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Utility of clinical exome sequencing in the evaluation of neonates with suspected genetic condition - An observational study from tertiary neonatal care unit in South India. Eur J Med Genet 2021; 64:104247. [PMID: 34000440 DOI: 10.1016/j.ejmg.2021.104247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/27/2021] [Accepted: 05/10/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES To study the utility of clinical exome sequencing (CES) using next generation sequencing (NGS) in evaluating neonates with suspected genetic conditions. METHODS This is an observational study conducted in a tertiary care neonatal unit. We included neonates with suspected genetic conditions, for whom CES were done either by direct sampling or from stored DNA. Data was collected from the Sri Ramachandra centre of excellence in perinatal health (SCOPE) case records of 2016-2019. Yield of CES, percentage of pathogenic, non-pathogenic and variant of uncertain significance (VUS) and associated disorders were studied. RESULTS CES was done in 36 neonates. Variants were detected in 78% (28/36). However, significant variants with clinical correlation were present in 20 (56%) babies. Test was carried out from the stored sample in 10 (28%) babies. Mean turn-around time was 39 ± 7 days. Specialist was involved in 1 and treatment changes were done in 5 neonates. Five out of 8 VUS were clinically correlating. Inborn errors of metabolism were the commonest (60%). Two VUS were ascertained as likely pathogenic after parental segregation analysis. CONCLUSION CES has a definite role in evaluation of suspected genetic conditions for diagnosis and prognostication. It also helps scientific society to build in additional evidence so that the "VUS" could be asserted as "likely pathogenic" . Our experience reiterates the importance of storing and archiving DNA of the affected child.
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Giardina T, Robinson C, Grieu-Iacopetta F, Millward M, Iacopetta B, Spagnolo D, Amanuel B. Implementation of next generation sequencing technology for somatic mutation detection in routine laboratory practice. Pathology 2018; 50:389-401. [DOI: 10.1016/j.pathol.2018.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 02/08/2023]
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Kaul KL, Sabatini LM, Tsongalis GJ, Caliendo AM, Olsen RJ, Ashwood ER, Bale S, Benirschke R, Carlow D, Funke BH, Grody WW, Hayden RT, Hegde M, Lyon E, Murata K, Pessin M, Press RD, Thomson RB. The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care. Acad Pathol 2017; 4:2374289517708309. [PMID: 28815200 PMCID: PMC5528950 DOI: 10.1177/2374289517708309] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/16/2022] Open
Abstract
An explosion of knowledge and technology is revolutionizing medicine and patient care. Novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. Under the oversight provided by the Clinical Laboratory Improvement Amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. Quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of Clinical Laboratory Improvement Amendments oversight of laboratory-developed procedures. Laboratories have a long history of successful service to patients operating under Clinical Laboratory Improvement Amendments. A series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. These examples also demonstrate how Clinical Laboratory Improvement Amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories.
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Affiliation(s)
- Karen L. Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Linda M. Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Gregory J. Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
- Laboratory Medicine, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Angela M. Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | | | | | - Robert Benirschke
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Dean Carlow
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Birgit H. Funke
- Laboratory for Molecular Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wayne W. Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics and Human Genetics, UCLA School of Medicine, Los Angeles, CA, USA
| | - Randall T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Elaine Lyon
- Pathology Department, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
| | - Kazunori Murata
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard D. Press
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Richard B. Thomson
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
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Shahsiah R, DeKoning J, Samie S, Latifzadeh SZ, Kashi ZM. Validation of a next generation sequencing panel for detection of hotspot cancer mutations in a clinical laboratory. Pathol Res Pract 2016; 213:98-105. [PMID: 28049581 DOI: 10.1016/j.prp.2016.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Abstract
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform. Important parameters for somatic mutations including the threshold for differentiation of a positive and a negative result, coverage, sensitivity, specificity, and limit of detection (LoD) were analyzed. Variant calls with coverage of <100x were found to be inaccurate. The limit of detection for identifying hotspot mutations was determined to be 4.3%. The sensitivity and specificity of the method were 96.1% and 97.8% respectively. No statistically significant difference was found between different gene targets in terms of performance of hotspot frequency measurement for the subset tested. In every validation study, the number of samples, the manner of sample selection, and the number and type of variants play a role in the outcome. Therefore, these parameters should be assessed according to the clinical needs of each laboratory undertaking the validation.
