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Shen W, Sellers HL, Choate LA, Stein MI, Tandale PP, Tan J, Setlem R, Sakai Y, Fadra N, Sosa C, McClelland SP, Barnett SS, Rasmussen KJ, Runke CK, Smoley SA, Tillmans LS, Marcou CA, Rowsey RA, Thorland EC, Boczek NJ, Kearney HM. Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders. J Mol Diagn 2023; 25:524-531. [PMID: 37088140 DOI: 10.1016/j.jmoldx.2023.04.001] [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: 01/20/2023] [Revised: 03/09/2023] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
Genome sequencing (GS) is a powerful clinical tool used for the comprehensive diagnosis of germline disorders. GS library preparation typically involves mechanical DNA fragmentation, end repair, and bead-based library size selection followed by adapter ligation, which can require a large amount of input genomic DNA. Tagmentation using bead-linked transposomes can simplify the library preparation process and reduce the DNA input requirement. Here we describe the clinical validation of tagmentation-based PCR-free GS as a clinical test for rare germline disorders. Compared with the Genome-in-a-Bottle Consortium benchmark variant sets, GS had a recall >99.7% and a precision of 99.8% for single nucleotide variants and small insertion-deletions. GS also exhibited 100% sensitivity for clinically reported sequence variants and the copy number variants examined. Furthermore, GS detected mitochondrial sequence variants above 5% heteroplasmy and showed reliable detection of disease-relevant repeat expansions and SMN1 homozygous loss. Our results indicate that while lowering DNA input requirements and reducing library preparation time, GS enables uniform coverage across the genome as well as robust detection of various types of genetic alterations. With the advantage of comprehensive profiling of multiple types of genetic alterations, GS is positioned as an ideal first-tier diagnostic test for germline disorders.
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Affiliation(s)
- Wei Shen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Heidi L Sellers
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lauren A Choate
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mariam I Stein
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Pratyush P Tandale
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Jiayu Tan
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Rohit Setlem
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Yuta Sakai
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Numrah Fadra
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Carlos Sosa
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Shawn P McClelland
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sarah S Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kristen J Rasmussen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cassandra K Runke
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lori S Tillmans
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cherisse A Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ross A Rowsey
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Nicole J Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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2
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Riggs ER, Andersen EF, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL. Response to Spurdle et al. Genet Med 2023:100869. [PMID: 37261438 DOI: 10.1016/j.gim.2023.100869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 06/02/2023] Open
Affiliation(s)
- Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Erica F Andersen
- ARUP Laboratories, Salt Lake City, UT; University of Utah, Salt Lake City, UT
| | - Sibel Kantarci
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA
| | - Hutton Kearney
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA
| | - Deborah I Ritter
- Texas Children's Cancer Center, Baylor College of Medicine Houston, TX
| | - Sarah T South
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Swaroop Aradhya
- Invitae, San Francisco, CA; Stanford University School of Medicine, Stanford, CA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
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3
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Gagnon MF, Berg HE, Meyer RG, Sukov WR, Van Dyke DL, Jenkins RB, Greipp PT, Thorland EC, Hoppman NL, Xu X, Baughn LB, Reichard KK, Ketterling RP, Peterson JF. Typical, atypical and cryptic t(15;17)(q24;q21) (PML::RARA) observed in acute promyelocytic leukemia: a retrospective review of 831 patients with concurrent chromosome and PML::RARA dual-color dual-fusion FISH studies. Genes Chromosomes Cancer 2022; 61:629-634. [PMID: 35639830 DOI: 10.1002/gcc.23070] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/07/2022] Open
Abstract
The diagnosis of acute promyelocytic leukemia (APL) relies on the identification of PML::RARA fusion. While the majority of APL cases harbor a typical t(15;17)(q24;q21), atypical genetic mechanisms leading to the oncogenic PML::RARA fusion have been reported yet their frequency and scope remain poorly characterized. We assessed the genetic findings of 831 cases with APL investigated with concurrent chromosome banding analysis and dual-color dual-fusion fluorescence in situ hybridization (D-FISH) analysis at our institution over an 18.5-year timeframe. Seven-hundred twenty-three (87%) cases had a typical balanced t(15;17) with both testing modalities. Atypical karyotypic results including complex translocations, unbalanced rearrangements and insertional events occurred in 50 (6%) cases, while 6 (0.7%) cases were cryptic by conventional chromosome studies despite PML::RARA fusion by D-FISH evaluation. Atypical FISH patterns were observed in 48 (6%) cases despite apparently balanced t(15;17) on chromosome banding analysis. Two-hundred fifty (30%) cases displayed additional chromosome abnormalities of which trisomy/tetrasomy 8 (37%), del(7q)/add(7q) (12%) and del(9q) (7%) were most frequent. Complex and very complex karyotypes were observed in 81 (10%) and 34 (4%) cases, respectively. In addition, 4 (0.5%) cases presented as an apparently doubled, near-tetraploid stemline clone. This report provides the largest appraisal of cytogenetic findings in APL with conventional chromosome and PML::RARA D-FISH analysis. By characterizing the frequency and breadth of typical and atypical results through the lens of these cytogenetic testing modalities, this study serves as a pragmatic source of information for those involved in the investigation of APL in both the clinical and research laboratory settings.
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Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Holly E Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - William R Sukov
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel L Van Dyke
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robert B Jenkins
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erik C Thorland
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kaaren K Reichard
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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4
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Gonzales PR, Andersen EF, Brown TR, Horner VL, Horwitz J, Rehder CW, Rudy NL, Robin NH, Thorland EC, On Behalf Of The Acmg Laboratory Quality Assurance Committee. Interpretation and reporting of large regions of homozygosity and suspected consanguinity/uniparental disomy, 2021 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:255-261. [PMID: 34906464 DOI: 10.1016/j.gim.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/18/2022] Open
Abstract
Genomic testing, including single-nucleotide variation (formerly single-nucleotide polymorphism)-based chromosomal microarray and exome and genome sequencing, can detect long regions of homozygosity (ROH) within the genome. Genomic testing can also detect possible uniparental disomy (UPD). Platforms that can detect ROH and possible UPD have matured since the initial American College of Medical Genetics and Genomics (ACMG) standard was published in 2013, and the detection of ROH and UPD by these platforms has shown utility in diagnosis of patients with genetic/genomic disorders. The presence of these segments, when distributed across multiple chromosomes, may indicate a familial relationship between the proband's parents. This technical standard describes the detection of possible consanguinity and UPD by genomic testing, as well as the factors confounding the inference of a specific parental relationship or UPD. Current bioethical and legal issues regarding detection and reporting of consanguinity are also discussed.
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Affiliation(s)
| | - Erica F Andersen
- ARUP Laboratories, Salt Lake City, UT; The University of Utah, Salt Lake City, UT
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5
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Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL. Correction: Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 2021; 23:2230. [PMID: 33731880 DOI: 10.1038/s41436-021-01150-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA.
| | - Erica F Andersen
- ARUP Laboratories, Salt Lake City, UT, USA.,Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | | | - Sibel Kantarci
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Hutton Kearney
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Deborah I Ritter
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Swaroop Aradhya
- Stanford University School of Medicine, Stanford, CA, USA.,Invitae, San Francisco, CA, USA
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6
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Tester DJ, Bombei HM, Fitzgerald KK, Giudicessi JR, Pitel BA, Thorland EC, Russell BG, Hamrick SK, Kim CSJ, Haglund-Turnquist CM, Johnsrude CL, Atkins DL, Ochoa Nunez LA, Law I, Temple J, Ackerman MJ. Identification of a Novel Homozygous Multi-Exon Duplication in RYR2 Among Children With Exertion-Related Unexplained Sudden Deaths in the Amish Community. JAMA Cardiol 2021; 5:13-18. [PMID: 31913406 DOI: 10.1001/jamacardio.2019.5400] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance The exome molecular autopsy may elucidate a pathogenic substrate for sudden unexplained death. Objective To investigate the underlying cause of multiple sudden deaths in young individuals and sudden cardiac arrests that occurred in 2 large Amish families. Design, Setting, and Participants Two large extended Amish families with multiple sudden deaths in young individuals and sudden cardiac arrests were included in the study. A recessive inheritance pattern was suggested based on an extended family history of sudden deaths in young individuals and sudden cardiac arrests, despite unaffected parents. A family with exercise-associated sudden deaths in young individuals occurring in 4 siblings was referred for postmortem genetic testing using an exome molecular autopsy. Copy number variant (CNV) analysis was performed on exome data using PatternCNV. Chromosomal microarray validated the CNV identified. The nucleotide break points of the CNV were determined by mate-pair sequencing. Samples were collected for this study between November 2004 and June 2019. Main Outcomes and Measures The identification of an underlying genetic cause for sudden deaths in young individuals and sudden cardiac arrests consistent with the recessive inheritance pattern observed in the families. Results A homozygous duplication, involving approximately 26 000 base pairs of intergenic sequence, RYR2's 5'UTR/promoter region, and exons 1 through 4 of RYR2, was identified in all 4 siblings of a family. Multiple distantly related relatives experiencing exertion-related sudden cardiac arrest also had the identical RYR2 homozygous duplication. A second, unrelated family with multiple exertion-related sudden deaths and sudden cardiac arrests in young individuals, with the same homozygous duplication, was identified. Several living, homozygous duplication-positive symptomatic patients from both families had nondiagnostic cardiologic testing, with only occasional ventricular ectopy occurring during exercise stress tests. Conclusions and Relevance In this analysis, we identified a novel, highly penetrant, homozygous multiexon duplication in RYR2 among Amish youths with exertion-related sudden death and sudden cardiac arrest but without an overt phenotype that is distinct from RYR2-mediated catecholaminergic polymorphic ventricular tachycardia. Considering that no cardiac tests reliably identify at-risk individuals and given the high rate of consanguinity in Amish families, identification of unaffected heterozygous carriers may provide potentially lifesaving premarital counseling and reproductive planning.
