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Scott S, Levy B. New ADCs bring new questions in EGFR NSCLC and beyond. Ann Oncol 2024; 35:412-413. [PMID: 38484972 DOI: 10.1016/j.annonc.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 04/15/2024] Open
Affiliation(s)
- S Scott
- Johns Hopkins School of Medicine, Baltimore; Johns Hopkins Sidney Kimmel Cancer Center at Sibley Memorial Hospital, Washington, USA
| | - B Levy
- Johns Hopkins School of Medicine, Baltimore; Johns Hopkins Sidney Kimmel Cancer Center at Sibley Memorial Hospital, Washington, USA.
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Levy B, Kanagal-Shamanna R, Sahajpal NS, Neveling K, Rack K, Dewaele B, Olde Weghuis D, Stevens-Kroef M, Puiggros A, Mallo M, Clifford B, Mantere T, Hoischen A, Espinet B, Kolhe R, Solé F, Raca G, Smith AC. A framework for the clinical implementation of optical genome mapping in hematologic malignancies. Am J Hematol 2024; 99:642-661. [PMID: 38164980 DOI: 10.1002/ajh.27175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/09/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost-effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth "the Consortium") to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrina Rack
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Mallo
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Francesc Solé
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Adam C Smith
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Pandya P, Levy B, Sistermans EA. Current controversies in prenatal diagnosis: Noninvasive prenatal testing should replace other screening strategies for fetal trisomies 13, 18, 21. Prenat Diagn 2024; 44:381-388. [PMID: 38047733 DOI: 10.1002/pd.6477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/05/2023]
Abstract
This is a written summary of the oral debate presented at the International Society for Prenatal Diagnosis annual conference in Edinburgh in 2023. The topic under debate is whether noninvasive prenatal testing (NIPT) using cell-free fetal DNA should replace other screening strategies for the detection of fetal trisomies 13, 18, 21. There is no disagreement that NIPT is far more sensitive and has better positive predictive values for identifying trisomies 13, 18, and 21 than traditional screening approaches using biochemical markers and measurement of nuchal translucency. The major issue lies in the potential adverse consequences associated with abandoning traditional screening methods. The source of disagreement stems primarily from whether you consider the role of ultrasound in the context of screening to be strictly for nuchal translucency measurement or whether it should be combined with a fetal anatomy scan. The debate featured two experts who presented evidence in favor of each argument.
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Affiliation(s)
- Pranav Pandya
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Brynn Levy
- Columbia University Irving Medical Center, New York, New York, USA
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4
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Broeckel U, Iqbal MA, Levy B, Sahajpal N, Nagy PL, Scharer G, Rodriguez V, Bossler A, Stence A, Skinner C, Skinner SA, Kolhe R, Stevenson R. Detection of Constitutional Structural Variants by Optical Genome Mapping: A Multisite Study of Postnatal Samples. J Mol Diagn 2024; 26:213-226. [PMID: 38211722 DOI: 10.1016/j.jmoldx.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024] Open
Abstract
Optical genome mapping is a high-resolution technology that can detect all types of structural variations in the genome. This second phase of a multisite study compares the performance of optical genome mapping and current standard-of-care methods for diagnostic testing of individuals with constitutional disorders, including neurodevelopmental impairments and congenital anomalies. Among the 627 analyses in phase 2, 405 were of retrospective samples supplied by five diagnostic centers in the United States and 94 were prospective samples collected over 18 months by two diagnostic centers (June 2021 to October 2022). Additional samples represented a family cohort to determine inheritance (n = 119) and controls (n = 9). Full concordance of results between optical genome mapping and one or more standard-of-care diagnostic tests was 98.6% (618/627), with partial concordance in an additional 1.1% (7/627).
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Affiliation(s)
- Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - M Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Brynn Levy
- Columbia University Medical Center, New York, New York
| | | | - Peter L Nagy
- Columbia University Medical Center, New York, New York
| | - Gunter Scharer
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | - Aaron Stence
- University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | | | | | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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5
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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Bi X, Mulhern MS, Spiegel E, Wapner RJ, Levy B, Bain JM, Liao J. 3' UTR Deletion of FBXO28 in a Patient with Brain Abnormalities and Developmental Delay. Genes (Basel) 2023; 14:1687. [PMID: 37761828 PMCID: PMC10530825 DOI: 10.3390/genes14091687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Constitutional deletions of chromosome 1q42 region are rare. The phenotype spectrum associated with this copy number change is variable, including developmental delay, intellectual disability, seizures, and dysmorphology. This study describes a patient with developmental delays and brain abnormalities. G-banded karyotype, FISH, SNP oligonucleotide microarray analysis (SOMA), and whole exome sequencing analysis were performed. Postnatal reanalysis of prenatal SOMA and follow-up parental testing revealed a paternally inherited 63 kb deletion at 1q42.11 in the patient. We characterized the clinical features of this patient, providing insight into the clinical phenotype associated with deletions of the 1q42.11 sub-band. Our study provides new evidence supporting the potential functional importance of the FBXO28 3' UTR region and the hypothesis that FBXO28 is a critical gene in the pathogenesis of chromosome 1q41q42 microdeletion syndrome. It also highlights the different goals and reporting criteria between prenatal and postnatal microarray tests.
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Affiliation(s)
- Xin Bi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maureen S. Mulhern
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Erica Spiegel
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jennifer M. Bain
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jun Liao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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7
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Greer SU, Botello J, Hongo D, Levy B, Shah P, Rabinowitz M, Miller DE, Im K, Kumar A. Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic. J Transl Med 2023; 21:378. [PMID: 37301971 PMCID: PMC10257846 DOI: 10.1186/s12967-023-04243-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular diagnoses using a single assay capable of detecting variants, characterizing methylation patterns, resolving complex rearrangements, and assigning findings to long-range haplotypes. Here, we demonstrate the clinical utility of Nanopore long-read sequencing by validating a confirmatory test for copy number variants (CNVs) in neurodevelopmental disorders and illustrate the broader applications of this platform to assess genomic features with significant clinical implications. METHODS We used adaptive sampling on the Oxford Nanopore platform to sequence 25 genomic DNA samples and 5 blood samples collected from patients with known or false-positive copy number changes originally detected using short-read sequencing. Across the 30 samples (a total of 50 with replicates), we assayed 35 known unique CNVs (a total of 55 with replicates) and one false-positive CNV, ranging in size from 40 kb to 155 Mb, and assessed the presence or absence of suspected CNVs using normalized read depth. RESULTS Across 50 samples (including replicates) sequenced on individual MinION flow cells, we achieved an average on-target mean depth of 9.5X and an average on-target read length of 4805 bp. Using a custom read depth-based analysis, we successfully confirmed the presence of all 55 known CNVs (including replicates) and the absence of one false-positive CNV. Using the same CNV-targeted data, we compared genotypes of single nucleotide variant loci to verify that no sample mix-ups occurred between assays. For one case, we also used methylation detection and phasing to investigate the parental origin of a 15q11.2-q13 duplication with implications for clinical prognosis. CONCLUSIONS We present an assay that efficiently targets genomic regions to confirm clinically relevant CNVs with a concordance rate of 100%. Furthermore, we demonstrate how integration of genotype, methylation, and phasing data from the Nanopore sequencing platform can potentially simplify and shorten the diagnostic odyssey.
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Affiliation(s)
| | | | - Donna Hongo
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
| | - Brynn Levy
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Premal Shah
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
| | - Matthew Rabinowitz
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
- Natera Inc., San Carlos, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Department of Laboratory Medicine and Pathology, University of Washington, WA, Seattle, USA
| | - Kate Im
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
| | - Akash Kumar
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA.
