1
|
McGill BC, Wakefield CE, Tucker KM, Daly RA, Donoghoe MW, Vetsch J, Warby M, Fuentes‐Bolanos NA, Barlow‐Stewart K, Kirk J, Courtney E, O’Brien TA, Marshall GM, Pinese M, Cowley MJ, Tyrrell V, Deyell RJ, Ziegler DS, Hetherington K. Parents' expectations, preferences, and recall of germline findings in a childhood cancer precision medicine trial. Cancer 2023; 129:3620-3632. [PMID: 37382186 PMCID: PMC10952780 DOI: 10.1002/cncr.34917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Germline genome sequencing in childhood cancer precision medicine trials may reveal pathogenic or likely pathogenic variants in cancer predisposition genes in more than 10% of children. These findings can have implications for diagnosis, treatment, and the child's and family's future cancer risk. Understanding parents' perspectives of germline genome sequencing is critical to successful clinical implementation. METHODS A total of 182 parents of 144 children (<18 years of age) with poor-prognosis cancers enrolled in the Precision Medicine for Children with Cancer trial completed a questionnaire at enrollment and after the return of their child's results, including clinically relevant germline findings (received by 13% of parents). Parents' expectations of germline genome sequencing, return of results preferences, and recall of results received were assessed. Forty-five parents (of 43 children) were interviewed in depth. RESULTS At trial enrollment, most parents (63%) believed it was at least "somewhat likely" that their child would receive a clinically relevant germline finding. Almost all expressed a preference to receive a broad range of germline genomic findings, including variants of uncertain significance (88%). Some (29%) inaccurately recalled receiving a clinically relevant germline finding. Qualitatively, parents expressed confusion and uncertainty after the return of their child's genome sequencing results by their child's clinician. CONCLUSIONS Many parents of children with poor-prognosis childhood cancer enrolled in a precision medicine trial expect their child may have an underlying cancer predisposition syndrome. They wish to receive a wide scope of information from germline genome sequencing but may feel confused by the reporting of trial results.
Collapse
|
2
|
Gutierrez AM, Robinson JO, Raesz-Martinez R, Canfield I, Majumder MA, Scollon S, Desrosiers LR, Hsu RL, Allen-Rhoades W, Parsons DW, Plon SE, McGuire AL, Malek J. Views of Adolescents and Young Adults with Cancer and Their Oncologists Toward Patients' Participation in Genomic Research. J Adolesc Young Adult Oncol 2023; 12:773-781. [PMID: 36595372 PMCID: PMC10611971 DOI: 10.1089/jayao.2022.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Purpose: With increased use of genomic testing in cancer research and clinical care, it is important to understand the perspectives and decision-making preferences of adolescents and young adults (AYAs) with cancer and their treating oncologists. Methods: We conducted an interview substudy of the BASIC3 Study, which enrolled newly diagnosed cancer patients <18 years of age with assent. Of 32 young adults (YAs) with cancer who reached the age of majority (AOM; 18 years) while on study, 12 were successfully approached and all consented to study continuation at AOM. Of those, seven completed an interview. Patients' oncologists, who enrolled and participated in return of clinical genomic results, were also interviewed (n = 12). Interviews were transcribed, deidentified, and analyzed using thematic analysis. Results: YAs cited the possibility of helping others and advancing science as major reasons for their assent to initial study enrollment and their willingness to consent at AOM. YAs thought obtaining informed consent from research participants for study continuation at AOM was a good idea in case they changed their minds or wanted to make their own decisions, and to keep them aware of study activities. There was diversity in what YAs understood and learned from genomic testing: some recalled specific findings, while some remembered minimal information about their results. Oncologists varied in their assessment of adolescents' engagement with the study and understanding of their results. Conclusion: Given the different ways AYAs engage with genomic information, careful assessment of AYAs' diverse communication and decision-making preferences is needed to tailor interactions accordingly.
Collapse
Affiliation(s)
- Amanda M. Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Jill O. Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Robin Raesz-Martinez
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel Canfield
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Mary A. Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Sarah Scollon
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Lauren R. Desrosiers
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Rebecca L. Hsu
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Wendy Allen-Rhoades
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - D. Williams Parsons
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sharon E. Plon
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
3
|
Cakici JA, Dimmock D, Caylor S, Gaughran M, Clarke C, Triplett C, Clark MM, Kingsmore SF, Bloss CS. Assessing Diversity in Newborn Genomic Sequencing Research Recruitment: Race/Ethnicity and Primary Spoken Language Variation in Eligibility, Enrollment, and Reasons for Declining. Clin Ther 2023; 45:736-744. [PMID: 37429778 DOI: 10.1016/j.clinthera.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE Diagnostic genomic research has the potential to directly benefit participants. This study sought to identify barriers to equitable enrollment of acutely ill newborns into a diagnostic genomic sequencing research study. METHODS We reviewed the 16-month recruitment process of a diagnostic genomic research study enrolling newborns admitted to the neonatal intensive care unit at a regional pediatric hospital that primarily serves English- and Spanish-speaking families. Differences in eligibility, enrollment, and reasons for not enrolling were examined as functions of race/ethnicity and primary spoken language. FINDINGS Of the 1248 newborns admitted to the neonatal intensive care unit, 46% (n = 580) were eligible, and 17% (n = 213) were enrolled. Of the 16 languages represented among the newborns' families, 4 (25%) had translated consent documents. Speaking a language other than English or Spanish increased a newborn's likelihood of being ineligible by 5.9 times (P < 0.001) after controlling for race/ethnicity. The main reason for ineligibility was documented as the clinical team declined having their patient recruited (41% [51 of 125]). This reason significantly affected families who spoke languages other than English or Spanish and was able to be remediated with training of the research staff. Stress (20% [18 of 90]) and the study intervention(s) (20% [18 of 90]) were the main reasons given for not enrolling. IMPLICATIONS This analysis of eligibility, enrollment, and reasons for not enrolling in a diagnostic genomic research study found that recruitment generally did not differ as a function of a newborn's race/ethnicity. However, differences were observed depending on the parent's primary spoken language. Regular monitoring and training can improve equitable enrollment into diagnostic genomic research. There are also opportunities at the federal level to improve access to those with limited English proficiency and thus decrease disparities in representation in research participation.
Collapse
Affiliation(s)
- Julie A Cakici
- The Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, California, USA; School of Public Health, San Diego State University, San Diego, California, USA
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Mary Gaughran
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Christina Clarke
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | | | - Michelle M Clark
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Cinnamon S Bloss
- The Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, California, USA.
| |
Collapse
|
4
|
Nathe JM, Oskoui TT, Weiss EM. Parental Views of Facilitators and Barriers to Research Participation: Systematic Review. Pediatrics 2023; 151:e2022058067. [PMID: 36477217 PMCID: PMC9808610 DOI: 10.1542/peds.2022-058067] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Low enrollment within pediatric research increases the cost of research, decreases generalizability, and threatens to exacerbate existing health disparities. To assess barriers and facilitators to pediatric research participation and evaluate differences by enrollment status. METHODS Data Sources include PubMed, Embase, PsycInfo, Cumulative Index to Nursing and Allied Health Literature, and Web of Science. Study selection include peer reviewed articles that contained information related to facilitators and barriers to the parental decision whether to enroll their child in research and included the views of parents who declined. We extracted barriers and facilitators to research, enrollment status, and study characteristics, including study design, quality, and patient population. RESULTS Seventy articles were included for analysis. Facilitators of participation included: benefits, trust, support of research, informational and consent related, and relational issues. Common facilitators within those categories included health benefit to child (N = 39), altruism (N = 30), and the importance of research (N = 26). Barriers to participation included: study-related concerns, burdens of participation, lack of trust, general research concerns, informational and consent related, and relational issues. Common barriers within those categories included risks to child (N = 46), burdens of participation (N = 35), and the stress of the decision (N = 29). We had a limited ability to directly compare by enrollment status and no ability to analyze interactions between facilitators and barriers. We only included studies written in English. CONCLUSIONS This review identified key facilitators and barriers to research participation in pediatrics. The findings from this review may guide researchers aiming to create interventions to improve the parental experience of recruitment for pediatric studies and to optimize enrollment rates.
Collapse
Affiliation(s)
- Julia M. Nathe
- University of Washington School of Medicine, Seattle, Washington
| | - Tira T. Oskoui
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California
| | - Elliott Mark Weiss
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Research Institute, Seattle, Washington
| |
Collapse
|
5
|
Mandrell BN, Johnson LM, Caples M, Gattuso J, Maciaszek JL, Mostafavi R, Sharp KMH, Nichols KE. Parental Preferences Surrounding Timing and Content of Consent Conversations for Clinical Germline Genetic Testing Following a Child's New Cancer Diagnosis. JCO Precis Oncol 2022; 6:e2200323. [PMID: 36265116 PMCID: PMC9848596 DOI: 10.1200/po.22.00323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/10/2022] [Accepted: 08/30/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Clinical genomic testing is increasingly being used to direct pediatric cancer care. Many centers are interested in offering testing of tumors and paired germline tissues at or near the time of cancer diagnosis. We conducted this study to better understand parent preferences surrounding timing and content of consent conversations for clinical germline genetic testing of their children with cancer as a part of real-time cancer care. PATIENTS AND METHODS A seven-question survey developed by the Division of Cancer Predisposition and collaborators at St Jude Children's Research Hospital (St Jude) was distributed to members of the St Jude Patient Family Advisory Council, which included parents of childhood cancer survivors and bereaved parents whose children with cancer had died. Parents were asked to provide free text comments after each question. Qualitative methods were used to derive codes from parent comments, and survey results were depicted using descriptive statistics. RESULTS The survey was completed by 172 parents. Ninety-three (54%) endorsed an approach for consent conversations ≥ 1 month after cancer diagnosis, whereas 58 (34%) endorsed an approach at 1-2 weeks and 21 (12%) at 1-2 days. Needing time to adjust to a new or relapsed cancer diagnosis and feeling overwhelmed were frequent themes; however, parents acknowledged the urgency and importance of testing. Parents desired testing of as many cancer-related genes as possible, with clinical utility the most important factor for proceeding with testing. Most parents (75%) desired germline results to be disclosed in person, preferably by a genetic counselor. CONCLUSION Parents described urgency and benefits associated with germline testing, but desired flexibility in timing to allow for initial adjustment after their child's cancer diagnosis.
Collapse
Affiliation(s)
- Belinda N. Mandrell
- Division of Nursing Research, Department of Pediatrics, St Jude Children's Research Hospital, Memphis, TN
| | - Liza Marie Johnson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Mary Caples
- Division of Nursing Research, Department of Pediatrics, St Jude Children's Research Hospital, Memphis, TN
| | - Jami Gattuso
- Division of Nursing Research, Department of Pediatrics, St Jude Children's Research Hospital, Memphis, TN
| | - Jamie L. Maciaszek
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Roya Mostafavi
- Division of Cancer Predisposition, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | | | - Kim E. Nichols
- Division of Cancer Predisposition, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| |
Collapse
|
6
|
Hirsch S, Dikow N, Pfister SM, Pajtler KW. Cancer predisposition in pediatric neuro-oncology-practical approaches and ethical considerations. Neurooncol Pract 2021; 8:526-538. [PMID: 34594567 DOI: 10.1093/nop/npab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A genetic predisposition to tumor development can be identified in up to 10% of pediatric patients with central nervous system (CNS) tumors. For some entities, the rate of an underlying predisposition is even considerably higher. In recent years, population-based approaches have helped to further delineate the role of cancer predisposition in pediatric oncology. Investigations for cancer predisposition syndrome (CPS) can be guided by clinical signs and family history leading to directed testing of specific genes. The increasingly adopted molecular analysis of tumor and often parallel blood samples with multi-gene panel, whole-exome, or whole-genome sequencing identifies additional patients with or without clinical signs. Diagnosis of a genetic predisposition may put an additional burden on affected families. However, information on a given cancer predisposition may be critical for the patient as potentially influences treatment decisions and may offer the patient and healthy carriers the chance to take part in intensified surveillance programs aiming at early tumor detection. In this review, we discuss some of the practical and ethical challenges resulting from the widespread use of new diagnostic techniques and the most important CPS that may manifest with brain tumors in childhood.
