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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [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: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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2
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Lawrence SM, Goshia T, Sinha M, Fraley SI, Williams M. Decoding human cytomegalovirus for the development of innovative diagnostics to detect congenital infection. Pediatr Res 2024; 95:532-542. [PMID: 38146009 PMCID: PMC10837078 DOI: 10.1038/s41390-023-02957-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Abstract
Cytomegalovirus is the most common cause of congenital infectious disease and the leading nongenetic etiology of sensorineural hearing loss. Although most infected neonates are asymptomatic at birth, congenital cytomegalovirus infection is responsible for nearly 400 infant deaths annually in the United States and may lead to significant long-term neurodevelopmental impairments in survivors. The resulting financial and social burdens of congenital cytomegalovirus infection have led many medical centers to initiate targeted testing after birth, with a growing advocacy to advance universal newborn screening. While no cures or vaccines are currently available to eliminate or prevent cytomegalovirus infection, much has been learned over the last five years regarding disease pathophysiology and viral replication cycles that may enable the development of innovative diagnostics and therapeutics. This Review will detail our current understanding of congenital cytomegalovirus infection, while focusing our discussion on routine and emerging diagnostics for viral detection, quantification, and long-term prognostication. IMPACT: This review highlights our current understanding of the fetal transmission of human cytomegalovirus. It details clinical signs and physical findings of congenital cytomegalovirus infection. This submission discusses currently available cytomegalovirus diagnostics and introduces emerging platforms that promise improved sensitivity, specificity, limit of detection, viral quantification, detection of genomic antiviral resistance, and infection staging (primary, latency, reactivation, reinfection).
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Affiliation(s)
- Shelley M Lawrence
- University of Utah, College of Medicine, Department of Pediatrics, Division of Neonatology, Salt Lake City, UT, USA.
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | | | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Marvin Williams
- University of Oklahoma, College of Medicine, Department of Obstetrics and Gynecology, Division of Fetal-Maternal Medicine, Oklahoma City, OK, USA
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3
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Li X, Zhong Y, Qiao Y, Li H, Hu X, Imani S, Zheng S, Li J. Advances and Challenges in Cytomegalovirus Detection Methods for Liver Transplant Donors. Diagnostics (Basel) 2023; 13:3310. [PMID: 37958206 PMCID: PMC10649722 DOI: 10.3390/diagnostics13213310] [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: 09/06/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
Cytomegalovirus (CMV) infection is a highly prevalent opportunistic infection among liver transplant recipients. When the liver donor is infected with CMV, there is a risk of transmission to the recipient, leading to CMV infection. To improve the postoperative outcome of liver transplantation, it is crucial to shift the focus of CMV detection to the donor and achieve early diagnosis, as well as implement effective preventative and therapeutic measures. However, the commonly used CMV detection methods in the past had limitations that prevented their early and accurate diagnosis in liver transplant donors. This review focuses on the latest advancements in CMV detection methods that can potentially be applied to liver transplant donors. The objective is to compare and evaluate their clinical utility, thereby providing guidance and support for rapid and accurate diagnosis of CMV infection in the clinic. The clustered regularly interspaced short palindromic repeats-associated proteins (CRISPR-Cas) system-based assay emerges as a promising method for detecting the virus, offering great prospects for early and expedient CMV infection diagnosis in clinical settings.
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Affiliation(s)
- Xiaoping Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yiwu Zhong
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yinbiao Qiao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou 310022, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
| | - Haoyu Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
| | - Xu Hu
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Saber Imani
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou 310022, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
| | - Jianhui Li
- Zhejiang Chinese Medical University, Hangzhou 310053, China
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou 310022, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
- The Organ Repair and Regeneration Medicine Institute of Hangzhou, Hangzhou 310003, China
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Thompson WS, Greenmyer JR, Lanpher BC, Brumbaugh JE, Bendel-Stenzel EM, Dimmock DP, Hobbs CA, Ibrahim SH, Hildreth AN. Ultra-rapid whole genome sequencing: A paradigm shift in the pre-transplant evaluation of neonatal acute liver failure. Liver Transpl 2023; 29:118-121. [PMID: 35861277 DOI: 10.1002/lt.26547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/27/2022] [Accepted: 07/10/2022] [Indexed: 01/14/2023]
Affiliation(s)
- Whitney S Thompson
- Department of Pediatric and Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA.,Center for Individualized Medicine , Mayo Clinic , Rochester , Minnesota , USA
| | - Jacob R Greenmyer
- Department of Pediatric and Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA
| | - Brendan C Lanpher
- Department of Clinical Genomics , Mayo Clinic , Rochester , Minnesota , USA
| | - Jane E Brumbaugh
- Division of Neonatal-Perinatal Medicine , Mayo Clinic , Rochester , Minnesota , USA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine , San Diego , California , USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine , San Diego , California , USA
| | - Samar H Ibrahim
- Pediatric Gastroenterology and Transplant Hepatology , Mayo Clinic , Rochester , Minnesota , USA
| | - Amber N Hildreth
- Rady Children's Institute for Genomic Medicine , San Diego , California , USA.,Department of Pediatrics, Division of Gastroenterology , University of California San Diego , San Diego , California , USA
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Plotogea M, Isam AJ, Frincu F, Zgura A, Bacinschi X, Sandru F, Duta S, Petca RC, Edu A. An Overview of Cytomegalovirus Infection in Pregnancy. Diagnostics (Basel) 2022; 12:diagnostics12102429. [PMID: 36292118 PMCID: PMC9600407 DOI: 10.3390/diagnostics12102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
The objective of this review was to bring to attention cytomegalovirus (CMV) infection during pregnancy, taking into consideration all relevant aspects, such as maternal diagnosis, fetal infection and prevention, prenatal diagnosis, and postnatal prognosis. A literature review was performed regarding adult and congenital infection. General information regarding this viral infection and potential related medical conditions was provided, considering the issues of maternal infection during pregnancy, transmission to the fetus, and associated congenital infection management. Prenatal diagnosis includes maternal serum testing and the confirmation of the infection in amniotic fluid or fetal blood. Additionally, prenatal diagnosis requires imaging techniques, ultrasound, and complementary magnetic resonance to assess cortical and extracortical anomalies. Imaging findings can predict both fetal involvement and the postnatal prognosis of the newborn, but they are difficult to assess, even for highly trained physicians. In regard to fetal sequelae, the early diagnosis of a potential fetal infection is crucial, and methods to decrease fetal involvement should be considered. Postnatal evaluation is also important, because many newborns may be asymptomatic and clinical anomalies can be diagnosed when sequelae are permanent.
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Affiliation(s)
- Mihaela Plotogea
- Department of Obstetrics and Gynecology, “Nicolae Malaxa” Clinical Hospital, 022441 Bucharest, Romania
| | - Al Jashi Isam
- Faculty of Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
- Correspondence: (A.J.I.); (F.F.)
| | - Francesca Frincu
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Correspondence: (A.J.I.); (F.F.)
| | - Anca Zgura
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Xenia Bacinschi
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Florica Sandru
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Simona Duta
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Razvan Cosmin Petca
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Antoine Edu
- Department of Obstetrics and Gynecology, “Nicolae Malaxa” Clinical Hospital, 022441 Bucharest, Romania
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
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6
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Sanford Kobayashi EF, Dimmock DP. Better and faster is cheaper. Hum Mutat 2022; 43:1495-1506. [PMID: 35723630 DOI: 10.1002/humu.24422] [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: 02/11/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.
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Affiliation(s)
- Erica F Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
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