1
|
Shickh S, Sebastian A, Clausen M, Mighton C, Elser C, Eisen A, Waldman L, Panchal S, Ward T, Carroll JC, Glogowski E, Schrader KA, Lerner-Ellis J, Kim RH, Thorpe KE, Bombard Y. Great expectations: patients' preferences for clinically significant results from genomic sequencing. Hum Genet 2023; 142:553-562. [PMID: 36943453 PMCID: PMC11249280 DOI: 10.1007/s00439-023-02543-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
We aimed to describe patient preferences for a broad range of secondary findings (SF) from genomic sequencing (GS) and factors driving preferences. We assessed preference data within a trial of the Genomics ADvISER, (SF decision aid) among adult cancer patients. Participants could choose from five categories of SF: (1) medically actionable; (2) polygenic risks; (3) rare diseases; (4) early-onset neurological diseases; and (5) carrier status. We analyzed preferences using descriptive statistics and drivers of preferences using multivariable logistic regression models. The 133 participants were predominantly European (74%) or East Asian or mixed ancestry (13%), female (90%), and aged > 50 years old (60%). The majority chose to receive SF. 97% (129/133) chose actionable findings with 36% (48/133) choosing all 5 categories. Despite the lack of medical actionability, participants were interested in receiving SF of polygenic risks (74%), carrier status (75%), rare diseases (59%), and early-onset neurologic diseases (53%). Older participants were more likely to be interested in receiving results for early-onset neurological diseases, while those exhibiting lower decisional conflict were more likely to select all categories. Our results highlight a disconnect between cancer patient preferences and professional guidelines on SF, such as ACMG's recommendations to only return medically actionable secondary findings. In addition to clinical evidence, future guidelines should incorporate patient preferences.
Collapse
Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Agnes Sebastian
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Christine Elser
- University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Larissa Waldman
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Thomas Ward
- Zane Cohen Centre, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - June C Carroll
- Ray D Wolfe Department of Family Medicine, Sinai Health, Toronto, ON, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Raymond H Kim
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network and Sinai Health, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kevin E Thorpe
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Applied Health Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
| |
Collapse
|
2
|
Rost C, Dent KM, Botkin J, Rothwell E. Experiences and lessons learned by genetic counselors in returning secondary genetic findings to patients. J Genet Couns 2020; 29:1234-1244. [PMID: 32453499 DOI: 10.1002/jgc4.1292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/06/2022]
Abstract
Few studies have explored the real-world experiences and strategies of genetic counselors involved in the process of returning secondary findings (SFs). This study aimed to describe and categorize the experiences for the return of SFs from clinical sequencing. Semi-structured telephone interviews with 21 genetic counselors representing 56 incidences were conducted. A content analysis was conducted on the transcripts through an iterative, team-based approach. Four common categories emerged across all interviews. These included (a) the importance of pretest counseling for the return of SFs, (b) how primary test results influenced the level of importance placed on the SFs, (c) patients' emotional reactions from receiving SF results, and (d) how returning SFs changed future pretest counseling and consent. This study identified experiences and common practices by genetic counselors who returned SFs. More research is needed to assess how genetic counselors' specific strategies improve patient comprehension and medical actions.
Collapse
Affiliation(s)
- Carly Rost
- University of Utah Graduate Program in Genetic Counseling, Salt Lake City, Utah
| | - Karin M Dent
- University of Utah Graduate Program in Genetic Counseling, Salt Lake City, Utah.,Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Jeffrey Botkin
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Erin Rothwell
- Department of OB/GYN, University of Utah, Salt Lake City, Utah
| |
Collapse
|
3
|
A comparison of genomic diagnostics in adults and children with epilepsy and comorbid intellectual disability. Eur J Hum Genet 2020; 28:1066-1077. [PMID: 32238909 DOI: 10.1038/s41431-020-0610-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/13/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
Next generation sequencing provides an important opportunity for improved diagnosis in epilepsy. To date, the majority of diagnostic genetic testing is conducted in the paediatric arena, while the utility of such testing is less well understood in adults with epilepsy. We conducted whole exome sequencing (WES) and copy number variant analyses in an Irish cohort of 101 people with epilepsy and co-morbid intellectual disability to compare the diagnostic yield of genomic testing between adult and paediatric patients. Variant interpretation followed American College of Medical Genetics and Genomics (ACMG) guidelines. We demonstrate that WES, in combination with array-comparative genomic hybridisation, provides a diagnostic rate of 27% in unrelated adult epilepsy patients and 42% in unrelated paediatric patients. We observe a 2.7% rate of ACMG-defined incidental findings. Our findings indicate that WES has similar utility in both adult and paediatric cohorts and is appropriate for diagnostic testing in both epilepsy patient groups.