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Affiliation(s)
- Reza Shahsiah
- Cancer Research Center, Tehran University of Medical Sciences, Iran.
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Onyido EK, Sweeney E, Nateri AS. Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches. Mol Cancer 2016; 15:56. [PMID: 27590724 PMCID: PMC5010773 DOI: 10.1186/s12943-016-0541-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/26/2016] [Indexed: 02/02/2023] Open
Abstract
Over the past few years, microRNAs (miRNAs) have not only emerged as integral regulators of gene expression at the post-transcriptional level but also respond to signalling molecules to affect cell function(s). miRNAs crosstalk with a variety of the key cellular signalling networks such as Wnt, transforming growth factor-β and Notch, control stem cell activity in maintaining tissue homeostasis, while if dysregulated contributes to the initiation and progression of cancer. Herein, we overview the molecular mechanism(s) underlying the crosstalk between Wnt-signalling components (canonical and non-canonical) and miRNAs, as well as changes in the miRNA/Wnt-signalling components observed in the different forms of cancer. Furthermore, the fundamental understanding of miRNA-mediated regulation of Wnt-signalling pathway and vice versa has been significantly improved by high-throughput genomics and bioinformatics technologies. Whilst, these approaches have identified a number of specific miRNA(s) that function as oncogenes or tumour suppressors, additional analyses will be necessary to fully unravel the links among conserved cellular signalling pathways and miRNAs and their potential associated components in cancer, thereby creating therapeutic avenues against tumours. Hence, we also discuss the current challenges associated with Wnt-signalling/miRNAs complex and the analysis using the biomedical experimental and bioinformatics approaches.
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Affiliation(s)
- Emenike K Onyido
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Eloise Sweeney
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Abdolrahman Shams Nateri
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
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McGann P, Bunin JL, Snesrud E, Singh S, Maybank R, Ong AC, Kwak YI, Seronello S, Clifford RJ, Hinkle M, Yamada S, Barnhill J, Lesho E. Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time? Diagn Microbiol Infect Dis 2016; 85:277-282. [PMID: 27185645 DOI: 10.1016/j.diagmicrobio.2016.04.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/30/2016] [Accepted: 04/27/2016] [Indexed: 12/20/2022]
Abstract
Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations.
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Affiliation(s)
- Patrick McGann
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Jessica L Bunin
- Department of Critical Care, Tripler Army Medical Center, Honolulu, HI, USA
| | - Erik Snesrud
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Seema Singh
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Rosslyn Maybank
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ana C Ong
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yoon I Kwak
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Scott Seronello
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Robert J Clifford
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mary Hinkle
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Stephen Yamada
- Infectious Diseases Service, Tripler Army Medical Center, Honolulu, HI, USA
| | - Jason Barnhill
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Emil Lesho
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Abstract
The field of clinical genetics has advanced at an unprecedented pace. Today, with the aid of several high-resolution and high-precision technologies, physicians are able to make molecular genetic diagnoses for many infants affected with genetic disease. It is imperative, however, that perinatologists and neonatologists understand the strengths and limitations of genetic testing. This article discusses the different genetic testing options available for perinatal and neonatal diagnostics, along with their clinical utilities and indications. From variant-specific testing to whole-exome and genome sequencing, the article covers the whole gamut of genetic testing, with some thoughts on the changing paradigm of medical genetics.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
| | - Madhuri R Hegde
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA.