Collapse
Affiliation(s)
- Steffen Hirsch
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
7
|
Pediatric Oncologists' Experiences Returning and Incorporating Genomic Sequencing Results into Cancer Care. J Pers Med 2021; 11:jpm11060570. [PMID: 34207141 PMCID: PMC8235493 DOI: 10.3390/jpm11060570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/27/2022] Open
Abstract
Pediatric oncologists’ perspectives around returning and incorporating tumor and germline genomic sequencing (GS) results into cancer care are not well-described. To inform optimization of cancer genomics communication, we assessed oncologists’ experiences with return of genomic results (ROR), including their preparation/readiness for ROR, collaboration with genetic counselors (GCs) during ROR, and perceived challenges. The BASIC3 study paired pediatric oncologists with GCs to return results to patients’ families. We thematically analyzed 24 interviews with 12 oncologists at two post-ROR time points. Oncologists found pre-ROR meetings with GCs and geneticists essential to interpreting patients’ reports and communicating results to families. Most oncologists took a collaborative ROR approach where they discussed tumor findings and GCs discussed germline findings. Oncologists perceived many roles for GCs during ROR, including answering families’ questions and describing information in lay language. Challenges identified included conveying uncertain information in accessible language, limits of oncologists’ genetics expertise, and navigating families’ emotional responses. Oncologists emphasized how GCs’ and geneticists’ support was essential to ROR, especially for germline findings. GS can be successfully integrated into cancer care, but to account for the GC shortage, alternative ROR models and access to genetics resources will be needed to better support families and avoid burdening oncologists.
Collapse
|
8
|
Lee BM, Kraft SA. Fostering Relationships in Pediatric Oncology Research: A Relational Ethics Approach to Clinically Integrated Research. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2021; 21:85-88. [PMID: 33825652 DOI: 10.1080/15265161.2021.1891350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Brittany M Lee
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and University of Washington School of Medicine
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and University of Washington School of Medicine
| |
Collapse
|
9
|
Riggs MJ, Huang B, Chen Q, Bocklage T, Schuh MR, Poi M, Villano JL, Cavnar MJ, Arnold SM, Miller RW, Ueland FR, Kolesar JM. Factors Predicting Participation in the Prospective Genomic Sequencing Study, Total Cancer Care (TCC), in Kentucky. J Rural Health 2020; 38:5-13. [PMID: 32633045 DOI: 10.1111/jrh.12492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE Large-scale genomic sequencing studies are driving oncology drug development. However, rural populations, like those residing in Appalachian Kentucky, are underrepresented in these efforts. In this study, we determined the frequency of participation, reasons for nonparticipation, and factors predicting the decision to participate in the Total Cancer Care (TCC) prospective genomic cohort study. METHODS A total of 1,188 patients were invited to enroll in the TCC prospective cohort from December 2018 to May 2019. Declining patients were queried for their rationale for nonparticipation and their patient data were obtained from the Kentucky Cancer Registry (KCR). Logistic regression was used to assess the association between characteristics and study participation. The association of study participation with survival was modeled with Cox proportional-hazards regression. RESULTS 90.9% (1,081) patients consented to participate. In multivariate analysis, factors significantly associated with participation were age, gender, treatment status, and race. Though overall more women participated in the study, men were more likely to participate than women when invited (OR 1.57). Younger, Caucasian individuals who had received chemotherapy, but not surgery, were also more likely to participate. Patients in the Kentucky Appalachian cohort were primarily rural, had less educational attainment, and lower socioeconomic status. Kentucky Appalachian patients were no less likely to enroll in TCC than non-Appalachian patients. Consented individuals had higher overall survival compared to those who declined. CONCLUSION Though minorities, those with low socioeconomic status, and rural populations are underrepresented in genomic studies, they were no less likely to participate when given the opportunity, and participation was associated with better clinical outcomes.
Collapse
Affiliation(s)
- McKayla J Riggs
- Department of Obstetrics and Gynecology/Division of Gynecologic Oncology, University of Kentucky, Lexington, Kentucky
| | - Bin Huang
- Biostatistics and Bioinformatics Shared Resource Facility, Markey Cancer Center, Lexington, Kentucky
| | - Quan Chen
- Biostatistics and Bioinformatics Shared Resource Facility, Markey Cancer Center, Lexington, Kentucky
| | - Therese Bocklage
- Department of Pathology, University of Kentucky, Lexington, Kentucky
| | - Marissa R Schuh
- Precision Medicine Center, Markey Cancer Center, Lexington, Kentucky
| | | | - John L Villano
- Department of Hematology & Oncology, Internal Medicine, University of Kentucky, Lexington, Kentucky
| | - Michael J Cavnar
- Department of Surgery/Division of Surgical Oncology, University of Kentucky, Lexington, Kentucky
| | - Susanne M Arnold
- Department of Hematology & Oncology, Internal Medicine, University of Kentucky, Lexington, Kentucky
| | - Rachel W Miller
- Department of Obstetrics and Gynecology/Division of Gynecologic Oncology, University of Kentucky, Lexington, Kentucky
| | - Frederick R Ueland
- Department of Obstetrics and Gynecology/Division of Gynecologic Oncology, University of Kentucky, Lexington, Kentucky
| | - Jill M Kolesar
- Department of Pharmacy, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
10
|
Ryan NAJ, Donnelly L, Stocking K, Evans DG, Crosbie EJ. Feasibility of Gynaecologist Led Lynch Syndrome Testing in Women with Endometrial Cancer. J Clin Med 2020; 9:E1842. [PMID: 32545685 PMCID: PMC7355853 DOI: 10.3390/jcm9061842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/30/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022] Open
Abstract
A barrier to Lynch syndrome testing is the need for prior genetic counselling, a resource demanding process for both patients and healthcare services. We explored the impact of gynaecologist led Lynch syndrome testing in women with endometrial cancer. Women were approached before surgery, on the day of surgery or during routine follow up. Lynch syndrome testing was offered irrespective of age, family history or tumour characteristics. Women's reasons for being tested were explored using the Motivations and Concerns for GeNEtic Testing (MACGNET) instrument. The short form State-Trait Anxiety Inventory (STAI-6) was used to measure anxiety levels. Only 3/305 women declined Lynch syndrome testing. In total, 175/220 completed MACGNET and STAI-6 psychological instruments. The consent process took an average of 7min 36sec (SD 5min 16sec) to complete. The point of care at which consent was taken (before, day of surgery, during follow up) did not influence motivation for Lynch syndrome testing. Anxiety levels were significantly lower when women were consented during follow up (mean reversed STAI-6 score 32 vs 42, p = 0.001). Anxiety levels were not affected by familial cancer history (p = 0.41). Gynaecologist led Lynch syndrome testing is feasible and may even be desirable in endometrial cancer, especially when offered during routine follow up.
Collapse
Affiliation(s)
- Neil A. J. Ryan
- Division of Evolution and Genomic Medicine, University of Manchester, St Mary’s Hospital, Manchester M13 9WL, UK; (N.A.J.R.); (D.G.E.)
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary’s Hospital, Manchester M13 9WL, UK
| | - Louise Donnelly
- Nightingale and Prevent Breast Cancer Research Unit, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK;
- NIHR Greater Manchester Patient Safety Translational Research Centre, University of Manchester, Manchester M13 9PL, UK
| | - Katie Stocking
- Centre for Biostatistics, Faculty of Biology, Medicine and Health, University of Manchester, St Mary’s Hospital, Manchester M13 9WL, UK;
| | - D. Gareth Evans
- Division of Evolution and Genomic Medicine, University of Manchester, St Mary’s Hospital, Manchester M13 9WL, UK; (N.A.J.R.); (D.G.E.)
- Nightingale and Prevent Breast Cancer Research Unit, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK;
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Emma J. Crosbie
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary’s Hospital, Manchester M13 9WL, UK
- Division of Gynaecology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| |
Collapse
|
11
|
Barsan V, Paul M, Gorsi H, Malicki D, Elster J, Kuo DJ, Crawford J. Clinical Impact of Next-generation Sequencing in Pediatric Neuro-Oncology Patients: A Single-institutional Experience. Cureus 2019; 11:e6281. [PMID: 31827999 PMCID: PMC6892579 DOI: 10.7759/cureus.6281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The implementation of next-generation sequencing (NGS) in pediatric neuro-oncology may impact diagnosis, prognosis, therapeutic strategies, clinical trial enrollment, and germline risk. We retrospectively analyzed 58 neuro-oncology patients (31 boys, 27 girls, average age 7.4 years) who underwent NGS tumor profiling using a single commercially available platform on paraffin-embedded tissue obtained at diagnosis (20 low-grade gliomas, 12 high-grade gliomas, 11 embryonal tumors, four ependymal tumors, three meningeal tumors, and eight other CNS tumors) from May 2014 to December 2016. NGS results were analyzed for actionable mutations, variants of unknown significance and clinical impact. Seventy-four percent of patients (43 of 57) had actionable mutations; 26% had only variants of uncertain significance (VUS). NGS findings impacted treatment decisions in 55% of patients; 24% were given a targeted treatment based on NGS findings. Seven of eight patients with low-grade tumors treated with targeted therapy (everolimus, trametinib, or vemurafenib) experienced partial response or stable disease. All high-grade tumors had progressive disease on targeted therapy. Forty percent of patients had a revision or refinement of their diagnosis, and nine percent of patients were diagnosed with a previously unconfirmed cancer predisposition syndrome. Turnaround time between sample shipment and report generation averaged 13.4 ± 6.4 days. One sample failed due to insufficient DNA quantity. Our experience highlights the feasibility and clinical utility of NGS in the management of pediatric neuro-oncology patients. Future prospective clinical trials using NGS are needed to establish efficacy.
Collapse
Affiliation(s)
- Valentin Barsan
- Pediatric Hematology/Oncology, Stanford University School of Medicine, Palo Alto, USA
| | - Megan Paul
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - Hamza Gorsi
- Pediatric Hematology/Oncology, Children's Hospital of Michigan, Michigan, USA
| | - Denise Malicki
- Pathology, University of California San Diego, La Jolla, USA
| | - Jennifer Elster
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - Dennis J Kuo
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - John Crawford
- Neurosciences and Pediatrics, University of California San Diego, La Jolla, USA
| |
Collapse
|
12
|
Yang HT, Shah RH, Tegay D, Onel K. Precision oncology: lessons learned and challenges for the future. Cancer Manag Res 2019; 11:7525-7536. [PMID: 31616176 PMCID: PMC6698584 DOI: 10.2147/cmar.s201326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
The decreasing cost of and increasing capacity of DNA sequencing has led to vastly increased opportunities for population-level genomic studies to discover novel genomic alterations associated with both Mendelian and complex phenotypes. To translate genomic findings clinically, a number of health care institutions have worked collaboratively or individually to initiate precision medicine programs. These precision medicine programs involve designing patient enrollment systems, tracking electronic health records, building biobank repositories, and returning results with actionable matched therapies. As cancer is a paradigm for genetic diseases and new therapies are increasingly tailored to attack genetic susceptibilities in tumors, these precision medicine programs are largely driven by the urgent need to perform genetic profiling on cancer patients in real time. Here, we review the current landscape of precision oncology and highlight challenges to be overcome and examples of benefits to patients. Furthermore, we make suggestions to optimize future precision oncology programs based upon the lessons learned from these "first generation" early adopters.
