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Billington CJ, Chapman KA, Leon E, Meltzer BW, Berger SI, Olson M, Figler RA, Hoang SA, Wanxing C, Wamhoff BR, Collado MS, Cusmano‐Ozog K. Genomic and biochemical analysis of repeatedly observed variants in DBT in individuals with maple syrup urine disease of Central American ancestry. Am J Med Genet A 2022; 188:2738-2749. [PMID: 35799415 PMCID: PMC9542135 DOI: 10.1002/ajmg.a.62893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 01/25/2023]
Abstract
Maple syrup urine disease (MSUD) is an intoxication-type inherited metabolic disorder in which hyperleucinemia leads to brain swelling and death without treatment. MSUD is caused by branched-chain alpha-ketoacid dehydrogenase deficiency due to biallelic loss of the protein products from the genes BCKDHA, BCKDHB, or DBT, while a distinct but related condition is caused by loss of DLD. In this case series, eleven individuals with MSUD caused by two pathogenic variants in DBT are presented. All eleven individuals have a deletion of exon 2 (delEx2, NM_001918.3:c.48_171del); six individuals are homozygous and five individuals are compound heterozygous with a novel missense variant (NM_001918.5:c.916 T > C [p.Ser306Pro]) confirmed to be in trans. Western Blot indicates decreased amount of protein product in delEx2;c.916 T > C liver cells and absence of protein product in delEx2 homozygous hepatocytes. Ultrahigh performance liquid chromatography-tandem mass spectrometry demonstrates an accumulation of branched-chain amino acids and alpha-ketoacids in explanted hepatocytes. Individuals with these variants have a neonatal-onset, non-thiamine-responsive, classical form of MSUD. Strikingly, the entire cohort is derived from families who immigrated to the Washington, DC, metro area from Honduras or El Salvador suggesting the possibility of a founder effect.
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Affiliation(s)
- Charles J. Billington
- Children's National Rare Disease InstituteWashingtonDistrict of ColumbiaUSA
- Department of PediatricsUniversity of MinnesotaMinneapolisMinnesotaUSA
| | | | - Eyby Leon
- Children's National Rare Disease InstituteWashingtonDistrict of ColumbiaUSA
| | - Beatrix W. Meltzer
- Laboratory Medicine, Children's National HospitalWashingtonDistrict of ColumbiaUSA
| | - Seth I. Berger
- Children's National Rare Disease InstituteWashingtonDistrict of ColumbiaUSA
| | - Matthew Olson
- HemoShear Therapeutics, Inc.CharlottesvilleVirginiaUSA
| | | | | | - Cui Wanxing
- Georgetown University HospitalWashingtonDistrict of ColumbiaUSA
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2
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Christopherson PA, Haberichter SL, Flood VH, Perry CL, Sadler BE, Bellissimo DB, Di Paola J, Montgomery RR. Molecular pathogenesis and heterogeneity in type 3 VWD families in U.S. Zimmerman program. J Thromb Haemost 2022; 20:1576-1588. [PMID: 35343054 DOI: 10.1111/jth.15713] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Type 3 von Willebrand Disease (VWD) is a rare and severe form of VWD characterized by the absence of von Willebrand factor (VWF). OBJECTIVES As part of the Zimmerman Program, we sought to explore the molecular pathogenesis, correlate bleeding phenotype and severity, and determine the inheritance pattern found in type 3 VWD families. PATIENTS/METHODS 62 index cases with a pre-existing diagnosis of type 3 VWD were analyzed. Central testing included FVIII, VWF:Ag, VWF:RCo, and VWFpp. Bleeding symptoms were quantified using the ISTH bleeding score. Genetic analysis included VWF sequencing, comparative genomic hybridization and predictive computational programs. RESULTS 75% of subjects (46) had central testing confirming type 3, while 25% were re-classified as type 1-Severe or type 1C. Candidate VWF variants were found in all subjects with 93% of expected alleles identified. The majority were null alleles including frameshift, nonsense, splice site, and large deletions, while 13% were missense variants. Additional studies on 119 family members, including 69 obligate carriers, revealed a wide range of heterogeneity in VWF levels and bleeding scores, even amongst those with the same variant. Co-dominant inheritance was present in 51% of families and recessive in 21%, however 28% were ambiguous. CONCLUSION This report represents a large cohort of VWD families in the U.S. with extensive phenotypic and genotypic data. While co-dominant inheritance was seen in approximately 50% of families, this study highlights the complexity of VWF genetics due to the heterogeneity found in both VWF levels and bleeding tendencies amongst families with type 3 VWD.
