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Loll D, Bauermeister J, Ela E, Manu A, Morhe E, Dozier J, Harris L, Dalton V, Hall K. Reproductive autonomy and contraceptive use among adolescent and young adult women in Ghana. Contraception 2016. [DOI: 10.1016/j.contraception.2016.07.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Pan JC, Booth J, Ross V, Harris L, Pan P. Abstract PR213. Anesth Analg 2016. [DOI: 10.1213/01.ane.0000492611.92153.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Kohut SA, Stinson J, Forgeron P, Luca S, Harris L. (490) Being a peer mentor to youth with painful chronic conditions: perceived benefits and challenges. The Journal of Pain 2016. [DOI: 10.1016/j.jpain.2016.01.297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Stinson J, Lalloo C, Harris L, Cafazzo J, Campbell F, Chorney J, Clark J, Dick B, Forgeron P, Gordon A, Ingelmo P, Jibb L, McGillion M, Montgomery L, Palermo T, Rashiq S, Ruskin D, Simmonds M, Tupper S, Ware M. (540) iCanCope with Pain: User-centered design of an integrated smartphone and web-based pain self-management program for youth and young adults with chronic pain. The Journal of Pain 2016. [DOI: 10.1016/j.jpain.2016.01.347] [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] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Agrawal V, Varadan V, Banerjee N, Miskimen K, Vadodkar A, Abu-Khalaf M, Sikov W, Harris L, Dimitrova N. Abstract P6-03-08: Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-03-08] [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: Recent discoveries of recurrent and targetable gene fusions in breast cancer suggest the need to characterize the functional significance of such genomic aberrations within larger cohorts. We quantified fusion transcript expression in patient samples using RNASeq to identify recurrent gene fusion events in breast cancer as well as study the fusions post-brief exposure to mono-therapy.
Methods: We sequenced transcriptomes of core biopsy RNA from 130 breast tumors obtained from brief-exposure preoperative clinical trials BrUOG 211A/211B. HER2- patients were treated with brief exposure to bevacizumab (B) or nab-paclitaxel (nP) followed by treatment with B/nP/carboplatin while HER2+ patients received brief exposure to trastuzumab (T) or nP followed by T/nP/carboplatin. Paired-end sequencing on 75 baseline biopsies and 55 post-exposure biopsies using amplified total RNA yielded 55 million reads on average perlsample. Fusion transcript abundance was evaluated using 2 pipelines, TopHat-Fusion and deFuse, due to their complementary strategies in fusion detection. We eliminated gene-pseuodogene fusion pairs as likely false positives arising due to alignment artifacts. Fusions that met 1 or more of the following 3 criteria were considered high confidence:
i) Called by both deFuse and TopHat. ii) Called by deFuse with probability >95% iii) Called by TopHat with > 15 reads supporting the fusion.
Results: We identified high confidence gene fusions, detected by both TopHat and deFuse, in 73 of the 75 baseline biopsies with 16 fusions on average per sample. We looked for modulation of gene fusions upon brief exposure to therapy in 55 patients that had post exposure biopsy data and found that out of the 545 high confidence fusions detected across these patients, 62 (11.37%) of the fusions were found to be still present after the therapy exposure. For the recurrent fusion analyses, we considered the 75 baseline samples. We found a total of 1158 unique candidate fusions. Out of these, 116 (10%) were recurrent in more than 1 patient. After further filtering, we were able to narrow down to 9 (0.77%) fusions that were reliable since they were predicted by both the algorithms in different patients. 2 of these 9 fusions involved GAS5 as a partner gene. GAS5 have been studied to have a role in apoptosis and its down-regulation has been associated with cell proliferation, which makes it a very interesting fusion candidate.
Conclusions: We find that gene fusions in breast cancer are highly heterogeneous but are enriched with cancer-related pathway genes. This is the first study to report 2 novel gene-lincRNA fusion transcripts: MDN1-GAS5 and GABRB3-GAS5. Both these fusions are called in the baseline & post-therapy for atleast 1 patient (different patients each). GAS5 has been found as participating in a fusion in B-cell lymphoma. We are currently in the process of validating the fusion calls using qRT-PCR. The heterogeneity of detected fusions suggests that multiple mechanisms could underlie the selective advantage of tumor cells expressing fusion transcripts. The brief-exposure preoperative paradigm provides a unique opportunity to evaluate modulation of fusion transcripts that can shed light on their functional importance.
Citation Format: Agrawal V, Varadan V, Banerjee N, Miskimen K, Vadodkar A, Abu-Khalaf M, Sikov W, Harris L, Dimitrova N. Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-08.
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Affiliation(s)
- V Agrawal
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - V Varadan
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - N Banerjee
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - K Miskimen
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - A Vadodkar
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - M Abu-Khalaf
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - W Sikov
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - L Harris
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
| | - N Dimitrova
- Philips Research North America, Briarcliff Manor, NY; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown University, Providence, RI; Seidman Cancer Center, University Hospitals, Cleveland, OH
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Albrecht C, Caniggia I, Clifton V, Göhner C, Harris L, Hemmings D, Jawerbaum A, Johnstone E, Jones H, Keelan J, Lewis R, Mitchell M, Murthi P, Powell T, Saffery R, Smith R, Vaillancourt C, Wadsack C, Salomon C. IFPA meeting 2015 workshop report III: nanomedicine applications and exosome biology, xenobiotics and endocrine disruptors and pregnancy, and lipid. Placenta 2016; 48 Suppl 1:S12-S16. [PMID: 27094788 DOI: 10.1016/j.placenta.2016.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 10/27/2015] [Revised: 12/29/2015] [Accepted: 01/04/2016] [Indexed: 11/29/2022]
Abstract
Workshops are an important part of the IFPA annual meeting, as they allow for discussion of specialized topics. At the IFPA meeting 2015 there were twelve themed workshops, three of which are summarized in this report. These workshops were related to various aspects of placental biology but collectively covered areas of pregnancy pathologies and placental metabolism: 1) nanomedicine applications and exosome biology; 2) xenobiotics and endocrine disruptors and pregnancy; 3) lipid mediators and placental function.
