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Bao YK, Situ BA, Runner M, Moshfeghi A, Ameri H. Comparison of The Results of Sponsored Genetic Testing Panels for Inherited Retinal Diseases. J Clin Med 2024; 13:3118. [PMID: 38892829 PMCID: PMC11172676 DOI: 10.3390/jcm13113118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Background/Objectives: Gene therapy's emergence has made molecular diagnosis for inherited retinal diseases clinically significant. Free genetic testing panels have improved testing access in clinical practice, yet the interpretation of results, especially variants of unknown significance (VUS), remains challenging and requires expertise. This study shares our experience in utilizing sponsored IRD panel tests by Invitae and Blueprint Genetics (BG), reporting their positivity rates, and comparing their reclassification of variants through amendments. Methods: This retrospective study analyzed genetic test reports from patients who underwent testing via Invitae or BG panels. A positive test was determined if there was a pathogenic mutation in an autosomal dominant gene, two pathogenic mutations in an autosomal recessive gene, or a pathogenic mutation in an X-linked gene in a male patient. Results: The testing positivity rates were 34.9% for Invitae (n = 109) and 42.1% for BG (n = 107). Invitae had more pathogenic variants per report (0.87 vs. 0.58 variants, p = 0.0038) and issued more amendments than BG (0.54 vs. 0.03 amendments; p < 0.01). Of the Invitae variant classification changes, 66.2% switched a VUS to benign. In the BG group, 75% of variant reclassifications changed a VUS to pathogenic. As a result of the Invitae amendments, 88% did not change the overall report result. Conclusions: While free-of-charge genetic testing panels offer valuable insights for diagnosing IRD, limitations such as low diagnostic yield and variant classification discrepancies persist between Invitae and BG. VUS should not be considered pathogenic in the clinical decision-making process. Careful interpretation of genetic testing is required.
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Affiliation(s)
- Yicheng K. Bao
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
| | - Betty A. Situ
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
| | | | - Andrew Moshfeghi
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
| | - Hossein Ameri
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
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Redman MG, Horton RH, Carley H, Lucassen A. Ancestry, race and ethnicity: the role and relevance of language in clinical genetics practice. J Med Genet 2024; 61:313-318. [PMID: 38050060 PMCID: PMC10982622 DOI: 10.1136/jmg-2023-109370] [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: 04/28/2023] [Accepted: 09/28/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND The terms ancestry, race and ethnicity are used variably within the medical literature and within society and clinical care. Biological lineage can provide an important context for the interpretation of genomic data, but the language used, and practices around when to ascertain this, vary. METHODS Using a fictional case scenario we explore the relevance of questions around ancestry, race and ethnicity in clinical genetic practice. RESULTS In the UK, data on 'ethnicity' are routinely collected by those using genomic medicine, as well as within the wider UK National Health Service, although the reasons for this are not always clear to practitioners and patients. Sometimes it is requested as a proxy for biological lineage to aid variant interpretation, refine estimations of carrier frequency and guide decisions around the need for pharmacogenetic testing. CONCLUSION There are many challenges around the use and utility of these terms. Currently, genomic databases are populated primarily with data from people of European descent, and this can lead to health disparities and poorer service for minoritised or underserved populations. Sensitivity and consideration are needed when communicating with patients around these areas. We explore the role and relevance of language around biological lineage in clinical genetics practice.
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Affiliation(s)
- Melody Grace Redman
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rachel Helen Horton
- Centre for Personalised Medicine, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, UK
| | - Helena Carley
- South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Anneke Lucassen
- Centre for Personalised Medicine, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, UK
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Hazel JW, Hammack-Aviran C, Brelsford KM, Malin BA, Beskow LM, Clayton EW. Direct-to-consumer genetic testing: Prospective users' attitudes toward information about ancestry and biological relationships. PLoS One 2021; 16:e0260340. [PMID: 34843533 PMCID: PMC8629298 DOI: 10.1371/journal.pone.0260340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
Direct-to-consumer genetic testing is marketed as a tool to uncover ancestry and kin. Recent studies of actual and potential users have demonstrated that individuals’ responses to the use of these tests for these purposes are complex, with privacy, disruptive consequences, potential for misuse, and secondary use by law enforcement cited as potential concerns. We conducted six focus groups with a diverse sample of participants (n = 62) who were aware of but had not used direct-to-consumer genetic tests, in an effort to understand more about what people considering these tests think about the potential value, risks, and benefits of such testing, taking into account use by third parties, such as potential kin and law enforcement. Participants differed widely in the perceived value of direct-to-consumer genetic tests for ancestry and kinship information for their own lives, including the desirability of contact with previously unknown relatives. Some perceived ancestry testing as mere curiosity or entertainment, while others, particularly those who had gaps in their family history, few living relatives, or who were adopted, saw greater value. Concerns about intrusion into one’s life by purported kin and control of data were widespread, with many participants expressing concern about secondary uses of data that could harm users or their families. The use of direct-to-consumer genetic tests data for forensic genealogy elicited a particularly wide array of reactions, both spontaneously and in response to specific discussion prompts, mirroring the current public debate about law enforcement access to such data. The themes uncovered through our investigation warrant specific attention in the continued development of the science, policy, and practice of commercial direct-to-consumer genetic testing.