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Affiliation(s)
- David J Tester
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hannah M Bombei
- Stead Family Children's Hospital, Division of Pediatric Cardiology, University of Iowa, Iowa City
| | - Kristi K Fitzgerald
- Nemours Cardiac Center, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - John R Giudicessi
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Barbara G Russell
- Division of Pediatric Cardiology, University of Louisville, Louisville, Kentucky
| | - Samantha K Hamrick
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - C S John Kim
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Carla M Haglund-Turnquist
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Dianne L Atkins
- Stead Family Children's Hospital, Division of Pediatric Cardiology, University of Iowa, Iowa City
| | - Luis A Ochoa Nunez
- Stead Family Children's Hospital, Division of Pediatric Cardiology, University of Iowa, Iowa City
| | - Ian Law
- Stead Family Children's Hospital, Division of Pediatric Cardiology, University of Iowa, Iowa City
| | - Joel Temple
- Nemours Cardiac Center, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Michael J Ackerman
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
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7
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Palmer EE, Carroll R, Shaw M, Kumar R, Minoche AE, Leffler M, Murray L, Macintosh R, Wright D, Troedson C, McKenzie F, Townshend S, Ward M, Nawaz U, Ravine A, Runke CK, Thorland EC, Hummel M, Foulds N, Pichon O, Isidor B, Le Caignec C, Demeer B, Andrieux J, Albarazi SH, Bye A, Sachdev R, Kirk EP, Cowley MJ, Field M, Gecz J. RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features. Am J Hum Genet 2020; 107:1157-1169. [PMID: 33159883 PMCID: PMC7820564 DOI: 10.1016/j.ajhg.2020.10.005] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.
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Affiliation(s)
- Elizabeth E Palmer
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia; School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute, Darlinghurst, Sydney, NSW 2010, Australia.
| | - Renee Carroll
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Raman Kumar
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Andre E Minoche
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | | | - Dale Wright
- Discipline of Genomic Medicine and Discipline of Child & Adolescent Health, University of Sydney, Sydney, NSW 2010, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Chris Troedson
- Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Fiona McKenzie
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6009, Australia; Genetic Services of Western Australia, Perth, WA 6008, Australia
| | | | - Michelle Ward
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Urwah Nawaz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anja Ravine
- Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Pathwest Laboratory Medicine WA, Perth, WA 6008, Australia
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Marybeth Hummel
- West Virginia University School of Medicine, Department of Pediatrics, Section of Medical Genetics Morgantown, WV 26506-9600, USA
| | - Nicola Foulds
- Wessex Clinical Genetics Services, Southampton SO16 5YA, UK
| | - Olivier Pichon
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Bertrand Isidor
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Cédric Le Caignec
- Service de génétique médicale, Institut fédératif de Biologie, CHU Hopital Purpan, Toulouse 31059, France
| | - Bénédicte Demeer
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, Amiens 80080, France; CHIMERE EA 7516, University Picardie Jules Verne, Amiens 80025, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille 59000, France
| | | | - Ann Bye
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Rani Sachdev
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Edwin P Kirk
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW 2033, Australia
| | - Mike Field
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
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8
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Marcou CA, Pitel B, Hagen CE, Boczek NJ, Rowsey RA, Baughn LB, Hoppman NL, Thorland EC, Kearney HM. Limited diagnostic impact of duplications <1 Mb of uncertain clinical significance: a 10-year retrospective analysis of reporting practices at the Mayo Clinic. Genet Med 2020; 22:2120-2124. [PMID: 32820244 DOI: 10.1038/s41436-020-0932-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Copy-number variants (CNVs) of uncertain clinical significance are routinely reported in a clinical setting only when exceeding predetermined reporting thresholds, typically based on CNV size. Given that very few genes are associated with triplosensitive phenotypes, it is not surprising that many interstitial duplications <1 Mb are found to be inherited and anticipated to be of limited or no clinical significance. METHODS In an effort to further refine our reporting criteria to maximize diagnostic yield while minimizing the return of uncertain variants, we performed a retrospective analysis of all clinical microarray cases reported in a 10-year window. A total of 1112 reported duplications had parental follow-up, and these were compared by size, RefSeq gene content, and inheritance pattern. De novo origin was used as a rough proxy for pathogenicity. RESULTS Approximately 6% of duplications 500 kb-1 Mb were de novo observations, compared with approximately 14% for 1-2 Mb duplications (p = 0.0005). On average, de novo duplications had higher gene counts than inherited duplications. CONCLUSION Our data reveal limited diagnostic utility for duplications of uncertain significance <1 Mb. Considerations for revised reporting criteria are discussed and are applicable to CNVs detected by any genome-wide exploratory methodology, including exome/genome sequencing.
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Affiliation(s)
- Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Beth Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Clinton E Hagen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ross A Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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9
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Riggs ER, Andersen EF, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL. Response to Maya et al. Genet Med 2020; 22:1278-1279. [PMID: 32341575 DOI: 10.1038/s41436-020-0796-3] [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: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Erica F Andersen
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Sibel Kantarci
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Hutton Kearney
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Deborah I Ritter
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Swaroop Aradhya
- Invitae, San Francisco, CA, USA.,Stanford University School of Medicine, Stanford, CA, USA
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10
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Riggs ER, Nelson T, Merz A, Ackley T, Bunke B, Collins CD, Collinson MN, Fan YS, Goodenberger ML, Golden DM, Haglund-Hazy L, Krgovic D, Lamb AN, Lewis Z, Li G, Liu Y, Meck J, Neufeld-Kaiser W, Runke CK, Sanmann JN, Stavropoulos DJ, Strong E, Su M, Tayeh MK, Kokalj Vokac N, Thorland EC, Andersen E, Martin CL. Copy number variant discrepancy resolution using the ClinGen dosage sensitivity map results in updated clinical interpretations in ClinVar. Hum Mutat 2019; 39:1650-1659. [PMID: 30095202 DOI: 10.1002/humu.23610] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 11/07/2022]
Abstract
Conflict resolution in genomic variant interpretation is a critical step toward improving patient care. Evaluating interpretation discrepancies in copy number variants (CNVs) typically involves assessing overlapping genomic content with focus on genes/regions that may be subject to dosage sensitivity (haploinsufficiency (HI) and/or triplosensitivity (TS)). CNVs containing dosage sensitive genes/regions are generally interpreted as "likely pathogenic" (LP) or "pathogenic" (P), and CNVs involving the same known dosage sensitive gene(s) should receive the same clinical interpretation. We compared the Clinical Genome Resource (ClinGen) Dosage Map, a publicly available resource documenting known HI and TS genes/regions, against germline, clinical CNV interpretations within the ClinVar database. We identified 251 CNVs overlapping known dosage sensitive genes/regions but not classified as LP or P; these were sent back to their original submitting laboratories for re-evaluation. Of 246 CNVs re-evaluated, an updated clinical classification was warranted in 157 cases (63.8%); no change was made to the current classification in 79 cases (32.1%); and 10 cases (4.1%) resulted in other types of updates to ClinVar records. This effort will add curated interpretation data into the public domain and allow laboratories to focus attention on more complex discrepancies.
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Affiliation(s)
- Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Tristan Nelson
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Andrew Merz
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Todd Ackley
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | | | | | - Morag N Collinson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire, UK
| | - Yao-Shan Fan
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - McKinsey L Goodenberger
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Denae M Golden
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Linda Haglund-Hazy
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Danijela Krgovic
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Allen N Lamb
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Zoe Lewis
- ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Yajuan Liu
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Whitney Neufeld-Kaiser
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer N Sanmann
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Emma Strong
- Genome Diagnostics, The Hospital for Sick Children, University of Toronto, Canada
| | - Meng Su
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marwan K Tayeh
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Nadja Kokalj Vokac
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erica Andersen
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
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11
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Aypar U, Smoley SA, Pitel BA, Pearce KE, Zenka RM, Vasmatzis G, Johnson SH, Smadbeck JB, Peterson JF, Geiersbach KB, Van Dyke DL, Thorland EC, Jenkins RB, Ketterling RP, Greipp PT, Kearney HM, Hoppman NL, Baughn LB. Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia. Eur J Haematol 2018; 102:87-96. [PMID: 30270457 PMCID: PMC7379948 DOI: 10.1111/ejh.13179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 07/03/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Acute myeloid leukemia (AML) can be subtyped based on recurrent cytogenetic and molecular genetic abnormalities with diagnostic and prognostic significance. Although cytogenetic characterization classically involves conventional chromosome and/or fluorescence in situ hybridization (FISH) assays, limitations of these techniques include poor resolution and the inability to precisely identify breakpoints. METHOD We evaluated whether an NGS-based methodology that detects structural abnormalities and copy number changes using mate pair sequencing (MPseq) can enhance the diagnostic yield for patients with AML. RESULTS Using 68 known abnormal and 20 karyotypically normal AML samples, each recurrent primary AML-specific abnormality previously identified in the abnormal samples was confirmed using MPseq. Importantly, in eight cases with abnormalities that could not be resolved by conventional cytogenetic studies, MPseq was utilized to molecularly define eight recurrent AML-fusion events. In addition, MPseq uncovered two cryptic abnormalities that were missed by conventional cytogenetic studies. Thus, MPseq improved the diagnostic yield in the detection of AML-specific structural rearrangements in 10/88 (11%) of cases analyzed. CONCLUSION Utilization of MPseq represents a precise, molecular-based technique that can be used as an alternative to conventional cytogenetic studies for newly diagnosed AML patients with the potential to revolutionize the diagnosis of hematologic malignancies.
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Beth A Pitel
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Roman M Zenka
- Bioinformatics Systems, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Katherine B Geiersbach
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Daniel L Van Dyke
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
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12
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Boczek NJ, Lahner CA, Nguyen TM, Ferber MJ, Hasadsri L, Thorland EC, Niu Z, Gavrilova RH. Developmental delay and failure to thrive associated with a loss-of-function variant in WHSC1 (NSD2). Am J Med Genet A 2018; 176:2798-2802. [PMID: 30345613 DOI: 10.1002/ajmg.a.40498] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/12/2018] [Accepted: 07/14/2018] [Indexed: 11/07/2022]
Abstract
Wolf-Hirschhorn syndrome (WHS) is a microdeletion syndrome characterized by distinctive facial features consisting of "Greek warrior helmet" appearance, prenatal and postnatal growth deficiency, developmental disability, and seizures. This disorder is caused by heterozygous deletions on chromosome 4p16.3 often identified by cytogenetic techniques. Many groups have attempted to identify the critical region within this deletion to establish which genes are responsible for WHS. Herein, clinical whole exome sequencing (WES) was performed on a child with developmental delays, mild facial dysmorphisms, short stature, failure to thrive, and microcephaly, and revealed a de novo frameshift variant, c.1676_1679del (p.Arg559Tfs*38), in WHSC1 (NSD2). While WHSC1 falls within the WHS critical region, individuals with only disruption of this gene have only recently been described in the literature. Loss-of-function de novo variations in WHSC1 were identified in large developmental delay, autism, diagnostic, and congenital cardiac cohorts, as well as recent case reports, suggesting that de novo loss-of-function WHSC1 variants may be related to disease. These findings, along with our patient suggest that loss-of-function variation in WHSC1 may lead to a mild form of Wolf-Hirschhorn syndrome, and also may suggest that the developmental delays, facial dysmorphisms, and short stature seen in WHS may be due to disruption of WHSC1 gene.