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8
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Levy B, Baughn LB, Akkari Y, Chartrand S, LaBarge B, Claxton D, Lennon PA, Cujar C, Kolhe R, Kroeger K, Pitel B, Sahajpal N, Sathanoori M, Vlad G, Zhang L, Fang M, Kanagal-Shamanna R, Broach JR. Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Adv 2023; 7:1297-1307. [PMID: 36417763 PMCID: PMC10119592 DOI: 10.1182/bloodadvances.2022007583] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/25/2022] Open
Abstract
Detection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for diagnostic subtyping, prognosis, and patient management. However, cytogenetic/cytogenomic techniques used to identify those aberrations, such as karyotyping, fluorescence in situ hybridization (FISH), or chromosomal microarray analysis (CMA), are limited by the need for skilled personnel as well as significant time, cost, and labor. Optical genome mapping (OGM) provides a single, cost-effective assay with a significantly higher resolution than karyotyping and with a comprehensive genome-wide analysis comparable with CMA and the added unique ability to detect balanced structural variants (SVs). Here, we report in a real-world setting the performance of OGM in a cohort of 100 AML cases that were previously characterized by karyotype alone or karyotype and FISH or CMA. OGM identified all clinically relevant SVs and copy number variants (CNVs) reported by these standard cytogenetic methods when representative clones were present in >5% allelic fraction. Importantly, OGM identified clinically relevant information in 13% of cases that had been missed by the routine methods. Three cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. In 4% of cases, OGM findings would have altered recommended clinical management, and in an additional 8% of cases, OGM would have rendered the cases potentially eligible for clinical trials. The results from this multi-institutional study indicate that OGM effectively recovers clinically relevant SVs and CNVs found by standard-of-care methods and reveals additional SVs that are not reported. Furthermore, OGM minimizes the need for labor-intensive multiple cytogenetic tests while concomitantly maximizing diagnostic detection through a standardized workflow.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yassmine Akkari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Brandon LaBarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, PA
| | - David Claxton
- Department of Hematology and Oncology, Department of Medicine, Penn State College of Medicine, Hershey, PA
| | | | - Claudia Cujar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | - Kate Kroeger
- Cytogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | | | - George Vlad
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - James R. Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
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Verbitsky M, Krishnamurthy S, Krithivasan P, Hughes D, Khan A, Marasà M, Vena N, Khosla P, Zhang J, Lim TY, Glessner JT, Weng C, Shang N, Shen Y, Hripcsak G, Hakonarson H, Ionita-Laza I, Levy B, Kenny EE, Loos RJ, Kiryluk K, Sanna-Cherchi S, Crosslin DR, Furth S, Warady BA, Igo RP, Iyengar SK, Wong CS, Parsa A, Feldman HI, Gharavi AG. Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 2023; 34:607-618. [PMID: 36302597 PMCID: PMC10103259 DOI: 10.1681/asn.2022060725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
SIGNIFICANCE STATEMENT Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis. BACKGROUND Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility. METHODS We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II ( n =248), Chronic Renal Insufficiency Cohort (CRIC) study ( n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort. RESULTS We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk. CONCLUSION Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Pavan Khosla
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Joseph T. Glessner
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology and Columbia Genome Center, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David R. Crosslin
- Division of Biomedical Informatics and Genomics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Susan Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Iqbal MA, Broeckel U, Levy B, Skinner S, Sahajpal NS, Rodriguez V, Stence A, Awayda K, Scharer G, Skinner C, Stevenson R, Bossler A, Nagy PL, Kolhe R. Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases. J Mol Diagn 2023; 25:175-188. [PMID: 36828597 PMCID: PMC10851778 DOI: 10.1016/j.jmoldx.2022.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 02/24/2023] Open
Abstract
This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders.
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Affiliation(s)
- M Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brynn Levy
- Columbia University Medical Center, New York, New York
| | | | - Nikhil S Sahajpal
- Greenwood Genetic Center, Greenwood, South Carolina; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | - Aaron Stence
- Department of Pathology, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Kamel Awayda
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Gunter Scharer
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | | | | | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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11
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Tshiaba PT, Ratman DK, Sun JM, Tunstall TS, Levy B, Shah PS, Weitzel JN, Rabinowitz M, Kumar A, Im KM. Integration of a Cross-Ancestry Polygenic Model With Clinical Risk Factors Improves Breast Cancer Risk Stratification. JCO Precis Oncol 2023; 7:e2200447. [PMID: 36809055 DOI: 10.1200/po.22.00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
PURPOSE To develop and validate a cross-ancestry integrated risk score (caIRS) that combines a cross-ancestry polygenic risk score (caPRS) with a clinical estimator for breast cancer (BC) risk. We hypothesized that the caIRS is a better predictor of BC risk than clinical risk factors across diverse ancestry groups. METHODS We used diverse retrospective cohort data with longitudinal follow-up to develop a caPRS and integrate it with the Tyrer-Cuzick (T-C) clinical model. We tested the association between the caIRS and BC risk in two validation cohorts including > 130,000 women. We compared model discrimination for 5-year and remaining lifetime BC risk between the caIRS and T-C and assessed how the caIRS would affect screening in the clinic. RESULTS The caIRS outperformed T-C alone for all populations tested in both validation cohorts and contributed significantly to risk prediction beyond T-C. The area under the receiver operating characteristic curve improved from 0.57 to 0.65, and the odds ratio per standard deviation increased from 1.35 (95% CI, 1.27 to 1.43) to 1.79 (95% CI, 1.70 to 1.88) in validation cohort 1 with similar improvements observed in validation cohort 2. We observed the largest gain in positive predictive value using the caIRS in Black/African American women across both validation cohorts, with an approximately two-fold increase and an equivalent negative predictive value as the T-C. In a multivariate, age-adjusted logistic regression model including both caIRS and T-C, caIRS remained significant, indicating that caIRS provides information over T-C alone. CONCLUSION Adding a caPRS to the T-C model improves BC risk stratification for women of multiple ancestries, which could have implications for screening recommendations and prevention.