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Affiliation(s)
| | - Sandra L Haberichter
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Hematology/Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Veronica H Flood
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Hematology/Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Brooke E Sadler
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel B Bellissimo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jorge Di Paola
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert R Montgomery
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Hematology/Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
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3
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Chalmers SJ, Murphy SJ, Thompson LL, Hoppman NL, Smadbeck JB, Balcom JR, Harris FR, Frantz RP, Vasmatzis G, E Wylam M. Mate-pair sequencing identifies a cryptic BMPR2 mutation in hereditary pulmonary arterial hypertension. Pulm Circ 2021; 10:2045894020933081. [PMID: 34290857 PMCID: PMC8278463 DOI: 10.1177/2045894020933081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/11/2020] [Indexed: 11/29/2022] Open
Abstract
Current guidelines suggest screening all patients with idiopathic pulmonary arterial hypertension for genetic aberrations, particularly mutations in Bone Morphogenic Protein Receptor Type II (BMPR2), the gene most commonly implicated in the pathogenesis of PAH. Herein, we present a novel technique used to identify a pathogenic germline BMPR2 alteration in a 36-year-old female and family members with hereditary pulmonary arterial hypertension who each screened negative by standard cytogenetics and molecular genetics testing.
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Affiliation(s)
- Sarah J Chalmers
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Stephen J Murphy
- Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Laura L Thompson
- Department of Laboratory Genetics and Genomics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Nicole L Hoppman
- Department of Laboratory Genetics and Genomics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - James B Smadbeck
- Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jessica R Balcom
- Department of Laboratory Genetics and Genomics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Faye R Harris
- Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Robert P Frantz
- Department of Cardiovascular Disease, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - George Vasmatzis
- Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mark E Wylam
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
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4
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Macke EL, Morales-Rosado JA, Gupta A, Schmitz CT, Kruisselbrink T, Lanpher B, Klee EW. A novel missense variant and multiexon deletion causing a delayed presentation of xeroderma pigmentosum, group C. Cold Spring Harb Mol Case Stud 2020; 6:a005165. [PMID: 32843428 PMCID: PMC7476405 DOI: 10.1101/mcs.a005165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/23/2020] [Indexed: 12/02/2022] Open
Abstract
Pathogenic variants in the XPC complex subunit, DNA damage recognition, and repair factor (XPC) are the cause of xeroderma pigmentosum, group C (MIM: 278720). Xeroderma pigmentosum is an inherited condition characterized by hypersensitivity to ultraviolet (UV) irradiation and increased risk of skin cancer due to a defect in nucleotide excision repair (NER). Here we describe an individual with a novel missense variant and deletion of exons 14-15 in XPC presenting with a history of recurrent melanomas. The proband is a 39-yr-old female evaluated through the Mayo Clinic Department of Clinical Genomics. Prior to age 36, she had more than 60 skin biopsies that showed dysplastic nevi, many of which had atypia. At age 36 she presented with her first melanoma in situ, and since then has had more than 10 melanomas. The proband underwent research whole-exome sequencing (WES) through the Mayo Clinic's Center for Individualized Medicine and a novel heterozygous variant of uncertain significance (VUS) in XPC (c.1709T > G, p.Val570Gly) was identified. Clinical confirmation pursued via XPC gene sequencing and deletion/duplication analysis of XPC revealed a pathogenic heterozygous deletion of ∼1 kb within XPC, including exons 14 and 15. Research studies determined the alterations to be in trans Although variants in XPC generally result in early-onset skin cancer in childhood, the proband is atypical in that she did not present with her first melanoma until age 36. Review of the patient's clinical, pathological, and genetic findings points to a diagnosis of delayed presentation of xeroderma pigmentosum.
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Affiliation(s)
- Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Joel A Morales-Rosado
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Aditi Gupta
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | | | - Brendan Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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5
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Jezkova J, Heath J, Williams A, Barrell D, Norton J, Collinson MN, Beal SJ, Corrin S, Morgan S. Exon-focused targeted oligonucleotide microarray design increases detection of clinically relevant variants across multiple NHS genomic centres. NPJ Genom Med 2020; 5:28. [PMID: 32714564 PMCID: PMC7374691 DOI: 10.1038/s41525-020-0136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
In recent years, chromosomal microarrays have been widely adopted by clinical diagnostic laboratories for postnatal constitutional genome analysis and have been recommended as the first-line test for patients with intellectual disability, developmental delay, autism and/or congenital abnormalities. Traditionally, array platforms have been designed with probes evenly spaced throughout the genome and increased probe density in regions associated with specific disorders with a resolution at the level of whole genes or multiple exons. However, this level of resolution often cannot detect pathogenic intragenic deletions or duplications, which represent a significant disease-causing mechanism. Therefore, new high-resolution oligonucleotide comparative genomic hybridisation arrays (oligo-array CGH) have been developed with probes targeting single exons of disease relevant genes. Here we present a retrospective study on 27,756 patient samples from a consortium of state-funded diagnostic UK genomic centres assayed by either oligo-array CGH of a traditional design (Cytosure ISCA v2) or by an oligo-array CGH with enhanced exon-level coverage of genes associated with developmental disorders (CytoSure Constitutional v3). The new targeted design used in Cytosure v3 array has been designed to capture intragenic aberrations that would have been missed on the v2 array. To assess the relative performance of the two array designs, data on a subset of samples (n = 19,675), generated only by laboratories using both array designs, were compared. Our results demonstrate that the new high-density exon-focused targeted array design that uses updated information from large scale genomic studies is a powerful tool for detection of intragenic deletions and duplications that leads to a significant improvement in diagnostic yield.
