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Haidar H, Iskander R. Non-invasive Prenatal Testing for Fetal Whole Genome Sequencing: An Interpretive Critical Review of the Ethical, Legal, Social, and Policy Implications. CANADIAN JOURNAL OF BIOETHICS 2022. [DOI: 10.7202/1087199ar] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Best S, Wou K, Vora N, Van der Veyver IB, Wapner R, Chitty LS. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat Diagn 2018; 38:10-19. [PMID: 28654730 PMCID: PMC5745303 DOI: 10.1002/pd.5102] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Abstract
Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sunayna Best
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karen Wou
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Neeta Vora
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignatia B. Van der Veyver
- Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - 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 Great Ormond Street Institute of Child Health, London, UK
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Fujikura K. Global Carrier Rates of Rare Inherited Disorders Using Population Exome Sequences. PLoS One 2016; 11:e0155552. [PMID: 27219052 PMCID: PMC4878778 DOI: 10.1371/journal.pone.0155552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 12/22/2022] Open
Abstract
Exome sequencing has revealed the causative mutations behind numerous rare, inherited disorders, but it is challenging to find reliable epidemiological values for rare disorders. Here, I provide a genetic epidemiology method to identify the causative mutations behind rare, inherited disorders using two population exome sequences (1000 Genomes and NHLBI). I created global maps of carrier rate distribution for 18 recessive disorders in 16 diverse ethnic populations. Out of a total of 161 mutations associated with 18 recessive disorders, I detected 24 mutations in either or both exome studies. The genetic mapping revealed strong international spatial heterogeneities in the carrier patterns of the inherited disorders. I next validated this methodology by statistically evaluating the carrier rate of one well-understood disorder, sickle cell anemia (SCA). The population exome-based epidemiology of SCA [African (allele frequency (AF) = 0.0454, N = 2447), Asian (AF = 0, N = 286), European (AF = 0.000214, N = 4677), and Hispanic (AF = 0.0111, N = 362)] was not significantly different from that obtained from a clinical prevalence survey. A pair-wise proportion test revealed no significant differences between the two exome projects in terms of AF (46/48 cases; P > 0.05). I conclude that population exome-based carrier rates can form the foundation for a prospectively maintained database of use to clinical geneticists. Similar modeling methods can be applied to many inherited disorders.
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Affiliation(s)
- Kohei Fujikura
- Kobe University School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
- * E-mail:
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Wilkinson DJC, Barnett C, Savulescu J, Newson AJ. Genomic intensive care: should we perform genome testing in critically ill newborns? Arch Dis Child Fetal Neonatal Ed 2016; 101:F94-8. [PMID: 26369368 PMCID: PMC4789714 DOI: 10.1136/archdischild-2015-308568] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/05/2015] [Indexed: 11/24/2022]
Affiliation(s)
- Dominic JC Wilkinson
- Faculty of Philosophy, Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, UK,Robinson Institute, Discipline of Obstetrics and Gynaecology, University of Adelaide, Adelaide, South Australia, Australia,Newborn care unit, John Radcliffe Hospital, Oxford, UK
| | - Christopher Barnett
- SA Clinical Genetics Service, Women's and Children's Hospital/SA Pathology, North Adelaide, South Australia, Australia,School of Paediatrics and Reproductive Health, University of Adelaide,Adelaide, South Australia, Australia
| | - Julian Savulescu
- Faculty of Philosophy, Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, UK
| | - Ainsley J Newson
- Centre for Values, Ethics and the Law in Medicine, School of Public Health, University of Sydney, Sydney, New South Wales, Australia