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Affiliation(s)
- C Albrecht
- Institute of Biochemistry and Molecular Medicine, University of Bern, Switzerland
| | - I Caniggia
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - V Clifton
- Mater Research, Matter Hospital, Brisbane, Australia
| | - C Göhner
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - D Hemmings
- University of Alberta, Edmonton, Alberta, Canada
| | - A Jawerbaum
- University of Buenos Aires, Buenos Aires, Argentina
| | | | - H Jones
- Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - J Keelan
- The University of Western Australia, Perth, WA, Australia
| | - R Lewis
- University of Southampton, UK
| | - M Mitchell
- UQ Centre for Clinical Research, The University of Queensland, Australia
| | - P Murthi
- Department of Medicine, Monash University, Clayton Victoria 3168, Australia
| | - T Powell
- University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - R Saffery
- Murdoch Childrens Research Institute, Department of Paediatrics, University of Melbourne, Australia
| | - R Smith
- The Mothers and Babies Research Centre, University of Newcastle, Australia
| | - C Vaillancourt
- INRS Institut Armand Frappier, Université du Québec, Canada
| | - C Wadsack
- Medical University of Graz, Graz, Austria
| | - C Salomon
- Exosome Biology Laboratory, Center for Clinical Diagnostics, UQ Centre for Clinical Research, Faculty of Medicine + Biomedical Sciences, The University of Queensland, Australia.
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Jones N, Melville CA, Harris L, Bleazard L, Hankey CR. A qualitative study exploring why adults with intellectual disabilities and obesity want to lose weight and views of their carers. BMC Obes 2015; 2:49. [PMID: 26693285 PMCID: PMC4683767 DOI: 10.1186/s40608-015-0080-2] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/09/2015] [Indexed: 11/19/2022]
Abstract
Background Obesity is more prevalent in adults with intellectual disabilities (ID) compared to the general population. Motivations for weight loss may influence engagement with weight management programmes and have only been studied in adults without ID. Aims: To determine reasons given by adults with ID and obesity for seeking weight loss and whether these reasons differ from those of their carers. Methods Prior to a multi-component weight management intervention, participants were asked “why do you want to lose weight?” Carers were asked their views and these were compared to the answers given by the adult with ID. Responses were themed. The Fisher’s Exact analysis was used to test for any relationship between reasons for seeking weight loss and participants’ level of ID, age, gender and BMI. Results Eighteen men and 32 women; age 41.6 SD 14.6 years; BMI 40.8 SD 7.5 kg/m2; Level ID Mild (28 %), Moderate (42 %), Severe (22 %), Profound (8 %). Eleven were unable to respond. Six themes emerged; Health; Fitness / Activity / Mobility; Appearance / Clothes; Emotional / Happiness; For Others; Miscellaneous. The most frequent reason given overall and by women was “appearance.” Carers cited “health” most frequently and “appearance” least, rarely agreeing with participants. “Health” was given as a reason more from older adults and those with milder ID. No statistically significant associations were found between reasons for seeking weight loss and BMI age, gender or level of ID but the differing views of adults with ID and their carers were clear. Conclusions Views of adults with obesity and mild or moderate ID can be collected. The opposing views of adults and their carers may affect motivation for weight loss.
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Affiliation(s)
- N Jones
- Mental Health and Wellbeing, University of Glasgow, 1st Floor Admin Building, Gartnavel Royal Hospital, 1055 Great Western Road, Glasgow, G12 0XH UK
| | - C A Melville
- Mental Health and Wellbeing, University of Glasgow, 1st Floor Admin Building, Gartnavel Royal Hospital, 1055 Great Western Road, Glasgow, G12 0XH UK
| | - L Harris
- Mental Health and Wellbeing, University of Glasgow, 1st Floor Admin Building, Gartnavel Royal Hospital, 1055 Great Western Road, Glasgow, G12 0XH UK
| | - L Bleazard
- Mental Health and Wellbeing, University of Glasgow, 1st Floor Admin Building, Gartnavel Royal Hospital, 1055 Great Western Road, Glasgow, G12 0XH UK
| | - C R Hankey
- Human Nutrition Section, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow, G31 2ER UK
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Harris L, Worsfold J, Favi E, Aboutaleb E, Cacciola R, Puliatti C, Sammartino C, Sivaprakasam R. Incidence and outcomes of polyomavirus infection in 639 kidney transplant recipients: Are high immunological risk characteristics more relevant than specific induction or maintenance immunosuppressive regimens? Int J Surg 2015. [DOI: 10.1016/j.ijsu.2015.07.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Harris L, Fioratou E, Broadis E. Paediatric burns in Blantyre, Malawi: A follow up study. Int J Surg 2015. [DOI: 10.1016/j.ijsu.2015.07.437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Harris L, Ho L, Rae P, O'Donnell D, Warrillow SJ, Moten S, Weinberg L. Pacemaker-induced R-on-T phenomenon leading to ventricular fibrillation post cardiac surgery. Anaesth Intensive Care 2015; 43:795-797. [PMID: 26603815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Worsfold J, Harris L, Aboutaleb E, Favi E, Cacciola R, Puliatti C, Sammartino C, Sivaprakasam R. New onset diabetes after transplantation: Is it a big deal? Risk factors and impact after kidney transplantation. A single centre experience. Int J Surg 2015. [DOI: 10.1016/j.ijsu.2015.07.506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hall K, Manu A, Morhe E, Zochowski M, Boakye A, Challa S, Loll D, Dozier J, Harris L, Adanu R, Dalton V. Understanding “Bad Girl:” qualitative findings on stigma and adolescent sexual and reproductive health in Ghana. Contraception 2015. [DOI: 10.1016/j.contraception.2015.06.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hall K, Dalton V, Zochowski M, Johnson T, Harris L. An exploratory study of unintended pregnancy, stressful life events and chronic and mental health conditions among a national probability sample of US women. Contraception 2015. [DOI: 10.1016/j.contraception.2015.06.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Porta-Sanchez A, Alqubbany A, Das M, Downar E, Masse S, Harris L, Cameron D, Nair K, Chauhan V, Spears D, Ha A, Gollob M, Jackson N, Nanthakumar K. USING TIMING RELATIONSHIPS OF SINGLE DIASTOLIC ELECTROGRAMS DURING RAPID ACTIVATION MAPPING TO DETERMINE CRITICAL SITE DURING VENTRICULAR TACHYCARDIA ABLATION. Can J Cardiol 2015. [DOI: 10.1016/j.cjca.2015.07.600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Harris L, Czarnecki D, Dunn M, Hauschildt K, Anspach R, De Vries R. Moral diversity and abortion care in labor and delivery. Contraception 2015. [DOI: 10.1016/j.contraception.2015.06.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Harris L, Hankey C, Murray H, Melville C. The effects of physical activity interventions on preventing weight gain and the effects on body composition in young adults with intellectual disabilities: systematic review and meta-analysis of randomized controlled trials. Clin Obes 2015; 5:198-210. [PMID: 26126951 DOI: 10.1111/cob.12103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 01/13/2015] [Revised: 03/31/2015] [Accepted: 05/08/2015] [Indexed: 01/19/2023]