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Affiliation(s)
| | | | | | | | - Brynn Levy
- MyOme Inc, Menlo Park, CA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
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12
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Cherbi M, Maury P, Schneider F, Bonnefoy-Cudraz E, Roubille F, Puymirat E, Bonello L, Leurent G, Levy B, Lamblin N, Bourenne J, Quentin C, Delabranche X, Combaret N, Marchandot B, Lattuca B, Leborgne L, Fillippi E, Gerbaud E, Delmas C. 1-year outcomes in cardiogenic shock triggered by ventricular tachycardia: An analysis of the FRENSHOCK nationwide multicenter prospective registry. Archives of Cardiovascular Diseases Supplements 2023. [DOI: 10.1016/j.acvdsp.2022.10.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Smith A, Kanagal-Shamanna R, Dewaele B, Rack K, Hoischen A, Neveling K, Raca G, Levy B, Kolhe R, Espinet B, Puiggros A, Sole F, Mallo M. 16. International working group recommendations for the implementation of optical genome mapping in Hematologic Malignancies. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Wei S, D'Alton M, Levy B, Williams Z. THE SUCCESSFUL DEVELOPMENT AND CLINICAL VALIDATION OF STORK, A RAPID ANEUPLOIDY DETECTION METHOD USING NANOPORE SEQUENCING. Fertil Steril 2022. [DOI: 10.1016/j.fertnstert.2022.08.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Scott S, Hu C, Smith K, Anagnostou V, Lee J, Spicer J, Illei P, Prophet E, Rosner S, Ettinger D, Feliciano J, Hann C, Lam V, Levy B, Murray J, Brahmer J, Forde P, Marrone K. EP02.04-007 Phase 2 Trial of Neoadjuvant KRASG12C Directed Therapy with Adagrasib (MRTX849) With or Without Nivolumab in Resectable NSCLC (Neo-KAN). J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Ozguroglu M, Levy B, Horinouchi H, Yu J, Grainger E, Phuong P, Peterson D, Newton M, Spira A. 971TiP Phase III trial of durvalumab combined with domvanalimab following concurrent chemoradiotherapy (cCRT) in patients with unresectable stage III NSCLC (PACIFIC-8). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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17
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Rosner S, Zaidi N, Wang H, Smith K, Nauroth J, Guo M, Fitzpatrick P, Riemer J, Barnes A, Wenga P, Feliciano J, Hann C, Lam V, Murray J, Scott S, Anagnostou V, Levy B, Forde P, Brahmer J, Jaffee E, Marrone K. EP08.01-086 Pooled Mutant KRAS-Targeted Peptide Vaccine with Nivolumab and Ipilimumab in Advanced KRAS Mutated Non-Small Cell Lung Cancer. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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18
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Shachar E, Raz Y, Hasson SP, Levy B, Adar L, Honig Z, Mischan N, Laskov I, Grisaru D, Wolf I, Safra T. 543P Can we predict the long and short-term survivors with advanced ovarian cancer? Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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19
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Wei S, Djandji A, Lattin MT, Nahum O, Hoffman N, Cujar C, Kayali R, Cinnioglu C, Wapner R, D'Alton M, Levy B, Williams Z. Rapid Nanopore Sequencing-Based Screen for Aneuploidy in Reproductive Care. N Engl J Med 2022; 387:658-660. [PMID: 36070716 DOI: 10.1056/nejmc2201810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Shan Wei
- Columbia University Irving Medical Center, New York, NY
| | | | | | - Odelia Nahum
- Columbia University Irving Medical Center, New York, NY
| | | | - Claudia Cujar
- Columbia University Irving Medical Center, New York, NY
| | | | | | - Ronald Wapner
- Columbia University Irving Medical Center, New York, NY
| | - Mary D'Alton
- Columbia University Irving Medical Center, New York, NY
| | - Brynn Levy
- Columbia University Irving Medical Center, New York, NY
| | - Zev Williams
- Columbia University Irving Medical Center, New York, NY
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20
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Dharmadhikari AV, Pereira EM, Andrews CC., Macera M, Harkavy N, Wapner R, Jobanputra V, Levy B, Ganapathi M, Liao J. Case Report: Prenatal Identification of a De Novo Mosaic Neocentric Marker Resulting in 13q31.1→qter Tetrasomy in a Mildly Affected Girl. Front Genet 2022; 13:906077. [PMID: 35928455 PMCID: PMC9343796 DOI: 10.3389/fgene.2022.906077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Partial tetrasomy of distal 13q has a reported association with a variable phenotype including microphthalmia, ear abnormalities, hypotelorism, facial dysmorphisms, urogenital defects, pigmentation and skin defects, and severe learning difficulties. A wide range of mosaicism has been reported, which may, to some extent, account for the variable spectrum of observed phenotypes. We report here a pregnancy conceived using intrauterine insemination in a 32-year-old female with a history of infertility. Non-invasive prenatal screening (NIPS) was performed in the first trimester which reported an increased risk for trisomy 13. Follow-up cytogenetic workup using chorionic villus sampling (CVS) and amniotic fluid samples showed a mosaic karyotype with a small supernumerary marker chromosome (sSMC). Chromosomal microarray analysis (CMA) identified a mosaic 31.34 Mb terminal gain on chr13q31.1q34 showing the likely origin of the sSMC to distal chromosome 13q. Follow-up metaphase FISH testing suggested an inverted duplication rearrangement involving 13q31q34 in the marker chromosome and the presence of a neocentromere. At 21 months of age, the proband has a history of gross motor delay, hypotonia, left microphthalmia, strabismus, congenital anomaly of the right optic nerve, hemangiomas, and a tethered spinal cord. Postnatal chromosome analyses in buccal, peripheral blood, and spinal cord ligament tissues were consistent with the previous amniocentesis and CVS findings, and the degree of mosaicism varied from 25 to 80%. It is often challenging to pinpoint the chromosomal identity of sSMCs using banding cytogenetics. A combination of low-pass genome sequencing of cell-free DNA, chromosomal microarray, and FISH enabled the identification of the precise chromosomal rearrangement in this patient. This study adds to the growing list of clinically identified neocentric marker chromosomes and is the first described instance of partial tetrasomy 13q31q34 identified in a mosaic state prenatally. Since NIPS is now being routinely performed along with invasive testing for advanced maternal age, an increased prenatal detection rate for mosaic sSMCs in otherwise normal pregnancies is expected. Future studies investigating how neocentromeres mediate gene expression changes could help identify potential epigenetic targets as treatment options to rescue or reverse the phenotypes seen in patients with congenital neocentromeres.
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Affiliation(s)
- Avinash V. Dharmadhikari
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Elaine M. Pereira
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Carli C . Andrews
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Michael Macera
- Clinical Cytogenetics Laboratory, New York Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Nina Harkavy
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Jun Liao
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- *Correspondence: Jun Liao,
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21
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Iqbal MA, Broeckel U, Levy B, Skinner S, Sahajpal N, Rodriguez V, Stence A, Awayda K, Scharer G, Skinner C, Stevenson R, Bossler A, Nagy PL, Kolhe R. 6. Optical genome mapping as a potential Tier1 test for Postnatal Chromosomal Disorders – results of multi-institutional validation study of 331 retrospective clinical samples. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Tshiaba P, Sun J, Ratman D, Tunstall T, Levy B, Shah P, Rabinowitz M, Kumar A, Im K. Cross-ancestry polygenic risk score for breast cancer risk assessment. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.10540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
10540 Background: Breast cancer (BC) risk is influenced by many common variants with small effects. Polygenic risk scores (PRS) weight these variants based on genome-wide association studies (GWAS) and aggregate them into a single measure. PRS has primarily shown benefit in Caucasian women. We established a cross-ancestry polygenic model (caPRS) which assesses risk of breast cancer across multiple ancestries. Methods: Performance of multiple BC polygenic models, both published and developed in-house, were evaluated for each of five ancestry groups: European, African, South Asian, East Asian, and Admixed American. To account for ancestry-specific mean and variance, we computed principal components (PCs) for all women by projecting their genotypes onto PCs calculated on individuals in the 1000 Genomes Project (1KGP). We next centered each ancestry-specific PRS by subtracting the PRS predicted from a linear regression of PRS against the first four PCs in unaffected individuals. Each centered PRS was then divided by the SD of the corresponding 1KGP population. We defined a cross-ancestry polygenic model as a linear combination of the best performing PRS model for each ancestry group weighted by fractional ancestry. Association of the caPRS with breast cancer risk was tested in a validation cohort of >130,000 women consisting of multiple independent cohorts (the Women’s Health Initiative, the Multiethnic Cohort, the ROOT cohort and the UK Biobank) using a multivariate logistic regression model that included caPRS, age, self-reported ancestry, personal history of ovarian cancer (when available) and first-degree family history of BC. Discrimination was assessed by the odds ratio (OR) per SD and the area under the receiver-operator curve (AUC). Results: This study included women with African/Black, East Asian, Caucasian/White, Hispanic/Latino, South Asian and ‘Other’ self-reported ancestry. The ancestry-specific models included in the caPRS ranged in size from 173 to >800,000 variants. The caPRS was associated with BC risk for women in each self-reported ancestry (Table). The caPRS offered a modest increase in performance over a commonly implemented 313-SNP PRS in non-European ancestries, most significantly in African/Black women where the OR per SD increased from 1.24 (1.08 - 1.43), p-value 2.3x10-3. Conclusions: The caPRS performed well for women of any ancestry and allows flexibility to update ancestry-specific models. These results suggest the caPRS has the potential to improve the clinical utility of existing clinical risk predictors. [Table: see text]
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23
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Akkari YM, Baughn LB, Dubuc AM, Smith AC, Mallo M, Dal Cin P, Diez Campelo M, Gallego MS, Granada Font I, Haase DT, Schlegelberger B, Slavutsky I, Mecucci C, Levine RL, Hasserjian RP, Solé F, Levy B, Xu X. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood 2022; 139:2273-2284. [PMID: 35167654 PMCID: PMC9710485 DOI: 10.1182/blood.2021014309] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.