Collapse
Affiliation(s)
- Hsih-Te Yang
- Medical Genetics and Human Genomics, Department of Pediatrics, Northwell Health, New York, NY, USA
| | - Ronak H Shah
- Medical Genetics and Human Genomics, Department of Pediatrics, Northwell Health, New York, NY, USA
- Center for Research Informatics and Innovation, The Feinstein Institute for Medical Research, Northwell Health, New York, NY, USA
| | - David Tegay
- Medical Genetics and Human Genomics, Department of Pediatrics, Northwell Health, New York, NY, USA
| | - Kenan Onel
- The Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| |
Collapse
|
13
|
Yu JH, Appelbaum PS, Brothers KB, Joffe S, Kauffman TL, Koenig BA, Prince AE, Scollon S, Wolf SM, Bernhardt BA, Wilfond BS. Consent for clinical genome sequencing: considerations from the Clinical Sequencing Exploratory Research Consortium. Per Med 2019; 16:325-333. [PMID: 31313633 DOI: 10.2217/pme-2018-0076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Implementing genome and exome sequencing in clinical practice presents challenges, including obtaining meaningful informed consent. Consent may be challenging due to test limitations such as uncertainties associated with test results and interpretation, complexity created by the potential for additional findings and high patient expectations. We drew on the experiences of research teams within the Clinical Sequencing Exploratory Research (CSER1) Consortium on informed consent for clinical genome and exome sequencing (CGES) to negotiate consensus considerations. We present six considerations for clinicians and 12 key points to communicate as they support patients in deciding whether to undergo CGES. These considerations and key points provide a helpful starting point for informed consent to CGES, grounded in the Clinical Sequencing Exploratory Research (CSER1) experience.
Collapse
Affiliation(s)
- Joon-Ho Yu
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.,Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital & Research Institute, Seattle, WA 98101, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center, NY, 10032, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Tia L Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Barbara A Koenig
- Program in Bioethics, University of California, San Francisco, CA 94143, USA
| | - Anya Er Prince
- College of Law, University of Iowa, Iowa City, IA 52242, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Wolf
- Law School; Medical School; Consortium on Law & Values in Health, Environment & the Life Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine & Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin S Wilfond
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.,Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital & Research Institute, Seattle, WA 98101, USA
| | | |
Collapse
|
14
|
Malek J, Pereira S, Robinson JO, Gutierrez AM, Slashinski MJ, Parsons DW, Plon SE, McGuire AL. Responsibility, culpability, and parental views on genomic testing for seriously ill children. Genet Med 2019; 21:2791-2797. [PMID: 31186522 DOI: 10.1038/s41436-019-0570-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/28/2019] [Indexed: 01/09/2023] Open
Abstract
PURPOSE We describe parental perceptions of and experiences with genomic sequencing (GS) in the care of seriously ill children. Understanding parents' perspectives is vital for clinicians caring for children, given the uptake of genomic technologies into clinical practice. METHODS Longitudinal, semistructured interviews were conducted with parents of pediatric cancer patients who underwent exome sequencing (ES) as a part of the BASIC3 study. Interviews were conducted at baseline, one to eight months after results disclosure, and approximately one year after disclosure. Using thematic qualitative analysis, parent interviews were coded with both inductive and deductive approaches. RESULTS Before receiving genomic information, parents indicated that they saw ES as something responsible parents would agree to if their child had cancer. Some parents talked about the possibility of sequencing affecting feelings of culpability for their child's cancer, worrying that they passed on a cancer-causing gene or made parenting decisions that caused the disease. However, after receiving their child's ES results many reported feeling relieved of guilt and worry, and felt they had fulfilled parental duties by agreeing to ES for their child. CONCLUSION These results reveal a layer of meaning that parents associate with GS that may inform clinicians' approach to care.
Collapse
Affiliation(s)
- Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA.
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Melody J Slashinski
- School of Public Health & Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - D Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
15
|
Gutierrez AM, Statham EE, Robinson JO, Slashinski MJ, Scollon S, Bergstrom KL, Street RL, Parsons DW, Plon SE, McGuire AL. Agents of empathy: How medical interpreters bridge sociocultural gaps in genomic sequencing disclosures with Spanish-speaking families. PATIENT EDUCATION AND COUNSELING 2019; 102:895-901. [PMID: 30581014 PMCID: PMC7197396 DOI: 10.1016/j.pec.2018.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 11/26/2018] [Accepted: 12/08/2018] [Indexed: 05/09/2023]
Abstract
OBJECTIVES To describe how linguistic tools used by interpreters during return of genomic sequencing results may have impacted communication with Spanish-speaking families, and to discuss the implications for the role of medical interpreters. METHODS Using discourse analysis, we identified and categorized the various ways hospital-based interpreters adapted clinicians' language in 37 audio-recorded sessions in which Spanish-speaking parents participating in a clinical trial received their child's genomic sequencing results from English-speaking clinicians. RESULTS We found that interpreters adapted clinicians' statements using five empathic linguistic tools: contextualization, encouragement, checking comprehension, endearment, and softening. Interpreters used an average of four linguistic tools per session, with contextualization and encouragement being the most frequently used. CONCLUSIONS Interpreters used empathic linguistic tools to alter clinicians' statements when communicating genomic information to Spanish-speaking families. Our findings demonstrate the critical role of interpreters as cultural mediators and facilitators of understanding for Spanish-speaking families. PRACTICE IMPLICATIONS This study expands upon the definition of clinical empathy in interpreter-mediated sessions. Our findings suggest that revisions of standards of medical interpretation practice may be warranted regarding interpreters' ability to adapt clinicians' language in a culturally sensitive manner during interpretation.
Collapse
Affiliation(s)
- Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, USA.
| | - Emily E Statham
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, USA.
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, USA.
| | - Melody J Slashinski
- School of Public Health & Health Sciences, University of Massachusetts at Amherst, Amherst, USA.
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, USA.
| | - Katie L Bergstrom
- Department of Pediatrics, Baylor College of Medicine, Houston, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, USA.
| | - Richard L Street
- Department of Communication, Texas A&M University, College Station, USA; Department of Medicine, Baylor College of Medicine, Houston, USA; Center for Innovation in Healthcare Quality, Effectiveness, & Safety, Michael E. DeBakey Veterans Affairs Medical Center, Houston, USA.
| | - D Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, USA.
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, USA.
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, USA.
| |
Collapse
|
16
|
Scollon S, Majumder MA, Bergstrom K, Wang T, McGuire AL, Robinson JO, Gutierrez AM, Lee CH, Hilsenbeck SG, Plon SE, Parsons DW, Street RL. Exome sequencing disclosures in pediatric cancer care: Patterns of communication among oncologists, genetic counselors, and parents. PATIENT EDUCATION AND COUNSELING 2019; 102:680-686. [PMID: 30482469 PMCID: PMC6440863 DOI: 10.1016/j.pec.2018.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/10/2018] [Accepted: 11/09/2018] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To examine communication patterns and behaviors during disclosure of exome sequencing (ES) results to parents of pediatric cancer patients, and describe common themes in parental communication. METHODS Using mixed methods, we analyzed transcripts of sessions where parents of pediatric cancer patients received ES results from an oncologist and genetic counselor. Seventy-six transcripts were analyzed for frequency of clinician information-giving, partnering-supportive talk, and active parent participation. A subset of 40 transcripts were analyzed using thematic content analysis. RESULTS Disclosures consisted mostly of clinician talk (84% of total talk), which was focused on providing information (62% of clinicians' utterances) with occasional partnering-supportive talk (7% of clinicians' utterances). Most parents assumed a passive, listening role (16% of total talk). Themes in parental communication included expressing relief and the significance of an answer, concern about sharing results and responsibility for inheritance, and seeking clarification of health implications of results. CONCLUSION Our finding of low levels of active parent participation during ES disclosures highlights the need to improve patient/parent engagement and understanding in a genetic setting. PRACTICE IMPLICATIONS Clinician communication strategies that could encourage parent participation and understanding include checking for parent understanding, partnership-building, and tailoring ES discussions to address parent concerns and preferences.
Collapse
Affiliation(s)
- Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States.
| | - Mary A Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, 1 Baylor Plaza, Suite 310D, Houston, TX 77030, United States.
| | - Katie Bergstrom
- Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States.
| | - Tao Wang
- Dan L Duncan Cancer Center, Baylor College of Medicine, 6620 Main St., Houston, TX 77030, United States.
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, 1 Baylor Plaza, Suite 310D, Houston, TX 77030, United States.
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, 1 Baylor Plaza, Suite 310D, Houston, TX 77030, United States.
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, 1 Baylor Plaza, Suite 310D, Houston, TX 77030, United States.
| | - Caroline H Lee
- Rice University, 6100 Main St., Houston, TX 77005, United States.
| | - Susan G Hilsenbeck
- Dan L Duncan Cancer Center, Baylor College of Medicine, 6620 Main St., Houston, TX 77030, United States.
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States; Dan L Duncan Cancer Center, Baylor College of Medicine, 6620 Main St., Houston, TX 77030, United States.
| | - D Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States.
| | - Richard L Street
- Department of Medicine, Baylor College of Medicine, 6620 Main St., Houston, TX 77030, United States; Department of Communication, Texas A&M University, TAMU 4234, College Station, TX 77843, United States; Center for Innovation in Healthcare Quality, Effectiveness, & Safety, Michael E. DeBakey Veterans Affairs Medical Center, 2450 Holcombe Blvd., Suite 01Y, Houston, TX 77021, United States.
| |
Collapse
|
17
|
Dheensa S, Crawford G, Salter C, Parker M, Fenwick A, Lucassen A. How do clinical genetics consent forms address the familial approach to confidentiality and incidental findings? A mixed-methods study. Fam Cancer 2019; 17:155-166. [PMID: 28405783 PMCID: PMC5770491 DOI: 10.1007/s10689-017-9994-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genetic test results can be relevant to patients and their relatives. Questions thus arise around whether clinicians regard genetic information as confidential to individuals or to families, and about how they broach this and other issues, including the potential for incidental findings, in consent (forms) for genetic testing. We conducted a content analysis of UK-wide genetic testing consent forms and interviewed 128 clinicians/laboratory scientists. We found that almost all genetic services offered patients multiple, sometimes unworkable, choices on forms, including an option to veto the use of familial genetic information to benefit relatives. Participants worried that documented choices were overriding professional judgement and cautioned against any future forms dictating practice around incidental findings. We conclude that ‘tick-box’ forms, which do little to enhance autonomy, are masking valid consent processes in clinical practice. As genome-wide testing becomes commonplace, we must re-consider consent processes, so that they protects patients’—and relatives’—interests.