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Affiliation(s)
- Nicole J Boczek
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Thuy-Mi Nguyen
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Matthew J Ferber
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Zhiyv Niu
- Department of Laboratory Medicine and Pathology; Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Ralitza H Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota.,Department of Neurology, Mayo Clinic, Rochester, Minnesota
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13
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Thorland EC, Weinshenker BG, Liu JZ, Ketterling RP, Vielhaber EL, Kasper CK, Ambriz R, Paredes R, Sommer SS. Molecular Epidemiology of Factor IX Germline Mutations in Mexican Hispanics: Pattern of Mutation and Potential Founder Effects. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1649957] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryGermline mutations in patients with hemophilia B generally have arisen within the past 150 years. Evidence suggests that these germline mutations generally result from endogenous processes. However, a unique pattern would be expected if a population were exposed to a physiologically important germline mutagen since mutagens generally produce characteristic patterns, or “fingerprints”, of mutation. To determine the pattern of mutation in Mexican Hispanics, the regions of likely functional significance in the factor IX gene were screened by di-deoxy fingerprinting (ddF) in 31 families with hemophilia B. Mutations were found in 30 of these families. Haplotype analysis was performed on individuals with identical mutations to help distinguish independent, recurrent mutations from founder effects. Analysis of these 30 mutations, along with 7 mutations reported previously in Mexican Hispanic families, reveals a pattern of independent mutation that is similar to the pattern of mutation observed in 127 U. S. Caucasian families (p = 0.89). These results may reflect either an underlying pattern of germline mutation due to endogenous processes or the presence of an ubiquitous mutagen. Further analyses of the recurrent mutations revealed that two mutations, T296M and R248Q, accounted for 19% of the mutations found in the Mexicans. Haplotype data suggest that the multiple occurrences of T296M and R248Q are associated with founder effects and that screening for these mutations may allow rapid mutation detection and carrier diagnosis in a significant minority of Mexican families with hemophilia B. These two mutations also are associated with founder effects in the U. S. Caucasian population. However, the haplotypes are different in these two populations, indicating independent origins. The occurrence of identical founder mutations in distinct populations provides evidence for the previous hypothesis that the number of different mutations giving rise to mild or borderline mild/moderate hemophilia B is small compared to deleterious mutations causing more severe disease.
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Affiliation(s)
- Erik C Thorland
- The Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota, USA
| | - Brian G Weinshenker
- The Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota, USA
| | - Jing-zhong Liu
- The Institute of Basic Medical Science, Chinese Academy of Medical Science, Beijing, China
| | - Rhett P Ketterling
- The Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota, USA
| | - Erica L Vielhaber
- The Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota, USA
| | - Carol K Kasper
- The Orthopaedic Hospital, University of Southern California, Los Angeles, California, USA
| | - Raul Ambriz
- The Banco Central de Sangre del C. M. N. Siglo XXI, Mexico, DF
| | | | - Steve S Sommer
- The Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota, USA
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14
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Uddin M, Pellecchia G, Thiruvahindrapuram B, D'Abate L, Merico D, Chan A, Zarrei M, Tammimies K, Walker S, Gazzellone MJ, Nalpathamkalam T, Yuen RKC, Devriendt K, Mathonnet G, Lemyre E, Nizard S, Shago M, Joseph-George AM, Noor A, Carter MT, Yoon G, Kannu P, Tihy F, Thorland EC, Marshall CR, Buchanan JA, Speevak M, Stavropoulos DJ, Scherer SW. Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay. Sci Rep 2016; 6:28663. [PMID: 27363808 PMCID: PMC4929460 DOI: 10.1038/srep28663] [Citation(s) in RCA: 28] [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: 01/12/2016] [Accepted: 06/06/2016] [Indexed: 01/03/2023] Open
Abstract
A challenge in clinical genomics is to predict whether copy number variation (CNV) affecting a gene or multiple genes will manifest as disease. Increasing recognition of gene dosage effects in neurodevelopmental disorders prompted us to develop a computational approach based on critical-exon (highly expressed in brain, highly conserved) examination for potential etiologic effects. Using a large CNV dataset, our updated analyses revealed significant (P < 1.64 × 10−15) enrichment of critical-exons within rare CNVs in cases compared to controls. Separately, we used a weighted gene co-expression network analysis (WGCNA) to construct an unbiased protein module from prenatal and adult tissues and found it significantly enriched for critical exons in prenatal (P < 1.15 × 10−50, OR = 2.11) and adult (P < 6.03 × 10−18, OR = 1.55) tissues. WGCNA yielded 1,206 proteins for which we prioritized the corresponding genes as likely to have a role in neurodevelopmental disorders. We compared the gene lists obtained from critical-exon and WGCNA analysis and found 438 candidate genes associated with CNVs annotated as pathogenic, or as variants of uncertain significance (VOUS), from among 10,619 developmental delay cases. We identified genes containing CNVs previously considered to be VOUS to be new candidate genes for neurodevelopmental disorders (GIT1, MVB12B and PPP1R9A) demonstrating the utility of this strategy to index the clinical effects of CNVs.
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Affiliation(s)
- Mohammed Uddin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ada Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Neuropsychiatric Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew J Gazzellone
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Emmanuelle Lemyre
- CHU Sainte-Justine, University de Montreal, Montreal, Quebec, Canada
| | - Sonia Nizard
- CHU Sainte-Justine, University de Montreal, Montreal, Quebec, Canada
| | - Mary Shago
- Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ann M Joseph-George
- Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Abdul Noor
- Department of Pathology and Laboratory Medicine, Division of Diagnostic Medical Genetics, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Melissa T Carter
- Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 2L3, Canada
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 2L3, Canada
| | - Frédérique Tihy
- CHU Sainte-Justine, University de Montreal, Montreal, Quebec, Canada
| | - Erik C Thorland
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Janet A Buchanan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
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15
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Marcou CA, Halling G, Johnson SH, Smoley S, Pearce K, Vasmatzis G, Thorland EC, Aypar U, Hoppman NL. What's Next in Cytogenetics: Molecular Characterization of De Novo Apparently Balanced Chromosomal Rearrangements to Assess Pathogenicity by Whole Genome Mate Pair Sequencing. Cancer Genet 2016. [DOI: 10.1016/j.cancergen.2016.04.048] [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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16
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Porath B, Johnson SH, Smoley SA, Pitel B, Gliem T, Vasmatzis G, Kearney HM, Hoppman NL, Thorland EC. Molecular Characterization of Recurrent Partial Gene Duplications by Whole Genome Mate-Pair Sequencing (MPseq) to Improve the Accuracy of Chromosomal Microarray Reporting. Cancer Genet 2016. [DOI: 10.1016/j.cancergen.2016.04.051] [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: 11/25/2022]
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17
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Wang W, Wang C, Dawson DB, Thorland EC, Lundquist PA, Eckloff BW, Wu Y, Baheti S, Evans JM, Scherer SS, Dyck PJ, Klein CJ. Target-enrichment sequencing and copy number evaluation in inherited polyneuropathy. Neurology 2016; 86:1762-71. [PMID: 27164712 DOI: 10.1212/wnl.0000000000002659] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 01/05/2016] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To assess the efficiency of target-enrichment next-generation sequencing (NGS) with copy number assessment in inherited neuropathy diagnosis. METHODS A 197 polyneuropathy gene panel was designed to assess for mutations in 93 patients with inherited or idiopathic neuropathy without known genetic cause. We applied our novel copy number variation algorithm on NGS data, and validated the identified copy number mutations using CytoScan (Affymetrix). Cost and efficacy of this targeted NGS approach was compared to earlier evaluations. RESULTS Average coverage depth was ∼760× (median = 600, 99.4% > 100×). Among 93 patients, 18 mutations were identified in 17 cases (18%), including 3 copy number mutations: 2 PMP22 duplications and 1 MPZ duplication. The 2 patients with PMP22 duplication presented with bulbar and respiratory involvement and had absent extremity nerve conductions, leading to axonal diagnosis. Average onset age of these 17 patients was 25 years (2-61 years), vs 45 years for those without genetic discovery. Among those with onset age less than 40 years, the diagnostic yield of targeted NGS approach is high (27%) and cost savings is significant (∼20%). However, the cost savings for patients with late onset age and without family history is not demonstrated. CONCLUSIONS Incorporating copy number analysis in target-enrichment NGS approach improved the efficiency of mutation discovery for chronic, inherited, progressive length-dependent polyneuropathy diagnosis. The new technology is facilitating a simplified genetic diagnostic algorithm utilizing targeted NGS, clinical phenotypes, age at onset, and family history to improve diagnosis efficiency. Our findings prompt a need for updating the current practice parameters and payer guidelines.
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Affiliation(s)
- Wei Wang
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Chen Wang
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - D Brian Dawson
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Erik C Thorland
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Patrick A Lundquist
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Bruce W Eckloff
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Yanhong Wu
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Saurabh Baheti
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Jared M Evans
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Steven S Scherer
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Peter J Dyck
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Christopher J Klein
- From the Departments of Neurology, Peripheral Nerve Division (W.W., P.J.D., C.J.K.), Department of Health Science Research (C.W., S.B., J.M.E.), Laboratory Medicine and Pathology (D.B.D., E.C.T., P.A.L., Y.W., C.J.K.), Medical Genome Facility (B.W.E., Y.W.), and Medical Genetics (C.J.K., D.B.D.), Mayo Clinic, Rochester, MN; Department of Neurology (W.W.), China-Japan Friendship Hospital, Beijing, China; and Department of Neurology (S.S.S.), Perelman School of Medicine, University of Pennsylvania, Philadelphia.