Collapse
|
4
|
Interpreting Genomic Reports. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
5
|
Wang LJ, Zhang CW, Su SC, Chen HIH, Chiu YC, Lai Z, Bouamar H, Ramirez AG, Cigarroa FG, Sun LZ, Chen Y. An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data. BMC Genomics 2019; 20:1007. [PMID: 31888480 PMCID: PMC6936141 DOI: 10.1186/s12864-019-6333-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Europeans and American Indians were major genetic ancestry of Hispanics in the U.S. These ancestral groups have markedly different incidence rates and outcomes in many types of cancers. Therefore, the genetic admixture may cause biased genetic association study with cancer susceptibility variants specifically in Hispanics. For example, the incidence rate of liver cancer has been shown with substantial disparity between Hispanic, Asian and non-Hispanic white populations. Currently, ancestry informative marker (AIM) panels have been widely utilized with up to a few hundred ancestry-informative single nucleotide polymorphisms (SNPs) to infer ancestry admixture. Notably, current available AIMs are predominantly located in intron and intergenic regions, while the whole exome sequencing (WES) protocols commonly used in translational research and clinical practice do not cover these markers. Thus, it remains challenging to accurately determine a patient’s admixture proportion without additional DNA testing. Results In this study we designed an unique AIM panel that infers 3-way genetic admixture from three distinct and selective continental populations (African (AFR), European (EUR), and East Asian (EAS)) within evolutionarily conserved exonic regions. Initially, about 1 million exonic SNPs from selective three populations in the 1000 Genomes Project were trimmed by their linkage disequilibrium (LD), restricted to biallelic variants, and finally we optimized to an AIM panel with 250 SNP markers, or the UT-AIM250 panel, using their ancestral informativeness statistics. Comparing to published AIM panels, UT-AIM250 performed better accuracy when we tested with three ancestral populations (accuracy: 0.995 ± 0.012 for AFR, 0.997 ± 0.007 for EUR, and 0.994 ± 0.012 for EAS). We further demonstrated the performance of the UT-AIM250 panel to admixed American (AMR) samples of the 1000 Genomes Project and obtained similar results (AFR, 0.085 ± 0.098; EUR, 0.665 ± 0.182; and EAS, 0.250 ± 0.205) to previously published AIM panels (Phillips-AIM34: AFR, 0.096 ± 0.127, EUR, 0.575 ± 0.290, and EAS, 0.330 ± 0.315; Wei-AIM278: AFR, 0.070 ± 0.096, EUR, 0.537 ± 0.267, and EAS, 0.393 ± 0.300). Subsequently, we applied the UT-AIM250 panel to a clinical dataset of 26 self-reported Hispanic patients in South Texas with hepatocellular carcinoma (HCC). We estimated the admixture proportions using WES data of adjacent non-cancer liver tissues (AFR, 0.065 ± 0.043; EUR, 0.594 ± 0.150; and EAS, 0.341 ± 0.160). Similar admixture proportions were identified from corresponding tumor tissues. In addition, we estimated admixture proportions of The Cancer Genome Atlas (TCGA) collection of hepatocellular carcinoma (TCGA-LIHC) samples (376 patients) using the UT-AIM250 panel. The panel obtained consistent admixture proportions from tumor and matched normal tissues, identified 3 possible incorrectly reported race/ethnicity, and/or provided race/ethnicity determination if necessary. Conclusions Here we demonstrated the feasibility of using evolutionarily conserved exonic regions to infer admixture proportions and provided a robust and reliable control for sample collection or patient stratification for genetic analysis. R implementation of UT-AIM250 is available at https://github.com/chenlabgccri/UT-AIM250.
Collapse
Affiliation(s)
- Li-Ju Wang
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Catherine W Zhang
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Sophia C Su
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Hung-I H Chen
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yu-Chiao Chiu
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.,Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Hakim Bouamar
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Amelie G Ramirez
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.,Institute for Health Promotion Research, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Francisco G Cigarroa
- Department of Surgery, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Lu-Zhe Sun
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA. .,Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
| |
Collapse
|
6
|
A proposal on the first Japanese practical guidance for the return of individual genomic results in research settings. J Hum Genet 2019; 65:251-261. [PMID: 31873219 DOI: 10.1038/s10038-019-0697-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022]
Abstract
Large-scale, low-cost genome analysis has become possible with next-generation sequencing technology, which is currently used in research and clinical practice. Many attempts of returning individual genomic results have commenced not only in clinical practice, but also in research settings of several countries. In Japan, the government guidelines include a section on the disclosure of genetic information regarding genome analysis in research. However, no practical guidance for the return of individual genomic results in research settings (ROGRR) currently exists. We propose practical guidance regarding ROGRR in Japan based on extensive research, including a literature review of related previous studies, an examination of the relevant legislation in Japan, and interviews with stakeholders. The guidance we developed consists of "Points to consider" and "Issues for further discussion and consideration." The "Points to consider" were divided into five parts, from preliminary review before discussion of policy, to the actual return and follow-up process, in the order of the assumed ROGRR process. It is anticipated that a situation will arise where numerous research projects will consider ROGRR carefully and realistically in the future, and in the process of drafting such practical guidance, various issues requiring continuous discussion will emerge. The necessities of continuous discussion concerning ROGRR in Japan's context is increasing, particularly in terms of the ethical, legal, and social implications. We believe such discussions and considerations may contribute to creating a new system that will increase availability of personalized medicine and prevention using genetic information, allowing them to become useful to the broader population.