Abstract
The aim of this study was to examine the literature on randomized controlled trials examining the efficacy of physical activity interventions to prevent weight gain and the effects on body composition in young adults with intellectual disabilities.A systematic search of Medline, Emabse, CINHAL, PsychINFO, Cochrane library and ERIC was conducted from 1946 to September 2014. Eligibility criteria included; randomized controlled trials of a physical activity intervention: objective measure of body weight and body composition; young adults (age range 16-24 years) with intellectual disabilities. Six studies met the eligibility criteria. The interventions varied in their prescription of physical activity including aerobic and strength-based activities. The mean duration of the interventions was 15.3 (range 10-21 weeks). There was no significant effect of physical activity interventions on body weight (weighted mean difference: -0.17 kg, 95% confidence interval, -1.04 kg to 0.72 kg) and body composition outcomes. The meta-analysis showed that physical activity interventions did not prevent weight gain in young adults with intellectual disabilities. Published studies are inadequate to form firm conclusions. Future longer term studies of interventions specifically designed for this population group are required to elucidate the effects of physical activity interventions on body composition and the prevention of weight gain in young adults with intellectual disabilities.
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Affiliation(s)
- L Harris
- College of Medical Veterinary and Life Sciences, Institute of Mental Health & Wellbeing, University of Glasgow, Glasgow, UK
| | - C Hankey
- Human Nutrition, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - H Murray
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - C Melville
- College of Medical Veterinary and Life Sciences, Institute of Mental Health & Wellbeing, University of Glasgow, Glasgow, UK
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Tonidandel A, Booth J, D’Angelo R, Harris L, Tonidandel S. Corrigendum to “Anesthetic and obstetric outcomes in morbidly obese parturients: a 20-year follow-up retrospective cohort study” Int J Obstet Anesth 2014; 23: 357–64. Int J Obstet Anesth 2015. [DOI: 10.1016/j.ijoa.2014.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Rogers L, Varadan V, Palkar A, Miskimen K, Williams N, Morton M, Maximuk S, Vinayak S, Sloan A, Barnholtz-Sloan J, Gilmore H, Harris L. BM-28 * BIOLOGICAL PATHWAYS ASSOCIATED WITH BREAST CANCER METASTASIS TO THE BRAIN. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou240.28] [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: 11/12/2022] Open
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Tonidandel A, Booth J, D’Angelo R, Harris L, Tonidandel S. Anesthetic and obstetric outcomes in morbidly obese parturients: a 20-year follow-up retrospective cohort study. Int J Obstet Anesth 2014; 23:357-64. [DOI: 10.1016/j.ijoa.2014.05.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 05/12/2014] [Accepted: 05/19/2014] [Indexed: 11/16/2022]
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Viswanathan K, Patra S, King B, Silversides C, Oechslin E, Roche L, Cameron D, Chauhan V, Harris L, Downar E, Nair K. 49 * Tachyarrhythmias in adults with previous rastelli repair: mechanistic insights from single center expereince. Europace 2014. [DOI: 10.1093/europace/euu240.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Martin L, Hassinger J, Harris L. Evaluation of the abortion provider stigma scale. Contraception 2014. [DOI: 10.1016/j.contraception.2014.05.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kahn C, Upadhyay U, Stidham Hall K, Kolenic G, Zochowski M, Dalton V, Harris L. Reproductive autonomy: adapting a scale to account for religious influences on women’s contraceptive use. Contraception 2014. [DOI: 10.1016/j.contraception.2014.05.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kahn C, Torell E, Zochowski M, Stidham Hall K, Dalton V, Harris L. Family planning and reproductive autonomy among highly religious women: a qualitative study. Contraception 2014. [DOI: 10.1016/j.contraception.2014.05.213] [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: 11/16/2022]
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Dunn G, Henrich N, Holmes B, Harris L, Prystajecky N. Microbial water quality communication: public and practitioner insights from British Columbia, Canada. J Water Health 2014; 12:584-595. [PMID: 25252362 DOI: 10.2166/wh.2014.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This work examines the communication interactions of water suppliers and health authorities with the general public regarding microbial source water quality for recreational and drinking water. We compare current approaches to risk communication observable in British Columbia (BC), Canada, with best practices derived from the communications literature, finding significant gaps between theory and practice. By considering public views and government practices together, we identify key disconnects, leading to the conclusion that at present, neither the public's needs nor public health officials' goals are being met. We find: (1) there is a general lack of awareness and poor understanding by the public of microbial threats to water and the associated health implications; (2) the public often does not know where to find water quality information; (3) public information needs are not identified or met; (4) information sharing by authorities is predominantly one-way and reactive (crisis-oriented); and (5) the effectiveness of communications is not evaluated. There is a need for both improved public understanding of water quality-related risks, and new approaches to ensure information related to water quality reaches audiences. Overall, greater attention should be given to planning and goal setting related to microbial water risk communication.
