of Toronto, Canada.
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Connor AA, Burkes R, Gallinger S. Strategies in the Multidisciplinary Management of Synchronous Colorectal Cancer and Resectable Liver Metastases. Curr Colorectal Cancer Rep 2014. [DOI: 10.1007/s11888-014-0222-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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