Collapse
|
7
|
Savatt J, Pisieczko CJ, Zhang Y, Lee MTM, Faucett WA, Williams JL. Biobanks in the Era of Genomic Data. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00171-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
8
|
Saelaert M, Mertes H, Moerenhout T, De Baere E, Devisch I. Criteria for reporting incidental findings in clinical exome sequencing - a focus group study on professional practices and perspectives in Belgian genetic centres. BMC Med Genomics 2019; 12:123. [PMID: 31429751 PMCID: PMC6702726 DOI: 10.1186/s12920-019-0561-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 07/24/2019] [Indexed: 12/16/2022] Open
Abstract
Background Incidental and secondary findings (IFs and SFs) are subject to ongoing discussion as potential consequences of clinical exome sequencing (ES). International policy documents vary on the reporting of these findings. Discussion points include the practice of unintentionally identified IFs versus deliberately pursued SFs, patient opt-out possibilities and the spectrum of reportable findings. The heterogeneity of advice permits a non-standardised disclosure but research is lacking on actual reporting practices. Therefore, this study assessed national reporting practices for IFs and SFs in clinical ES and the underlying professional perspectives. Methods A qualitative focus group study has been undertaken, including professionals from Belgian centres for medical genetics (CMGs). Data were analysed thematically. Results All Belgian CMGs participated in this study. Data analysis resulted in six main themes, including one regarding the reporting criteria used for IFs. All CMGs currently use ES-based panel testing. They have limited experience with IFs in clinical ES and are cautious about the pursuit of SFs. Two main reporting criteria for IFs were referred to by all CMGs: the clinical significance of the IF (including pathogenicity and medical actionability) and patient-related factors (including the patient’s preference to know and patient characteristics). The consensus over the importance of these criteria contrasted with their challenging interpretation and application. Points of concern included IFs’ pathogenicity in non-symptomatic persons, IFs concerning variants of uncertain significance, the requirement and definition of medical actionability and patient opt-out possibilities. Finally, reporting decisions were guided by the interaction between the clinical significance of the IF and patient characteristics. This interaction questions the possible disclosure of findings with context-dependent and personal utility, such as IFs concerning a carrier status. To evaluate the IF’s final relevance, a professional and case-by-case deliberation was considered essential. Conclusions The challenging application of reporting criteria for IFs results in diversified practices and policy perspectives within Belgian CMGs. This echoes international concerns and may have consequences for effective policy recommendations.
Collapse
Affiliation(s)
- Marlies Saelaert
- Department of Public Health and Primary Care, Philosophy of Medicine and Ethics Research Group, Ghent University, Campus Heymans (UZ Gent), Corneel Heymanslaan 10 - Building 6K3, 9000, Ghent, Belgium.
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Bioethics Institute Ghent, Ghent University, Ghent, Belgium
| | - Tania Moerenhout
- Department of Public Health and Primary Care, Philosophy of Medicine and Ethics Research Group, Ghent University, Campus Heymans (UZ Gent), Corneel Heymanslaan 10 - Building 6K3, 9000, Ghent, Belgium.,Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Ignaas Devisch
- Department of Public Health and Primary Care, Philosophy of Medicine and Ethics Research Group, Ghent University, Campus Heymans (UZ Gent), Corneel Heymanslaan 10 - Building 6K3, 9000, Ghent, Belgium
| |
Collapse
|
9
|
Wou K, Weitz T, McCormack C, Wynn J, Spiegel E, Giordano J, Wapner RJ, Chung WK. Parental perceptions of prenatal whole exome sequencing (PPPWES) study. Prenat Diagn 2018; 38:801-811. [PMID: 30035818 DOI: 10.1002/pd.5332] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/06/2018] [Accepted: 07/11/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The objective of the study is to investigate the experiences of couples who underwent prenatal whole-exome sequencing (WES) for fetal anomalies and the amount/type of information couples want from prenatal WES. METHOD Participants in the Fetal Sequencing Study who had genetic testing for fetal anomalies were invited for a semistructured interview about their experience with prenatal WES. A constructivist grounded theory approach with an inductive coding style was used for coding and analysis. RESULTS We interviewed 29 participants from 17 pregnancies. Two pregnancies had positive prenatal WES results, and 4 were terminated prior to receipt of WES results. The main themes were anxiety and stress around the time of diagnosis, education and consent for WES, coping and support while waiting for results, and receiving genetic testing results. In response to hypothetical scenarios probing the desire for uncertain results, 86% would like to be told about results for which the provider had some degree of uncertainty, and the percent desiring results decreased as the certainty of the results decreased. CONCLUSION Participants' experience with exome sequence was similar to other prenatal genetic diagnostic tests, except for the longer wait time for results. When probed with hypothetical scenarios, participants desired more results than were provided in the study, including uncertain results that might diagnose the fetal condition. This highlights the need for specialized prenatal genetic counseling to have nuanced discussions of multiple dimensions of uncertainty with implementation of prenatal WES.