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Affiliation(s)
- G Dunn
- Program on Water Governance, University of British Columbia, 439-2202 Main Mall, Vancouver, BC, V6T 1Z4 Canada E-mail:
| | - N Henrich
- Centre for Health Evaluation and Outcome Sciences, 588-1081 Burrard Street St. Paul's Hospital, Vancouver, BC, V6Z 1Y6, Canada
| | - B Holmes
- School of Population and Public Health, University of British Columbia, 2206 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - L Harris
- Program on Water Governance, University of British Columbia, 439-2202 Main Mall, Vancouver, BC, V6T 1Z4 Canada E-mail: ; Institute of Resources, Environment and Sustainability, University of British Columbia, 439-2202 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - N Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, G227-2211 Wesbrook Mall Vancouver, Vancouver, BC, V6T 2B5, Canada
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Pundir J, Kopeika J, Harris L, Krishnan N, Uwins C, Siozos A, Khalaf Y, El-Toukhy T. Reproductive outcome following abdominal myomectomy for a very large fibroid uterus. J OBSTET GYNAECOL 2014; 35:37-41. [DOI: 10.3109/01443615.2014.930097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Gizurarson S, Spears D, Sivagangabalan G, Farid T, Ha ACT, Masse S, Kusha M, Chauhan VS, Nair K, Harris L, Downar E, Nanthakumar K. Bipolar ablation for deep intra-myocardial circuits: human ex vivo development and in vivo experience. Europace 2014; 16:1684-8. [DOI: 10.1093/europace/euu001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Connelly T, Berg A, Harris L, Hegarty J, Deiling S, Stewart D, Koltun W. The Expression of Colonic TAGAP is Affected By Severity of Crohn's Disease Inflammation and The Rs212388 Allele. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Madabhushi A, Doyle S, Basavanhally A, Gilmore H, Harris L, Shih N, Mies C, Feldman M, Tomaszewski J, Ganesan S. Abstract P4-03-04: Computer extracted image measurements of nuclear shape and texture from H&E images appear to stratify low and high risk ER+ breast cancers assessed via oncotype DX. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p4-03-04] [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: In this study we investigate the ability of computer extracted image features (nuclear morphology and texture) from digitized H&E tissue slides to stratify women with lymph node negative (LN-), estrogen receptor positive (ER+) breast cancer (BCa) as low or high risk as determined by Oncotype DX (ODX), a 21 gene-expression assay. Each year, over 120,000 women in the United States (1 million worldwide) are diagnosed with ER+ BCa. Treatment guidelines recommend hormone therapy (HT) plus chemotherapy (CT); however, up to 85% of ER+ BCa patients will not benefit from CT, yet will still suffer its side effects. ODX yields a numeric risk score (RS) ranging from 1-100; RS<18 suggests patients will respond to HT alone while RS>30 indicates need for adjuvant CT. Unfortunately, this test is expensive (>$4000), time-consuming, and involves destructive tissue testing. The goal of this study is to show that quantitative features calculated from H&E images can accurately predict risk stratification as determined by ODX in women with LN-, ER+ BCa, suggesting a histologic image based classifier could serve as a low-cost alternative.
Methods: Digitized H&E-stained ER+ BCa tissue sampled from 111 patients (34 high and 77 low-risk as determined by ODX) were obtained from the University of Pennsylvania, the University of Medicine and Dentistry of NJ, and Case Western Reserve University. Regions of cancer were annotated manually by an expert pathologist, and representative fields of view (FOV) were chosen at 20x magnification (2000 by 2000 pixels) for each patient. A selection of nuclear boundaries was annotated manually in each FOV. For each nucleus, a set of 2343 features was extracted, including 21 morphological (size, shape, and boundary) and 2322 texture (Gabor, Local Binary Pattern, Greylevel, and Laws filter features). Using Minimum Redundancy Maximum Relevance (mRMR) feature selection, the 3 features best able to separate low and high ODX risk categories were identified and used to build a supervised Bayesian classifier. Classifier training employed a randomized 3-fold cross-validation scheme; in each trial, two-thirds of the dataset were randomly selected for training, and the remaining one-third employed for independent testing. Classifier performance was evaluated using area under the receiver operating characteristic curve (AUC), positive predictive value (PPV), and negative predictive value (NPV) with respect to low and high ODX risk categorization. Performance metrics were averaged over 100 trials of 3-fold cross-validation (see table).