Collapse
Affiliation(s)
- Sandi Dheensa
- Clinical Ethics and Law, Faculty of Medicine, Southampton General Hospital, University of Southampton, Room AB 203, MP 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, UK.
| | - Gillian Crawford
- Clinical Ethics and Law, Faculty of Medicine, Southampton General Hospital, University of Southampton, Room AB 203, MP 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, UK.,Wessex Clinical Genetic Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Claire Salter
- Wessex Clinical Genetic Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Michael Parker
- The Ethox Centre, Institute of Health Sciences, University of Oxford, Old Rd, Oxford, OX3 7LF, UK
| | - Angela Fenwick
- Clinical Ethics and Law, Faculty of Medicine, Southampton General Hospital, University of Southampton, Room AB 203, MP 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, UK
| | - Anneke Lucassen
- Clinical Ethics and Law, Faculty of Medicine, Southampton General Hospital, University of Southampton, Room AB 203, MP 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, UK.,Wessex Clinical Genetic Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| |
Collapse
|
18
|
Roberts JS, Gornick MC, Le LQ, Bartnik NJ, Zikmund-Fisher BJ, Chinnaiyan AM. Next-generation sequencing in precision oncology: Patient understanding and expectations. Cancer Med 2019; 8:227-237. [PMID: 30600607 PMCID: PMC6346219 DOI: 10.1002/cam4.1947] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Implementation of precision oncology interventions poses several challenges to informed consent and patient education. This study assessed cancer patients' understanding, expectations, and outcomes regarding participation in research examining the impact of matched tumor and germline sequencing on their clinical care. METHODS A total of 297 patients (mean age: 59 years; 50% female; 96% white) with refractory, metastatic cancer were surveyed, including 217 who completed surveys both before and after undergoing integrated whole exome and transcriptome sequencing as part of a larger clinical research study. RESULTS At baseline, the vast majority of patients expected to receive several potential direct benefits from study participation, including written reports of sequencing findings (88%), greater understanding of the causes of their cancer (74%), and participation in clinical trials for which sequencing results would make them eligible (84%). In most cases, these benefits were not realized by study completion. Despite explanations from study personnel to the contrary, most participants (67%-76%) presumed that incidental germline sequencing findings relevant to noncancerous health conditions (eg, diabetes) would automatically be disclosed to them. Patients reported low levels of concern about study risks at baseline and low levels of regret about study participation at follow-up. CONCLUSIONS Findings suggest that cancer patients participating in precision oncology intervention research have largely unfulfilled expectations of direct benefits related to their study participation. Increased focus on patient education to supplement the informed consent process may help manage patients' expectations regarding the extent and likelihood of benefits received as a result of undergoing genomic sequencing.
Collapse
Affiliation(s)
- J. Scott Roberts
- Department of Health Behavior and Health EducationUniversity of Michigan School of Public HealthAnn ArborMichigan
- Center for Bioethics & Social Sciences in MedicineUniversity of Michigan Medical SchoolAnn ArborMichigan
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichigan
| | - Michele C. Gornick
- Center for Bioethics & Social Sciences in MedicineUniversity of Michigan Medical SchoolAnn ArborMichigan
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichigan
- Department of Internal MedicineUniversity of Michigan Medical SchoolAnn ArborMichigan
| | - Lan Q. Le
- Department of Health Behavior and Health EducationUniversity of Michigan School of Public HealthAnn ArborMichigan
| | - Natalie J. Bartnik
- Department of Health Behavior and Health EducationUniversity of Michigan School of Public HealthAnn ArborMichigan
| | - Brian J. Zikmund-Fisher
- Department of Health Behavior and Health EducationUniversity of Michigan School of Public HealthAnn ArborMichigan
- Center for Bioethics & Social Sciences in MedicineUniversity of Michigan Medical SchoolAnn ArborMichigan
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichigan
- Department of Internal MedicineUniversity of Michigan Medical SchoolAnn ArborMichigan
| | - Arul M. Chinnaiyan
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichigan
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichigan
- Michigan Center for Translational PathologyUniversity of Michigan Medical SchoolAnn ArborMichigan
- Department of UrologyUniversity of Michigan Medical SchoolAnn ArborMichigan
- Howard Hughes Medical InstituteUniversity of Michigan Medical SchoolAnn ArborMichigan
| |
Collapse
|
19
|
Vos S, van Diest PJ, Ausems MGEM, van Dijk MR, de Leng WWJ, Bredenoord AL. Ethical considerations for modern molecular pathology. J Pathol 2018; 246:405-414. [DOI: 10.1002/path.5157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Shoko Vos
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Paul J van Diest
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Margreet GEM Ausems
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Marijke R van Dijk
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Wendy WJ de Leng
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Annelien L Bredenoord
- Department of Medical Humanities; University Medical Center Utrecht; Utrecht The Netherlands
| |
Collapse
|
20
|
Byrjalsen A, Stoltze U, Wadt K, Hjalgrim LL, Gerdes AM, Schmiegelow K, Wahlberg A. Pediatric cancer families’ participation in whole-genome sequencing research in Denmark: Parent perspectives. Eur J Cancer Care (Engl) 2018; 27:e12877. [DOI: 10.1111/ecc.12877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 04/04/2018] [Accepted: 06/08/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Anna Byrjalsen
- Department of Clinical Genetics; Rigshospitalet; Copenhagen Denmark
- Department of Paediatrics and Adolescent Medicine; Rigshospitalet; Copenhagen Denmark
| | - Ulrik Stoltze
- Department of Paediatrics and Adolescent Medicine; Rigshospitalet; Copenhagen Denmark
| | - Karin Wadt
- Department of Clinical Genetics; Rigshospitalet; Copenhagen Denmark
| | - Lisa Lyngsie Hjalgrim
- Department of Paediatrics and Adolescent Medicine; Rigshospitalet; Copenhagen Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics; Rigshospitalet; Copenhagen Denmark
- Department of Clinical Medicine; University of Copenhagen; Copenhagen Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine; Rigshospitalet; Copenhagen Denmark
- Department of Clinical Medicine; University of Copenhagen; Copenhagen Denmark
| | - Ayo Wahlberg
- Department of Anthropology; University of Copenhagen; Copenhagen Denmark
| |
Collapse
|
21
|
Oberg JA, Ruiz J, Ali-Shaw T, Schlechtweg KA, Ricci A, Kung AL, Chung WK, Appelbaum PS, Glade Bender JL, Levine JM. Whole-Genome and Whole-Exome Sequencing in Pediatric Oncology: An Assessment of Parent and Young Adult Patient Knowledge, Attitudes, and Expectations. JCO Precis Oncol 2018; 2:1700104. [PMID: 32913997 DOI: 10.1200/po.17.00104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Purpose The complexity of results generated from whole-genome sequencing (WGS) and whole-exome sequencing (WES) adds challenges to obtaining informed consent in pediatric oncology. Little is known about knowledge of WGS and WES in this population, and no validated tools exist in pediatric oncology. Methods We developed and psychometrically evaluated a novel WGS and WES knowledge questionnaire, the Precision in Pediatric Sequencing Knowledge Questionnaire (PIPseqKQ), to identify levels of understanding among parents and young adult cancer survivors (≥ 18 years old), off therapy for at least 1 year from a single-institution pediatric oncology outpatient clinic. Participants also completed health literacy and numeracy questionnaires. All participants provided written informed consent. Results One hundred eleven participants were enrolled: 76 were parents, and 35 were young adults. Of the total cohort, 77 (69%) were female, 63 (57%) self-identified as white, and 74 (67%) self-identified as non-Hispanic. Sixty-six (59%) had less than a college degree. Adequate health literacy (n = 87; 80%) and numeracy (n = 89; 80%) were demonstrated. Internal consistency was high (Cronbach's α = .88), and test-retest reliability was greater than the 0.7 minimum requirement. Scores were highest for genetic concepts related to health and cancer and lowest for WGS and WES concepts. Health literacy and educational attainment were significantly associated with PIPseqKQ scores. Overall, participants felt the benefits of WGS and WES outweighed the potential risks. Conclusion Parents and young adult cancer survivors have some genetics knowledge, but they lack knowledge about WGS and WES. The PIPseqKQ is a reliable tool that can identify deficits in knowledge, identify perceptions of risks and benefits of WGS and WES, and help clinicians tailor their consent discussions to best fit families. The PIPseqKQ also may inform the development of educational tools to better facilitate the informed consent process in pediatric oncology.
Collapse
Affiliation(s)
- Jennifer A Oberg
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Jenny Ruiz
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Trisha Ali-Shaw
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Kathryn A Schlechtweg
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Angela Ricci
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Andrew L Kung
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Wendy K Chung
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Paul S Appelbaum
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Julia L Glade Bender
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| | - Jennifer M Levine
- , , , , , , and , Herbert Irving Comprehensive Cancer Center and Columbia University Medical Center; and , NewYork-Presbyterian Hospital; and , Columbia University College of Physicians and Surgeons, New York, NY
| |
Collapse
|
22
|
Amendola LM, Robinson JO, Hart R, Biswas S, Lee K, Bernhardt BA, East K, Gilmore MJ, Kauffman TL, Lewis KL, Roche M, Scollon S, Wynn J, Blout C. Why Patients Decline Genomic Sequencing Studies: Experiences from the CSER Consortium. J Genet Couns 2018; 27:1220-1227. [PMID: 29497922 DOI: 10.1007/s10897-018-0243-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/18/2018] [Indexed: 01/02/2023]
Abstract
Clinical and research settings are increasingly incorporating genomic sequencing (GS) technologies. Previous research has explored reasons for declining genetic testing and participation in genetic studies; however, there is a dearth of literature regarding why potential participants decline participation in GS research, and if any of these reasons are unique to GS. This knowledge is essential to promote informed decision-making and identify potential barriers to research participation and clinical implementation. We aggregated data from seven sites across the National Institutes of Health's Clinical Sequencing Exploratory Research (CSER) consortium on each project's procedures for recruitment, and rates of and reasons for decline. Data were analyzed using descriptive statistics. The decline rate for enrollment at the seven CSER sites ranged from 12 to 64% (median 28%) and varied based on age and disease status. Projects differed in their protocols for approaching potential participants and obtaining informed consent. Reasons for declining GS research were reported for 1088 potential participants. Commonly cited reasons were similar to those reported for clinical single gene testing and non-GS genetic research. The most frequently cited reason for decline was study logistics (35%); thus, addressing logistical barriers to enrollment may positively impact GS study recruitment. Privacy and discrimination concerns were cited by 13% of decliners, highlighting the need for researchers and providers to focus educational efforts in this area. The potential psychological burden of pursuing and receiving results from GS and not wanting to receive secondary findings, a concern specific to GS, have been cited as concerns in the literature. A minority of potential participants cited psychological impact (8%) or not wanting to receive secondary findings (2%) as reasons for decline, suggesting that these concerns were not major barriers to participation in these GS studies. Further research is necessary to explore the impact, if any, of different participant groups or study protocols on rates of decline for GS studies. Future studies exploring GS implementation should consider using standardized collection methods to examine reasons for decline in larger populations and more diverse healthcare settings.
Collapse
Affiliation(s)
- Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ragan Hart
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sawona Biswas
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kaitlyn Lee
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Marian J Gilmore
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR, 97227, USA
| | - Tia L Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, 97227, USA
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Myra Roche
- Departments of Pediatrics and Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY, 10032, USA
| | - Carrie Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| |
Collapse
|
23
|
Ahmed AA, Abedalthagafi M. Cancer diagnostics: The journey from histomorphology to molecular profiling. Oncotarget 2018; 7:58696-58708. [PMID: 27509178 PMCID: PMC5295463 DOI: 10.18632/oncotarget.11061] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management.