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18
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Aypar U, Hoppman NL, Thorland EC, Dawson DB. Patients with mosaic methylation patterns of the Prader-Willi/Angelman Syndrome critical region exhibit AS-like phenotypes with some PWS features. Mol Cytogenet 2016; 9:26. [PMID: 27006693 PMCID: PMC4802915 DOI: 10.1186/s13039-016-0233-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 12/03/2015] [Accepted: 03/09/2016] [Indexed: 01/29/2023] Open
Abstract
Background Loss of expression of imprinted genes in the 15q11.2-q13 region is known to cause either Prader-Willi syndrome (PWS) or Angelman syndrome (AS), depending on the parent of origin. In some patients (1 % in PWS and 2–4 % in AS), the disease is due to aberrant imprinting or gene silencing, or both. Results We report here a 4-year-old boy on whom a chromosomal microarray (CMA) was performed due to mild hand tremors, mild developmental delays, and clumsiness. CMA revealed absence of heterozygosity (AOH) spanning the entire chromosome 15, suggesting uniparental isodisomy 15. The patient had no definitive phenotypic features of PWS or AS. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed to determine the parent of origin of the uniparental disomy (UPD) by examining methylation status at maternally imprinted sites. Interestingly, our patient had a mosaic methylation pattern. We identified nine additional previously tested patients with a similar mosaic methylation pattern. CMA was performed on these individuals retrospectively to test whether patients with mosaic methylation are more likely to have UPD of chromosome 15. Of the nine patients, only one had regions of AOH on chromosome 15; however, this patient had numerous regions of AOH on multiple chromosomes suggestive of consanguinity. Conclusion The patients with mosaic methylation had milder or atypical features of AS, and the majority also had some features characteristic of PWS. We suggest that quantitative methylation analysis be performed for cases of atypical PWS or AS. It is also important to follow up with methylation testing when whole-chromosome isodisomy is detected.
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - D Brian Dawson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
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19
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Lyon SM, Waggoner D, Halbach S, Thorland EC, Khorasani L, Reid RR. Syndromic craniosynostosis associated with microdeletion of chromosome 19p13.12-19p13.2. Genes Dis 2015; 2:347-352. [PMID: 26966713 PMCID: PMC4782977 DOI: 10.1016/j.gendis.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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] [Indexed: 11/27/2022] Open
Abstract
Craniosynostosis, a condition in which the cranial sutures prematurely fuse, can lead to elevated intracranial pressure and craniofacial abnormalities in young children. Currently surgical intervention is the only therapeutic option for patients with this condition. Craniosynostosis has been associated with a variety of different gene mutations and chromosome anomalies. Here we describe three cases of partial deletion of chromosome 19p. Two of the cases present with syndromic craniosynostosis while one has metopic ridging. A review of the genes involved in the rearrangements between the three cases suggests several gene candidates for craniosynostosis. CALR and DAND5, BMP regulators involved in osteoblast differentiation, and MORG1, a mediator of osteoclast dysregulation may play a role in abnormal cranial vault development. Additionally, CACNA1A, a gene that when mutated is associated with epilepsy and CC2D1A, a gene associated with non-syndromic mental retardation may contribute to additional phenotypic features seen in the patients we describe. In addition, these findings further support the need for genetic testing in cases of syndromic craniosynostosis.
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Affiliation(s)
- Sarah M Lyon
- Pritzker School of Medicine, University of Chicago
| | - Darrel Waggoner
- Department of Human Genetics and Pediatrics, University of Chicago, 5841 S. Maryland Ave, M/C 0077, Chicago, IL 60637
| | - Sara Halbach
- Department of Human Genetics and Pediatrics, University of Chicago, 5841 S. Maryland Ave, M/C 0077, Chicago, IL 60637
| | - Erik C Thorland
- Lab Medicine & Pathology, 200 First St SW, Hilton 970, Rochester, MN 55905-0001
| | - Leila Khorasani
- Department of Surgery, University of Chicago, 5841 S. Maryland Ave, M/C 0077, Chicago, IL 60637
| | - Russell R Reid
- Department of Surgery, University of Chicago, 5841 S. Maryland Ave, M/C 0077, Chicago, IL 60637
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20
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Cuturilo G, Hodge JC, Runke CK, Thorland EC, Al-Owain MA, Ellison JW, Babovic-Vuksanovic D. Phenotype analysis impacts testing strategy in patients with Currarino syndrome. Clin Genet 2015; 89:109-14. [PMID: 25691298 DOI: 10.1111/cge.12572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/12/2015] [Accepted: 02/12/2015] [Indexed: 12/11/2022]
Abstract
Currarino syndrome (OMIM 175450) presents with sacral, anorectal, and intraspinal anomalies and presacral meningocele or teratoma. Autosomal dominant loss-of-function mutations in the MNX1 gene cause nearly all familial and 30% of sporadic cases. Less frequently, a complex phenotype of Currarino syndrome can be caused by microdeletions of 7q containing MNX1. Here, we report one familial and three sporadic cases of Currarino syndrome. To determine the most efficient genetic testing approach for these patients, we have compared results from MNX1 sequencing, chromosomal microarray, and performed a literature search with analysis of genotype-phenotype correlation. Based on the relationship between the type of mutation (intragenic MNX1 mutations vs 7q microdeletion) and the presence of intellectual disability, growth retardation, facial dysmorphism, and associated malformations, we propose a testing algorithm. Patients with the classic Currarino triad of malformations but normal growth, intellect, and facial appearance should have MNX1 sequencing first, and only in the event of a normal result should the clinician proceed with chromosomal microarray testing. In contrast, if growth delay and/or facial dysmorphy and/or intellectual disability are present, chromosomal microarray should be the first method of choice for genetic testing.
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Affiliation(s)
- G Cuturilo
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Department of Medical Genetics, University Children's Hospital, Belgrade, Serbia
| | - J C Hodge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - C K Runke
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - E C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - M A Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - J W Ellison
- Department of Genetics, Kaiser Permanente Medical Center, San Francisco, CA, USA
| | - D Babovic-Vuksanovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Department of Medical Genetics, Mayo Clinic, Rochester, MN, USA
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21
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Vasmatzis G, Feldman AL, Johnson SH, Thorland EC, Fonseca R, Braggio E, Gliem TJ. Abstract 3572: Copy number detection using genomics technologies: A comparison between aCGH and NGS. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3572] [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: 11/16/2022]
Abstract
Abstract
Introduction: Identification of causal DNA copy number variations (CNVs) is critical to the understanding of cancer development and progression, and is important clinically for accurate prognosis and efficient treatment. T-cell lymphomas are replete with amplifications and deletions that result in over- and under-expression of genes. Array comparative genomic hybridization (aCGH) has been the technology of choice to detect CNVs but recently, it has been proposed that mate-pair Next Generation Sequencing (mpNGS) can produce similar results. Here, we report a comparison between the two techniques.
Methods: We have developed an algorithm based on extreme value theory to identify CNVs across the genome at high resolution from mate-pair NGS data. The algorithm is based on plotting the distribution of read-counts in windows across the genome, and detecting deletions and gains by finding the windows that differ significantly from the distribution of the normal part of the genome. We compared this algorithm with aCGH data to detect CNVs. We ran five cases of T-cell lymphoma with both techniques and compared the results using concordance statistics.
Results: With 50kb lower cutoff for a CNV, mpNGS detected 98% of the cumulative deleted genome and 94% of the amplified/gained genome that were called by aCGH. Most of the discordant CNVs that were detected by only aCGH were in regions of repetitive areas where mapping fails. Conversely, aCGH detected 75% of the cumulative deleted genome and 74% of the amplified/gained genome that were called by mpNGS.
Conclusion: A detailed comparison of these techniques showed that both have pros and cons. In general, mpNGS can detect most CNVs detected by aCGH, as long as they are more than 50KB. Additionally, mpNGS offers confirmatory data, particularly for deletions, based on detection of aberrant mate pairs that map to the rejoined ends of deleted regional. Finally, the mate-pair technology can also detect balanced translocations and can also predict fusion genes.
Citation Format: George Vasmatzis, Andrew L. Feldman, Sarah H. Johnson, Erik C. Thorland, Rafael Fonseca, Esteban Braggio, Troy J. Gliem. Copy number detection using genomics technologies: A comparison between aCGH and NGS. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3572. doi:10.1158/1538-7445.AM2014-3572
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22
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Aypar U, Brodersen PR, Lundquist PA, Dawson DB, Thorland EC, Hoppman N. Does parent of origin matter? Methylation studies should be performed on patients with multiple copies of the Prader-Willi/Angelman syndrome critical region. Am J Med Genet A 2014; 164A:2514-20. [DOI: 10.1002/ajmg.a.36663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 05/22/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Umut Aypar
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - Pamela R. Brodersen
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - Patrick A. Lundquist
- Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - D. Brian Dawson
- Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - Erik C. Thorland
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - Nicole Hoppman
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
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23
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Goldlust IS, Hermetz KE, Catalano LM, Barfield RT, Cozad R, Wynn G, Ozdemir AC, Conneely KN, Mulle JG, Dharamrup S, Hegde MR, Kim KH, Angle B, Colley A, Webb AE, Thorland EC, Ellison JW, Rosenfeld JA, Ballif BC, Shaffer LG, Demmer LA, Rudd MK. Mouse model implicates GNB3 duplication in a childhood obesity syndrome. Proc Natl Acad Sci U S A 2013; 110:14990-4. [PMID: 23980137 PMCID: PMC3773733 DOI: 10.1073/pnas.1305999110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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] [Indexed: 12/13/2022] Open
Abstract
Obesity is a highly heritable condition and a risk factor for other diseases, including type 2 diabetes, cardiovascular disease, hypertension, and cancer. Recently, genomic copy number variation (CNV) has been implicated in cases of early onset obesity that may be comorbid with intellectual disability. Here, we describe a recurrent CNV that causes a syndrome associated with intellectual disability, seizures, macrocephaly, and obesity. This unbalanced chromosome translocation leads to duplication of over 100 genes on chromosome 12, including the obesity candidate gene G protein β3 (GNB3). We generated a transgenic mouse model that carries an extra copy of GNB3, weighs significantly more than its wild-type littermates, and has excess intraabdominal fat accumulation. GNB3 is highly expressed in the brain, consistent with G-protein signaling involved in satiety and/or metabolism. These functional data connect GNB3 duplication and overexpression to elevated body mass index and provide evidence for a genetic syndrome caused by a recurrent CNV.