Results: The mRMR method selected one morphological feature (nuclear area) and two Laws-based texture features as being highly discriminating between risk categories. The Bayesian classifier trained with these 3 features yielded high AUC, PPV, and NPV measures with low variance in distinguishing ODX risk categories. The supervised classification results indicate that quantitative image features from H&E-stained histopathology are able to accurately discriminate between low and high risk patients as determined by ODX.
Classification PerformancePerformance MetricAverage (100 Trials)Standard DeviationAUC0.870.018PPV0.810.039NPV0.880.017
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-03-04.
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Affiliation(s)
- A Madabhushi
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - S Doyle
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - A Basavanhally
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - H Gilmore
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - L Harris
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - N Shih
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - C Mies
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - M Feldman
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - J Tomaszewski
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
| | - S Ganesan
- Case Western Reserve University, Cleveland, OH; Ibris Incorporated, Monmouth Junction, NJ; University of Pennsylvania, Philadelphia, PA; University at Buffalo, Buffalo, NY; Cancer Institute of New Jersey, New Brunswick, NJ
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Madabhushi A, Wan T, Bloch B, Plecha D, Thompson C, Gilmore H, Avril N, Jaffe C, Harris L. Abstract P2-02-12: Computer derived image features on DCE-MRI appear to distinguish estrogen receptor-positive breast cancers with low and high oncotype DX recurrence scores. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p2-02-12] [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
The Oncotype DX (ODX) is a 21 panel gene-expression based assay for identifying which Estrogen Receptor-positive (ER+) breast cancer (BCa) patients are candidates for adjuvant chemotherapy. The objective of this research was to identify whether computerized texture features on a staging DCE-MRI can distinguish ER+ BCa with low and high ODX recurrence scores (RS) (i.e. to distinguish which ER+ BCa patients are more likely to benefit from adjuvant hormonal therapy from those who require chemotherapy). This would provide a non-invasive, imaging based, pre-therapeutic assessment tool for predicting the appropriate treatment regimen. This work, to the best of our knowledge, is the first attempt to quantitatively correlate low versus high risk stratification via computer derived MRI measurements to corresponding risk stratification via the ODX assay.
52 ER+ BCa patient studies with high (>30, N = 28) and low (<18, N = 24) ODX RS were available for this study from two sites; 16 breast MRIs from the Boston Medical Center using a Phillips 1.5T magnet with a 7-channel breast coil, and 36 MRIs from the Case Medical Center using a Siemens 1.5T magnet with a 8-channel breast coil. All datasets included T1w images obtained prior to, during, and after administration of 0.1 mmol/kg of Gd-DTPA and corresponding ODX RS. For each study a radiologist picked a representative slice showing the tumor and then manually segmented the region of interest (ROI) containing the lesion. Computerized image analysis tools developed in-house via the MATLAB© programming platform were applied to the manually segmented lesion ROI for each of the 52 MRI studies to quantitatively characterize the lesion via a set of (a) 6 shape, (b) 3 pharmacokinetic (Ktrans, ve, kep) based on Tofts model (PK), (c) 12 enhancement kinetic (EK), (d) 12 intensity kinetic (IK), (e) 312 textural kinetic (TK), (f) 6 dynamic local binary pattern (DLBP), and (g) 5 dynamic histogram of oriented gradient (DHoG) features. The computer extracted features were evaluated via a linear discriminant analysis (LDA) classifier in terms of their ability to distinguish ER+ BCa as having a low or high ODX RS via a 2-fold randomized cross validation scheme. At each iteration, half of the studies were randomly selected from the 52 cases and used for training the LDA classifier and the remaining 26 studies were used for independent testing. This process was repeated 200 times. Classification performance was evaluated by area under the ROC curve (AUC). Higher AUC values suggest a stronger relationship between risk stratification via MRI attributes and ODX.
Table 1Feature classAccuracy (μ±Δ)AUC (μ±Δ)DHoG87.07%±5.66%0.89±0.04DLBP85.86%±7.82%0.83±0.07EK82.36%±8.46%0.80±0.06PK81.14%±7.55%0.78±0.07TK75.93%±6.65%0.76±0.08IK76.43%±7.23%0.75±0.12Shape71.04%±6.81%0.70±0.06
Table 1 illustrates the mean and standard deviation in accuracy and AUC values over 200 runs of randomized cross validation. DHoG, DBLP and EK features yielded the highest classification accuracy and AUC. Although lesion shape has been shown to be important for discriminating benign and malignant lesions on MRI, shape appears to be less useful in distinguishing between ER+ BCa lesions with low and high ODX RS.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-02-12.