Collapse
Affiliation(s)
- Karen Wou
- Department of Pediatrics, Division of Clinical Genetics, Columbia University, New York, NY, USA
| | - Talia Weitz
- College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Clare McCormack
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Division of Clinical Genetics, Columbia University, New York, NY, USA
| | - Erica Spiegel
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Jessica Giordano
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Division of Clinical Genetics, Columbia University, New York, NY, USA.,Department of Pediatrics, Division of Molecular Genetics, and Department of Medicine, Columbia University, New York, NY, USA
| |
Collapse
|
10
|
Saelaert M, Mertes H, De Baere E, Devisch I. Incidental or secondary findings: an integrative and patient-inclusive approach to the current debate. Eur J Hum Genet 2018; 26:1424-1431. [PMID: 29970927 DOI: 10.1038/s41431-018-0200-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/13/2018] [Accepted: 05/24/2018] [Indexed: 12/18/2022] Open
Abstract
Incidental or secondary findings (ISFs) in whole exome or whole genome sequencing have been widely debated in recent literature. The American College of Medical Genetics and Genomics' recommendations on diagnostic ISFs have strongly catalyzed the discussion, resulting in worldwide reactions and a variety of international guidelines. This article will outline how propositions on levels of terminology, policy, and underlying values are still internationally criticized and adjusted. Unsolved questions regarding ISFs include a suitable terminology, adequate counseling or informed consent procedures, opt-out possibilities, reporting ISFs to (parents of) minors and values regarding professional duty, patient autonomy, and actionability. These questions will be characterized as intrinsically related and reciprocally maintained and hence, symptomatic, single-level reflections will be marked as ineffective. Instead, a level-integrative approach of the debate that explicitly acknowledges this interaction and considers a balance between internationally significant and case-specific solutions, will be advocated. Second, the inclusion of a patient perspective will be strongly encouraged to complement the professional preponderance in the current debate. The examination of lived patient experiences, a qualitative focus on the subjective meaning of ISFs, and a contextualization of meaning processes will be suggested as specific concretizations. This integrative and inclusive approach aims for a more comprehensive understanding of ISFs, a consideration of all relevant stakeholders' perspective and, ultimately, an effective health-care policy.
Collapse
Affiliation(s)
- Marlies Saelaert
- Department of Family Medicine and Primary Health Care, Ghent University, Ghent, Belgium.
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Bioethics Institute Ghent, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Ignaas Devisch
- Department of Family Medicine and Primary Health Care, Ghent University, Ghent, Belgium
| |
Collapse
|
11
|
Fu F, Li R, Li Y, Nie ZQ, Lei T, Wang D, Yang X, Han J, Pan M, Zhen L, Ou Y, Li J, Li FT, Jing X, Li D, Liao C. Whole exome sequencing as a diagnostic adjunct to clinical testing in fetuses with structural abnormalities. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:493-502. [PMID: 28976722 DOI: 10.1002/uog.18915] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES. METHODS Karyotyping, chromosomal microarray analysis (CMA) and WES were performed sequentially on stored samples from a cohort of 3949 pregnancies with fetal structural abnormalities detected on ultrasound and/or magnetic resonance imaging, referred between January 2011 and December 2015. Diagnostic rates of the three techniques were investigated overall, for phenotypic subgroups and for proband-only vs fetus-mother-father samples. Information on pathogenic variants was identified by WES. RESULTS Overall, 18.2% (720/3949) of fetuses had an abnormal karyotype. Pathogenic copy number variants were detected on CMA in 8.2% (138/1680) of fetuses that had a normal karyotype result. WES performed on a subgroup of 196 fetuses with normal CMA and karyotype results revealed the putative genetic variants responsible for the abnormal phenotypes in 47 cases (24%). The molecular diagnosis rates for fetus-mother-father and proband-only samples were 26.5% (13/49) and 23.1% (34/147), respectively. Variants of uncertain significance were detected in 12.8% (25/196) of fetuses, of which 22 were identified in the fetal proband-only group (15%; 22/147) and three in the fetus-mother-father group (6.1%; 3/49). The incidental finding rate was 6.1% (12/196). CONCLUSIONS WES is a promising method for the identification of genetic variants that cause structural abnormalities in fetuses with normal results on karyotyping and CMA. This enhanced diagnostic yield has the potential to improve the clinical management of pregnancies and to inform better the reproductive decisions of affected families. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- F Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - R Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Li
- Guanzghou Umbilical Cord Blood Bank, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Z-Q Nie
- Epidemiology Division, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangzhou, Guangdong, China