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Affiliation(s)
- Jana Jezkova
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Jade Heath
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Angharad Williams
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Deborah Barrell
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Jessica Norton
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK.,Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Morag N Collinson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK
| | - Sarah J Beal
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Sian Morgan
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
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6
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Brusius-Facchin AC, Rojas Malaga D, Leistner-Segal S, Giugliani R. Recent advances in molecular testing to improve early diagnosis in children with mucopolysaccharidoses. Expert Rev Mol Diagn 2018; 18:855-866. [DOI: 10.1080/14737159.2018.1523722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - Diana Rojas Malaga
- Medical Genetics Service, HCPA, Porto Alegre, RS, Brazil
- Postgraduate Program of Genetics and Molecular Biology, UFRGS, Porto Alegre, RS, Brazil
| | - Sandra Leistner-Segal
- Medical Genetics Service, HCPA, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Science, UFRGS, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, HCPA, Porto Alegre, RS, Brazil
- Postgraduate Program of Genetics and Molecular Biology, UFRGS, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Science, UFRGS, Porto Alegre, RS, Brazil
- Department of Genetics, UFRGS, Porto Alegre, RS, Brazil
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7
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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8
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Vazač J, Füssy Z, Hladová I, Killi S, Oborník M. Ploidy and Number of Chromosomes in the Alveolate Alga Chromera velia. Protist 2017; 169:53-63. [PMID: 29367153 DOI: 10.1016/j.protis.2017.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/06/2017] [Accepted: 12/09/2017] [Indexed: 11/16/2022]
Abstract
Chromera velia is an alveolate alga which represents the closest known phototrophic relative to apicomplexan parasites. Although the nuclear, mitochondrial, and plastid genomes of this alga have been sequenced, the number of chromosomes and ploidy of C. velia are unknown. We explored ploidy in the vegetative cell, the predominant stage in cultures of Chromera, using the tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH) in isolated nuclei of C. velia. Probes were derived from three single copy genes coding for 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) synthase and Topoisomerase II. Our results indicate that the vegetative cell of C. velia is haploid, as each probe produced a single fluorescent signal, although the possibility of diploidy with somatic pairing of homologous chromosomes cannot be completely excluded. Restriction analysis and hybridization with the telomere probe produced eight bands suggesting the presence of four chromosomes in haploid vegetative cells of C. velia. However, when the chromerid-specific telomere probe (TTTAGGG)4 was used for TSA-FISH, we consistently obtained a double signal. This may indicate that the four chromosomes are organized in clusters in interphase nuclei of C. velia, which is a chromosome organization similar to that of their apicomplexan relatives.
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Affiliation(s)
- Jan Vazač
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Irena Hladová
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Sireesha Killi
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Miroslav Oborník
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic; Institute of Microbiology, Czech Academy of Sciences, Algatech, Novohradská 237, Opatovický mlýn, 37901 Třeboň, Czech Republic.
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9
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Abstract
PURPOSE OF REVIEW Copy number variation (CNV) disorders arise from the dosage imbalance of one or more gene(s), resulting from deletions, duplications or other genomic rearrangements that lead to the loss or gain of genetic material. Several disorders, characterized by multiple birth defects and neurodevelopmental abnormalities, have been associated with relatively large (>1 Mb) and often recurrent CNVs. CNVs have also been implicated in the etiology of neuropsychiatric disorders including autism and schizophrenia as well as other common complex diseases. Thus, CNVs have a significant impact on human health and disease. RECENT FINDINGS The use of increasingly higher resolution, genomewide analysis has greatly enhanced the detection of genetic variation, including CNVs. Furthermore, the availability of comprehensive genetic variation data from large cohorts of healthy controls has the potential to greatly improve the identification of disease associated genetic variants in patient samples. SUMMARY This review discusses the current knowledge about CNV disorders, including the mechanisms underlying their formation and phenotypic outcomes, and the advantages and limitations of current methods of detection and disease association.