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Affiliation(s)
- Ian S. Goldlust
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Karen E. Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Lisa M. Catalano
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Rebecca Cozad
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Grace Wynn
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Alev Cagla Ozdemir
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Karen N. Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Departments of Biostatistics and Bioinformatics and
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Epidemiology, Emory University School of Public Health, Atlanta, GA 30322
| | - Shikha Dharamrup
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Madhuri R. Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Katherine H. Kim
- Division of Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614
| | - Brad Angle
- Division of Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614
| | - Alison Colley
- Department of Clinical Genetics, South Western Sydney Local Health District, Liverpool, NSW 1871, Australia
| | - Amy E. Webb
- Amy E. Webb Pediatrics, Pismo Beach, CA 93449
| | - Erik C. Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Jay W. Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Blake C. Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Lisa G. Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Laurie A. Demmer
- Division of Genetics and Metabolism, Tufts University School of Medicine, Boston, MA 02111; and
| | | | - M. Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
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24
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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25
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Banck MS, Kanwar R, Kulkarni AA, Boora GK, Metge F, Kipp BR, Zhang L, Thorland EC, Minn KT, Tentu R, Eckloff BW, Wieben ED, Wu Y, Cunningham JM, Nagorney DM, Gilbert JA, Ames MM, Beutler AS. The genomic landscape of small intestine neuroendocrine tumors. J Clin Invest 2013; 123:2502-8. [PMID: 23676460 DOI: 10.1172/jci67963] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/22/2013] [Indexed: 12/12/2022] Open
Abstract
Small intestine neuroendocrine tumors (SI-NETs) are the most common malignancy of the small bowel. Several clinical trials target PI3K/Akt/mTOR signaling; however, it is unknown whether these or other genes are genetically altered in these tumors. To address the underlying genetics, we analyzed 48 SI-NETs by massively parallel exome sequencing. We detected an average of 0.1 somatic single nucleotide variants (SNVs) per 106 nucleotides (range, 0-0.59), mostly transitions (C>T and A>G), which suggests that SI-NETs are stable cancers. 197 protein-altering somatic SNVs affected a preponderance of cancer genes, including FGFR2, MEN1, HOOK3, EZH2, MLF1, CARD11, VHL, NONO, and SMAD1. Integrative analysis of SNVs and somatic copy number variations identified recurrently altered mechanisms of carcinogenesis: chromatin remodeling, DNA damage, apoptosis, RAS signaling, and axon guidance. Candidate therapeutically relevant alterations were found in 35 patients, including SRC, SMAD family genes, AURKA, EGFR, HSP90, and PDGFR. Mutually exclusive amplification of AKT1 or AKT2 was the most common event in the 16 patients with alterations of PI3K/Akt/mTOR signaling. We conclude that sequencing-based analysis may provide provisional grouping of SI-NETs by therapeutic targets or deregulated pathways.
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Affiliation(s)
- Michaela S Banck
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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26
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McDonnell SK, Riska SM, Klee EW, Thorland EC, Kay NE, Thibodeau SN, Parker AS, Eckel-Passow JE. Experimental designs for array comparative genomic hybridization technology. Cytogenet Genome Res 2013; 139:250-7. [PMID: 23548696 DOI: 10.1159/000348815] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2012] [Indexed: 01/31/2023] Open
Abstract
Array comparative genomic hybridization (aCGH) technology is commonly used to estimate genome-wide copy-number variation and to evaluate associations between copy number and disease. Although aCGH technology is well developed and there are numerous algorithms available for estimating copy number, little attention has been paid to the important issue of the statistical experimental design. Herein, we review classical statistical experimental designs and discuss their relevance to aCGH technology as well as their importance for downstream statistical analyses. Furthermore, we provide experimental design guidance for various study objectives.
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Affiliation(s)
- S K McDonnell
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minn 55905, USA
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27
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DeScipio C, Conlin L, Rosenfeld J, Tepperberg J, Pasion R, Patel A, McDonald MT, Aradhya S, Ho D, Goldstein J, McGuire M, Mulchandani S, Medne L, Rupps R, Serrano AH, Thorland EC, Tsai ACH, Hilhorst-Hofstee Y, Ruivenkamp CAL, Van Esch H, Addor MC, Martinet D, Mason TBA, Clark D, Spinner NB, Krantz ID. Subtelomeric deletion of chromosome 10p15.3: clinical findings and molecular cytogenetic characterization. Am J Med Genet A 2012; 158A:2152-61. [PMID: 22847950 DOI: 10.1002/ajmg.a.35574] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 06/28/2012] [Indexed: 11/06/2022]
Abstract
We describe 19 unrelated individuals with submicroscopic deletions involving 10p15.3 characterized by chromosomal microarray (CMA). Interestingly, to our knowledge, only two individuals with isolated, submicroscopic 10p15.3 deletion have been reported to date; however, only limited clinical information is available for these probands and the deleted region has not been molecularly mapped. Comprehensive clinical history was obtained for 12 of the 19 individuals described in this study. Common features among these 12 individuals include: cognitive/behavioral/developmental differences (11/11), speech delay/language disorder (10/10), motor delay (10/10), craniofacial dysmorphism (9/12), hypotonia (7/11), brain anomalies (4/6) and seizures (3/7). Parental studies were performed for nine of the 19 individuals; the 10p15.3 deletion was de novo in seven of the probands, not maternally inherited in one proband and inherited from an apparently affected mother in one proband. Molecular mapping of the 19 individuals reported in this study has identified two genes, ZMYND11 (OMIM 608668) and DIP2C (OMIM 611380; UCSC Genome Browser), mapping within 10p15.3 which are most commonly deleted. Although no single gene has been identified which is deleted in all 19 individuals studied, the deleted region in all but one individual includes ZMYND11 and the deleted region in all but one other individual includes DIP2C. There is not a clearly identifiable phenotypic difference between these two individuals and the size of the deleted region does not generally predict clinical features. Little is currently known about these genes complicating a direct genotype/phenotype correlation at this time. These data however, suggest that ZMYND11 and/or DIP2C haploinsufficiency contributes to the clinical features associated with 10p15 deletions in probands described in this study.
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Affiliation(s)
- Cheryl DeScipio
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S, Kearney HM, Ledbetter DH, South ST, Thorland EC, Martin CL. Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet 2011; 81:403-12. [PMID: 22097934 DOI: 10.1111/j.1399-0004.2011.01818.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The evidence-based review (EBR) process has been widely used to develop standards for medical decision-making and to explore complex clinical questions. This approach can be applied to genetic tests, such as chromosomal microarrays, in order to assist in the clinical interpretation of certain copy number variants (CNVs), particularly those that are rare, and guide array design for optimal clinical utility. To address these issues, the International Standards for Cytogenomic Arrays Consortium has established an EBR Work Group charged with building a framework to systematically assess the potential clinical relevance of CNVs throughout the genome. This group has developed a rating system enumerating the evidence supporting or refuting dosage sensitivity for individual genes and regions that considers the following criteria: number of causative mutations reported; patterns of inheritance; consistency of phenotype; evidence from large-scale case-control studies; mutational mechanisms; data from public genome variation databases; and expert consensus opinion. The system is designed to be dynamic in nature, with regions being reevaluated periodically to incorporate emerging evidence. The evidence collected will be displayed within a publically available database, and can be used in part to inform clinical laboratory CNV interpretations as well as to guide array design.
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Affiliation(s)
- E R Riggs
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 2011; 13:680-5. [PMID: 21681106 DOI: 10.1097/gim.0b013e3182217a3a] [Citation(s) in RCA: 655] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genomic microarrays used to assess DNA copy number are now recommended as first-tier tests for the postnatal evaluation of individuals with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. Application of this technology has resulted in the discovery of widespread copy number variation in the human genome, both polymorphic variation in healthy individuals and novel pathogenic copy number imbalances. To assist clinical laboratories in the evaluation of copy number variants and to promote consistency in interpretation and reporting of genomic microarray results, the American College of Medical Genetics has developed the following professional guidelines for the interpretation and reporting of copy number variation. These guidelines apply primarily to evaluation of constitutional copy number variants detected in the postnatal setting.
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Affiliation(s)
- Hutton M Kearney
- Fullerton Genetics Center, Mission Health System, 267 McDowell St., Asheville, NC 28803, USA.
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Moreno-De-Luca D, Mulle JG, Kaminsky EB, Sanders SJ, Myers SM, Adam MP, Pakula AT, Eisenhauer NJ, Uhas K, Weik L, Guy L, Care ME, Morel CF, Boni C, Salbert BA, Chandrareddy A, Demmer LA, Chow EW, Surti U, Aradhya S, Pickering DL, Golden DM, Sanger WG, Aston E, Brothman AR, Gliem TJ, Thorland EC, Ackley T, Iyer R, Huang S, Barber JC, Crolla JA, Warren ST, Martin CL, Ledbetter DH. Deletion 17q12 Is a Recurrent Copy Number Variant that Confers High Risk of Autism and Schizophrenia. Am J Hum Genet 2011. [DOI: 10.1016/j.ajhg.2010.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Babovic N, Simmons PS, Moir C, Thorland EC, Scheithauer B, Gliem TJ, Babovic-Vuksanovic D. Mucinous cystadenoma of ovary in a patient with juvenile polyposis due to 10q23 microdeletion: expansion of phenotype. Am J Med Genet A 2010; 152A:2623-7. [PMID: 20815035 DOI: 10.1002/ajmg.a.33637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Juvenile polyposis syndrome (JPS) is a hereditary condition characterized by development of gastrointestinal polyps, and caused by mutations in SMAD4 or BMPR1A genes. Juvenile polyps can also be found in a related group of syndromes with multisystemic involvement including Cowden disease, Lhermitte-Duclos disease, Bannayan-Riley-Ruvalcaba syndrome, and Proteus-like syndrome, all grouped as PTEN hamartoma tumor syndromes (PHTS). In all these conditions including JPS, polyps manifest in older childhood or early adulthood. Infantile juvenile polyposis (JPI) is a rare entity, presenting in the first year of life with severe gastrointestinal symptoms. Many of these patients have associated macrocephaly, hypotonia, and congenital anomalies. It was recently recognized that patients with infantile polyposis have a 10q23 microdeletion, involving both BMPR1A and PTEN genes. There is a major risk for gastrointestinal malignancies in these patients, but the risk for development of other tumors is not known. We describe a patient with a history of infantile polyposis, macrocephaly, developmental delay, hypotonia, and a 10q23 microdeletion. At age 14 she presented with bilateral mucinous cystadenoma of the ovary. This type of tumor was not previously reported in association with JPS, 10q23 microdeletion syndrome, or infantile polyposis. We believe that ovarian cystadenomas may be another neoplastic complication of infantile polyposis, and that our report widens the spectrum of the 10q23 microdeletion phenotype.