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Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DGB, Merker JD, Nagarajan R, Palicki LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV. College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests. Arch Pathol Lab Med 2015; 139:481-93. [DOI: 10.5858/arpa.2014-0250-cp] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hegde M, Bale S, Bayrak-Toydemir P, Gibson J, Jeng LJB, Joseph L, Laser J, Lubin IM, Miller CE, Ross LF, Rothberg PG, Tanner AK, Vitazka P, Mao R. Reporting incidental findings in genomic scale clinical sequencing--a clinical laboratory perspective: a report of the Association for Molecular Pathology. J Mol Diagn 2015; 17:107-17. [PMID: 25684271 DOI: 10.1016/j.jmoldx.2014.10.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/27/2014] [Accepted: 10/21/2014] [Indexed: 12/17/2022] Open
Abstract
Advances in sequencing technologies have facilitated concurrent testing for many disorders, and the results generated may provide information about a patient's health that is unrelated to the clinical indication, commonly referred to as incidental findings. This is a paradigm shift from traditional genetic testing in which testing and reporting are tailored to a patient's specific clinical condition. Clinical laboratories and physicians are wrestling with this increased complexity in genomic testing and reporting of the incidental findings to patients. An enormous amount of discussion has taken place since the release of a set of recommendations from the American College of Medical Genetics and Genomics. This discussion has largely focused on the content of the incidental findings, but the laboratory perspective and patient autonomy have been overlooked. This report by the Association of Molecular Pathology workgroup discusses the pros and cons of next-generation sequencing technology, potential benefits, and harms for reporting of incidental findings, including the effect on both the laboratory and the patient, and compares those with other areas of medicine. The importance of genetic counseling to preserve patient autonomy is also reviewed. The discussion and recommendations presented by the workgroup underline the need for continued research and discussion among all stakeholders to improve our understanding of the effect of different policies on patients, providers, and laboratories.
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Affiliation(s)
- Madhuri Hegde
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia; Emory Genetics Laboratory, Emory University, Decatur, Georgia.
| | - Sherri Bale
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; GeneDx, Gaithersburg, Maryland
| | - Pinar Bayrak-Toydemir
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah; Department of Molecular Genetics, ARUP Laboratories, Salt Lake City, Utah
| | - Jane Gibson
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Clinical Sciences, University of Central Florida College of Medicine, Orlando, Florida
| | - Linda Jo Bone Jeng
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, Department of Pathology, and Division of Human Genetics, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Loren Joseph
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Pathology, University of Chicago, Chicago, Illinois
| | - Jordan Laser
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Division of Cytogenetics and Molecular Pathology, North Shore Long Island Jewish Health System, New Hyde Park, New York
| | - Ira M Lubin
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Division of Laboratory Programs, Standards, and Services, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Christine E Miller
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Molecular Genetics, ARUP Laboratories, Salt Lake City, Utah
| | - Lainie F Ross
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Pediatrics, University of Chicago, Chicago, Illinois; MacLean Center for Clinical Medical Ethics, University of Chicago, Chicago, Illinois
| | - Paul G Rothberg
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Alice K Tanner
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia; Emory Genetics Laboratory, Emory University, Decatur, Georgia
| | - Patrik Vitazka
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; GeneDx, Gaithersburg, Maryland
| | - Rong Mao
- Incidental Findings Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee and the Whole Genome Analysis Working Group, Bethesda, Maryland; Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah; Department of Molecular Genetics, ARUP Laboratories, Salt Lake City, Utah
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Ankala A, da Silva C, Gualandi F, Ferlini A, Bean LJH, Collins C, Tanner AK, Hegde MR. A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield. Ann Neurol 2014; 77:206-14. [PMID: 25380242 DOI: 10.1002/ana.24303] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Neuromuscular diseases (NMDs) are a group of >200 highly genetically as well as clinically heterogeneous inherited genetic disorders that affect the peripheral nervous and muscular systems, resulting in gross motor disability. The clinical and genetic heterogeneities of NMDs make disease diagnosis complicated and expensive, often involving multiple tests. METHODS To expedite the molecular diagnosis of NMDs, we designed and validated several next generation sequencing (NGS)-based comprehensive gene panel tests that include complementary deletion and duplication testing through comparative genomic hybridization arrays. Our validation established the targeted gene panel test to have 100% sensitivity and specificity for single nucleotide variant detection. To compare the clinical diagnostic yields of single gene (NMD-associated) tests with the various NMD NGS panel tests, we analyzed data from all clinical tests performed at the Emory Genetics Laboratory from October 2009 through May 2014. We further compared the clinical utility of the targeted NGS panel test with that of exome sequencing (ES). RESULTS We found that NMD comprehensive panel testing has a 3-fold greater diagnostic yield (46%) than single gene testing (15-19%). Sanger fill-in of low-coverage exons, copy number variation analysis, and thorough in-house validation of the assay all complement panel testing and allow the detection of all types of causative pathogenic variants, some of which (about 18%) may be missed by ES. INTERPRETATION Our results strongly indicate that for molecular diagnosis of heterogeneous disorders such as NMDs, targeted panel testing has the highest clinical yield and should therefore be the preferred first-tier approach.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
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