| | - T Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - D Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - X Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - J Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - M Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - L Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Ou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - J Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - F-T Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - X Jing
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - D Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - C Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
12
|
Lei TY, Fu F, Li R, Wang D, Wang RY, Jing XY, Deng Q, Li ZZ, Liu ZQ, Yang X, Li DZ, Liao C. Whole-exome sequencing for prenatal diagnosis of fetuses with congenital anomalies of the kidney and urinary tract. Nephrol Dial Transplant 2018; 32:1665-1675. [PMID: 28387813 DOI: 10.1093/ndt/gfx031] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/20/2017] [Indexed: 12/18/2022] Open
Abstract
Background In the absence of cytogenetic abnormality, fetuses with congenital anomalies of the kidney and urinary tract (CAKUT) with/without other structural anomalies show a higher likelihood of monogenic causes; however, defining the underlying pathology can be challenging. Here, we investigate the value of whole-exome sequencing (WES) in fetuses with CAKUT but normal findings upon karyotyping and chromosome microarray analysis. Methods WES was performed on DNA from the cord blood of 30 fetuses with unexplained CAKUT with/without other structural anomalies. In the first 23 cases, sequencing was initially performed on fetal DNA only; for the remaining seven cases, the trio of fetus, mother and father was sequenced simultaneously. Results Of the 30 cases, pathogenic variants were identified in 4 (13%) (UMOD, NEK8, HNF1B and BBS2) and incidental variants in 2 (7%) (HSPD1 and GRIN2B). Furthermore, two of the above four cases had other anomalies in addition to CAKUT. Thus, the detection rate was only 2/22 (9.1%) for isolated CAKUT and 2/8 (25%) for CAKUT with other abnormalities. Conclusions Applying WES to the prenatal diagnostic approach in CAKUT fetuses with or without other anomalies allows for an accurate and early etiology-based diagnosis and improved clinical management. To expedite interpretation of the results, trio sequencing should be employed; however, interpretation may nevertheless be compromised by incomplete coverage of all relevant genes.
Collapse
Affiliation(s)
- Ting-Ying Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Fang Fu
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Ru Li
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Dan Wang
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Rong-Yue Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Xiang-Yi Jing
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Qiong Deng
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Zhou-Zhou Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Ze-Qun Liu
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| |
Collapse
|
13
|
Kuderer NM, Burton KA, Blau S, Senecal F, Gadi VK, Parker S, Mahen E, Veenstra D, Carlson JJ, Lyman GH, Blau CA. Participant Attitudes Toward an Intensive Trial of Multiple Biopsies, Multidimensional Molecular Analysis, and Reporting of Results in Metastatic Triple-Negative Breast Cancer. JCO Precis Oncol 2017; 1:PO.17.00076. [PMID: 32913975 PMCID: PMC7446457 DOI: 10.1200/po.17.00076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Multidimensional molecular analysis of tumor tissue intensively over space and time can provide insight into how cancers evolve and escape treatment. Attitudes of participants in such trials have not been assessed. We explored patient views regarding an intensive study incorporating multiple biopsies, multidimensional molecular testing, and drug response predictions that are reported to the oncologist and patient. PATIENTS AND METHODS A structured, self-administered survey was conducted among the first 15 patients enrolled in ITOMIC-001 (Intensive Trial of Omics in Cancer). Patients with metastatic triple-negative breast cancer were accrued at two sites in Washington state. Surveys containing 17 items were administered at enrollment and after the return of results. Surveys explored perceptions regarding risks, personal benefits, benefits to others, uncertainties associated with interpreting complex molecular results, concerns regarding multiple biopsies, and potential loss of confidentiality. At follow-up, three additional unique items explored patient coping. RESULTS All participants expressed a strong desire for their experiences to benefit others, and all perceived a higher likelihood of deriving benefit than described during detailed consent discussions. Loss of confidentiality ranked lowest among patient concerns. Despite acknowledging uncertainties and risks inherent in complex molecular testing for clinical reporting, participants wanted access to findings in evaluating treatment choices, even if the best available evidence was weak. Follow-up surveys demonstrated relatively little change in attitudes, although concern about study biopsies generally declined. Study participation helped several patients cope better with their disease. CONCLUSION In advanced breast cancer, these findings demonstrate the feasibility of engaging motivated patients in trials that navigate the uncertainties associated with intensive spatial and longitudinal multidimensional molecular testing for the purpose of advancing precision medicine.