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Affiliation(s)
- Yassmine M.N. Akkari
- Departments of Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Adam C. Smith
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Mar Mallo
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Maria Diez Campelo
- Hematology Department University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Marta S. Gallego
- Laboratory of Cytogenetics and Molecular Cytogenetics, Department of Clinical Pathology, Italian Hospital, Buenos Aires, Argentina
| | - Isabel Granada Font
- Hematology Laboratory, Germans Trias i Pujol University Hospital–Catalan Institute of Oncology, Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Detlef T. Haase
- Clinics of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Irma Slavutsky
- Laboratory Genetics of Lymphoid Malignancies, Institute of Experimental Medicine, Buenos Aires, Argentina
| | - Cristina Mecucci
- Laboratory of Cytogenetics and Molecular Medicine, Hematology University of Perugia, Perugia, Italy
| | - Ross L. Levine
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Francesc Solé
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Brynn Levy
- College of Physicians and Surgeons, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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24
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Kumar A, Im K, Banjevic M, Ng PC, Tunstall T, Garcia G, Galhardo L, Sun J, Schaedel ON, Levy B, Hongo D, Kijacic D, Kiehl M, Tran ND, Klatsky PC, Rabinowitz M. Whole-genome risk prediction of common diseases in human preimplantation embryos. Nat Med 2022; 28:513-516. [PMID: 35314819 PMCID: PMC8938270 DOI: 10.1038/s41591-022-01735-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022]
Abstract
Preimplantation genetic testing (PGT) of in-vitro-fertilized embryos has been proposed as a method to reduce transmission of common disease; however, more comprehensive embryo genetic assessment, combining the effects of common variants and rare variants, remains unavailable. Here, we used a combination of molecular and statistical techniques to reliably infer inherited genome sequence in 110 embryos and model susceptibility across 12 common conditions. We observed a genotype accuracy of 99.0–99.4% at sites relevant to polygenic risk scoring in cases from day-5 embryo biopsies and 97.2–99.1% in cases from day-3 embryo biopsies. Combining rare variants with polygenic risk score (PRS) magnifies predicted differences across sibling embryos. For example, in a couple with a pathogenic BRCA1 variant, we predicted a 15-fold difference in odds ratio (OR) across siblings when combining versus a 4.5-fold or 3-fold difference with BRCA1 or PRS alone. Our findings may inform the discussion of utility and implementation of genome-based PGT in clinical practice. A computational approach combining whole-genome sequencing of parental genomes and genotyping of preimplantation embryos allows accurate prediction of the inherited genomes of embryos and calculation of polygenic risk scores.
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Affiliation(s)
| | - Kate Im
- MyOme, Inc., Menlo Park, CA, USA
| | | | | | | | | | | | | | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | - Nam D Tran
- Spring Fertility, San Francisco, CA, USA
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25
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Barua S, Pereira EM, Jobanputra V, Anyane-Yeboa K, Levy B, Liao J. 3q27.1 microdeletion causes prenatal and postnatal growth restriction and neurodevelopmental abnormalities. Mol Cytogenet 2022; 15:7. [PMID: 35241116 PMCID: PMC8895857 DOI: 10.1186/s13039-022-00587-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Overlapping microdeletions of chromosome 3q26-3q28 have been reported in eight individuals. The common phenotype observed in these individuals include intrauterine growth restriction, short stature, microcephaly, feeding difficulties, facial dysmorphisms, limb abnormalities and developmental delay. The most striking clinical features shared among all reported cases is prenatal and postnatal growth restriction and neurodevelopmental abnormalities. CASE PRESENTATION We identified two additional individuals with overlapping deletions and shared clinical features by high-resolution SNP oligonucleotide microarray, and refined the smallest region of overlap (SRO) to a 1.2 Mb genomic location in chromosome 3q27.1 by reviewing and comparing all published cases. We evaluated the SRO using ACMG/ClinGen current recommendations for classifying copy number variants (CNVs), and discussed the contribution of the genes deleted in the SRO to the abnormal phenotype observed in these individuals. CONCLUSIONS This study provides further evidence supporting the existence of a novel 3q27.1 microdeletion syndrome and suggests that haploinsufficiency of potential candidate genes, DVL3, AP2M1, and PARL in the SRO in 3q27.1 is responsible for the phenotype.
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Affiliation(s)
- Subit Barua
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jun Liao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
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26
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Sahajpal N, Rodriguez V, Kanyo L, Stence A, Skinner S, Iqbal A, Awayda K, Levy B, Broeckel U, Scharer G, Hackman J, Mondal A, Bossler A, Nagy P, Kolhe R. eP391: Optical genome mapping for constitutional postnatal SV, CNV, and repeat array sizing: A multi-site clinical study. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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27
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Levy B, Leventakos K, Lou Y, Savvides P, Rixe O, Tolcher A, Yin J, Xie J, Guevara F, Goto Y. P47.04 TROPION-Lung02: Datopotamab Deruxtecan (Dato-DXd) Plus Pembrolizumab and Platinum-Based Chemotherapy in Advanced NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Levy B. Inhibiteurs du système rénine angiotensine aldostérone et COVID-19 : que faut-il retenir ? JMV-Journal de Médecine Vasculaire 2021. [PMCID: PMC8464182 DOI: 10.1016/j.jdmv.2021.08.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
L’enzyme de conversion de type 2 ou ACE2 est une enzyme de clairance de l’angiotensine 2 qui clive cette dernière en un peptide (Ang 1-7) dont les effets sont opposés à ceux de l’angiotensine 2 : vasodilatateurs, anti-inflammatoires et anti-fibrosants. ACE2 est surexprimée dans toutes les situations de risque cardiovasculaire élevé : maladies coronaires, insuffisance cardiaque, hypertension, obésité, diabète. Le virus SARS-CoV-2 se lie à l’ACE2 membranaire pour pénétrer dans les cellules qu’il infecte. L’abondance de l’ACE2 chez les malades à risque cardiovasculaire élevé est probablement un facteur d’augmentation du risque d’infection virale. Il existe très peu ou pas de mesures des concentration tissulaire de ACE2 chez l’homme. Encore moins chez des patients recevant un traitement par un bloqueur du système rénine angiotensine. À partir des études expérimentales, on peut avancer que les inhibiteurs de l’enzyme de conversion n’ont semble-t-il pas d’effet sur les concentrations plasmatiques et tissulaires d’ACE2 alors que les bloqueurs des récepteurs de l’angiotensine augmenteraient l’activité de l’ACE2. Enfin, les premiers grands essais cliniques observationnels publiés montrent clairement que les traitements chroniques par des bloqueurs du SRAA n’ont pas d’effet sur l’incidence et la gravité de l’infection virale. Ces traitements ne doivent donc pas être interrompus ni pour prévenir une éventuelle infection par le SARS-CoV-2 ni en cas de survenue avérée de COVID-19.