Collapse
Affiliation(s)
- Atif A Ahmed
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Malak Abedalthagafi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Saudi Human Genome Laboratory, Department of Pathology, King Fahad Medical City, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| |
Collapse
|
24
|
Perakslis ED, Kohane IS. Treating the enigmatic "exceptional responders" as patients with undiagnosed diseases. Sci Transl Med 2018; 8:340ed8. [PMID: 27225181 DOI: 10.1126/scitranslmed.aaf6146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Eric D Perakslis
- Eric D. Perakslis is Senior Vice President, Data Science, Takeda Oncology, and Visiting Faculty, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA. S. Kohane is Chair and Marion V. Nelson Professor of the Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
| | - Isaac S Kohane
- Eric D. Perakslis is Senior Vice President, Data Science, Takeda Oncology, and Visiting Faculty, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA. S. Kohane is Chair and Marion V. Nelson Professor of the Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
25
|
Leavey PJ, Hilden JM, Matthews D, Dandoy C, Badawy SM, Shah M, Wayne AS, Hord J. The American Society of Pediatric Hematology/Oncology workforce assessment: Part 2-Implications for fellowship training. Pediatr Blood Cancer 2018; 65. [PMID: 29068565 DOI: 10.1002/pbc.26765] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/18/2017] [Indexed: 11/10/2022]
Abstract
The American Society of Pediatric Hematology/Oncology (ASPHO) solicited information from division directors and fellowship training program directors to capture pediatric hematology/oncology (PHO) specific workforce data of 6 years (2010-2015), in response to an increase in graduating fellows during that time. Observations included a stable number of physicians and advanced practice providers (APPs) in clinical PHO, an increased proportion of APPs hired compared to physicians, and an increase in training-level first career positions. Rapid changes in the models of PHO care have significant implications to current and future trainees and require continued analysis to understand the evolving discipline of PHO.
Collapse
Affiliation(s)
- P J Leavey
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - J M Hilden
- Children's Hospital Colorado, Denver, Colorado
| | - D Matthews
- Fred Hutchinson Cancer Research Center, Seattle Children's Hospital, Seattle, Washington
| | - C Dandoy
- Cincinnati Children's Hospital, Cincinnati, Ohio
| | - S M Badawy
- Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - M Shah
- Texas Children's Hospital, Houston, Texas
| | - A S Wayne
- Children's Hospital Los Angeles, The Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - J Hord
- Children's Medical Center of Akron, Akron, Ohio
| | | |
Collapse
|
26
|
Roberts JS, Robinson JO, Diamond PM, Bharadwaj A, Christensen KD, Lee KB, Green RC, McGuire AL. Patient understanding of, satisfaction with, and perceived utility of whole-genome sequencing: findings from the MedSeq Project. Genet Med 2018; 20:1069-1076. [PMID: 29300387 PMCID: PMC6034997 DOI: 10.1038/gim.2017.223] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/02/2017] [Indexed: 12/02/2022] Open
Abstract
Purpose To examine patients’ experiences with clinical use of whole genome sequencing (WGS). Methods A randomized trial compared primary care and cardiology patients receiving WGS and family health history (FH) information or FH information alone. 202 patients were surveyed before (BL) and up to six months (6M) after disclosure of results. Results Patients (mean age = 55 years; 50% female; 81% college graduates) reported low levels of decisional regret (mean: 7.1/100) and high satisfaction with physicians’ disclosure of results (median = 29 / 30). Compared to the FH-only arm, patients receiving WGS results were more likely to report learning accurate disease risk information (OR = 7.45) and findings influential for medical treatment (OR = 2.39). Sessions where WGS results were disclosed took longer (30 vs. 15 minutes), particularly for primary care patients. Patients’ expected utility of sequencing at BL was higher than perceived utility at 6M in several domains, including impacting medical decision-making (87% vs. 54%) and influencing medication choice (73% vs. 32%). Conclusions Patients were satisfied with their physicians’ communication of WGS results and perceived them as medically useful. Discrepancies in expected versus perceived utility of WGS results suggest a need to temper patients’ expectations about its potential benefits.
Collapse
Affiliation(s)
- J Scott Roberts
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Pamela M Diamond
- Division of Health Promotion & Behavioral Sciences, University of Texas Houston School of Public Health, Houston, Texas, USA
| | - Archana Bharadwaj
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Kurt D Christensen
- Division of Genetics, Department of Medicine, Brigham and Women's, Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn B Lee
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's, Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | | |
Collapse
|
27
|
Gutierrez AM, Robinson JO, Statham EE, Scollon S, Bergstrom KL, Slashinski MJ, Parsons DW, Plon SE, McGuire AL, Street RL. Portero versus portador: Spanish interpretation of genomic terminology during whole exome sequencing results disclosure. Per Med 2017; 14:503-514. [PMID: 29749861 DOI: 10.2217/pme-2017-0040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIM Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. PATIENTS & METHODS Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. RESULTS Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. CONCLUSION Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.
Collapse
Affiliation(s)
- Amanda M Gutierrez
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Jill O Robinson
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Emily E Statham
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Katie L Bergstrom
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Melody J Slashinski
- School of Public Health & Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Donald W Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Amy L McGuire
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Richard L Street
- Department of Communication, Texas A&M University, College Station, TX, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Center for Innovation in Healthcare Quality, Effectiveness, & Safety, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| |
Collapse
|
28
|
Scherr CL, Dean M, Clayton MF, Hesse BW, Silk K, Street RL, Krieger J. A Research Agenda for Communication Scholars in the Precision Medicine Era. JOURNAL OF HEALTH COMMUNICATION 2017; 22:839-848. [PMID: 28956728 DOI: 10.1080/10810730.2017.1363324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The 2015 announcement of the Precision Medicine Initiative (PMI) galvanized and energized efforts to reconsider medical practice through tailoring of prevention and treatment recommendations based on genetics, environment, and lifestyle. Numerous disciplines contributed white papers identifying challenges associated with PMI and calling for discipline-specific research that might provide solutions to such challenges. Throughout these white papers, the prominence of communication in achieving the PMI's goals is obviously apparent. In this article, we highlight opportunities for communication scholars' contributions to the PMI based on challenges identified in white papers from other disciplines and work already conducted by research teams in the field of communication.
Collapse
Affiliation(s)
- Courtney L Scherr
- a Department of Communication Studies , Northwestern University , Evanston , Illinois , USA
| | - Marleah Dean
- b Department of Communication , University of South, Florida , Tampa , Florida , USA
| | | | - Bradford W Hesse
- d Health Communication and Informatics Research Branch , National Cancer Institute , Bethesda , Maryland , USA
| | - Kami Silk
- e Department of Communication , Michigan State University , East Lansing , Michigan , USA
| | - Richard L Street
- f Department of Communication , Texas A&M University , College Station , Texas , USA
| | - Janice Krieger
- g STEM Translational Communication Center, College of Journalism and Communications , University of Florida , Gainesville , Florida , USA
| |
Collapse
|
29
|
Malek J, Slashinski MJ, Robinson JO, Gutierrez AM, Parsons DW, Plon SE, McCullough LB, McGuire AL. Parental Perspectives on Whole Exome Sequencing in Pediatric Cancer: A Typology of Perceived Utility. JCO Precis Oncol 2017; 1. [PMID: 31886451 DOI: 10.1200/po.17.00010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Purpose To explore how parents of pediatric cancer patients perceived the utility of clinical tumor and germline whole-exome sequencing (WES) results. Patients and Methods We conducted longitudinal interviews with parents of a diverse pediatric cancer population before disclosure of WES results (n=64), then one to eight months (n=33) after disclosure. Interview transcripts were analyzed using a thematic qualitative approach. Results Parents identified a broad range of types of utility for their child's WES results. Even when results did not affect their child's current treatment, they expressed optimism about future clinical utility for their child, themselves, and other family members. Parents also reported experiencing psychological utility including peace of mind, relief of guilt, and satisfaction of curiosity. Pragmatic utility, such as the ability to plan for the future and make better reproductive decisions, was also described. Conclusion Parents of pediatric cancer patients perceive WES to have broad utility, including psychological and pragmatic utility, even if there is no direct impact on clinical care. Further work will need to consider how the value of genomic information should be characterized, how risks and benefits should be described, and how these results should inform recommendations and decisions about using WES.
Collapse
Affiliation(s)
- Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Melody J Slashinski
- School of Public Health & Health Sciences, University of Massachusetts, Amherst, MA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - D Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Laurence B McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| |
Collapse
|
30
|
Johnson LM, Hamilton KV, Valdez JM, Knapp E, Baker JN, Nichols KE. Ethical considerations surrounding germline next-generation sequencing of children with cancer. Expert Rev Mol Diagn 2017; 17:523-534. [PMID: 28399664 DOI: 10.1080/14737159.2017.1316665] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The advent of next-generation sequencing (NGS) has introduced an exciting new era in biomedical research. NGS forms the foundation of current genetic testing approaches, including targeted gene panel testing, as well as more comprehensive whole-exome and whole-genome sequencing. Together, these approaches promise to provide critical insights into the understanding of health and disease. However, with NGS testing come many ethical questions and concerns, particularly when testing involves children. These concerns are especially relevant for children with cancer, where the testing of tumor and germline tissues is increasingly being incorporated into clinical care. Areas covered: In this manuscript, we explore the key ethical considerations related to conducting germline NGS testing in pediatric oncology, focusing on the four main principles of beneficence, non-maleficence, autonomy and justice. Expert commentary: The ethical issues surrounding germline NGS testing are complex and result in part from our limited understanding of the medical relevance of many of the results obtained and poor knowledge of the impacts of testing, both beneficial and detrimental, on patients and their families. In this article we discuss the risks and benefits of germline NGS testing and the arguments for and against such testing in children with cancer.
Collapse
Affiliation(s)
- Liza-Marie Johnson
- a Section of Bioethics , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Kayla V Hamilton
- b Division of Cancer Predisposition , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Jessica M Valdez
- b Division of Cancer Predisposition , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Esther Knapp
- c Department of Pediatrics , University of Louisville , Louisville , KY , USA
| | - Justin N Baker
- d Division of Quality of Life and Palliative Care , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Kim E Nichols
- b Division of Cancer Predisposition , St. Jude Children's Research Hospital , Memphis , TN , USA
| |
Collapse
|
31
|
Potter SL, Venkatramani R, Wenderfer S, Graham BH, Vasudevan SA, Sher A, Wu H, Wheeler DA, Yang Y, Eng CM, Gibbs RA, Roy A, Plon SE, Parsons DW. Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia. Pediatr Blood Cancer 2017; 64:10.1002/pbc.26286. [PMID: 27748010 PMCID: PMC5469213 DOI: 10.1002/pbc.26286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/25/2016] [Accepted: 09/08/2016] [Indexed: 01/10/2023]
Abstract
Pediatric renal cell carcinoma (RCC) is a rare cancer that can be associated with inherited diseases including tuberous sclerosis complex (TSC) caused by germline mutations in TSC1 or TSC2. Somatic mutations in TSC1 and TSC2 have also been reported in adult RCC, which predict response to mTOR inhibitors. Here, we present the first case of RCC in a child with methylmalonic acidemia (MMA). Clinical whole exome sequencing of blood and tumor samples confirmed the diagnosis of MMA and revealed two somatic inactivating mutations in TSC2, suggesting the potential consideration of an mTOR inhibitor in the event of tumor recurrence.
Collapse
Affiliation(s)
- Samara L. Potter
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Rajkumar Venkatramani
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Scott Wenderfer
- Department of Pediatric, Division of Nephrology, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sanjeev A. Vasudevan
- Department of Surgery, Texas Children’s Hospital, Houston, Texas,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas,The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Andrew Sher
- Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - Hao Wu
- Department of Pathology, Texas Children’s Hospital, Houston, Texas,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - David A. Wheeler
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Angshumoy Roy
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, Texas,The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Department of Pathology, Texas Children’s Hospital, Houston, Texas,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Sharon E. Plon
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, Texas,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - D. Williams Parsons
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, Texas,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
32
|
Reasons for Declining Preconception Expanded Carrier Screening Using Genome Sequencing. J Genet Couns 2017; 26:971-979. [PMID: 28315134 DOI: 10.1007/s10897-017-0074-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/18/2017] [Indexed: 01/03/2023]
Abstract
Genomic carrier screening can identify more disease-associated variants than existing carrier screening methodologies, but its utility from patients' perspective is not yet established. A randomized controlled trial for preconception genomic carrier screening provided an opportunity to understand patients' decisions about whether to accept or decline testing. We administered a survey to potential genomic carrier screening recipients who declined participation (N = 240) to evaluate their reasons for doing so. Two thirds of women declined participation. We identified major themes describing reasons these individuals declined to participate; the most common were time limitation, lack of interest, not wanting to know the information, and potential cause of worry or anxiety. Most women eligible for genomic carrier screening indicated that their reasons for opting out were due to logistical issues rather than opposing the rationale for testing. As expanded carrier screening and genomic sequencing become a more routine part of clinical care, it is anticipated there will be variable uptake from individuals for this testing. Thus, the advancement of clinical carrier screening from single genes, to expanded screening panels, to an exome- or genome-wide platform, will require approaches that respect individual choice to receive genetic testing for reproductive risk assessment.