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Affiliation(s)
- Nikola Babovic
- Mayo Medical School, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.
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Moreno-De-Luca D, Mulle JG, Kaminsky EB, Sanders SJ, Myers SM, Adam MP, Pakula AT, Eisenhauer NJ, Uhas K, Weik L, Guy L, Care ME, Morel CF, Boni C, Salbert BA, Chandrareddy A, Demmer LA, Chow EW, Surti U, Aradhya S, Pickering DL, Golden DM, Sanger WG, Aston E, Brothman AR, Gliem TJ, Thorland EC, Ackley T, Iyer R, Huang S, Barber JC, Crolla JA, Warren ST, Martin CL, Ledbetter DH, Warren ST, Martin CL, Ledbetter DH. Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia. Am J Hum Genet 2010; 87:618-30. [PMID: 21055719 DOI: 10.1016/j.ajhg.2010.10.004] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 09/23/2010] [Accepted: 10/07/2010] [Indexed: 01/17/2023] Open
Abstract
Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻⁵). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.
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Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010; 86:749-64. [PMID: 20466091 PMCID: PMC2869000 DOI: 10.1016/j.ajhg.2010.04.006] [Citation(s) in RCA: 1798] [Impact Index Per Article: 128.4] [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: 02/15/2010] [Revised: 04/12/2010] [Accepted: 04/19/2010] [Indexed: 12/11/2022] Open
Abstract
Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.
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Affiliation(s)
- David T. Miller
- Division of Genetics and Department of Laboratory Medicine, Children's Hospital Boston and Harvard Medical School, Boston, MA, USA
| | - Margaret P. Adam
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Leslie G. Biesecker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arthur R. Brothman
- Department of Pediatrics, Human Genetics, Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Deanna M. Church
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - John A. Crolla
- National Genetics Reference Laboratory (Wessex), Salisbury UK
| | - Evan E. Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Charles J. Epstein
- Institute for Human Genetics and Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - W. Andrew Faucett
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lars Feuk
- Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, and Child & Family Research Institute, Vancouver, British Columbia, Canada
| | - Ada Hamosh
- Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laird Jackson
- Department of Obstetrics and Gynecology, Drexel University College of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin B. Kaminsky
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Klaas Kok
- Department of Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands
| | - Ian D. Krantz
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James M. Ostell
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, University Sao Paulo, Brazil
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genetic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Nancy B. Spinner
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Erik C. Thorland
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Darrel J. Waggoner
- Department of Human Genetics and Pediatrics, University of Chicago, Chicago, IL, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David H. Ledbetter
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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Dewald GW, Smyrk TC, Thorland EC, McWilliams RR, Van Dyke DL, Keefe JG, Belongie KJ, Smoley SA, Knutson DL, Fink SR, Wiktor AE, Petersen GM. Fluorescence in situ hybridization to visualize genetic abnormalities in interphase cells of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas. Mayo Clin Proc 2009; 84:801-10. [PMID: 19720778 PMCID: PMC2735430 DOI: 10.1016/s0025-6196(11)60490-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To use fluorescence in situ hybridization (FISH) to visualize genetic abnormalities in interphase cell nuclei (interphase FISH) of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas. PATIENTS AND METHODS Between April 4, 2007, and December 4, 2008, interphase FISH was used to study paraffin-embedded preparations of tissue obtained from 18 patients listed in the Mayo Clinic Biospecimen Resource for Pancreas Research with a confirmed diagnosis of acinar cell carcinoma, ductal adenocarcinoma, islet cell carcinoma, or pancreas without evidence of neoplasia. FISH probes were used for chromosome loci of APC (see glossary at end of article for expansion of all gene symbols), BRCA2, CTNNB1, EGFR, ERBB2, CDKN2A, TP53, TYMP, and TYMS. These FISH probes were used with control probes to distinguish among various kinds of chromosome abnormalities of number and structure. RESULTS FISH abnormalities were observed in 12 (80%) of 15 patients with pancreatic cancer: 5 of 5 patients with acinar cell carcinoma, 5 of 5 patients with ductal adenocarcinoma, and 2 (40%) of 5 patients with islet cell carcinoma. All 3 specimens of pancreatic tissue without neoplasia had normal FISH results. Gains of CTNNB1 due to trisomy 3 occurred in each tumor with acinar cell carcinoma but in none of the other tumors in this study. FISH abnormalities of all other cancer genes studied were observed in all forms of pancreatic tumors in this investigation. CONCLUSION FISH abnormalities of CTNNB1 due to trisomy 3 were observed only in acinar cell carcinoma. FISH abnormalities of genes implicated in familial cancer, tumor progression, and the 5-fluorouracil pathway were common but were not associated with specific types of pancreatic cancer.
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Affiliation(s)
- Gordon W Dewald
- Division of Laboratory Genetics, Mayo Clinic, Rochester, MN 55905, USA.
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35
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Dewald GW, Smyrk TC, Thorland EC, McWilliams RR, Van Dyke DL, Keefe JG, Belongie KJ, Smoley SA, Knutson DL, Fink SR, Wiktor AE, Petersen GM. Fluorescence in situ hybridization to visualize genetic abnormalities in interphase cells of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas. Mayo Clin Proc 2009; 84:801-10. [PMID: 19720778 PMCID: PMC2735430 DOI: 10.4065/84.9.801] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
OBJECTIVE To use fluorescence in situ hybridization (FISH) to visualize genetic abnormalities in interphase cell nuclei (interphase FISH) of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas. PATIENTS AND METHODS Between April 4, 2007, and December 4, 2008, interphase FISH was used to study paraffin-embedded preparations of tissue obtained from 18 patients listed in the Mayo Clinic Biospecimen Resource for Pancreas Research with a confirmed diagnosis of acinar cell carcinoma, ductal adenocarcinoma, islet cell carcinoma, or pancreas without evidence of neoplasia. FISH probes were used for chromosome loci of APC (see glossary at end of article for expansion of all gene symbols), BRCA2, CTNNB1, EGFR, ERBB2, CDKN2A, TP53, TYMP, and TYMS. These FISH probes were used with control probes to distinguish among various kinds of chromosome abnormalities of number and structure. RESULTS FISH abnormalities were observed in 12 (80%) of 15 patients with pancreatic cancer: 5 of 5 patients with acinar cell carcinoma, 5 of 5 patients with ductal adenocarcinoma, and 2 (40%) of 5 patients with islet cell carcinoma. All 3 specimens of pancreatic tissue without neoplasia had normal FISH results. Gains of CTNNB1 due to trisomy 3 occurred in each tumor with acinar cell carcinoma but in none of the other tumors in this study. FISH abnormalities of all other cancer genes studied were observed in all forms of pancreatic tumors in this investigation. CONCLUSION FISH abnormalities of CTNNB1 due to trisomy 3 were observed only in acinar cell carcinoma. FISH abnormalities of genes implicated in familial cancer, tumor progression, and the 5-fluorouracil pathway were common but were not associated with specific types of pancreatic cancer.
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Affiliation(s)
- Gordon W Dewald
- Division of Laboratory Genetics, Mayo Clinic, Rochester, MN 55905, USA.
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Mefford HC, Cooper GM, Zerr T, Smith JD, Baker C, Shafer N, Thorland EC, Skinner C, Schwartz CE, Nickerson DA, Eichler EE. A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Res 2009; 19:1579-85. [PMID: 19506092 DOI: 10.1101/gr.094987.109] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Copy-number variants (CNVs) are substantial contributors to human disease. A central challenge in CNV-disease association studies is to characterize the pathogenicity of rare and possibly incompletely penetrant events, which requires the accurate detection of rare CNVs in large numbers of individuals. Cost and throughput issues limit our ability to perform these studies. We have adapted the Illumina BeadXpress SNP genotyping assay and developed an algorithm, SNP-Conditional OUTlier detection (SCOUT), to rapidly and accurately detect both rare and common CNVs in large cohorts. This approach is customizable, cost effective, highly parallelized, and largely automated. We applied this method to screen 69 loci in 1105 children with unexplained intellectual disability, identifying pathogenic variants in 3.1% of these individuals and potentially pathogenic variants in an additional 2.3%. We identified seven individuals (0.7%) with a deletion of 16p11.2, which has been previously associated with autism. Our results widen the phenotypic spectrum of these deletions to include intellectual disability without autism. We also detected 1.65-3.4 Mbp duplications at 16p13.11 in 1.1% of affected individuals and 350 kbp deletions at 15q11.2, near the Prader-Willi/Angelman syndrome critical region, in 0.8% of affected individuals. Compared to published CNVs in controls they are significantly (P = 4.7 x 10(-5) and 0.003, respectively) enriched in these children, supporting previously published hypotheses that they are neurocognitive disease risk factors. More generally, this approach offers a previously unavailable balance between customization, cost, and throughput for analysis of CNVs and should prove valuable for targeted CNV detection in both research and diagnostic settings.