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29
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Okur V, Hamm L, Kavus H, Mebane C, Robinson S, Levy B, Chung WK. Clinical and genomic characterization of 8p cytogenomic disorders. Genet Med 2021; 23:2342-2351. [PMID: 34282301 DOI: 10.1038/s41436-021-01270-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To provide a detailed clinical and cytogenomic summary of individuals with chromosome 8p rearrangements of invdupdel(8p), del(8p), and dup(8p). METHODS We enrolled 97 individuals with invdupdel(8p), del(8p), and dup(8p). Clinical and molecular data were collected to delineate and compare the clinical findings and rearrangement breakpoints. We included additional 5 individuals with dup(8p) from the literature for a total of 102 individuals. RESULTS Eighty-one individuals had recurrent rearrangements of invdupdel(8p) (n = 49), del(8p)_distal (n = 4), del(8p)_proximal (n = 9), del(8p)_proximal&distal (n = 12), and dup(8p)_proximal (n = 7). Twenty-one individuals had nonrecurrent rearrangements. While all individuals had neurodevelopmental features, the frequency and severity of clinical findings were higher in individuals with invdupdel(8p), and with larger duplications. All individuals with GATA4 deletion had structural congenital heart defects; however, the presence of structural heart defects in some individuals with normal GATA4 copy number suggests there are other potentially contributing gene(s) on 8p. CONCLUSION Our study may inform families and health-care providers about the associated clinical findings and severity in individuals with chromosome 8p rearrangements, and guide researchers in investigating the underlying molecular and biological mechanisms by providing detailed clinical and cytogenomic information about individuals with distinct 8p rearrangements.
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Affiliation(s)
- Volkan Okur
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Laura Hamm
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Haluk Kavus
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Caroline Mebane
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Scott Robinson
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA. .,Department of Medicine, Columbia University Medical Center, New York, NY, USA.
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30
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Jacobson BF, Schapkaitz E, Mer M, Louw S, Haas S, Buller HR, Brenner B, Abdool-Carrim ATO, De Jong P, Hsu P, Jankelow D, Lebos M, Levy B, Radford H, Rowji P, Redman L, Sussman M, Van der Jagt D, Wessels PF, Williams PG, Society Of Thrombosis And Haemostasis OBOTSA. Recommendations for the diagnosis and management of vaccine-induced immune thrombotic thrombocytopenia. S Afr Med J 2021; 111:535-537. [PMID: 34382561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 06/13/2023] Open
Abstract
There have recently been safety concerns regarding an increased risk of vaccine-induced immune thrombotic thrombocytopenia (VITT) following administration of SARS-CoV-2 adenoviral vector vaccines. The Southern African Society of Thrombosis and Haemostasis reviewed the emerging literature on this idiosyncratic complication. A draft document was produced and revised by consensus agreement by a panel of professionals from various specialties. The recommendations were adjudicated by independent international experts to avoid local bias. We present concise, practical guidelines for the clinical management of VITT.
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Affiliation(s)
- B F Jacobson
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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31
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Hofmeyr GJ, Bernitz S, Bonet M, Bucagu M, Dao B, Downe S, Galadanci H, Homer C, Hundley V, Lavender T, Levy B, Lissauer D, Lumbiganon P, McConville FE, Pattinson R, Qureshi Z, Souza JP, Stanton ME, Ten Hoope-Bender P, Vannevel V, Vogel JP, Oladapo OT. WHO next-generation partograph: revolutionary steps towards individualised labour care. BJOG 2021; 128:1658-1662. [PMID: 33686760 PMCID: PMC9291293 DOI: 10.1111/1471-0528.16694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 11/27/2022]
Affiliation(s)
- G J Hofmeyr
- Department of Obstetrics and Gynaecology, University of Botswana, Gaborone, Botswana.,Effective Care Research Unit, University of the Witwatersrand and Walter Sisulu University, East London, South Africa
| | - S Bernitz
- Department of Obstetrics and Gynecology, Østfold Hospital Trust, Grålum, Norway.,Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - M Bonet
- UNDP/UNFPA/UNICEF/WHO/World Bank Special Programme of Research, Development and Research Training in Human Reproduction (HRP), Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - M Bucagu
- Department of Maternal, Newborn, Child, Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland
| | - B Dao
- Jhpiego, Baltimore, MD, USA
| | - S Downe
- Research in Childbirth and Health (ReaCH) Group, University of Central Lancashire, Preston, UK
| | - H Galadanci
- Africa Centre of Excellence for Population Health and Policy, Bayero University, Bayero, Nigeria
| | - Cse Homer
- Maternal, Child and Adolescent Health Programme, Burnet Institute, Melbourne, Vic., Australia
| | - V Hundley
- Centre for Midwifery, Maternal and Perinatal Health, Bournemouth University, Bournemouth, UK
| | - T Lavender
- Department of International Global Health, Liverpool School of Tropical Medicine, Liverpool, UK
| | - B Levy
- Department of Obstetrics and Gynecology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - D Lissauer
- Malawi-Liverpool-Wellcome Trust Research Institute, Queen Elizabeth Central Hospital, College of Medicine, Chichiri, Blantyre, Malawi
| | - P Lumbiganon
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - F E McConville
- Department of Maternal, Newborn, Child, Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland
| | - R Pattinson
- South African Medical Research Council/University of Pretoria Maternal and Infant Health Care Strategies Unit, Pretoria, South Africa
| | - Z Qureshi
- Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya
| | - J P Souza
- Department of Social Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - M E Stanton
- Bureau for Global Health, United States Agency for International Development, Washington, DC, USA
| | | | - V Vannevel
- South African Medical Research Council/University of Pretoria Maternal and Infant Health Care Strategies Unit, Pretoria, South Africa
| | - J P Vogel
- Maternal, Child and Adolescent Health Programme, Burnet Institute, Melbourne, Vic., Australia
| | - O T Oladapo
- UNDP/UNFPA/UNICEF/WHO/World Bank Special Programme of Research, Development and Research Training in Human Reproduction (HRP), Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
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32
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Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Andersen EF, Herriges J, Coe B, Conlin L, Goodenberger M, Hilton B, Jobanputra V, Levy B, Paulraj P, Riggs ER, Runke C, Schleede J, Speevak M, Zhang S, Thorland E, Martin CL. 3. Standardizing recurrent copy number variant classification – From benign to reduced and high penetrance regions. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Levy B, Hoffmann ER, McCoy RC, Grati FR. Chromosomal mosaicism: Origins and clinical implications in preimplantation and prenatal diagnosis. Prenat Diagn 2021; 41:631-641. [PMID: 33720449 DOI: 10.1002/pd.5931] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
The diagnosis of chromosomal mosaicism in the preimplantation and prenatal stage is fraught with uncertainty and multiple factors need to be considered in order to gauge the likely impact. The clinical effects of chromosomal mosaicism are directly linked to the type of the imbalance (size, gene content, and copy number), the timing of the initial event leading to mosaicism during embryogenesis/fetal development, the distribution of the abnormal cells throughout the various tissues within the body as well as the ratio of normal/abnormal cells within each of those tissues. Additional factors such as assay noise and culture artifacts also have an impact on the significance and management of mosaic cases. Genetic counseling is an important part of educating patients about the likelihood of having a liveborn with a chromosome abnormality and these risks differ according to the time of ascertainment and the tissue where the mosaic cells were initially discovered. Each situation needs to be assessed on a case-by-case basis and counseled accordingly. This review will discuss the clinical impact of finding mosaicism through: embryo biopsy, chorionic villus sampling, amniocentesis, and noninvasive prenatal testing using cell-free DNA.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Francesca R Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays, S.p.A. (Impact Lab), Busto Arsizio, Varese, Italy
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35
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Thomson D, Joubert I, De Vasconcellos K, Paruk F, Mokogong S, Mathivha R, McCulloch M, Morrow B, Baker D, Rossouw B, Mdladla N, Richards GA, Welkovics N, Levy B, Coetzee I, Spruyt M, Ahmed N, Gopalan D. South African guidelines on the determination of death. South Afr J Crit Care 2021; 37:10.7196/SAJCC.2021v37i1b.466. [PMCID: PMC10193841 DOI: 10.7196/sajcc.2021v37i1b.466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 05/20/2023] Open
Abstract
Summary
Death is a medical occurrence that has social, legal, religious and cultural consequences requiring common clinical standards for its diagnosis
and legal regulation. This document compiled by the Critical Care Society of Southern Africa outlines the core standards for determination
of death in the hospital context. It aligns with the latest evidence-based research and international guidelines and is applicable to the South
African context and legal system. The aim is to provide clear medical standards for healthcare providers to follow in the determination
of death, thereby promoting safe practices and high-quality care through the use of uniform standards. Adherence to such guidelines will
provide assurance to medical staff, patients, their families and the South African public that the determination of death is always undertaken
with diligence, integrity, respect and compassion, and is in accordance with accepted medical standards and latest scientific evidence.