Collapse
Affiliation(s)
- Nicole M. Kuderer
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Kimberly A. Burton
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Sibel Blau
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Francis Senecal
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Vijayakrishna K. Gadi
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Stephanie Parker
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Elisabeth Mahen
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - David Veenstra
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Josh J. Carlson
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - Gary H. Lyman
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| | - C. Anthony Blau
- All authors: University of Washington; Vijayakrishna K. Gadi and Gary H. Lyman, Fred Hutchinson Cancer Research Center, Seattle; and Sibel Blau, Francis Senecal, and Stephanie Parker, Northwest Medical Specialties, Puyallup and Tacoma, WA
| |
Collapse
|
14
|
Mackley MP, Fletcher B, Parker M, Watkins H, Ormondroyd E. Stakeholder views on secondary findings in whole-genome and whole-exome sequencing: a systematic review of quantitative and qualitative studies. Genet Med 2016; 19:283-293. [PMID: 27584911 PMCID: PMC5447864 DOI: 10.1038/gim.2016.109] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/17/2016] [Indexed: 12/24/2022] Open
Abstract
PURPOSE As whole-exome sequencing (WES) and whole-genome sequencing (WGS) move into routine clinical practice, it is timely to review data that might inform the debate regarding secondary findings (SF) and the development of policies that maximize participant benefit. METHODS We systematically searched for qualitative and quantitative studies that explored stakeholder views on SF in WES/WGS. Framework analysis was undertaken to identify major themes. RESULTS Forty-four articles reporting the views of 11,566 stakeholders were included. Stakeholders were broadly supportive of returning "actionable" findings, but definitions of actionability varied. Stakeholder views on SF disclosure exist along a spectrum: potential WES/WGS recipients' views were largely influenced by a sense of rights, whereas views of genomics professionals were informed by a sense of professional responsibility. Experience with genetic illness and testing resulted in greater caution about SF, suggesting that truly informed decisions require an understanding of the implications and limitations of WES/WGS and possible findings. CONCLUSION This review suggests that bidirectional interaction during consent might best facilitate informed decision making about SF and that dynamic forms of consent, allowing for changing preferences, should be considered. Research exploring views from wider perspectives and from recipients who have received SF is critical if evidence-based policies are to be achieved.Genet Med 19 3, 283-293.
Collapse
Affiliation(s)
- Michael P Mackley
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin Fletcher
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Michael Parker
- Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
15
|
Yushak ML, Han G, Bouberhan S, Epstein L, DiGiovanna MP, Mougalian SS, Sanft TB, Abu-Khalaf MM, Chung GG, Stein SM, Goldberg SB, Pusztai L, Hofstatter EW. Patient preferences regarding incidental genomic findings discovered during tumor profiling. Cancer 2016; 122:1588-97. [PMID: 26970385 DOI: 10.1002/cncr.29951] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 01/10/2023]
Abstract
BACKGROUND During the process of tumor profiling, there is the potential to detect germline variants. To the authors' knowledge, there currently is no accepted standard of care for how to deal with these incidental findings. The goal of the current study was to assess disclosure preferences among patients with cancer regarding incidental genomic variants that may be discovered during tumor profiling. METHODS A 45-item questionnaire was administered to 413 patients in ambulatory oncology clinics. The survey captured demographic and disease variables and personal and family history, and presented case scenarios for different types of incidental germline variants that could theoretically be detected during genomic analysis of a patient's tumor. RESULTS The possibility of discovering non-cancer-related, germline variants did not deter patients from tumor profiling: 77% wanted to be informed concerning variants that could increase their risk of a serious but preventable illness, 56% wanted to know about variants that cause a serious but unpreventable illness, and 49% wanted to know about variants of uncertain significance. The majority of patients (75%) indicated they would share hereditary information regarding predisposition to preventable diseases with family and 62% would share information concerning unpreventable diseases. The most frequent concerns about incidental findings were ability to obtain health (48%) or life (41%) insurance. Only 21% of patients were concerned about privacy of information. CONCLUSIONS Patients with cancer appear to prefer to receive information regarding incidental germline variants, but there is substantial variability with regard to what information patients wish to learn. The authors recommend that personal preferences for the disclosure of different types of incidental findings be clarified before a tumor profiling test is ordered. Cancer 2016;122:1588-97. © 2016 American Cancer Society.