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Affiliation(s)
- Tamim H. Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045
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10
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Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SHL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 2017; 9:83. [PMID: 28934986 PMCID: PMC5607840 DOI: 10.1186/s13073-017-0472-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sailaja Golla
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Dengle
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Reuben Matalon
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lisa Emrick
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica B Proud
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Treadwell-Deering
- Department of Psychiatry and Behavioral Sciences, Child and Adolescent Psychiatry Division, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hannele Koillinen
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Chester Brown
- Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38105, USA.,Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | - Nora Urraca
- Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | | | | | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Patricia I Bader
- Northeast Indiana Genetic Counseling Center, Wayne, IN, 46804, USA
| | - Gary Bellus
- Section of Clinical Genetics & Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Cummings
- Department of Psychiatry Erie County Medical Center, Buffalo, NY, 14215, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Myla Ashfaq
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | | | - Robert Wildin
- St. Luke's Children's Hospital, Boise, ID, 83702, USA.,The National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Anita E Beck
- Seattle Children's Hospital, Seattle, WA, 98105, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lindsay Elton
- Child Neurology Consultants of Austin, Austin, TX, 78731, USA
| | - Shaun Varghese
- THINK Neurology for Kids/Children's Memorial Hermann Hospital, The Woodlands, TX, 77380, USA
| | - Edward Buchanan
- Division of Plastic Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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11
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Panny A, Glurich I, Haws RM, Acharya A. Oral and Craniofacial Anomalies of Bardet-Biedl Syndrome: Dental Management in the Context of a Rare Disease. J Dent Res 2017; 96:1361-1369. [PMID: 28662344 DOI: 10.1177/0022034517716913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Standardized guidelines for the oral health management of patients with rare diseases exhibiting morphologic anomalies are currently lacking. This review considers Bardet-Biedl syndrome (BBS), a monogenic autosomal recessive nonmotile ciliopathy, as an archetypal condition. Dental anomalies are present in a majority of individuals affected by BBS due to abnormal embryonic orofacial and tooth development. Genetically encoded intrinsic oral structural anomalies and heterogeneous BBS clinical phenotypes and consequent oral comorbidities confound oral health management. Since the comorbid spectrum of BBS phenotypes spans diabetes, renal disease, obesity, sleep apnea, cardiovascular disease, and cognitive disorders, a broad spectrum of collateral oral disease may be encountered. The genetic impact of BBS on the anatomic development of oral components and oral pathology encountered in the context of various BBS phenotypes and their associated comorbidities are reviewed herein. Challenges encountered in managing patients with BBS are highlighted, emphasizing the spectrum of oral pathology associated with heterogeneous clinical phenotypic expression. Guidelines for provision of care across the spectrum of BBS clinical phenotypes are considered. Establishment of integrated medical-dental delivery models of oral care in the context of rare diseases is emphasized, including involvement of caregivers in the context of managing these patients with special needs.
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Affiliation(s)
- A Panny
- 1 Institute for Oral and Systemic Health, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - I Glurich
- 1 Institute for Oral and Systemic Health, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - R M Haws
- 2 Center for Clinical Research, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - A Acharya
- 1 Institute for Oral and Systemic Health, Marshfield Clinic Research Foundation, Marshfield, WI, USA
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12
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Lantieri F, Malacarne M, Gimelli S, Santamaria G, Coviello D, Ceccherini I. Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation. Int J Mol Sci 2017; 18:E609. [PMID: 28287439 PMCID: PMC5372625 DOI: 10.3390/ijms18030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log₂ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log₂ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected.
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Affiliation(s)
- Francesca Lantieri
- Dipartimento di Scienzedella Salute, Sezione di Biostatistica, Università degli Studi di Genova, Via Pastore 1, 16132 Genoa, Italy.