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Affiliation(s)
- James W. Hazel
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Genetic Privacy and Identity in Community Settings (GetPreCiSe), Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Catherine Hammack-Aviran
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Genetic Privacy and Identity in Community Settings (GetPreCiSe), Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Kathleen M. Brelsford
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Genetic Privacy and Identity in Community Settings (GetPreCiSe), Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Bradley A. Malin
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Genetic Privacy and Identity in Community Settings (GetPreCiSe), Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Laura M. Beskow
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Genetic Privacy and Identity in Community Settings (GetPreCiSe), Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Genetic Privacy and Identity in Community Settings (GetPreCiSe), Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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Clayton J. Time considered as a helix of infinite possibilities. MEDICAL HUMANITIES 2021; 47:medhum-2020-012063. [PMID: 34088802 PMCID: PMC9396530 DOI: 10.1136/medhum-2020-012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 05/02/2023]
Abstract
This article explores the temporal implications of genomics through the lens of a classic science fiction story by Samuel R Delany, 'Time Considered as a Helix of Semi-Precious Stones'. Delany's futuristic vision of 'hologramic information storage', which allows the interplanetary Special Services to discover and predict everything a suspect has done or will be doing at any time in the past, present or future resembles 'genome time', the illusion that data encoded in your DNA can reveal your entire life-not only where you came from but what you will become-and that it is knowable from a single test in the present. The temporal implications of genomics are compared with 'queer time' and contrasted with the temporal implications of nanoscience and climate change in order to clarify what is distinctive about genome time. In conclusion, some practical consequences of genome time are discussed.
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Affiliation(s)
- Jay Clayton
- Curb Center, Vanderbilt University, Nashville, Tennessee, USA
- English, Vanderbilt University, Nashville, Tennessee, USA
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Basch CH, Hillyer GC, Wahrman MZ, Garcia P, Basch CE. DNA testing information on YouTube: Inadequate advice can mislead and harm the public. J Genet Couns 2020; 30:785-792. [PMID: 33382174 DOI: 10.1002/jgc4.1375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 01/07/2023]
Abstract
Direct-to-consumer (DTC) DNA (i.e., genetic) testing has become very popular, with close to 30 million Americans having used these services. The 100 most widely viewed DNA YouTube testing videos were analyzed to determine whether they are providing adequate information for consumers. The top 100 videos had more than 300 million cumulative views, showing the popularity and reach of the information source. While many videos addressed the specimen collection process, family roots and ancestry, and the prospect of uncovering unexpected information about family or health leading to possible distress, almost none of the videos addressed accuracy or confidentiality issues, which are major issues of DNA testing. It is recommended that further information on those issues be made readily available, and more vigilant oversight by regulatory agencies be implemented. Such oversight should include monitoring what information is and is not readily provided by each company, and the veracity of information being communicated to existing and prospective consumers. We also recommend that for medical issues, clinical genetic testing, along with genetic counseling by genetic counselors, be the method of choice.
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Affiliation(s)
- Corey H Basch
- Department of Public Health, William Paterson University, Wayne, NJ, USA
| | - Grace C Hillyer
- Department of Epidemiology, Mailman School of Public Health, Columbia University NY, New York, NY, USA
| | - Miryam Z Wahrman
- Department of Biology, William Paterson University, Wayne, NJ, USA
| | - Philip Garcia
- Department of Public Health, William Paterson University, Wayne, NJ, USA
| | - Charles E Basch
- Health and Behavior Studies, Teachers College, Columbia University NY, New York, NY, USA
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Resta R. Birds of a Feather? Genetic Counseling, Genetic Testing, and Humanism. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036673. [PMID: 31548221 DOI: 10.1101/cshperspect.a036673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Humanism is a philosophy that emphasizes rational, scientific, and empiric analysis of the world we live in to improve the physical, social, and psychological life of humanity. Although individual genetic counselors may or may not identify as humanists, genetic counseling and genetic testing are primarily humanistic endeavors because they are situated in the context of humanistic medicine in the westernized world. Humanistic goals are also implicit and explicit in the profession and practice of genetic counselors. This review examines the relationship between humanism and genetic counseling, highlighting situations in which the two may be discordant, and suggests ways that genetic counselors can reconcile these discordances.
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Affiliation(s)
- Robert Resta
- Swedish Cancer Institute, Swedish Medical Center, Seattle, Washington 98104, USA
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Batra P, Huang KL. Genotype concordance and polygenic risk score estimation across consumer genetic testing data. Ann Hum Genet 2020; 84:352-356. [PMID: 32436989 DOI: 10.1111/ahg.12389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 11/30/2022]
Abstract
The consumer genomics industry is steadily growing and delivering genetic information to over 10 million individuals. Yet, the implications of using data from different services remain unclear. We investigated the genotyped sites, concordance, and genetic risk estimation using data from three consumer services-two single nucleotide polymorphism (SNP)-array based and one sequencing based. In an N-of-one setting, we found the three services genotyped predominantly distinct sets of sites. While there was a high concordance between overlapping sites of the two SNP-array services (99.6%), there was a lower concordance between these services and a low-pass whole-genome service (73.0%). The discrepancy between the three sets of data resulted in different APOE genotypes and genetic risk scores of Alzheimer's disease. Our results demonstrate genotype results across consumer genomics platforms may lead to different genetic risk estimates, highlighting the need for careful quality control and interpretation.
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Affiliation(s)
- Prag Batra
- School of Medicine, New York University, New York, New York
| | - Kuan-Lin Huang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York.,Tisch Cancer Institute, New York, New York.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
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Affiliation(s)
- Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City
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