Collapse
Affiliation(s)
- Melinda L Yushak
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia
| | - Gang Han
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Sara Bouberhan
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Lianne Epstein
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Michael P DiGiovanna
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Sarah S Mougalian
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Tara B Sanft
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Maysa M Abu-Khalaf
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Gina G Chung
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Stacey M Stein
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Sarah B Goldberg
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Lajos Pusztai
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Erin W Hofstatter
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| |
Collapse
|
16
|
Ngeow J, Eng C. Precision medicine in heritable cancer: when somatic tumour testing and germline mutations meet. NPJ Genom Med 2016; 1:15006. [PMID: 29263804 PMCID: PMC5685292 DOI: 10.1038/npjgenmed.2015.6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 01/07/2023] Open
Abstract
Cancer is among the leading causes of death and disfigurement worldwide with an estimated global incidence of 14 million and ~8.2 million cancer-related deaths per annum. An estimated 5-10% of all cancers are hereditary, meaning a single gene mutation contributed to development of the cancer. In other words, inherited cancer has a worldwide incidence of ~1.4 million new cases per annum and a global prevalence of 300 million, and are often poorly recognised. The increase in genetic sequencing capability combined with the decrease in the cost of testing has altered both regulatory policy and clinical oncology practice Well-known examples of clinically important cancer susceptibility syndromes such as those caused by genetic mutations in highly penetrant genes such as BRCA1/2 hereditary breast-ovarian cancer syndrome genes have provided the framework for the practice of clinical cancer genetics. There is no question that these tests have provided clinical benefit to the patient and her/his family. However, with the expanding role of next generation sequencing in tumour profiling as well as in germline testing, clinicians are now faced with significant new challenges and potentially unexpected opportunities. Issues such as determining how best to deal with gene variants of uncertain clinical significance and the issue of incidental findings of hereditary cancer risk may be encountered during tumour genomic testing will require a concerted effort and dialogue on the part of the broad genomic community.
Collapse
Affiliation(s)
- Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Oncology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
- Germline High Risk Focus Group, Case Comprehensive Cancer Centre, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
17
|
Hofstatter E, Mehra K, Yushak M, Pusztai L. Tumor profiling and the incidentalome: patient decisions and risks. Future Oncol 2015; 11:3299-305. [DOI: 10.2217/fon.15.260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In recent years, the field of oncology has witnessed rapid advancements in genetic sequencing simultaneously with steeply declining costs of sequencing technology. As a result, genomics-driven cancer medicine and the use of tumor profiling are quickly becoming mainstays of cancer therapy. Oncology patients can benefit from tumor profiling by allowing the selection of targeted therapies tailored to their disease. However, it is increasingly recognized that the process of determining a tumor DNA sequence may lead to incidental discovery of underlying germline mutations which can impact other aspects of a patient’s health, and that of their family. How to handle the ‘incidentalome’ has been the subject of recent public debate, yet patient education about the potential risks of tumor profiling remains sparse. Patient perspectives and clinical implications of the tumor incidentalome must be specifically addressed by the oncology community as tumor profiling expands to become a new standard of care.
Collapse
Affiliation(s)
- Erin Hofstatter
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Karishma Mehra
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Melinda Yushak
- Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lajos Pusztai
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
18
|
Mallett A, Patel C, Maier B, McGaughran J, Gabbett M, Takasato M, Cameron A, Trnka P, Alexander SI, Rangan G, Tchan MC, Caruana G, John G, Quinlan C, McCarthy HJ, Hyland V, Hoy WE, Wolvetang E, Taft R, Simons C, Healy H, Little M. A protocol for the identification and validation of novel genetic causes of kidney disease. BMC Nephrol 2015; 16:152. [PMID: 26374634 PMCID: PMC4570515 DOI: 10.1186/s12882-015-0148-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic renal diseases (GRD) are a heterogeneous and incompletely understood group of disorders accounting for approximately 10 % of those diagnosed with kidney disease. The advent of Next Generation sequencing and new approaches to disease modelling may allow the identification and validation of novel genetic variants in patients with previously incompletely explained or understood GRD. METHODS/DESIGN This study will recruit participants in families/trios from a multidisciplinary sub-specialty Renal Genetics Clinic where known genetic causes of GRD have been excluded or where genetic testing is not available. After informed patient consent, whole exome and/or genome sequencing will be performed with bioinformatics analysis undertaken using a customised variant assessment tool. A rigorous process for participant data management will be undertaken. Novel genetic findings will be validated using patient-derived induced pluripotent stem cells via differentiation to renal and relevant extra-renal tissue phenotypes in vitro. A process for managing the risk of incidental findings and the return of study results to participants has been developed. DISCUSSION This investigator-initiated approach brings together experts in nephrology, clinical and molecular genetics, pathology and developmental biology to discover and validate novel genetic causes for patients in Australia affected by GRD without a known genetic aetiology or pathobiology.