The consensus guidelines were compiled using the AGREE II checklist with an 18-member expert panel participating in a three-round
modified Delphi process. Checklists and advice sheets were created to assist with application of these guidelines in the clinical environment
(https://criticalcare.org.za/resource/death-determination-checklists/). Key points Brain death and circulatory death are the accepted terms for defining death in the hospital context. Death determination is a clinical diagnosis which can be made with complete certainty provided that all preconditions are met. The determination of death in children is held to the same standard as in adults but cannot be diagnosed in children <36 weeks’ corrected
gestation. Brain-death testing while on extra-corporeal membrane oxygenation is outlined. Recommendations are given on handling family requests for accommodation and on consideration of the potential for organ donation. The use of a checklist combined with a rigorous testing process, comprehensive documentation and adequate counselling of the family
are core tenets of death determination. This is a standard of practice to which all clinicians should adhere in end-of-life care.
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Affiliation(s)
- D Thomson
- Division of Critical Care, Department of Surgery, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - I Joubert
- Division of Critical Care, Department of Anaesthesia and Peri-operative Medicine, University of Cape Town and Groote Schuur Hospital,
Cape Town, South Africa
| | - K De Vasconcellos
- Department of Critical Care, King Edward VIII Hospital, Durban, South Africa; Discipline of Anaesthesiology and Critical Care, School of Clinical
Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - F Paruk
- Department of Critical Care, University of Pretoria, South Africa
| | - S Mokogong
- Department of Neurosurgery, University of Pretoria, South Africa
| | - R Mathivha
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M McCulloch
- Paediatric Intensive Care Unit and Transplant Unit, Red Cross War Memorial Children’s Hospital and Faculty of Health Sciences, University of
Cape Town, South Africa
| | - B Morrow
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - D Baker
- Department of Adult Critical Care, Livingstone Hospital and Faculty of Health Sciences, Walter Sisulu University, Port Elizabeth, South Africa
| | - B Rossouw
- Paediatric Intensive Care Unit, Red Cross War Memorial Children’s Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
| | - N Mdladla
- Dr George Mukhari Academic Hospital, Sefako Makgatho University, Johannesburg, South Africa
| | - G A Richards
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N Welkovics
- Netcare Unitas Hospital, Centurion, South Africa
| | - B Levy
- Netcare Rosebank Hospital, Johannesburg, South Africa
| | - I Coetzee
- Department of Nursing Science, University of Pretoria, South Africa
| | - M Spruyt
- Busamed Bram Fischer International Airport Hospital, Bloemfontein, South Africa
| | - N Ahmed
- Consolidated Critical Care Unit, Tygerberg Hospital, Department of Surgical Sciences, Department of Anaesthesiology and Critical Care, Faculty
of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - D Gopalan
- Discipline of Anaesthesiology and Critical Care, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
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36
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Hsu M, Murray J, Zhang J, Barasa D, Turner M, Forde P, Ettinger D, Lam V, Marrone K, Levy B, Hann C, Brahmer J, Feliciano J, Naidoo J. MA07.05 Survivors from Anti-PD-(L)1 Immunotherapy in NSCLC: Clinical Features, Survival Outcomes and Long-term Toxicities. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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Bauml J, Mick R, Mccoach C, Weiss J, Marrone K, Nieva J, Villaruz L, Levy B, Moreno R, Murkherji R, Sun F, Schwartzman W, Shaverdashvili K, Wang X, Shah M, Woodley J, Miller N, Succe C, Ullah T, Lovly C, Doebele R, Iams W, Horn L, Dowell J, Liu G, Leighl N, Patil T, Liu S, Velcheti V, Aisner D, Camidge R. FP14.06 Multicenter Analysis of Mechanisms of Resistance to Osimertinib (O) in EGFR Mutated NSCLC: An ATOMIC Registry Study. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Thomson D, Joubert I, De Vasconcellos K, Paruk F, Mokogong S, Mathiva R, McCulloch M, Morrow B, Baker D, Rossouw B, Mdladla N, Richards GA, Welkovics N, Levy B, Coetzee I, Spruyt M, Ahmed N, Gopalan D. South African guidelines on the determination of death. S Afr Med J 2021; 111:367-380. [PMID: 37114488 DOI: 10.7196/samj.2021.v111i4b.15200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Death is a medical occurrence that has social, legal, religious and cultural consequences requiring common clinical standards for its diagnosis and legal regulation. This document compiled by the Critical Care Society of Southern Africa outlines the core standards for determination of death in the hospital context. It aligns with the latest evidence-based research and international guidelines and is applicable to the South African context and legal system. The aim is to provide clear medical standards for healthcare providers to follow in the determination of death, thereby promoting safe practices and high-quality care through the use of uniform standards. Adherence to such guidelines will provide assurance to medical staff, patients, their families and the South African public that the determination of death is always undertaken with diligence, integrity, respect and compassion, and is in accordance with accepted medical standards and latest scientific evidence. The consensus guidelines were compiled using the AGREE II checklist with an 18-member expert panel participating in a three-round modified Delphi process. Checklists and advice sheets were created to assist with application of these guidelines in the clinical environment (https://criticalcare.org.za/resource/death-determination-checklists/). Key points • Brain death and circulatory death are the accepted terms for defining death in the hospital context. • Death determination is a clinical diagnosis which can be made with complete certainty provided that all preconditions are met. • The determination of death in children is held to the same standard as in adults but cannot be diagnosed in children <36 weeks' corrected gestation. • Brain-death testing while on extra-corporeal membrane oxygenation is outlined. • Recommendations are given on handling family requests for accommodation and on consideration of the potential for organ donation. • The use of a checklist combined with a rigorous testing process, comprehensive documentation and adequate counselling of the family are core tenets of death determination. This is a standard of practice to which all clinicians should adhere in end-of-life care.