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Affiliation(s)
- A Madabhushi
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - T Wan
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - B Bloch
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - D Plecha
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - C Thompson
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - H Gilmore
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - N Avril
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - C Jaffe
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
| | - L Harris
- Case Western Reserve University, Cleveland, OH; Boston University School of Medicine, Boston, MA; UH MacDonald Women's Hospital Breast Centers, Cleveland, OH; University Hospitals Case Medical Center, Cleveland, OH; Seidman Cancer Center, Cleveland, OH
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Madabhushi A, Basavanhally AN, Doyle S, Wan T, Singanamalli A, Thompson C, Gilmore H, Plecha D, Harris L. Abstract P2-03-01: Computer extracted image texture features on T2-weighted MRI appear to correlate with nuclear morphologic descriptors from H&E-stained histopathology in estrogen receptor positive breast cancers. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p2-03-01] [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
Oncotype DX (ODX) is a 21 panel gene-expression based assay for predicting whether patients with estrogen receptor-positive (ER+) breast cancer (BCa) are candidates for adjuvant chemotherapy. However, the time and expense associated with genomic assays suggests the need for a non-invasive, imaging-based, pre-therapeutic tool for assessment of disease risk and selection of an appropriate treatment regimen. The objective of this research was to determine whether (a) computer extracted image features on T2-weighted (T2w) MRI and H&E stained histopathology are independently able to distinguish ER+ BCa with low and high ODX recurrence scores (RS) and (b) to determine whether there is a correlation between MRI and histologic features identified as being predictive of low and high ODX risk categories.
A total of 11 ER+ BCa patients were considered in this study, based on availability of in vivo 1.5 Tesla T2w MRI. For each study, the corresponding formalin-fixed paraffin-embedded H&E stained tissue specimens were digitized at 20x (0.5 μm/pixel) using a whole-slide scanner. Of the 11 patients, 8 were identified in the low ODX (RS < 18) and 3 in the high ODX (RS > 30) risk categories. Each dataset was accompanied by expert annotations of (a) the lesion ROI on MRI and (b) boundaries of epithelial nuclei from a representative field-of-view on the digitized histology slide.
For each MRI study, a multi-scale, multi-orientation Gabor filter bank was convolved with the annotated lesion area providing a set of 192 texture features (FMRI). For each corresponding histology image, 471 features (FHIST) were extracted describing both nuclear morphology (NM) and Laws texture (LT) within the nuclear regions. Independent 2-sample t-tests were used to identify salient features in FMRI and FHIST that are able to distinguish low and high ODX risk categories. We found that, for the MRI dataset, Gabor texture features at several scales and orientations yielded salient features (p < 0.05) while on histopathology, nuclear texture and convexity (shape) features were identified as the top discriminative features (p < 0.01). Relationships between significant features were evaluated via Spearman's rank correlation test (see table), where high correlations were observed between lesion texture on T2w MRI and nuclear texture and shape on histology.
Correlation of histologic and MRI features able to distinguish low and high ODX RSHistologic feature correlated with ODXMRI feature correlated with ODXCorrelation coefficient (ρ)p-valueLT: 70 Mean HSVGF: Scale 2: Orientation 3: min/max-0.85450.0008NM: ConvexityGF: Scale 5: Orientation 6: mean-0.85450.0008LT: 70 Mean HSVGF: Scale 2: Orientation 3: min/max-0.83640.0013LT: 70 Mean HSVGF: Scale 3: Orientation 8: mean-0.83640.0013LT: 70 Mean HSVGF: Scale 3: Orientation 2: mean-0.81820.0021
Our results suggest that quantitative features extracted on both T2w MRI and histopathology can independently distinguish between low and high risk ODX classes. Moreover, some of these MRI and histologic features appear to be significantly correlated, suggesting that information regarding tumor biology is reflected in both MRI and histologic image features.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-03-01.
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Affiliation(s)
- A Madabhushi
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - AN Basavanhally
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - S Doyle
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - T Wan
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - A Singanamalli
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - C Thompson
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - H Gilmore
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - D Plecha
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
| | - L Harris
- Case Western Reserve University, Cleveland, OH; Rutgers, The State University of New Jersey, Piscataway, NJ; Ibris, Inc., Monmouth Junction, NJ
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Williams N, Varadan V, Miskimen K, Vadodkar A, Poruban D, Edelheit S, Gilmore H, Maximuk S, Sinclair N, Lezon-Geyda K, Abu-Khalaf M, Sikov W, Harris L. Abstract P1-08-16: Deep sequencing of breast tumor biopsies reveals an association between pathologic complete response and reduction of TP53 clonal abundance upon brief exposure to therapy. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p1-08-16] [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: Next generation deep sequencing has revealed the existence of intra-tumor heterogeneity within subsets of breast tumors. The clinical implications of intra-tumor heterogeneity are not fully understood, however subclonal heterogeneity likely plays a role in treatment resistance. We quantify the clonal abundance of somatic mutations in breast tumor biopsies using deep targeted amplicon sequencing and assess their changes over the course of preoperative therapy (PT). We also evaluate the association of changes in clonal abundance upon brief exposure (BE) to therapy with clinical outcome.
Methods: DNA from 69 breast tumor samples obtained from BE preoperative clinical trials BrUOG 211A/211B were sequenced. Patients received a run-in dose of bevacizumab(B), nab-paclitaxel(N) or trastuzumab (T), followed by combination biologic/chemotherapy (HER2- with B/carboplatin/N; HER2+ with T/carboplatin/N). We sequenced biopsy pairs obtained pre/post 10 day exposure to run-in targeted therapy and germline and surgical tumor DNA for a subset of patients upon completion of PT. A TruSeqCustom Amplicon (Illumina) for targeted enrichment sequencing that included 1183 amplicons covering either hotspot regions or whole exonic regions from 35 commoly mutated genes in breast cancer (TCGA, Stephens, 2012; Shah); a total of 101,484 bp of the genome was represented. Sequencing was performed using IlluminaMiSeq platform and analyzed for variant calls using IlluminaBasespace. High confidence somatic mutations were identified in samples with matched germline data using VarScan2. In the absence of matched normal DNA, germline variants were eliminated using dbSNP and the 1000 Genomes Project. Minor allele frequencies (MAF) of somatic aberrations were estimated as the percentage of reads matching the variant.