Collapse
Affiliation(s)
- Andrew Mallett
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia. .,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia. .,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia. .,Kidney Health Service, Level 9, Ned Hanlon Building, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia.
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Barbara Maier
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Michael Gabbett
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia.,School of Medicine, Griffith University, Brisbane, Australia
| | - Minoru Takasato
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Anne Cameron
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Peter Trnka
- Queensland Child and Adolescent Renal Service, Lady Cilento Children's Hospital, Brisbane, Australia
| | - Stephen I Alexander
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gopala Rangan
- Department of Nephrology, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michel C Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Georgina Caruana
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - George John
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Cathy Quinlan
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Hugh J McCarthy
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia.,Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Valentine Hyland
- Molecular Genetics Laboratory, Pathology Queensland and Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Wendy E Hoy
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ryan Taft
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Helen Healy
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Melissa Little
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| |
Collapse
|
19
|
Drury S, Williams H, Trump N, Boustred C, Lench N, Scott RH, Chitty LS. Exome sequencing for prenatal diagnosis of fetuses with sonographic abnormalities. Prenat Diagn 2015; 35:1010-7. [DOI: 10.1002/pd.4675] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/21/2015] [Accepted: 08/08/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Suzanne Drury
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Hywel Williams
- Genetics and Genomic Medicine; UCL Institute of Child Health; London UK
| | - Natalie Trump
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Christopher Boustred
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Nicholas Lench
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Richard H. Scott
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Lyn S. Chitty
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
- Genetics and Genomic Medicine; UCL Institute of Child Health; London UK
| | | |
Collapse
|
20
|
Biancalana V, Laporte J. Diagnostic use of Massively Parallel Sequencing in Neuromuscular Diseases: Towards an Integrated Diagnosis. J Neuromuscul Dis 2015; 2:193-203. [PMID: 27858740 PMCID: PMC5240547 DOI: 10.3233/jnd-150092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is revolutionizing the genetic testing in diagnosis laboratories, replacing gene-by-gene investigations with a "gene panel" strategy. This new approach is particularly promising for the diagnosis of neuromuscular disorders affecting children as well as adults, which is constrained by strong clinical and genetic heterogeneity. While it leads to a strong improvement in molecular diagnosis, this new approach is dramatically changing the whole diagnosis process, establishing new decision trees and requiring integrated strategies between clinicians and laboratories. To have an overview of the implementation and benefit of these novel sequencing strategies for the diagnosis of neuromuscular disorders, we surveyed the current literature on the application of targeted genes panel sequencing, exome sequencing and genome sequencing. We highlight advantages and disadvantages of these different strategies in a diagnosis setting, discuss about unresolved cases, and point potential validation approaches and outcomes of massively parallel sequencing. It appears important to integrate such novel strategies with clinical, histopathological and imaging investigations, for a faster and more accurate diagnosis and patient care, and to foster research projects and clinical trials.
Collapse
Affiliation(s)
- Valérie Biancalana
- Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Strasbourg, France
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| |
Collapse
|
21
|
Abstract
Whole-exome sequencing has emerged as a fast and effective tool for the elucidation of genetic defects underlying both rare and common human diseases. Increased availability and decreased costs of next-generation sequencing have enabled investigators to use this approach not only in individual patients with rare diseases, but also to screen large cohorts or populations for the genetic determinants of diseases. Within the field of endocrinology, exome sequencing has led to major advancements in our understanding of many disorders including adrenal disease, growth and puberty disorders and type 2 diabetes mellitus, as well as a multitude of rare genetic syndromes with prominent endocrine involvement. In this Review, we provide an overview of these new insights and discuss the role that exome sequencing is expected to have in endocrine research and future clinical practice.
Collapse
Affiliation(s)
- Christiaan de Bruin
- Cincinnati Children's Hospital Medical Center, Division of Endocrinology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Andrew Dauber
- Cincinnati Children's Hospital Medical Center, Division of Endocrinology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| |
Collapse
|
22
|
Abstract
In this review, we describe key components of a computational infrastructure for a precision medicine program that is based on clinical-grade genomic sequencing. Specific aspects covered in this review include software components and hardware infrastructure, reporting, integration into Electronic Health Records for routine clinical use and regulatory aspects. We emphasize informatics components related to reproducibility and reliability in genomic testing, regulatory compliance, traceability and documentation of processes, integration into clinical workflows, privacy requirements, prioritization and interpretation of results to report based on clinical needs, rapidly evolving knowledge base of genomic alterations and clinical treatments and return of results in a timely and predictable fashion. We also seek to differentiate between the use of precision medicine in germline and cancer.
Collapse
|