Collapse
|
33
|
Mody RJ, Prensner JR, Everett J, Parsons DW, Chinnaiyan AM. Precision medicine in pediatric oncology: Lessons learned and next steps. Pediatr Blood Cancer 2017; 64:10.1002/pbc.26288. [PMID: 27748023 PMCID: PMC5683396 DOI: 10.1002/pbc.26288] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/19/2016] [Accepted: 09/05/2016] [Indexed: 01/01/2023]
Abstract
The maturation of genomic technologies has enabled new discoveries in disease pathogenesis as well as new approaches to patient care. In pediatric oncology, patients may now receive individualized genomic analysis to identify molecular aberrations of relevance for diagnosis and/or treatment. In this context, several recent clinical studies have begun to explore the feasibility and utility of genomics-driven precision medicine. Here, we review the major developments in this field, discuss current limitations, and explore aspects of the clinical implementation of precision medicine, which lack consensus. Lastly, we discuss ongoing scientific efforts in this arena, which may yield future clinical applications.
Collapse
Affiliation(s)
- Rajen J. Mody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - John R. Prensner
- Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts
| | - Jessica Everett
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - D. Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas,Texas Children’s Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Arul M. Chinnaiyan
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan,Department of Pathology and Michigan Center for Translational Pathology (MCTP), University of Michigan Medical School, Ann Arbor, Michigan,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan
| |
Collapse
|
34
|
Pediatric Whole Exome Sequencing: an Assessment of Parents’ Perceived and Actual Understanding. J Genet Couns 2016; 26:792-805. [DOI: 10.1007/s10897-016-0052-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 11/27/2016] [Indexed: 01/10/2023]
|
35
|
Marron JM, DuBois SG, Bender JG, Kim A, Crompton BD, Meyer SC, Janeway KA, Mack JW. Patient/parent perspectives on genomic tumor profiling of pediatric solid tumors: The Individualized Cancer Therapy (iCat) experience. Pediatr Blood Cancer 2016; 63:1974-82. [PMID: 27429135 PMCID: PMC5611837 DOI: 10.1002/pbc.26137] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/26/2016] [Accepted: 06/15/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND Genomic tumor profiling (GTP) plays an important role in the care of many adult cancer patients. Its role in pediatric oncology is still evolving, with only a subset of patients currently expected to receive clinically significant results. Little is known about perspectives of pediatric oncology patients/parents on GTP. PROCEDURE We surveyed individuals who previously underwent GTP through the iCat (Individualized Cancer Therapy) pilot study of molecular profiling in children with relapsed, refractory, and high-risk solid tumors at four pediatric cancer centers. Following return of profiling results, a cross-sectional survey was offered to the patient, if he or she was 18 years or older at enrollment, or parent, if he or she was under 18 years of age. Forty-five surveys (85% response) were completed. RESULTS Eighty-nine percent (39/44) of respondents reported hoping participation would help find cures for future patients, while 59% (26/44) hoped it would increase their/their child's chance of cure. Most had few concerns about GTP, but 12% (5/43) worried they would learn their/their child's cancer was less treatable or more aggressive than previously thought. Sixty-four percent (29/45) reported feeling their participation had helped others and 44% (20/45) felt they had helped themselves/their own child, despite only one substudy subject receiving targeted therapy matched to GTP findings. Fifty-four percent (21/39) wished to receive all available profiling data, including findings unrelated to cancer and of unclear significance. CONCLUSIONS Participants in pediatric GTP research perceive benefits of GTP to themselves and others, but expectations of personal benefits of GTP may exceed actual positive impact. These issues warrant consideration during consent discussions about GTP research participation.
Collapse
Affiliation(s)
- Jonathan M. Marron
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts,Office of Ethics, Boston Children’s Hospital, Boston, Massachusetts
| | - Steven G. DuBois
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Julia Glade Bender
- Division of Pediatric Hematology, Oncology, and Stem Cell Transplantation, Columbia University Medical Center, New York, New York
| | - AeRang Kim
- Department of Pediatric Oncology, Children’s National Medical Center, Washington, District of Columbia
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Stephanie C. Meyer
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Katherine A. Janeway
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Jennifer W. Mack
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| |
Collapse
|
36
|
Lin FY, Bergstrom K, Person R, Bavle A, Ballester LY, Scollon S, Raesz-Martinez R, Jea A, Birchansky S, Wheeler DA, Berg SL, Chintagumpala MM, Adesina AM, Eng C, Roy A, Plon SE, Parsons DW. Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle. Cold Spring Harb Mol Case Stud 2016; 2:a001057. [PMID: 27626068 PMCID: PMC5002928 DOI: 10.1101/mcs.a001057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individual's cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p.N546K) and PIK3CA (p.H1047R) and a germline pathogenic variant in PTPN11 (p.N308S) diagnostic for Noonan syndrome. The molecular landscape of RGNT is not well-described, but these data are consistent with prior observations regarding the importance of the interconnected MAPK and PI3K/AKT/mTOR signaling pathways in this rare tumor. The co-occurrence of FGFR1, PIK3CA, and PTPN11 alterations provides further evidence for consideration of RGNT as a distinct molecular entity from pediatric low-grade gliomas and suggests potential therapeutic strategies for this patient in the event of tumor recurrence as novel agents targeting these pathways enter pediatric clinical trials. Although RGNT has not been definitively linked with cancer predisposition syndromes, two prior cases have been reported in patients with RASopathies (Noonan syndrome and neurofibromatosis type 1 [NF1]), providing an additional link between these tumors and the mitogen-activated protein kinase (MAPK) signaling pathway. In summary, this case provides an example of the potential for genome-scale sequencing technologies to provide insight into the biology of rare tumors and yield both tumor and germline results of potential relevance to patient care.
Collapse
Affiliation(s)
- Frank Y Lin
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Katie Bergstrom
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard Person
- Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Abhishek Bavle
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Leomar Y Ballester
- Department of Pathology, Texas Children's Hospital Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sarah Scollon
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Robin Raesz-Martinez
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Andrew Jea
- Division of Pediatric Neurosurgery, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sherri Birchansky
- Department of Pediatric Radiology, Texas Children's Hospital Baylor College of Medicine, Houston, Texas 77030, USA
| | - David A Wheeler
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;; Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Stacey L Berg
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Murali M Chintagumpala
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adekunle M Adesina
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;; Department of Pathology, Texas Children's Hospital Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christine Eng
- Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Angshumoy Roy
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;; Department of Pathology, Texas Children's Hospital Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sharon E Plon
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;; Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - D Williams Parsons
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;; Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
37
|
Bissig-Choisat B, Kettlun-Leyton C, Legras XD, Zorman B, Barzi M, Chen LL, Amin MD, Huang YH, Pautler RG, Hampton OA, Prakash MM, Yang D, Borowiak M, Muzny D, Doddapaneni HV, Hu J, Shi Y, Gaber MW, Hicks MJ, Thompson PA, Lu Y, Mills GB, Finegold M, Goss JA, Parsons DW, Vasudevan SA, Sumazin P, López-Terrada D, Bissig KD. Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer. J Hepatol 2016; 65:325-33. [PMID: 27117591 PMCID: PMC5668139 DOI: 10.1016/j.jhep.2016.04.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Pediatric liver cancer is a rare but serious disease whose incidence is rising, and for which the therapeutic options are limited. Development of more targeted, less toxic therapies is hindered by the lack of an experimental animal model that captures the heterogeneity and metastatic capability of these tumors. METHODS Here we established an orthotopic engraftment technique to model a series of patient-derived tumor xenograft (PDTX) from pediatric liver cancers of all major histologic subtypes: hepatoblastoma, hepatocellular cancer and hepatocellular malignant neoplasm. We utilized standard (immuno) staining methods for histological characterization, RNA sequencing for gene expression profiling and genome sequencing for identification of druggable targets. We also adapted stem cell culturing techniques to derive two new pediatric cancer cell lines from the xenografted mice. RESULTS The patient-derived tumor xenografts recapitulated the histologic, genetic, and biological characteristics-including the metastatic behavior-of the corresponding primary tumors. Furthermore, the gene expression profiles of the two new liver cancer cell lines closely resemble those of the primary tumors. Targeted therapy of PDTX from an aggressive hepatocellular malignant neoplasm with the MEK1 inhibitor trametinib and pan-class I PI3 kinase inhibitor NVP-BKM120 resulted in significant growth inhibition, thus confirming this PDTX model as a valuable tool to study tumor biology and patient-specific therapeutic responses. CONCLUSIONS The novel metastatic xenograft model and the isogenic xenograft-derived cell lines described in this study provide reliable tools for developing mutation- and patient-specific therapies for pediatric liver cancer. LAY SUMMARY Pediatric liver cancer is a rare but serious disease and no experimental animal model currently captures the complexity and metastatic capability of these tumors. We have established a novel animal model using human tumor tissue that recapitulates the genetic and biological characteristics of this cancer. We demonstrate that our patient-derived animal model, as well as two new cell lines, are useful tools for experimental therapies.
Collapse
Affiliation(s)
- Beatrice Bissig-Choisat
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Claudia Kettlun-Leyton
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Xavier D. Legras
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Barry Zorman
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Mercedes Barzi
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Leon L. Chen
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mansi D. Amin
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yung-Hsin Huang
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Robia G. Pautler
- Small Animal Imaging Facility, Texas Children’s Hospital, Houston, TX, USA,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Oliver A. Hampton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Masand M. Prakash
- Department of Pediatric Radiology, Texas Children’s Hospital, Houston, TX, USA
| | - Diane Yang
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA,Graduate Program Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Malgorzata Borowiak
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA,Graduate Program Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA,McNair Medical Institute, Houston, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yan Shi
- Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation and Division of Hepatobiliary Surgery, Baylor College of Medicine, Houston, TX, USA,Department of Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - M. Waleed Gaber
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Small Animal Imaging Facility, Texas Children’s Hospital, Houston, TX, USA,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - M. John Hicks
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | | | - Yiling Lu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B. Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Milton Finegold
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA,Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - John A. Goss
- Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation and Division of Hepatobiliary Surgery, Baylor College of Medicine, Houston, TX, USA,Department of Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - D. Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Sanjeev A. Vasudevan
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA,Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation and Division of Hepatobiliary Surgery, Baylor College of Medicine, Houston, TX, USA,Department of Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - Pavel Sumazin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Dolores López-Terrada
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA,Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Karl-Dimiter Bissig
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA; Graduate Program Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
38
|
Green RC, Goddard KAB, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. Am J Hum Genet 2016; 98:1051-1066. [PMID: 27181682 DOI: 10.1016/j.ajhg.2016.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 12/11/2022] Open
Abstract
Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.