Results: Approximately 5 mutations on average were found baseline and post-exposure, with a maximum mutational burden of 15 mutations in one basal breast cancer. Recurrent somatic aberrations were observed in TP53 (42%), PIK3CA (16%) and FAT4 (13%), whereas sporadic aberrations were also seen in COL1A1, PTEN, CDH1. More than 85% of samples harboring TP53 mutations exhibited MAF≥40%. Similar high clonal abundance (MAF >50%) was observed for FAT4 mutations whereas PIK3CA mutations exhibited only subclonal frequencies (MAF≤30%). We evaluated changes in clonal architecture upon BE to therapy by scoring for a change in MAF of at least 10% from baseline to post-exposure sample. We scored a total of 16 cases for clonal abundance changes in TP53 mutations upon exposure to therapy. We found 6 cases that exhibited ≥10% reduction in MAF, of which 4 achieved pCR (p = 0.03) and the remaining 2 achieved RCB I. This association was independent of therapy arm and BE regimen.
Conclusions: We found that a reduction in TP53 clonal abundance upon BE to PT is associated with clinical outcome. We are currently integrating whole genome copy-number profiles with the deep sequencing data to more accurately assess clonal architecture and changes upon exposure to therapy. Clonal changes upon BE to therapy may provide early readouts of therapy benefit and provide biological insights into mechanisms of action.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-16.
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Affiliation(s)
- N Williams
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - V Varadan
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - K Miskimen
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - A Vadodkar
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - D Poruban
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - S Edelheit
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - H Gilmore
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - S Maximuk
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - N Sinclair
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - K Lezon-Geyda
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - M Abu-Khalaf
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - W Sikov
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
| | - L Harris
- University Hospitals/Case Medical Center, Cleveland, OH; Yale University School of Medicine; Yale Comprehensive Cancer Center, New Haven, CT; Warren Alpert Medical School of Brown, Providence, RI
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Wilson DM, Apps J, Bailey N, Bamford MJ, Beresford IJ, Brackenborough K, Briggs MA, Brough S, Calver AR, Crook B, Davis RK, Davis RP, Davis S, Dean DK, Harris L, Heslop T, Holland V, Jeffrey P, Panchal TA, Parr CA, Quashie N, Schogger J, Sehmi SS, Stean TO, Steadman JG, Trail B, Wald J, Worby A, Takle AK, Witherington J, Medhurst AD. Identification of clinical candidates from the benzazepine class of histamine H3 receptor antagonists. Bioorg Med Chem Lett 2013; 23:6890-6. [DOI: 10.1016/j.bmcl.2013.09.090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
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Wilson DM, Apps J, Bailey N, Bamford MJ, Beresford IJ, Briggs MA, Calver AR, Crook B, Davis RP, Davis S, Dean DK, Harris L, Heightman TD, Panchal T, Parr CA, Quashie N, Steadman JG, Schogger J, Sehmi SS, Stean TO, Takle AK, Trail BK, White T, Witherington J, Worby A, Medhurst AD. The discovery of the benzazepine class of histamine H3 receptor antagonists. Bioorg Med Chem Lett 2013; 23:6897-901. [DOI: 10.1016/j.bmcl.2013.09.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 11/16/2022]
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Roshan J, Gizurarson S, Kusha M, Dimagiba L, Khan K, Masse S, Harris L, Downar E, Nanthakumar K. Is There an Ideal Strategy to Maximize Endo- and Epicardial Late Potentials Mapping in Patients Undergoing Ablation for Ischemic Ventricular Tachycardia? Can J Cardiol 2013. [DOI: 10.1016/j.cjca.2013.07.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Roshan J, Das M, Khan F, Crean A, Harris L, Downar E, Spears D, Wanounou L, Chauhan V, Nair K, Ha A, Waxman M, Cameron D, Nanthakumar K. Pericardial Adhesions During Epicardial Ablation of Ventricular Tachycardia: Need for Imaging Techniques. Can J Cardiol 2013. [DOI: 10.1016/j.cjca.2013.07.396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Das M, Roshan J, Khan F, Wanounou L, Chemello D, Spears D, Cameron D, Harris L, Nair K, Ha A, Chauhan V, Gizurarson S, Downar E, Nanthakumar K. One-Year Mortality Outcomes Following Ventricular Tachycardia Ablation in Octogenarians. Can J Cardiol 2013. [DOI: 10.1016/j.cjca.2013.07.397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Martin L, Debbink M, Youatt E, Hassinger J, Bonnington A, Eagen-Torkko M, Harris L. Burnout, stigma and team cohesion among abortion providers participating in the providers share workshop. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Eagen-Torkko M, Martin L, Hassinger J, Youatt E, Bonnington A, Harris L. The “caring paradox”? Abortion care and nursing staff. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Harris L, Martin L, Youatt E, Eagen-Torrko M, Bonnington A, Hassinger J, Debbink M. Michigan’s HB5711: a case study of the role of abortion provider stigma in anti-abortion legislation. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.054] [Citation(s) in RCA: 4] [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: 11/25/2022]
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91
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Maniere E, Bonnington A, Hassinger J, Martin L, Youatt E, Eagen-Torkko M, Debbink M, Harris L. “I actually like children very much”: The false dichotomization of abortion provision and motherhood. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bonnington A, Martin L, Hassinger J, Youatt E, Eagen-Torkko M, Debbink M, Harris L. Abortion providers as stigmatizers: provider judgment and stereotyping of patients seeking abortion. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lance A, Harris L, Dalton V, Patel D. Can 16 and pregnant affect attitudes towards teen pregnancy among young women? A randomized controlled trial. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Koyak Z, Harris L, De Groot JR, Zwinderman AH, Silversides CK, Bouma BJ, Oechslin EN, Budts W, Van Gelder IC, Mulder BJM. Sudden cardiac death in adult congenital heart disease: can we predict the unpredictable? Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht308.p2098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Banerjee N, Maity S, Varadan V, Janevski A, Kamalakaran S, Sikov W, Abu-Khalaf M, Bossuyt V, Lannin D, Harris L, Cornfeld D, Dimitrova N. Abstract P4-01-02: Association of DCE-MRI texture features with molecular phenotypes and neoadjuvant therapy response in breast cancer. Cancer Res 2012. [DOI: 10.1158/0008-5472.sabcs12-p4-01-02] [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
Purpose: MRI imaging phenotype features such as volume and morphology are used to characterize tumor heterogeneity and tumor response. Texture-based imaging features are important in lesion characterization but their relationship to molecular phenotypes and response is unclear. Molecular stratification of breast cancer into luminal, basal, ERBB2, and normal-like can be made based on gene expression profiles. We investigate how texture-based imaging features relate to tumor biology, genetic subtypes and neoadjuvant therapy response using MRI, histopathological and RNA-sequencing data.