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Tonk VS, Wilson GN. Inaccuracy of non-invasive prenatal screening demands cautious counsel and follow-up. Am J Med Genet A 2015; 170A:1086-7. [PMID: 26708282 DOI: 10.1002/ajmg.a.37530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 12/10/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Vijay S Tonk
- Departments of Pediatrics, Obstetrics and Gynecology, Pathology Texas Tech University Health Science Centers, Dallas, Texas
| | - Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Science Center, Lubbock and Medical City Hospital, Dallas, Texas
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Butali A, Mossey P, Tiffin N, Adeyemo W, Eshete M, Mumena C, Audu R, Onwuamah C, Agbenorku P, Ogunlewe M, Adebola A, Olasoji H, Aregbesola B, Braimah R, Oladugba A, Onah I, Adebiyi E, Olaitan P, Abdur-Rahman L, Adeyemo A. Multidisciplinary approach to genomics research in Africa: the AfriCRAN model. Pan Afr Med J 2015; 21:229. [PMID: 26523171 PMCID: PMC4607986 DOI: 10.11604/pamj.2015.21.229.7380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/23/2015] [Indexed: 01/01/2023] Open
Abstract
This article is an outcome of the African Craniofacial Anomalies Research Network (AfriCRAN) Human Hereditary and Health (H3A) grant planning meeting in 2012 in Lagos, Nigeria. It describes the strengths of a multidisciplinary team approach to solving complex genetic traits in the craniofacial region. It also highlights the different components and argues for the composition of similar teams to fast track the discovery of disease genes, diagnostic tools, improved clinical treatment and ultimately prevention of diseases.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA. U.S.A
| | - Peter Mossey
- Department of Orthodontics, University of Dundee, Scotland. UK
| | - Nikki Tiffin
- South African National Bioinformatics Institute, University of the Western Cape, Private Bag, X17, Bellville 7535, South Africa
| | - Wasiu Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos. Nigeria
| | - Mekonen Eshete
- Department of surgery School of Medicine Faculty of health sciences Addis Ababa University, Addis Ababa. Ethiopia
| | - Chrispinanus Mumena
- Department of Oral and Maxillofacial Surgery, Kigali Health Institute, P.O. Box 3286, Kigali, Rwanda
| | - Rosemary Audu
- Human Virology Laboratory, Nigerian Institute of Medical Research, 6, Edmond Crescent, P.M.B. 2013, Yaba, Lagos, Nigeria
| | - Chika Onwuamah
- Human Virology Laboratory, Nigerian Institute of Medical Research, 6, Edmond Crescent, P.M.B. 2013, Yaba, Lagos, Nigeria
| | - Pius Agbenorku
- Department of Plastic Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, P.O. Box 448, KNUST, Kumasi, Ghana
| | - Mobolanle Ogunlewe
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos. Nigeria
| | - Adetokunbo Adebola
- Department of Oral and Maxillofacial Surgery, Aminu Kano University Teaching Hospital, Kano. Nigeria
| | - Hecto Olasoji
- Department of Oral and Maxillofacial Surgery, University of Maiduguri Teaching Hospital, Maiduguri. Nigeria
| | - Babatunde Aregbesola
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife. Nigeria
| | - Ramat Braimah
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife. Nigeria
| | | | - Ifeanyichukwu Onah
- Department of Plastic Surgery, National Orthopedic hospital, Enugu. Nigeria
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences and Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Peter Olaitan
- Department of Plastic and Reconstructive Surgery, Ladoke Akintola University Ogbomosho. Nigeria
| | | | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, U.S.A
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Michie M, Allyse M. Old Questions, New Paradigms: Ethical, Legal, and Social Complications of Noninvasive Prenatal Testing. AJOB Empir Bioeth 2015; 6:1-4. [PMID: 26185771 DOI: 10.1080/23294515.2014.993440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marsha Michie
- Institute for Health and Aging, University of California San Francisco
| | - Megan Allyse
- Institute for Health and Aging, University of California San Francisco