Collapse
Affiliation(s)
- Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA.
| | - Katrina A B Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, NY 10032, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sawona Biswas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Wylie Burke
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA; Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Pathology and Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI 48109, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10029, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN 37203, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jeremy R Garrett
- Children's Mercy Bioethics Center, Children's Mercy Hospital, Kansas City, MO 64108, USA; Departments of Pediatrics and Philosophy, University of Missouri - Kansas City, Kansas City, MO 64110, USA
| | - Stacy W Gray
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gail E Henderson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Carolyn M Hutter
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Pasi A Janne
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David Kaufman
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Barbara A Koenig
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Ian D Krantz
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Laurence McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean McEwen
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amy McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey Ou
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Donald W Parsons
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sharon E Plon
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA; Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, MA 02139, USA
| | - J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
| | - Joseph S Salama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Spinner
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Holly K Tabor
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Peter Tarczy-Hornoch
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington, Seattle, WA 98105, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Nikhil Wagle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Karen Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Benjamin S Wilfond
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Kirk Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan M Wolf
- Law School, Medical School, and Consortium on Law and Values in Health, Environment, & the Life Sciences, Minneapolis, University of Minnesota, MN 55455, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10029, USA
| | - Joon-Ho Yu
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
39
|
Recommendations for the integration of genomics into clinical practice. Genet Med 2016; 18:1075-1084. [PMID: 27171546 DOI: 10.1038/gim.2016.17] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/19/2016] [Indexed: 12/21/2022] Open
Abstract
The introduction of diagnostic clinical genome and exome sequencing (CGES) is changing the scope of practice for clinical geneticists. Many large institutions are making a significant investment in infrastructure and technology, allowing clinicians to access CGES, especially as health-care coverage begins to extend to clinically indicated genomic sequencing-based tests. Translating and realizing the comprehensive clinical benefits of genomic medicine remain a key challenge for the current and future care of patients. With the increasing application of CGES, it is necessary for geneticists and other health-care providers to understand its benefits and limitations in order to interpret the clinical relevance of genomic variants identified in the context of health and disease. New, collaborative working relationships with specialists across diverse disciplines (e.g., clinicians, laboratorians, bioinformaticians) will undoubtedly be key attributes of the future practice of clinical genetics and may serve as an example for other specialties in medicine. These new skills and relationships will also inform the development of the future model of clinical genetics training curricula. To address the evolving role of the clinical geneticist in the rapidly changing climate of genomic medicine, two Clinical Genetics Think Tank meetings were held that brought together physicians, laboratorians, scientists, genetic counselors, trainees, and patients with experience in clinical genetics, genetic diagnostics, and genetics education. This article provides recommendations that will guide the integration of genomics into clinical practice.Genet Med 18 11, 1075-1084.
Collapse
|
40
|
Parsons DW, Roy A, Yang Y, Wang T, Scollon S, Bergstrom K, Kerstein RA, Gutierrez S, Petersen AK, Bavle A, Lin FY, López-Terrada DH, Monzon FA, Hicks MJ, Eldin KW, Quintanilla NM, Adesina AM, Mohila CA, Whitehead W, Jea A, Vasudevan SA, Nuchtern JG, Ramamurthy U, McGuire AL, Hilsenbeck SG, Reid JG, Muzny DM, Wheeler DA, Berg SL, Chintagumpala MM, Eng CM, Gibbs RA, Plon SE. Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA Oncol 2016; 2:616-624. [PMID: 26822237 DOI: 10.1001/jamaoncol.2015.5699] [Citation(s) in RCA: 344] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Importance Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown. Objective To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors. Design Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic children's hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record. Main Outcomes and Measures Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations. Results Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%). Conclusions and Relevance Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.
Collapse
Affiliation(s)
- D Williams Parsons
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3The Human Genome Sequencing Center, Baylor College of Medicine, Houston, T
| | - Angshumoy Roy
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas5Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology a
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Tao Wang
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Sarah Scollon
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston
| | - Katie Bergstrom
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston
| | - Robin A Kerstein
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston
| | - Stephanie Gutierrez
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston
| | - Andrea K Petersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Abhishek Bavle
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston
| | - Frank Y Lin
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Dolores H López-Terrada
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas5Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology a
| | - Federico A Monzon
- Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - M John Hicks
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas5Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology a
| | - Karen W Eldin
- Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Norma M Quintanilla
- Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Adekunle M Adesina
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas5Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Carrie A Mohila
- Department of Pathology, Texas Children's Hospital, Houston6Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - William Whitehead
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas8Department of Surgery, Texas Children's Hospital, Houston
| | - Andrew Jea
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas8Department of Surgery, Texas Children's Hospital, Houston
| | - Sanjeev A Vasudevan
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas8Department of Surgery, Texas Children's Hospital, Houston9Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Jed G Nuchtern
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas8Department of Surgery, Texas Children's Hospital, Houston9Michael E. DeBakey Departme
| | - Uma Ramamurthy
- Dan L. Duncan Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Amy L McGuire
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas11Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Susan G Hilsenbeck
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Jeffrey G Reid
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Stacey L Berg
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Murali M Chintagumpala
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston4The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Sharon E Plon
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3The Human Genome Sequencing Center, Baylor College of Medicine, Houston, T
| |
Collapse
|
41
|
Mitchell G, Schrader KA. Testing for Hereditary Predisposition in Patients with Gynecologic Cancers, Quo Vadis? Surg Pathol Clin 2016; 9:301-6. [PMID: 27241110 DOI: 10.1016/j.path.2016.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genetic testing for a hereditary predisposition to gynecologic cancers has been available clinically since the 1990s. Since then, knowledge of the hereditary contribution to gynecologic cancers has dramatically increased, especially with respect to ovarian cancer. Although knowledge of the number of gynecologic cancer-predisposing genes has increased, the integration of genetic predisposition testing into routine clinical practice has been much slower. This article summarizes the technical and practical aspects of genetic testing in gynecologic cancers, the potential barriers to more widespread access and practice of genetic testing for hereditary predisposition to gynecologic cancers, and the potential solutions to these barriers.
Collapse
Affiliation(s)
- Gillian Mitchell
- Hereditary Cancer Program, BC Cancer Agency, 600 West 10th Ave, Vancouver, British Columbia V5Z 4E6, Canada; Department of Medical Oncology, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada.
| | - Kasmintan A Schrader
- Hereditary Cancer Program, Department of Molecular Oncology, BC Cancer Agency, 600 Wet 10th Ave, Vancouver, British Columbia V5Z 4E6, Canada; Department of Medical Genetics, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
| |
Collapse
|
42
|
Hingorani P, Janeway K, Crompton BD, Kadoch C, Mackall CL, Khan J, Shern JF, Schiffman J, Mirabello L, Savage SA, Ladanyi M, Meltzer P, Bult CJ, Adamson PC, Lupo PJ, Mody R, DuBois SG, Parsons DW, Khanna C, Lau C, Hawkins DS, Randall RL, Smith M, Sorensen PH, Plon SE, Skapek SX, Lessnick S, Gorlick R, Reed DR. Current state of pediatric sarcoma biology and opportunities for future discovery: A report from the sarcoma translational research workshop. Cancer Genet 2016; 209:182-94. [PMID: 27132463 DOI: 10.1016/j.cancergen.2016.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 01/09/2023]
Abstract
Sarcomas are a rare subgroup of pediatric cancers comprised of a variety of bone and soft-tissue tumors. While significant advances have been made in improving outcomes of patients with localized pediatric sarcomas since the addition of systemic chemotherapy to local control many decades ago, outcomes for patients with metastatic and relapsed sarcoma remain poor with few novel therapeutics identified to date. With the advent of new technologies to study cancer genomes, transcriptomes and epigenomes, our understanding of sarcoma biology has improved tremendously in a relatively short period of time. However, much remains to be accomplished in this arena especially with regard to translating all of this new knowledge to the bedside. To this end, a meeting was convened in Philadelphia, PA, on April 18, 2015 sponsored by the QuadW foundation, Children's Oncology Group and CureSearch for Children's Cancer that brought together sarcoma clinicians and scientists from North America to review the current state of pediatric sarcoma biology and ongoing/planned genomics based clinical trials in an effort to identify and bridge knowledge gaps that continue to exist at present. At the conclusion of the workshop, three key objectives that would significantly further our understanding of sarcoma were identified and a proposal was put forward to develop an all-encompassing pediatric sarcoma biology protocol that would address these specific needs. This review summarizes the proceedings of the workshop.
Collapse
Affiliation(s)
- Pooja Hingorani
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ, USA.
| | - Katherine Janeway
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Brian D Crompton
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Crystal L Mackall
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jack F Shern
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Schiffman
- Huntsman Cancer Institute & Primary Children's Medical Center, University of Utah, Salt Lake City, UT, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Meltzer
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Peter C Adamson
- Division of Clinical Pharmacology & Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Rajen Mody
- Department of Pediatrics, University Of Michigan, Ann Arbor, MI, USA
| | - Steven G DuBois
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - D Williams Parsons
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chand Khanna
- Molecular Oncology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ching Lau
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - R Lor Randall
- Huntsman Cancer Institute & Primary Children's Medical Center, University of Utah, Salt Lake City, UT, USA
| | | | - Poul H Sorensen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Sharon E Plon
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Stephen X Skapek
- Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Lessnick
- Division of Hematology/ Oncology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard Gorlick
- Division of Pediatric Hematology/Oncology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Damon R Reed
- Moffitt Cancer Center, Sarcoma Department, Adolescent and Young Adult Program, Tampa, FL, USA
| |
Collapse
|
43
|
McCullough LB, Slashinski MJ, McGuire AL, Street RL, Eng CM, Gibbs RA, Parsons DW, Plon SE. Is Whole-Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients With Solid Tumors. Pediatr Blood Cancer 2016; 63:511-5. [PMID: 26505993 PMCID: PMC4982513 DOI: 10.1002/pbc.25815] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND It has been anticipated that physician and parents will be ill prepared or unprepared for the clinical introduction of genome sequencing, making it ethically disruptive. PROCEDURE As a part of the Baylor Advancing Sequencing in Childhood Cancer Care study, we conducted semistructured interviews with 16 pediatric oncologists and 40 parents of pediatric patients with cancer prior to the return of sequencing results. We elicited expectations and attitudes concerning the impact of sequencing on clinical decision making, clinical utility, and treatment expectations from both groups. Using accepted methods of qualitative research to analyze interview transcripts, we completed a thematic analysis to provide inductive insights into their views of sequencing. RESULTS Our major findings reveal that neither pediatric oncologists nor parents anticipate sequencing to be an ethically disruptive technology, because they expect to be prepared to integrate sequencing results into their existing approaches to learning and using new clinical information for care. Pediatric oncologists do not expect sequencing results to be more complex than other diagnostic information and plan simply to incorporate these data into their evidence-based approach to clinical practice, although they were concerned about impact on parents. For parents, there is an urgency to protect their child's health and in this context they expect genomic information to better prepare them to participate in decisions about their child's care. CONCLUSIONS Our data do not support the concern that introducing genome sequencing into childhood cancer care will be ethically disruptive, that is, leave physicians or parents ill prepared or unprepared to make responsible decisions about patient care.