Materials and Methods: Data from 74 Stage IIA to IIIB breast cancer patients enrolled in neo-adjuvant clinical trials NCT00617942 and NCT00723125 were retrospectively reviewed. We evaluated 37 gray-level co-occurrence matrix features (GLCM) on post-contrast T1 fat-suppressed images of 38 HER2− tumors and 35 HER2+ tumors. The texture features included angular second moment, contrast, correlation, first diagonal moment, entropy, regularity, roughness, line likeness and other statistical summaries. We also performed RNA-sequencing on 23 tumors and compared RNAseq-based PAM50 clustering with texture-based clustering. Patients with pCR and RCB class=I were determined to be responders and the rest were labeled non-responders. Wilcoxon signed rank test was used to compare luminal vs. basal, ER+ vs. ER− and PR+ vs. PR- tumors and determine the discriminative power of the texture features. We then performed hierarchical clustering on our patient data set based on the significant texture features and evaluated their association with subtypes, hormone receptor status and response. Statistical significance of clusters was determined by hypergeometric test.
Results: We found five MRI texture features to be significantly associated with tumor subtypes: first diagonal moment, contrast range, correlation range and entropy range (p < 0.05). These five features together differentiated basal and luminal PAM50 subtypes with p = 0.001. Our analysis also showed an association between texture features and tumor hormone status. ER− tumors clustered strongly (13 of 20 ER− cases clustered, p = 0.009) with the 23 significant ER-associated texture features. Similarly, the PR- tumors formed tight grouping (15 of 24 PR- cases clustered, p = 0.006) with 26 significant PR-associated texture features in HER2− patients. Interestingly, only two texture features, entropy range and regularity, distinguished between responders and non-responders (p = 0.04). These features will be further evaluated with DCE-MRI data capturing post brief exposure dynamics.
Conclusion: Our results indicate that certain texture features from DCE-MRI images do capture biological heterogeneity in tumors and can potentially complement standard clinical evaluations. Texture features have previously been assessed for diagnostic settings but to our knowledge this is the first study that shows association of texture features with breast cancer subtyping and neoadjuvant therapy response. We speculate that this could potentially impact clinical management decisions and therapy selection.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-01-02.
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Affiliation(s)
- N Banerjee
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - S Maity
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - V Varadan
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - A Janevski
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - S Kamalakaran
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - W Sikov
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - M Abu-Khalaf
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - V Bossuyt
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - D Lannin
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - L Harris
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - D Cornfeld
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
| | - N Dimitrova
- Philips Research North America; Yale Comprehensive Cancer Center; Warren Alpert Medical School of Brown University; Yale-New Haven Hospital; Yale Breast Cancer Program; Seidman Cancer Center
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Khan F, Roshan J, Das M, Harris L, Wanounou L, Spears D, Chauhan V, Ing D, Cameron D, Waxman M, Ha A, Nair K, Downar E, Nanthakumar K. 735 Early Success of Ventricular Tachycardia Ablation in Patients With Structural Heart Disease: A Single Centre Experience. Can J Cardiol 2012. [DOI: 10.1016/j.cjca.2012.07.665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Das M, Khan F, Roshan J, Wanounou L, Chemello D, Harris L, Spears D, Cameron D, Nair K, Ha A, Chauhan V, Downar E, Nanthakumar K. 733 The Safety and Efficacy of Ventricular Tachycardia Ablation in Octogenarians. Can J Cardiol 2012. [DOI: 10.1016/j.cjca.2012.07.663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Masse S, Downar E, Sevaptsidis E, Asta J, Harris L, Cameron D, Nair K, Chauhan V, Spears D, Ha A, Nanthakumar K. 734 Exit Site of Ischemic Ventricular Tachycardia: Lessons From Simultaneous Multi-Electrode Mapping Era Applied to Sequential Mapping Era. Can J Cardiol 2012. [DOI: 10.1016/j.cjca.2012.07.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Harris L, Eagen-Torkko M, Youatt E, Hassinger J, Debbink M, Martin L. Abortion providers and pro-life patients. Contraception 2012. [DOI: 10.1016/j.contraception.2012.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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