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Allyse M, Minear MA, Berson E, Sridhar S, Rote M, Hung A, Chandrasekharan S. Non-invasive prenatal testing: a review of international implementation and challenges. Int J Womens Health 2015; 7:113-26. [PMID: 25653560 PMCID: PMC4303457 DOI: 10.2147/ijwh.s67124] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noninvasive prenatal genetic testing (NIPT) is an advance in the detection of fetal chromosomal aneuploidies that analyzes cell-free fetal DNA in the blood of a pregnant woman. Since its introduction to clinical practice in Hong Kong in 2011, NIPT has quickly spread across the globe. While many professional societies currently recommend that NIPT be used as a screening method, not a diagnostic test, its high sensitivity (true positive rate) and specificity (true negative rate) make it an attractive alternative to the serum screens and invasive tests currently in use. Professional societies also recommend that NIPT be accompanied by genetic counseling so that families can make informed reproductive choices. If NIPT becomes more widely adopted, States will have to implement regulation and oversight to ensure it fits into existing legal frameworks, with particular attention to returning fetal sex information in areas where sex-based abortions are prevalent. Although there are additional challenges for NIPT uptake in the developing world, including the lack of health care professionals and infrastructure, the use of NIPT in low-resource settings could potentially reduce the need for skilled clinicians who perform invasive testing. Future advances in NIPT technology promise to expand the range of conditions that can be detected, including single gene disorders. With these advances come questions of how to handle incidental findings and variants of unknown significance. Moving forward, it is essential that all stakeholders have a voice in crafting policies to ensure the ethical and equitable use of NIPT across the world.
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Affiliation(s)
- Megan Allyse
- Institute for Health and Aging, University of California San Francisco, San Francisco, California, USA
| | | | - Elisa Berson
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Shilpa Sridhar
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Margaret Rote
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Anthony Hung
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
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Farrell RM, Agatisa PK, Nutter B. What women want: lead considerations for current and future applications of noninvasive prenatal testing in prenatal care. Birth 2014; 41:276-82. [PMID: 24825739 PMCID: PMC4195446 DOI: 10.1111/birt.12113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/17/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) will change the delivery of prenatal care for all women, including those considered low risk for fetal chromosomal abnormalities. This study investigated pregnant women's attitudes, informational needs, and decision-making preferences with respect to current and future applications of NIPT. METHODS A survey instrument was used to identify aspects of the decision-making process for NIPT among low-risk and high-risk populations. RESULTS Both low-risk and high-risk women (n = 334) expressed interest in incorporating NIPT as a screening test into their prenatal care. Information specific to NIPT's detection rate (86%), indications (77%), and performance in comparison with conventional screens and diagnostic tests (63%) were identified as lead factors when considering its use. The future availability of NIPT as a diagnostic test increased women's willingness to undergo testing for fetal aneuploidy, cancer susceptibility, and childhood-onset and adult-onset diseases. Despite its noninvasive aspects, participants expressed the need for a formal informed consent process (71%) to take place before testing. CONCLUSIONS This study demonstrates that NIPT will introduce new challenges for pregnant women and their health care practitioners who will be charged with supporting informed decision making about its use. It is critical that obstetric professionals are prepared to facilitate a patient-centered decision-making process as its clinical application rapidly changes.