Collapse
Affiliation(s)
- Laurence B. McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, Correspondence to: Laurence B. McCullough, Ph.D., Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza MS 420, Houston, TX 77030-3411, Tel.:713 798 3505,
| | - Melody J. Slashinski
- Department of Community Health Education, University of Massachusetts at Amherst, Amherst, Massachusetts
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Richard L. Street
- Department of Communication, Texas A&M University, College Station, Texas,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - D. Williams Parsons
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas,Department of Pediatrics, Baylor College of Medicine Houston, Texas
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas,Department of Pediatrics, Baylor College of Medicine Houston, Texas
| |
Collapse
|
44
|
Maggi E, Montagna C. AACR precision medicine series: Highlights of the integrating clinical genomics and cancer therapy meeting. Mutat Res 2015; 782:44-51. [PMID: 26554403 DOI: 10.1016/j.mrfmmm.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/23/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
The American Association for Cancer Research (AACR) Precision Medicine Series "Integrating Clinical Genomics and Cancer Therapy" took place June 13-16, 2015 in Salt Lake City, Utah. The conference was co-chaired by Charles L. Sawyers form Memorial Sloan Kettering Cancer Center in New York, Elaine R. Mardis form Washington University School of Medicine in St. Louis, and Arul M. Chinnaiyan from University of Michigan in Ann Arbor. About 500 clinicians, basic science investigators, bioinformaticians, and postdoctoral fellows joined together to discuss the current state of Clinical Genomics and the advances and challenges of integrating Next Generation Sequencing (NGS) technologies into clinical practice. The plenary sessions and panel discussions covered current platforms and sequencing approaches adopted for NGS assays of cancer genome at several national and international institutions, different approaches used to map and classify targetable sequence variants, and how information acquired with the sequencing of the cancer genome is used to guide treatment options. While challenges still exist from a technological perspective, it emerged that there exists considerable need for the development of tools to aid the identification of the therapy most suitable based on the mutational profile of the somatic cancer genome. The process to match patients to ongoing clinical trials is still complex. In addition, the need for centralized data repositories, preferably linked to well annotated clinical records, that aid sharing of sequencing information is central to begin understanding the contribution of variants of unknown significance to tumor etiology and response to therapy. Here we summarize the highlights of this stimulating four-day conference with a major emphasis on the open problems that the clinical genomics community is currently facing and the tools most needed for advancing this field.
Collapse
Affiliation(s)
- Elaine Maggi
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department Pathology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.
| |
Collapse
|
45
|
Roy A, Kumar V, Zorman B, Fang E, Haines KM, Doddapaneni H, Hampton OA, White S, Bavle AA, Patel NR, Eldin KW, John Hicks M, Rakheja D, Leavey PJ, Skapek SX, Amatruda JF, Nuchtern JG, Chintagumpala MM, Wheeler DA, Plon SE, Sumazin P, Parsons DW. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun 2015; 6:8891. [PMID: 26573325 PMCID: PMC4660214 DOI: 10.1038/ncomms9891] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023] Open
Abstract
The X-linked BCL-6 co-repressor (BCOR) gene encodes a key constituent of a variant polycomb repressive complex (PRC) that is mutated or translocated in human cancers. Here we report on the identification of somatic internal tandem duplications (ITDs) clustering in the C terminus of BCOR in 23 of 27 (85%) pediatric clear cell sarcomas of the kidney (CCSK) from two independent cohorts. We profile CCSK tumours using a combination of whole-exome, transcriptome and targeted sequencing. Identical ITD mutations are found in primary and relapsed tumour pairs but not in adjacent normal kidney or blood. Mutant BCOR transcripts and proteins are markedly upregulated in ITD-positive tumours. Transcriptome analysis of ITD-positive CCSKs reveals enrichment for PRC2-regulated genes and similarity to undifferentiated sarcomas harbouring BCOR–CCNB3 fusions. The discovery of recurrent BCOR ITDs defines a major oncogenic event in this childhood sarcoma with significant implications for diagnostic and therapeutic approaches to this tumour. The genetic basis of clear cell sarcomas of the kidney is not well understood. In this study, Roy et al. perform whole-exome and RNA sequencing of these tumours and identify recurrent internal tandem duplications in BCOR, a key constituent of a variant polycomb repressive complex.
Collapse
Affiliation(s)
- Angshumoy Roy
- Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA.,Texas Children's Cancer Center, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vijetha Kumar
- Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Barry Zorman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erica Fang
- Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Katherine M Haines
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - HarshaVardhan Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Simon White
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Abhishek A Bavle
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nimesh R Patel
- Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Karen W Eldin
- Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA
| | - M John Hicks
- Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA.,Texas Children's Cancer Center, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pathology and Laboratory Medicine, Children's Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Patrick J Leavey
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stephen X Skapek
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - James F Amatruda
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jed G Nuchtern
- Texas Children's Cancer Center, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Division of Pediatric Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, USA.,Division of Pediatric Surgery, Department of Surgery, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Murali M Chintagumpala
- Texas Children's Cancer Center, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sharon E Plon
- Texas Children's Cancer Center, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Pavel Sumazin
- Texas Children's Cancer Center, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - D Williams Parsons
- Texas Children's Cancer Center, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
46
|
Bernhardt BA, Roche MI, Perry DL, Scollon SR, Tomlinson AN, Skinner D. Experiences with obtaining informed consent for genomic sequencing. Am J Med Genet A 2015; 167A:2635-46. [PMID: 26198374 PMCID: PMC4980577 DOI: 10.1002/ajmg.a.37256] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/06/2015] [Indexed: 01/11/2023]
Abstract
Despite the increased utilization of genome and exome sequencing, little is known about the actual content and process of informed consent for sequencing. We addressed this by interviewing 29 genetic counselors and research coordinators experienced in obtaining informed consent for sequencing in research and clinical settings. Interviews focused on the process and content of informed consent; patients/participants' common questions, concerns and misperceptions; and challenges to obtaining informed consent. Content analysis of transcribed interviews revealed that the main challenges to obtaining consent related to the broad scope and uncertainty of results, and patient/participants' unrealistic expectations about the likely number and utility of results. Interviewees modified their approach to sessions according to contextual issues surrounding the indication for testing, type of patient, and timing of testing. With experience, most interviewees structured sessions to place less emphasis on standard elements in the consent form and technological aspects of sequencing. They instead focused on addressing misperceptions and helping patients/participants develop realistic expectations about the types and implications of possible results, including secondary findings. These findings suggest that informed consent sessions should focus on key issues that may be misunderstood by patients/participants. Future research should address the extent to which various stakeholders agree on key elements of informed consent.
Collapse
Affiliation(s)
- Barbara A. Bernhardt
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Myra I. Roche
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | | | - Sarah R. Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ashley N. Tomlinson
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Debra Skinner
- FPG Child Development Institute, University of North Carolina, Chapel Hill, North Carolina
| |
Collapse
|
47
|
van den Veyver IB, Eng CM. Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023077. [PMID: 26253094 DOI: 10.1101/cshperspect.a023077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
New sequencing methods capable of rapidly analyzing the genome at increasing resolution have transformed diagnosis of single-gene or oligogenic genetic disorders in pediatric and adult medicine. Targeted tests, consisting of disease-focused multigene panels and diagnostic exome sequencing to interrogate the sequence of the coding regions of nearly all genes, are now clinically offered when there is suspicion for an undiagnosed genetic disorder or cancer in children and adults. Implementation of diagnostic exome and genome sequencing tests on invasively and noninvasively obtained fetal DNA samples for prenatal genetic diagnosis is also being explored. We predict that they will become more widely integrated into prenatal care in the near future. Providers must prepare for the practical, ethical, and societal dilemmas that accompany the capacity to generate and analyze large amounts of genetic information about the fetus during pregnancy.
Collapse
Affiliation(s)
- Ignatia B van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, The Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| |
Collapse
|
48
|
Oberg JA, Glade Bender JL, Cohn EG, Morris M, Ruiz J, Chung WK, Appelbaum PS, Kung AL, Levine JM. Overcoming challenges to meaningful informed consent for whole genome sequencing in pediatric cancer research. Pediatr Blood Cancer 2015; 62:1374-80. [PMID: 25832998 DOI: 10.1002/pbc.25520] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 02/19/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND Introducing whole genome sequencing (WGS) into pediatric cancer research at diagnosis poses unique challenges related to informed consent. WGS requires tissue obtained prior to initiating treatment, when families may be overwhelmed with uncertainty and fear. Motivation to participate may be high without fully understanding the range of possible results, including secondary findings. Little is known about parental knowledge, attitudes, and beliefs about this type of research. PROCEDURE A qualitative study was conducted to investigate parental knowledge about genetic concepts and WGS, thoughts about the informed consent process, and preferences for secondary findings. Focus groups were conducted with parents/guardians of children with cancer and semi-structured interviews were conducted in a control group without cancer. All transcripts were analyzed using content analysis. RESULTS Four focus groups included 15 participants; eight semi-structured interviews included 10 participants. Basic knowledge about genetics was limited to heredity. Some knowledge of genomic analysis was present in 3/15 focus group participants. Major factors related to participation in WGS research were: (i) hope for their child and future children; (ii) no additional procedures; (iii) and protection of privacy. All favored a two-step consent process, first to store extra tissue from a diagnostic biopsy/resection, followed by consenting to WGS research, one-to-two months later. The desire to receive secondary findings was high among both groups, but there were individuals who did not want these results, fearing increased anxiety. CONCLUSIONS Parents/guardians of children with cancer have limited knowledge about WGS. A two-step consent process may improve their ability to provide meaningful informed consent.
Collapse
Affiliation(s)
- Jennifer A Oberg
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Julia L Glade Bender
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Elizabeth G Cohn
- School of Nursing, Division of Academics, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Marilyn Morris
- Department of Pediatrics, Division of Pediatric Critical Care, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Jenny Ruiz
- College of Physicians and Surgeons, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Division of Pediatric Molecular Genetics, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Paul S Appelbaum
- Department of Psychiatry, Division of Law, Ethics, and Psychiatry, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Andrew L Kung
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| | - Jennifer M Levine
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation, Columbia University Medical Center, 161 Fort Washington Avenue, IP7, New York, New York
| |
Collapse
|
49
|
Pinto N, Volchenboum SL, Skol AD, Rhodes L, Doan A, Fein-Levy C, Lipton JM, Cunningham JM, Onel K. Establishing a translational genomics infrastructure in pediatric cancer: the GREAT KIDS experience. Per Med 2015; 12:221-229. [PMID: 29771652 DOI: 10.2217/pme.14.90] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have recently established a biobanking and sequencing pipeline at the University of Chicago dubbed Genomics for Risk Evaluation and Anticancer Therapy in Kids. We plan to intersect family and personal history of cancer and other diseases with multidimensional genomic profiling in order to: understand how genetics may have contributed to the development of cancer for each child, and investigate the spectrum of genomic alterations within a tumor spatially (e.g., primary site vs distant metastasis) and over time (e.g., diagnosis vs relapse). This review highlights some of the practical considerations involved in creating such a program including the capacity to use our platform for multi-institutional collaborations.
Collapse
Affiliation(s)
- Navin Pinto
- Department of Pediatrics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Samuel L Volchenboum
- Department of Pediatrics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA.,Center for Research Informatics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Andrew D Skol
- Department of Pediatrics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Lindsay Rhodes
- Department of Pediatrics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Andrew Doan
- Division of Hematology/Oncology, Steven & Alexandra Cohen Children's Medical Center, 269-01 76th Avenue, New Hyde Park, NY 11040, USA.,Feinstein Institute for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
| | - Carolyn Fein-Levy
- Division of Hematology/Oncology, Steven & Alexandra Cohen Children's Medical Center, 269-01 76th Avenue, New Hyde Park, NY 11040, USA.,Feinstein Institute for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
| | - Jeffrey M Lipton
- Division of Hematology/Oncology, Steven & Alexandra Cohen Children's Medical Center, 269-01 76th Avenue, New Hyde Park, NY 11040, USA.,Feinstein Institute for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA.,Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11549, USA
| | - John M Cunningham
- Department of Pediatrics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Kenan Onel
- Department of Pediatrics, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| |
Collapse
|
50
|
Unique Genetic Counseling Considerations in the Pediatric Oncology Setting. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0064-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|