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Marasa M, Ahram DF, Rehman AU, Mitrotti A, Abhyankar A, Jain NG, Weng PL, Piva SE, Fernandez HE, Uy NS, Chatterjee D, Kil BH, Nestor JG, Felice V, Robinson D, Whyte D, Gharavi AG, Appel GB, Radhakrishnan J, Santoriello D, Bomback A, Lin F, D’Agati VD, Jobanputra V, Sanna-Cherchi S. Implementation and Feasibility of Clinical Genome Sequencing Embedded Into the Outpatient Nephrology Care for Patients With Proteinuric Kidney Disease. Kidney Int Rep 2023; 8:1638-1647. [PMID: 37547535 PMCID: PMC10403677 DOI: 10.1016/j.ekir.2023.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/01/2023] [Accepted: 05/22/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction The diagnosis and management of proteinuric kidney diseases such as focal segmental glomerulosclerosis (FSGS) are challenging. Genetics holds the promise to improve clinical decision making for these diseases; however, it is often performed too late to enable timely clinical action and it is not implemented within routine outpatient nephrology visits. Methods We sought to test the implementation and feasibility of clinical rapid genome sequencing (GS) in guiding decision making in patients with proteinuric kidney disease in real-time and embedded in the outpatient nephrology setting. Results We enrolled 10 children or young adults with biopsy-proven FSGS (9 cases) or minimal change disease (1 case). The mean age at enrollment was 16.2 years (range 2-30). The workflow did not require referral to external genetics clinics but was conducted entirely during the nephrology standard-of-care appointments. The total turn-around-time from enrollment to return-of-results and clinical decision averaged 21.8 days (12.4 for GS), which is well within a time frame that allows clinically relevant treatment decisions. A monogenic or APOL1-related form of kidney disease was diagnosed in 5 of 10 patients. The genetic findings resulted in a rectified diagnosis in 6 patients. Both positive and negative GS findings determined a change in pharmacological treatment. In 3 patients, the results were instrumental for transplant evaluation, donor selection, and the immunosuppressive treatment. All patients and families received genetic counseling. Conclusion Clinical GS is feasible and can be implemented in real-time in the outpatient care to help guiding clinical management. Additional studies are needed to confirm the cost-effectiveness and broader utility of clinical GS across the phenotypic and demographic spectrum of kidney diseases.
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Affiliation(s)
- Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | | | - Namrata G. Jain
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, USA
| | - Patricia L. Weng
- Division of Pediatric Nephrology, Department of Pediatrics, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, California, USA
| | - Stacy E. Piva
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Hilda E. Fernandez
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Natalie S. Uy
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, USA
| | - Debanjana Chatterjee
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Byum H. Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Jordan G. Nestor
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | | | | | - Dilys Whyte
- Pediatric Specialty Center of Good Samaritan Hospital Medical Center, Babylon, New York, USA
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Gerald B. Appel
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Jai Radhakrishnan
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Dominick Santoriello
- Department of Pathology and Cell Biology, Renal Pathology Division, Columbia University Medical Center, New York, USA
| | - Andrew Bomback
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, USA
| | - Vivette D. D’Agati
- Department of Pathology and Cell Biology, Renal Pathology Division, Columbia University Medical Center, New York, USA
| | - Vaidehi Jobanputra
- The New York Genome Center, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, USA
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Abstract
OBJECTIVES Genetic disorders are a leading contributor to mortality in the neonatal ICU and PICU in the United States. Although individually rare, there are over 6,200 single-gene diseases, which may preclude a genetic diagnosis prior to ICU admission. Rapid whole genome sequencing is an emerging method of diagnosing genetic conditions in time to affect ICU management of neonates; however, its clinical utility has yet to be adequately demonstrated in critically ill children. This study evaluates next-generation sequencing in pediatric critical care. DESIGN Retrospective cohort study. SETTING Single-center PICU in a tertiary children's hospital. PATIENTS Children 4 months to 18 years admitted to the PICU who were nominated between July 2016 and May 2018. INTERVENTIONS Rapid whole genome sequencing with targeted phenotype-driven analysis was performed on patients and their parents, when parental samples were available. MEASUREMENTS AND MAIN RESULTS A molecular diagnosis was made by rapid whole genome sequencing in 17 of 38 children (45%). In four of the 17 patients (24%), the genetic diagnoses led to a change in management while in the PICU, including genome-informed changes in pharmacotherapy and transition to palliative care. Nine of the 17 diagnosed children (53%) had no dysmorphic features or developmental delay. Eighty-two percent of diagnoses affected the clinical management of the patient and/or family after PICU discharge, including avoidance of biopsy, administration of factor replacement, and surveillance for disorder-related sequelae. CONCLUSIONS This study demonstrates a retrospective evaluation for undiagnosed genetic disease in the PICU and clinical utility of rapid whole genome sequencing in a portion of critically ill children. Further studies are needed to identify PICU patients who will benefit from rapid whole genome sequencing early in PICU admission when the underlying etiology is unclear.