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Affiliation(s)
- D Thomson
- Division of Critical Care, Department of Surgery, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - I Joubert
- Division of Critical Care, Department of Anaesthesia and Peri-operative Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - K De Vasconcellos
- Department of Critical Care, King Edward VIII Hospital, Durban, South Africa; Discipline of Anaesthesiology and Critical Care, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - F Paruk
- Department of Critical Care, University of Pretoria, South Africa
| | - S Mokogong
- Department of Neurosurgery, University of Pretoria, South Africa
| | - R Mathiva
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M McCulloch
- Paediatric Intensive Care Unit and Transplant Unit, Red Cross War Memorial Children's Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
| | - B Morrow
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Cape Town, South Africa
| | - D Baker
- Department of Adult Critical Care, Livingstone Hospital and Faculty of Health Sciences, Walter Sisulu University, Port Elizabeth, South Africa
| | - B Rossouw
- Paediatric Intensive Care Unit, Red Cross War Memorial Children's Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
| | - N Mdladla
- Dr George Mukhari Academic Hospital, Sefako Makgatho University, Johannesburg, South Africa
| | - G A Richards
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N Welkovics
- Netcare Unitas Hospital, Centurion, South Africa
| | - B Levy
- Netcare Rosebank Hospital, Johannesburg, South Africa
| | - I Coetzee
- Department of Nursing Science, University of Pretoria, South Africa
| | - M Spruyt
- Busamed Bram Fischer International Airport Hospital, Bloemfontein, South Africa
| | - N Ahmed
- Consolidated Critical Care Unit, Tygerberg Hospital, Department of Surgical Sciences, Department of Anaesthesiology and Critical Care, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - D Gopalan
- Discipline of Anaesthesiology and Critical Care, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
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Zipfel S, Biancari F, Mariscalco G, Dalén M, Settembre N, Welp H, Perrotti A, Wiebe K, Leo E, Loforte A, Chocron S, Pacini D, Juvonen T, Broman LM, Di Perna D, Yusuff H, Harvey C, Mongardon N, Maureira JP, Levy B, Falk L, Ruggieri VG, Kluge S, Reichenspurner H, Folliguet T, Fiore A. Extracorporeal Membrane Oxygenation for Patients with Severe COVID-19-Related ARDS: A European Multicenter Analysis. Thorac Cardiovasc Surg 2021. [DOI: 10.1055/s-0041-1725648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Chitty LS, Ghidini A, Deprest J, Van Mieghem T, Levy B, Hui L, Bianchi DW. Right or wrong? Looking through the retrospectoscope to analyse predictions made a decade ago in prenatal diagnosis and fetal surgery. Prenat Diagn 2020; 40:1627-1635. [PMID: 33231306 DOI: 10.1002/pd.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, DC.,Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA
| | - Jan Deprest
- Department of Obstetrics and Gynaecology, University of Leuven, Leuven, Belgium and the Institute for Women's Health, UCL, London
| | - Tim Van Mieghem
- Fetal Medicine Unit and Ontario Fetal Centre, Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Brynn Levy
- Division of Personalized Genomic Medicine, Columbia University Medical Center & the New York Presbyterian Hospital, New York, New York, USA
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia.,Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,The Northern Hospital, Epping, Victoria, Australia
| | - Diana W Bianchi
- Division of Prenatal Genomics and Fetal Therapy, Medical Genomics and Metabolic Genetics Branch, National Human Genome Institute, National Human Genome Institute, National Institutes of Health, Bethesda, Maryland, USA
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41
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Maisenbacher MK, Merrion K, Levy B, Kutteh WH. SINGLE NUCLEOTIDE POLYMORPHISM (SNP) ARRAY ANALYSIS OF 63,277 PRODUCTS OF CONCEPTION (POC) SAMPLES: A 10-YEAR LABORATORY EXPERIENCE. Fertil Steril 2020. [DOI: 10.1016/j.fertnstert.2020.08.151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Bianchi DW, Deprest J, Levy B, Chitty LS, Ghidini A, Hui L, van Mieghem T, George ST. The 2019 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2020; 40:763-765. [PMID: 32597540 DOI: 10.1002/pd.5763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jan Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals, Leuven, Belgium
| | - Brynn Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Lyn S Chitty
- Genetic and Genomic Medicine, University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA, USA
| | - Lisa Hui
- Departments of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
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43
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Glen W, Wilson R, Znoyko I, Pasham V, Levy B, Fang M, Wolff D. 17. One test to rule them all? The utility of nanopore sequencing for variant detection in hematological malignancies. Cancer Genet 2020. [DOI: 10.1016/j.cancergen.2020.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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44
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Lennon PA, Raca G, Fang M, Wolff D, Li MM, Iqbal AM, Levy B, Schwartz S, Dubuc AM. Whole genome SNP arrays for best practice for detection of diagnostic, prognostic and therapy related copy number changes and copy neutral-loss of heterozygosity across solid tumors and hematologic malignancies. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e15575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15575 Background: High resolution single nucleotide polymorphism (SNP) chromosomal microarrays (CMA) detect copy number changes and copy neutral-loss of heterozygosity (CN-LOH) across the entire genome, currently providing the best assessment for these types of genomic variants. Chromosomal microarrays are first tier tests utilized in the postnatal detection of microdeletions, microduplications and uniparental disomy/regions of homozygosity in constitutional disorders involving congenital abnormalities, developmental delay and intellectual disability. Methods: In the oncology setting, aberrations detected may be diagnostic, prognostic, and therapeutic. Because CMA assesses the entire genome and can readily detect aberrations as small as a single exon to as large as a whole chromosome, this is an important clinical tool to bridge the gap between low resolution of metaphase chromosome analysis and PCR-based short read sequencing-based assays. Results: No single genomic technique (metaphase chromosome analysis, FISH, CMA or Next Generation Sequencing, including large targeted gene panels) has the ability to detect all relevant information. Therefore, CMA should be considered an important clinical tool for solid and liquid tumors. Across a wide variety of solid tumors, whole genome assessment (including oncogene amplification, tumor suppressor loss, and copy number burden) leads not only to possible therapy targets but also to opportunities for participation in active clinical trials. Recently, the Cancer Genomics Consortium has published evidenced-based reviews on the clinical utility of CMA for copy number and CN-LOH assessment in a variety of hematologic malignancies, and similar papers in solid tumors are in review. Recognizing the growing evidence for CMA, the American Medical Association (AMA) CPT editorial board recently created a new Tier 1 test for cytogenomic arrays in neoplasia, and Centers for Medicare and Medicaid Services (CMS) approved crosswalking the price of the new code to the well-established constitutional cytogenomic array CPT code. Conclusions: For this presentation, examples of diagnostic, prognostic, and therapeutic utility and inclusion in clinical trials across many hematologic and solid tumor neoplasms will be presented to demonstrate the efficacy, cost effectiveness and sensitivity of whole genome assessment of copy number and copy neutral loss of heterozygosity
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Affiliation(s)
| | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA
| | - Min Fang
- Seattle Cancer Care Alliance, Seattle, WA
| | - Daynna Wolff
- Medical University of South Carolina, Charleston, SC
| | | | | | | | - Stuart Schwartz
- Laboratory Corporation of America, Research Triangle Park, NC
| | - Adrian M. Dubuc
- Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA
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45
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Wei S, Levy B, Hoffman N, Cujar C, Rodney-Sandy R, Wapner R, D'Alton M, Williams Z. A rapid and simple bead-bashing-based method for genomic DNA extraction from mammalian tissue. Biotechniques 2020; 68:240-244. [PMID: 32054310 PMCID: PMC7252492 DOI: 10.2144/btn-2019-0172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
Conventional genomic DNA (gDNA) extraction methods can take hours to complete, may require fume hoods and represent the most time-consuming step in many gDNA-based molecular assays. We systematically optimized a bead bashing-based (BBB) approach for rapid gDNA extraction without the need for a fume hood. Human tissue specimens (n = 34) subjected to the 12-min BBB method yielded 0.40 ± 0.17 (mean ± SD) μg of gDNA per milligram of tissue, sufficient for many downstream applications, and 3- and 6-min extensions resulted in an additional 0.43 ± 0.23 μg and 0.48 ± 0.43 μg per milligram of tissue, respectively. The BBB method provides a simple and rapid method for gDNA extraction from mammalian tissue that is applicable to time-sensitive clinical applications.