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Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
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Tefferi A, Sirhan S, Sun Y, Lasho T, Finke CM, Weisberger J, Bale S, Compton J, LeDuc CA, Pardanani A, Thorland EC, Shevchenko Y, Grodman M, Chung WK. Oligonucleotide array CGH studies in myeloproliferative neoplasms: Comparison with JAK2V617F mutational status and conventional chromosome analysis. Leuk Res 2009; 33:662-4. [DOI: 10.1016/j.leukres.2008.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 11/27/2022]
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Feldman AL, Law M, Grogg KL, Thorland EC, Fink S, Kurtin PJ, Macon WR, Remstein ED, Dogan A. Incidence of TCR and TCL1 gene translocations and isochromosome 7q in peripheral T-cell lymphomas using fluorescence in situ hybridization. Am J Clin Pathol 2008; 130:178-85. [PMID: 18628085 DOI: 10.1309/pnxuka1cfjmvgcn1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Translocations involving the T-cell receptor (TCR) and TCL1 genes occur in T-cell precursor lymphoblastic leukemia/lymphoma and prolymphocytic leukemia; isochromosome 7q has been associated with hepatosplenic T-cell lymphoma. However, the incidence of these abnormalities in peripheral T-cell lymphomas (PTCLs) as a whole has not been well defined. We studied genetic abnormalities in 124 PTCLs seen at the Mayo Clinic, Rochester, MN, between 1987 and 2007. Tissue microarrays were screened using 2-color break-apart fluorescence in situ hybridization probes flanking the TCRalpha (TCRA, 14q11), TCRbeta (TCRB, 7q35), and TCRgamma (TCRG, 7p15) genes and the TCL1 gene (14q32). Isochromosome 7q was analyzed by using a 2-color probe to 7p and 7q32.1. Translocations involved TCRA in 3 (2.9%) of 102 cases and TCRB in 1 (1%) of 88. Isochromosome 7q was detected in 2 cases of extranodal NK/T-cell lymphoma, nasal type, and 2 cases of anaplastic lymphoma kinase-negative anaplastic large cell lymphoma. One of the latter cases also had a translocation of TCRA, and further studies confirmed a novel t(5;14) translocation.
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Sekulic A, Haluska P, Miller AJ, Genebriera De Lamo J, Ejadi S, Pulido JS, Salomao DR, Thorland EC, Vile RG, Swanson DL, Pockaj BA, Laman SD, Pittelkow MR, Markovic SN. Malignant melanoma in the 21st century: the emerging molecular landscape. Mayo Clin Proc 2008; 83:825-46. [PMID: 18613999 PMCID: PMC2739389 DOI: 10.4065/83.7.825] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Malignant melanoma presents a substantial clinical challenge. Current diagnostic methods are limited in their ability to diagnose early disease and accurately predict individual risk of disease progression and outcome. The lack of adequate approaches to properly define disease subgroups precludes rational treatment design and selection. Better tools are urgently needed to provide more accurate and personalized melanoma patient management. Recent progress in the understanding of the molecular aberrations that underlie melanoma oncogenesis will likely advance the diagnosis, prognosis, and treatment of melanoma. The emerging pattern of molecular complexity in melanoma tumors mirrors the clinical diversity of the disease and highlights the notion that melanoma, like other cancers, is not a single disease but a heterogeneous group of disorders that arise from complex molecular changes. Understanding of molecular aberrations involving important cellular processes, such as cellular signaling networks, cell cycle regulation, and cell death, will be essential for better diagnosis, accurate assessment of prognosis, and rational design of effective therapeutics. Defining an individual patient's unique tumor characteristics may lead to personalized prediction of outcomes and selection of therapy. We review the emerging molecular landscape of melanoma and its implications for better management of patients with melanoma.
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Thorland EC, Gonzales PR, Gliem TJ, Wiktor AE, Ketterling RP. Comprehensive validation of array comparative genomic hybridization platforms: how much is enough? Genet Med 2007; 9:632-41. [PMID: 17873652 DOI: 10.1097/gim.0b013e31814629fc] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Clinical testing using various array comparative genomic hybridization platforms is being incorporated rapidly into cytogenetic testing algorithms. Comprehensive validation of these complex assays presents unique challenges and very few studies reporting the validation of commercially available array platforms have been published. Sixty-seven patients with previously defined subtelomere abnormalities, representing deletions and/or duplications of all 41 clinically relevant sites, were tested in a blinded study using the Spectral Genomics Constitutional Chip 3.0. Overall, 72 of 74 (97%) subtelomeric abnormalities were concordant with previous cytogenetic studies. However, two false-negative results were documented, and issues with mismapped and suboptimal clone performance were identified that may result in failure to detect 6q and 20q subtelomeric abnormalities. The results of this study indicate that comprehensive validation is necessary before implementation of array comparative genomic hybridization platforms into a clinical setting. Specific suggestions for validation are discussed in the context of the recently proposed American College of Medical Genetics guidelines for microarray analysis for constitutional cytogenetic abnormalities.
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Affiliation(s)
- Erik C Thorland
- Cytogenetics Laboratory, Division of Laboratory Genetics, Department of Laboratory Genetics and Pathology, Mayo Clinic, 200 First St. SW, Rochester, Minnesota, USA.
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Shearer BM, Thorland EC, Gonzales PR, Ketterling RP. Evaluation of a commercially available focused aCGH platform for the detection of constitutional chromosome anomalies. Am J Med Genet A 2007; 143A:2357-70. [PMID: 17853469 DOI: 10.1002/ajmg.a.31954] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microarray-based comparative genomic hybridization (aCGH) allows for simultaneous high-resolution analysis of multiple genomic loci. Recently, focused aCGH platforms have emerged allowing for analysis of numerous clinically relevant chromosome loci. The purpose of our study was to evaluate the Spectral Genomics Constitutional Chip 1.0 (CC) for use in the clinical laboratory. The CC consisted of 429 BAC clones for 41 known genetic deletion/duplication syndromes, subtelomeric regions, and chromosomal backbone clones. We conducted a blinded study of 48 samples including 46 patients (one sample was run in triplicate) with previously determined constitutional chromosome anomalies and two negative controls. Patient samples included 31 microdeletions, four duplications, three derivative chromosomes, three trisomies, and five sex chromosome aneuploidies. Our results show that the CC identified the expected gains and/or losses in 46 of 48 samples. The two negative controls were considered to be normal and the three replicates of the same patient sample were concordant. Two samples yielded false-negative results; however, repeat analysis produced acceptable results for one of them. One sample ultimately had an insufficient amount of DNA precluding aCGH analysis. While promising, the results suggest that further studies are needed to reduce protocol variability and to establish standard analysis and interpretation criteria. Further, this study verifies the importance of extensive validation studies prior to clinical implementation of new clinically available methodologies.
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Affiliation(s)
- Brandon M Shearer
- Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
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Klein RD, Thorland EC, Gonzales PR, Beck PA, Dykas DJ, McGrath JM, Bale AE. A multiplex assay for the detection and mapping of complex glycerol kinase deficiency. Clin Chem 2006; 52:1864-70. [PMID: 16887896 DOI: 10.1373/clinchem.2006.072397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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] [Indexed: 11/06/2022]
Abstract
BACKGROUND Glycerol kinase deficiency (GKD) is an X-linked recessive disorder that presents in both isolated and complex forms. The contiguous deletion that leads to GKD also commonly affects NR0B1 (DAX1), the gene associated with adrenal hypoplasia congenita, and DMD, the Duchenne muscular dystrophy gene. Molecular testing to delineate this deletion is expensive and has only limited availability. METHODS We designed a multiplex PCR assay for the detection and mapping of a contiguous deletion potentially affecting the IL1RAPL1, NR0B1, GK, and DMD genes in a 29-month-old male patient with GKD. RESULTS Multiplex PCR detected a contiguous deletion that involved the IL1RAPL1, NR0B1, GK, and DMD genes. Although the patient had a creatine kinase concentration within the reference interval, further mapping with PCR revealed that exon 74 was the last intact exon at the 3' end of the DMD gene. CONCLUSIONS Multiplex PCR is an effective and inexpensive way to detect and map the contiguous deletion in cases of complex GKD. The extension of a deletion to include DMD exon 75 in a patient with a creatine kinase concentration within the reference interval suggests that this region of the gene may not be essential for protein function.
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Affiliation(s)
- Roger D Klein
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55901, USA.
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Fink SR, Smoley SA, Stockero KJ, Paternoster SF, Thorland EC, Van Dyke DL, Shanafelt TD, Zent CS, Call TG, Kay NE, Dewald GW. Loss of TP53 is due to rearrangements involving chromosome region 17p10 approximately p12 in chronic lymphocytic leukemia. ACTA ACUST UNITED AC 2006; 167:177-81. [PMID: 16737921 DOI: 10.1016/j.cancergencyto.2006.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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: 12/20/2005] [Accepted: 01/20/2006] [Indexed: 11/22/2022]
Abstract
Loss of tumor protein 53 (TP53) has been associated with aggressive disease and poor response to therapy in B-cell chronic lymphocytic leukemia (B-CLL). TP53 is located at chromosome band 17p13 and its absence can be detected by fluorescence in situ hybridization (FISH) in the interphase nuclei of 8-10% patients with B-CLL. To study the cytogenetic mechanism for loss of TP53, metaphase and interphase FISH studies were conducted on 16 B-CLL patients to investigate 17p10 to 17p12, a chromosome region known to be rich in low-copy DNA repeats. Loss of TP53 was caused by an isochromosome with breakpoints between 17p10 and 17p11.2 in four patients, an unbalanced translocation involving 17p10 to 17p11.2 in nine patients, and an unbalanced translocation involving 17p11.2 to 17p12 in three patients. These findings indicate that loss of TP53 results from the absence of nearly the entire chromosome 17 p-arm rather than to monosomy 17 or deletions of TP53. Translocations or isochromosome formations at sites of low-copy DNA repeats in 17p10 to 17p12 appear to be the mechanism for the loss of TP53 in B-CLL.
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Affiliation(s)
- Stephanie R Fink
- Cytogenetics Laboratory, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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Wiktor AE, Van Dyke DL, Stupca PJ, Ketterling RP, Thorland EC, Shearer BM, Fink SR, Stockero KJ, Majorowicz JR, Dewald GW. Preclinical validation of fluorescence in situ hybridization assays for clinical practice. Genet Med 2006; 8:16-23. [PMID: 16418595 DOI: 10.1097/01.gim.0000195645.00446.61] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Validation of fluorescence in situ hybridization assays is required before using them in clinical practice. Yet, there are few published examples that describe the validation process, leading to inconsistent and sometimes inadequate validation practices. The purpose of this article is to describe a broadly applicable preclinical validation process. METHODS Validation is performed using four consecutive experiments. The Familiarization experiment tests probe performance on metaphase cells to measure analytic sensitivity and specificity for normal blood specimens. The Pilot Study tests a variety of normal and abnormal specimens, using the intended tissue type, to set a preliminary normal cutoff and establish the analytic sensitivity. The Clinical Evaluation experiment tests these parameters in a series of normal and abnormal specimens to simulate clinical practice, establish the normal cutoff and abnormal reference ranges, and finalize the standard operating procedure. The Precision experiment measures the reproducibility of the new assay over 10 consecutive working days. To illustrate documentation and analysis of data with this process, the results for a new assay to detect fusion of IGH and BCL3 associated with t(14;19)(q32;q13.3) in lymphoproliferative disorders are provided in this report. RESULTS These four experiments determine the analytic sensitivity and specificity, normal values, precision, and reportable reference ranges for validation of the new test. CONCLUSION This report describes a method for preclinical validation of fluorescence in situ hybridization studies of metaphase cells and interphase nuclei using commercial or home brew probes.