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Affiliation(s)
- Ruth M. Farrell
- Department of Obstetrics and Gynecology, Cleveland Clinic, 9500 Euclid Avenue, A81, Cleveland, Ohio 44195 USA, , Department of Bioethics, Cleveland Clinic, 9500 Euclid Avenue, JJ-60, Cleveland, Ohio 44195 USA, , Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio, 44195 USA
| | - Patricia K. Agatisa
- Department of Bioethics, Cleveland Clinic, 9500 Euclid Avenue, JJ-60, Cleveland, Ohio 44195 USA,
| | - Benjamin Nutter
- Department of Quantitative Health Sciences, 9500 Euclid Avenue, JJN-3, Cleveland Clinic, Cleveland, Ohio 44195 USA,
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Santillan MK, Leslie KK, Hamilton WS, Boese BJ, Ahuja M, Hunter SK, Santillan DA. "Collection of a lifetime: a practical approach to developing a longitudinal collection of women's healthcare biological samples". Eur J Obstet Gynecol Reprod Biol 2014; 179:94-9. [PMID: 24965987 DOI: 10.1016/j.ejogrb.2014.05.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 05/20/2014] [Indexed: 01/16/2023]
Abstract
OBJECTIVE The objective is to develop a biorepository of samples that represent all stages of a women's life. Importantly, our goal is to collect longitudinal physical specimens as well as the associated short and long-term clinical information. STUDY DESIGN The Women's Health Tissue Repository was established to encompass four tissue banks: Well Women Tissue Bank, Reproductive Endocrinology and Infertility Tissue Bank, Maternal Fetal Tissue Bank, and the long-established Gynecologic Malignancies Tissue Bank. Based on their health status, women being seen in Women's Health at the University of Iowa are recruited to contribute samples and grant access to their electronic medical record to the biorepository. Samples are coded, processed, and stored for use by investigators. RESULTS The Maternal Fetal Tissue Bank was the first expansion of our department's biobanking efforts. Approximately 75% of the women approached consent to participate in the Maternal Fetal Tissue Bank. Enrollment has steadily increased. Samples have been used for over 20 projects in the first 3 years and are critical to 7 funded grants and 3 patent applications. CONCLUSION Patient samples with corresponding clinical data are initially important to women's health research. Our model demonstrates that many research projects by faculty, fellows, and residents have benefited from the existence of the Women's Health Tissue Repository. While challenging to achieve, longitudinal sampling allows for the greatest opportunity to study normal and pathological changes throughout all phases of a women's life, including pregnancy. This bank facilitates and accelerates the development of novel research, technologies, and possible therapeutic options in women's health. The establishment of more longitudinal biorepositories based on our model would enhance women's health research.
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Affiliation(s)
- Mark K Santillan
- University of Iowa Hospitals and Clinics, Department of Obstetrics and Gynecology, Iowa City, IA, United States
| | - Kimberly K Leslie
- University of Iowa Hospitals and Clinics, Department of Obstetrics and Gynecology, Iowa City, IA, United States
| | - Wendy S Hamilton
- University of Iowa Hospitals and Clinics, Department of Obstetrics and Gynecology, Iowa City, IA, United States
| | - Brenda J Boese
- University of Iowa Hospitals and Clinics, Department of Obstetrics and Gynecology, Iowa City, IA, United States
| | - Monika Ahuja
- University of Iowa, Institute for Clinical and Translational Science, Iowa City, IA, United States
| | - Stephen K Hunter
- University of Iowa Hospitals and Clinics, Department of Obstetrics and Gynecology, Iowa City, IA, United States
| | - Donna A Santillan
- University of Iowa Hospitals and Clinics, Department of Obstetrics and Gynecology, Iowa City, IA, United States.
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Snyder MW, Simmons LE, Kitzman JO, Santillan DA, Santillan MK, Gammill HS, Shendure J. Noninvasive fetal genome sequencing: a primer. Prenat Diagn 2013; 33:547-54. [PMID: 23553552 DOI: 10.1002/pd.4097] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We recently demonstrated whole genome sequencing of a human fetus using only parental DNA samples and plasma from the pregnant mother. This proof-of-concept study demonstrated how samples obtained noninvasively in the first or second trimester can be analyzed to yield a highly accurate and substantially complete genetic profile of the fetus, including both inherited and de novo variation. Here, we revisit our original study from a clinical standpoint, provide an overview of the scientific approach, and describe opportunities and challenges along the path toward clinical adoption of noninvasive fetal whole genome sequencing.
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Affiliation(s)
- Matthew W Snyder
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Dagle JM, Murray JC. Applying deep DNA sequencing to common, complex pediatric traits. Pediatrics 2012; 130:e1677-8. [PMID: 23166345 PMCID: PMC3507258 DOI: 10.1542/peds.2012-2870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Jeffrey C. Murray
- Departments of Pediatrics,,Biology,,Nursing, and,Epidemiology, University of Iowa, Iowa City, Iowa
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