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Affiliation(s)
- Shan Wei
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Clinical Cytogenetics Laboratory, Columbia University Medical Center & the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Nataly Hoffman
- Clinical Cytogenetics Laboratory, Columbia University Medical Center & the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Claudia Cujar
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Reunet Rodney-Sandy
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ronald Wapner
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Mary D'Alton
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zev Williams
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
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Chitty LS, Hui L, Ghidini A, Levy B, Deprest J, Van Mieghem T, Bianchi DW. In case you missed it: The Prenatal Diagnosis editors bring you the most significant advances of 2019. Prenat Diagn 2020; 40:287-293. [PMID: 31875323 DOI: 10.1002/pd.5632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022]
Affiliation(s)
- L S Chitty
- London North Genomic Laboratory, Great Ormond Street NHS Foundation Trust, and Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - L Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Ghidini
- Antenatal Testing Centre, Inova Alexandria Hospital, Alexandria, VA
| | - B Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY
| | - J Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - T Van Mieghem
- Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - D W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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Vossaert L, Wang Q, Salman R, McCombs AK, Patel V, Qu C, Mancini MA, Edwards DP, Malovannaya A, Liu P, Shaw CA, Levy B, Wapner RJ, Bi W, Breman AM, Van den Veyver IB, Beaudet AL. Validation Studies for Single Circulating Trophoblast Genetic Testing as a Form of Noninvasive Prenatal Diagnosis. Am J Hum Genet 2019; 105:1262-1273. [PMID: 31785788 PMCID: PMC6904821 DOI: 10.1016/j.ajhg.2019.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023] Open
Abstract
It has long been appreciated that genetic analysis of fetal or trophoblast cells in maternal blood could revolutionize prenatal diagnosis. We implemented a protocol for single circulating trophoblast (SCT) testing using positive selection by magnetic-activated cell sorting and single-cell low-coverage whole-genome sequencing to detect fetal aneuploidies and copy-number variants (CNVs) at ∼1 Mb resolution. In 95 validation cases, we identified on average 0.20 putative trophoblasts/mL, of which 55% were of high quality and scorable for both aneuploidy and CNVs. We emphasize the importance of analyzing individual cells because some cells are apoptotic, in S-phase, or otherwise of poor quality. When two or more high-quality trophoblast cells were available for singleton pregnancies, there was complete concordance between all trophoblasts unless there was evidence of confined placental mosaicism. SCT results were highly concordant with available clinical data from chorionic villus sampling (CVS) or amniocentesis procedures. Although determining the exact sensitivity and specificity will require more data, this study further supports the potential for SCT testing to become a diagnostic prenatal test.
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Affiliation(s)
- Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roseen Salman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne K McCombs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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48
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Ghidini A, Bianchi DW, Levy B, Van Mieghem T, Deprest J, Chitty LS. In case you missed it: The prenatal diagnosis editors bring you the most significant advances of 2018. Prenat Diagn 2019; 39:61-69. [PMID: 30593668 DOI: 10.1002/pd.5407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Alessandro Ghidini
- Antenatal Testing Center Alexandria Hospital, Alexandria, VA, USA.,Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, D.C., USA
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Brynn Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Tim Van Mieghem
- Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Canada
| | - Jan Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, Great Ormond Street NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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Joynt GM, Gopalan PD, Argent A, Chetty S, Wise R, Lai VKW, Hodgson E, Lee A, Joubert I, Mokgokong S, Tshukutsoane S, Richards GA, Menezes C, Mathivha LR, Espen B, Levy B, Asante K, Paruk F. The Critical Care Society of Southern Africa Consensus Guideline on ICU Triage and Rationing (ConICTri). South Afr J Crit Care 2019; 35:10.7196/SAJCC.2019.v35i1b.380. [PMID: 37719328 PMCID: PMC10503493 DOI: 10.7196/sajcc.2019.v35i1b.380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 11/08/2022] Open
Abstract
Background In South Africa (SA), administrators and intensive care practitioners are faced with the challenge of resource scarcity as well as an increasing demand for intensive care unit (ICU) services. ICU services are expensive, and practitioners in low- to middle-income countries experience the consequences of limited resources daily. Critically limited resources necessitate that rationing and triage (prioritisation) decisions are routinely necessary in SA, particularly in the publicly funded health sector. Purpose The purpose of this guideline is to utilise the relevant recommendations of the associated consensus meeting document and other internationally accepted principles to develop a guideline to inform frontline triage policy and ensure the best utilisation of adult intensive care in SA, while maintaining the fair distribution of available resources. Recommendations An overall conceptual framework for the triage process was developed. The components of the framework were developed on the basis that patients should be admitted preferentially when the likely incremental medical benefit derived from ICU admission justifies admission. An estimate of likely resource use should also form part of the triage decision, with those patients requiring relatively less resources to achieve substantial benefit receiving priority for admission. Thus, the triage system should maximise the benefits obtained from ICU resources available for the community. Where possible, practical examples of what the consensus group agreed would be considered appropriate practice under specified South African circumstances were provided, to assist clinicians with practical decision-making. It must be stressed that this guideline is not intended to be prescriptive for individual hospital or regional practice, and hospitals and regions are encouraged to develop specified local guidelines with locally relevant examples. The guideline should be reviewed and revised if appropriate within 5 years. Conclusion In recognition of the absolute need to limit patient access to ICU because of the lack of sufficient intensive care resources in public hospitals, this guideline has been developed to guide policy-making and assist frontline triage decision-making in SA. This document is not a complete plan for quality practice, but rather a template to support frontline clinicians, guide administrators and inform the public regarding appropriate triage decision-making.
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Affiliation(s)
- G M Joynt
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - P D Gopalan
- Department of Anaesthesiology and Critical Care, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - A Argent
- Department of Paediatrics and Child Health, University of Cape Town, South Africa
| | - S Chetty
- Department of Anaesthesiology and Critical Care, Stellenbosch University, Cape Town, South Africa
| | - R Wise
- Department of Anaesthesiology and Critical Care, School of Clinical Medicine, University of KwaZulu-Natal, Durban, and Edendale Hospital,
Pietermaritzburg, South Africa
| | - V K W Lai
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - E Hodgson
- Department of Anaesthesiology and Critical Care, School of Clinical Medicine, University of KwaZulu-Natal, Durban, and Inkosi Albert Luthuli
Central Hospital, Durban, South Africa
| | - A Lee
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - I Joubert
- Department of Anaesthesia and Peri-operative Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - S Mokgokong
- Department of Neurosurgery, University of Pretoria, South Africa
| | - S Tshukutsoane
- Chris Hani Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - G A Richards
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - C Menezes
- Chris Hani Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L R Mathivha
- Department of Critical Care, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - B Espen
- Centre for Health Professions Education, Stellenbosch University, Cape Town, South Africa
| | - B Levy
- Netcare Rosebank Hospital, Johannesburg, South Africa
| | - K Asante
- African Organization for Research and Training in Cancer, Cape Town, South Africa
| | - F Paruk
- Department of Critical Care, University of Pretoria, South Africa
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50
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Bianchi DW, Ghidini A, Levy B, Deprest J, van Mieghem T, Chitty LS, Hui L, McLean-Inglis A. The 2018 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2019; 39:835-837. [PMID: 31414475 DOI: 10.1002/pd.5533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Inova Alexandria Hospital, Alexandria, VA, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jan Deprest
- Academic Department of Development and Regeneration, Woman and Child, Biomedical Sciences, and Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium
| | - Tim van Mieghem
- Departments of Obstetrics and Gynaecology, Mount Sinai Hospital, Toronto, Canada
| | - Lyn S Chitty
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
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