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Weng C, Kahn MG. Clinical Research Informatics for Big Data and Precision Medicine. Yearb Med Inform 2016:211-218. [PMID: 27830253 DOI: 10.15265/iy-2016-019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES To reflect on the notable events and significant developments in Clinical Research Informatics (CRI) in the year of 2015 and discuss near-term trends impacting CRI. METHODS We selected key publications that highlight not only important recent advances in CRI but also notable events likely to have significant impact on CRI activities over the next few years or longer, and consulted the discussions in relevant scientific communities and an online living textbook for modern clinical trials. We also related the new concepts with old problems to improve the continuity of CRI research. RESULTS The highlights in CRI in 2015 include the growing adoption of electronic health records (EHR), the rapid development of regional, national, and global clinical data research networks for using EHR data to integrate scalable clinical research with clinical care and generate robust medical evidence. Data quality, integration, and fusion, data access by researchers, study transparency, results reproducibility, and infrastructure sustainability are persistent challenges. CONCLUSION The advances in Big Data Analytics and Internet technologies together with the engagement of citizens in sciences are shaping the global clinical research enterprise, which is getting more open and increasingly stakeholder-centered, where stakeholders include patients, clinicians, researchers, and sponsors.
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Affiliation(s)
- C Weng
- Chunhua Weng, PhD, FACMI, Department of Biomedical Informatics, Columbia University, 622 W 168 Street, PH-20, New York, NY 10032, USA, E-mail:
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Affiliation(s)
- David J Amor
- Royal Children's Hospital, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Abstract
With the recognition of genetic disorders in the newborn, there is the potential to offer new lifesaving therapies. For other conditions such as hypothyroidism in Down syndrome or hypercalemia in the 22q11 microdeltion syndrome, the early identification of an untreatable condition permits prompt screening for potential comorbid conditions. DNA testing for disorders and DNA-based screening are rapidly evolving. With new more powerful tests, there is an increasing ability to see into a potential future and change the outcome for newborns. However, there remain significant ethical and structural issues to be considered before routine implementation of DNA testing.
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Affiliation(s)
- David P Dimmock
- Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - David P Bick
- Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, WI 53226, USA
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Raje N, Soden S, Swanson D, Ciaccio CE, Kingsmore SF, Dinwiddie DL. Utility of next generation sequencing in clinical primary immunodeficiencies. Curr Allergy Asthma Rep 2014; 14:468. [PMID: 25149170 DOI: 10.1007/s11882-014-0468-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are a group of genetically heterogeneous disorders that present with very similar symptoms, complicating definitive diagnosis. More than 240 genes have hitherto been associated with PIDs, of which more than 30 have been identified in the last 3 years. Next generation sequencing (NGS) of genomes or exomes of informative families has played a central role in the discovery of novel PID genes. Furthermore, NGS has the potential to transform clinical molecular testing for established PIDs, allowing all PID differential diagnoses to be tested at once, leading to increased diagnostic yield, while decreasing both the time and cost of obtaining a molecular diagnosis. Given that treatment of PID varies by disease gene, early achievement of a molecular diagnosis is likely to enhance treatment decisions and improve patient outcomes.