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Affiliation(s)
- Anne E Wiktor
- Division of Laboratory Genetics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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Eklund EA, Sun L, Yang SP, Pasion RM, Thorland EC, Freeze HH. Congenital disorder of glycosylation Ic due to a de novo deletion and an hALG-6 mutation. Biochem Biophys Res Commun 2006; 339:755-60. [PMID: 16321363 DOI: 10.1016/j.bbrc.2005.11.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 10/25/2005] [Accepted: 11/08/2005] [Indexed: 10/25/2022]
Abstract
We describe a new cause of congenital disorder of glycosylation-Ic (CDG-Ic) in a young girl with a rather mild CDG phenotype. Her cells accumulated lipid-linked oligosaccharides lacking three glucose residues, and sequencing of the ALG6 gene showed what initially appeared to be a homozygous novel point mutation (338G>A). However, haplotype analysis showed that the patient does not carry any paternal DNA markers extending 33kb in the telomeric direction from the ALG6 region, and microsatellite analysis extended the abnormal region to at least 2.5Mb. We used high-resolution karyotyping to confirm a deletion (10-12Mb) [del(1)(p31.2p32.3)] and found no structural abnormalities in the father, suggesting a de novo event. Our findings extend the causes of CDG to larger DNA deletions and identify the first Japanese CDG-Ic mutation.
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Affiliation(s)
- Erik A Eklund
- Glycobiology and Carbohydrate Chemistry Program, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
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Zou YS, Van Dyke DL, Thorland EC, Chhabra HS, Michels VV, Keefe JG, Lega MA, Feely MA, Uphoff TS, Jalal SM. Mosaic ring 20 with no detectable deletion by FISH analysis: Characteristic seizure disorder and literature review. Am J Med Genet A 2006; 140:1696-706. [PMID: 16835934 DOI: 10.1002/ajmg.a.31332] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ring chromosome 20 is a rare chromosome disorder characterized by a typical seizure phenotype consisting of complex partial seizures, frequent progression to generalized tonic or tonic-clonic seizures, and nocturnal frontal lobe seizures with frequent episodes of non-convulsive status epilepticus. Development may be normal or mildly delayed, followed by cognitive and behavioral decline after seizure onset. Here, we describe a patient with a typical severe seizure phenotype and a mosaic ring chromosome 20 without loss of p or q subtelomere regions or telomeric sequences. The ring had a longer telomere length than either of the telomere ends of its homologous chromosome 20 by quantitative fluorescence in situ hybridization analysis, suggesting that it might be derived from telomere-telomere fusion. The phenotypic comparison of this patient and other chromosome 20 cases that had terminal deletions of 20qter (n = 1) and 20pter (n = 7), shows that the epilepsy phenotype and electroencephalographic abnormalities are characteristic in patients with ring chromosome 20. Several hypotheses have been proposed to address the elusive mechanisms underlying the seizure disorder in ring chromosome 20. These possibilities include haploinsufficiency of two epilepsy genes CHRNA4 and KCNQ2 located at 20qter, silencing of these genes by a telomere position effect, or microdeletions or rearrangements of genetic material during the ring formation.
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Affiliation(s)
- Ying S Zou
- Cytogenetics Laboratory, Mayo Clinic, Rochester, Minnesota 55905, USA.
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47
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Ferber MJ, Thorland EC, Brink AATP, Rapp AK, Phillips LA, McGovern R, Gostout BS, Cheung TH, Chung TKH, Fu WY, Smith DI. Preferential integration of human papillomavirus type 18 near the c-myc locus in cervical carcinoma. Oncogene 2003; 22:7233-42. [PMID: 14562053 DOI: 10.1038/sj.onc.1207006] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The development of cervical cancer is highly associated with human papillomavirus (HPV) infection. Greater than 99% of all cervical tumors contain HPV DNA. Integration of high-risk HPV has been temporally associated with the acquisition of a malignant phenotype. Recent work from our lab has shown that HPV16, the most common high-risk HPV associated with cervical carcinoma, preferentially integrates at loci containing human common fragile sites (CFSs). CFSs are regions of genomic instability that have also been associated with deletions, translocations, and gene amplification during cancer development. The current work shows that HPV18, the second most prevalent high-risk HPV type found in cervical tumors, preferentially targets the CFSs. We identified 27 unique HPV18 integrations in cervical tumors, of which 63% (P<0.001) occur in CFSs. However, the distribution of HPV18 integrations found were profoundly different from those found for HPV16. Specifically, 30% of all HPV18 integrations occurred within the chromosomal band 8q24 near the c-myc proto-oncogene. None of the HPV16 integrations occurred in this region. Previous low-resolution mapping suggested that c-myc may be a target of HPV integration. Our data at nucleotide resolution confirm that in HPV18-positive cervical tumors, the region surrounding c-myc is indeed a hot spot of viral integration. These results demonstrate that CFSs are preferred sites of integration for HPV18 in cervical tumors. In addition, we have identified multiple cellular genes that have been disrupted by HPV18 integration in cervical tumors. Our results suggest that the sites of HPV18 integration are nonrandom and may play an important role in the development of cervical tumors.
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Affiliation(s)
- Matthew J Ferber
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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48
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Lind T, Thorland EC, Sommer SS. Genomic amplification with transcript sequencing (GAWTS). Methods Mol Biol 2003; 65:193-200. [PMID: 8956267 DOI: 10.1385/0-89603-344-9:193] [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] [Indexed: 02/03/2023]
Affiliation(s)
- T Lind
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, MN, USA
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49
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Ensenauer RE, Adeyinka A, Flynn HC, Michels VV, Lindor NM, Dawson DB, Thorland EC, Lorentz CP, Goldstein JL, McDonald MT, Smith WE, Simon-Fayard E, Alexander AA, Kulharya AS, Ketterling RP, Clark RD, Jalal SM. Microduplication 22q11.2, an emerging syndrome: clinical, cytogenetic, and molecular analysis of thirteen patients. Am J Hum Genet 2003; 73:1027-40. [PMID: 14526392 PMCID: PMC1180483 DOI: 10.1086/378818] [Citation(s) in RCA: 253] [Impact Index Per Article: 12.0] [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: 05/15/2003] [Accepted: 07/29/2003] [Indexed: 11/03/2022] Open
Abstract
Chromosome 22, particularly band 22q11.2, is predisposed to rearrangements due to misalignments of low-copy repeats (LCRs). DiGeorge/velocardiofacial syndrome (DG/VCFS) is a common disorder resulting from microdeletion within the same band. Although both deletion and duplication are expected to occur in equal proportions as reciprocal events caused by LCR-mediated rearrangements, very few microduplications have been identified. We have identified 13 cases of microduplication 22q11.2, primarily by interphase fluorescence in situ hybridization (FISH). The size of the duplications, determined by FISH probes from bacterial artificial chromosomes and P(1) artificial chromosomes, range from 3-4 Mb to 6 Mb, and the exchange points seem to involve an LCR. Molecular analysis based on 15 short tandem repeats confirmed the size of the duplications and indicated that at least 1 of 15 loci has three alleles present. The patients' phenotypes ranged from mild to severe, sharing a tendency for velopharyngeal insufficiency with DG/VCFS but having other distinctive characteristics, as well. Although the present series of patients was ascertained because of some overlapping features with DG/VCF syndromes, the microduplication of 22q11.2 appears to be a new syndrome.
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Affiliation(s)
- Regina E. Ensenauer
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Adewale Adeyinka
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Heather C. Flynn
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Virginia V. Michels
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Noralane M. Lindor
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - D. Brian Dawson
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Erik C. Thorland
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Cindy Pham Lorentz
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Jennifer L. Goldstein
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Marie T. McDonald
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Wendy E. Smith
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Elba Simon-Fayard
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Alan A. Alexander
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Anita S. Kulharya
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Rhett P. Ketterling
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Robin D. Clark
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
| | - Syed M. Jalal
- Department of Medical Genetics, and Cytogenetics Laboratory and Molecular Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pediatrics, Duke University Medical Center, Durham, NC; Division of Genetics, Barbara Bush Children’s Hospital, Maine Medical Center, Portland, ME; Department of Pediatrics, Division of Neonatology, Loma Linda University Medical Center, and Division of Genetics, Loma Linda University Children’s Hospital, Loma Linda, CA; Desert Pediatrics, Inc., Palm Desert, CA; and Department of Pediatrics and Pathology, Medical College of Georgia, Augusta, GA
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50
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Ferber MJ, Montoya DP, Yu C, Aderca I, McGee A, Thorland EC, Nagorney DM, Gostout BS, Burgart LJ, Boix L, Bruix J, McMahon BJ, Cheung TH, Chung TKH, Wong YF, Smith DI, Roberts LR. Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene 2003; 22:3813-20. [PMID: 12802289 DOI: 10.1038/sj.onc.1206528] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [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] [Indexed: 01/02/2023]
Abstract
Chronic infections with the hepatitis B virus (HBV) and high-risk human papillomaviruses (HPVs) are important risk factors for hepatocellular carcinoma (HCC) and cervical cancer (CC), respectively. HBV and HPV are DNA viruses that almost invariably integrate into the host genome in invasive tumors. The viral integration sites occur throughout the genome, leading to the presumption that there are no preferred sites of integration. A number of viral integrations have been shown to occur within the vicinity of important cancer-related genes. In studies of HBV-induced HCC and HPV-induced CC, we have identified two HBV and three HPV integrations into the human telomerase reverse transcriptase (hTERT) gene. Detailed characterization of the integrations revealed that four integrations occurred within the hTERT promoter and upstream region and the fifth integration occurred in intron 3 of the hTERT gene. None of the integrations altered the hTERT coding sequence and all resulted in juxtaposition of viral enhancers near hTERT, with potential activation of hTERT expression. Our work supports the hypothesis that the sites of oncogenic viral integration are nonrandom and that genes at the sites of viral integration may play important roles in carcinogenesis.
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Affiliation(s)
- M J Ferber
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA
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