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Affiliation(s)
- Nikita Raje
- Children's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA,
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Abstract
INTRODUCTION Next-generation sequencing (NGS) is transforming the conduct of genetic research and diagnostic investigation. This creates new challenges as it generates additional information, including unsought and unwanted information. Nevertheless, this information must be deliberately managed-interpreted, disclosed and then either stored or destroyed. AREAS OF AGREEMENT Handling the process of consent to exome or genome sequencing should include discussion about the possible detection of variants of uncertain significance (VUSs) or incidental findings (IFs) that the patient may prefer not to hear about. A plan should be drawn up that specifies whether and how the patient would be recontacted in the future with new interpretations. AREAS OF CONTROVERSY There is an active debate about which IFs or VUSs should be disclosed to the patient when an exome or genome sequence has been performed, or whether all findings of any possible relevance should always be disclosed. How this is managed has important implications for the initial explanation of the test to the patient and the process of consent. The assumption is often made that all sequence information should be stored, but this may not be sustainable or useful. GROWING POINTS Efforts are being made to build a consensus on what 'incidental' information should be disclosed. These policy questions are being addressed in many centres and practices are evolving rapidly. AREAS TIMELY FOR DEVELOPING RESEARCH Those interested in genetics, public health, bioethics and medical ethics may wish to debate these issues and influence future practice in both genetic research and genetic diagnostic services.
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Affiliation(s)
- Angus J Clarke
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XW, UK
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Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde AK, Ben-Avraham D, Barzilai N, Oschwald D, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P. Disease variants in genomes of 44 centenarians. Mol Genet Genomic Med 2014; 2:438-50. [PMID: 25333069 PMCID: PMC4190879 DOI: 10.1002/mgg3.86] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 12/14/2022] Open
Abstract
To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE ε4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer's disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions. In genome sequences of 44 Ashkenazi centenarians, we identified many coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions.
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Affiliation(s)
- Yun Freudenberg-Hua
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030 ; Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Jan Freudenberg
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
| | - Vladimir Vacic
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Avinash Abhyankar
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Anne-Katrin Emde
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Danny Ben-Avraham
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Nir Barzilai
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Dayna Oschwald
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Erika Christen
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
| | - Jeremy Koppel
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030 ; Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Blaine Greenwald
- Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Robert B Darnell
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013 ; Department of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University 1230 York Avenue, New York, New York, 10065
| | - Soren Germer
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Gil Atzmon
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Peter Davies
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
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Hull SC, Berkman BE. Grappling with genomic incidental findings in the clinical realm. Chest 2014; 145:226-230. [PMID: 24493507 DOI: 10.1378/chest.13-1976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We have learned a remarkable amount in recent decades about genomics and its potential contributions to human health and medical practice. However, genomic sequencing technology, which is starting to become incorporated into clinical care, also raises ethical challenges. In particular, there has been significant debate about the appropriate management of genomic incidental findings (GIFs), which we define as pathogenic or likely pathogenic test results that are not apparently relevant to the diagnostic indications for which the tests were ordered. Although there is an emerging consensus that clinicians will have at least some obligation to disclose GIFs to patients, the scope of that obligation is unclear. This commentary identifies nuanced issues that clinicians will likely face in the foreseeable future regarding their emerging obligations to disclose clinically actionable GIFs. Will clinicians be expected to look actively for GIFs? Should GIFs for adult-onset disorders be disclosed to children? What obligations will clinicians have to disclose GIFs to family members of deceased patients? What role should informed consent play? There is value to exploring the range of views on these questions at this time, before genomic sequencing has fully matured as a technology, so that clinicians can anticipate how they will respond to the discovery of GIFs once sequencing becomes a more routine part of clinical care. Genomics is ultimately going to play an important role in the practice of pulmonary medicine, and it is important for pulmonologists and other subspecialists to be well informed about what to expect.
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Affiliation(s)
- Sara Chandros Hull
- Office of the Clinical Director, National Human Genome Research Institute.
| | - Benjamin E Berkman
- Office of the Clinical Director, National Human Genome Research Institute; Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD
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