| | - Michela Malacarne
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Stefania Gimelli
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Bâtiment de Base 8C-3-840.3, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Giuseppe Santamaria
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
| | - Domenico Coviello
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Isabella Ceccherini
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
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13
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A customized high-resolution array-comparative genomic hybridization to explore copy number variations in Parkinson's disease. Neurogenetics 2016; 17:233-244. [PMID: 27637465 PMCID: PMC5566182 DOI: 10.1007/s10048-016-0494-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Abstract
Parkinson’s disease (PD), the second most common progressive neurodegenerative disorder, was long believed to be a non-genetic sporadic syndrome. Today, only a small percentage of PD cases with genetic inheritance patterns are known, often complicated by reduced penetrance and variable expressivity. The few well-characterized Mendelian genes, together with a number of risk factors, contribute to the major sporadic forms of the disease, thus delineating an intricate genetic profile at the basis of this debilitating and incurable condition. Along with single nucleotide changes, gene-dosage abnormalities and copy number variations (CNVs) have emerged as significant disease-causing mutations in PD. However, due to their size variability and to the quantitative nature of the assay, CNV genotyping is particularly challenging. For this reason, innovative high-throughput platforms and bioinformatics algorithms are increasingly replacing classical CNV detection methods. Here, we report the design strategy, development, validation and implementation of NeuroArray, a customized exon-centric high-resolution array-based comparative genomic hybridization (aCGH) tailored to detect single/multi-exon deletions and duplications in a large panel of PD-related genes. This targeted design allows for a focused evaluation of structural imbalances in clinically relevant PD genes, combining exon-level resolution with genome-wide coverage. The NeuroArray platform may offer new insights in elucidating inherited potential or de novo structural alterations in PD patients and investigating new candidate genes.
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14
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Yap TA, Smith AD, Ferraldeschi R, Al-Lazikani B, Workman P, de Bono JS. Drug discovery in advanced prostate cancer: translating biology into therapy. Nat Rev Drug Discov 2016; 15:699-718. [DOI: 10.1038/nrd.2016.120] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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15
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Rosenfeld JA, Patel A. Chromosomal Microarrays: Understanding Genetics of Neurodevelopmental Disorders and Congenital Anomalies. J Pediatr Genet 2016; 6:42-50. [PMID: 28180026 DOI: 10.1055/s-0036-1584306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/23/2016] [Indexed: 01/09/2023]
Abstract
Chromosomal microarray (CMA) testing, used to identify DNA copy number variations (CNVs), has helped advance knowledge about genetics of human neurodevelopmental disease and congenital anomalies. It has aided in discovering new CNV syndromes and uncovering disease genes. It has discovered CNVs that are not fully penetrant and/or cause a spectrum of phenotypes, including intellectual disability, autism, schizophrenia, and dysmorphisms. Such CNVs can pose challenges to genetic counseling. They also have helped increase knowledge of genetic risk factors for neurodevelopmental disease and raised awareness of possible shared etiologies among these variable phenotypes. Advances in CMA technology allow CNV identification at increasingly finer scales, improving detection of pathogenic changes, although these sometimes are difficult to distinguish from normal population variation. This paper confronts some of the challenges uncovered by CMA testing while reviewing advances in genetics and the clinical use of this test that has replaced standard karyotyping in most genetic evaluations.
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Affiliation(s)
- Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
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16
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Giugliani R, Brusius-Facchin AC, Pasqualim G, Leistner-Segal S, Riegel M, Matte U. Current molecular genetics strategies for the diagnosis of lysosomal storage disorders. Expert Rev Mol Diagn 2015; 16:113-23. [DOI: 10.1586/14737159.2016.1121101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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Vairo F, Federhen A, Baldo G, Riegel M, Burin M, Leistner-Segal S, Giugliani R. Diagnostic and treatment strategies in mucopolysaccharidosis VI. APPLICATION OF CLINICAL GENETICS 2015; 8:245-55. [PMID: 26586959 PMCID: PMC4634832 DOI: 10.2147/tacg.s68650] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mucopolysaccharidosis VI (MPS VI) is a very rare autosomal recessive disorder caused by mutations in the ARSB gene, which lead to deficient activity of the lysosomal enzyme ASB. This enzyme is important for the breakdown of the glycosaminoglycans (GAGs) dermatan sulfate and chondroitin sulfate, which accumulate in body tissues and organs of MPS VI patients. The storage of GAGs (especially dermatan sulfate) causes bone dysplasia, joint restriction, organomegaly, heart disease, and corneal clouding, among several other problems, and reduced life span. Despite the fact that most cases are severe, there is a spectrum of severity and some cases are so attenuated that diagnosis is made late in life. Although the analysis of urinary GAGs and/or the measurement of enzyme activity in dried blood spots are useful screening methods, the diagnosis is based in the demonstration of the enzyme deficiency in leucocytes or fibroblasts, and/or in the identification of pathogenic mutations in the ARSB gene. Specific treatment with enzyme replacement has been available since 2005. It is safe and effective, bringing measurable benefits and increased survival to patients. As several evidences indicate that early initiation of therapy may lead to a better outcome, newborn screening is being considered for this condition, and it is already in place in selected areas where the incidence of MPS VI is increased. However, as enzyme replacement therapy is not curative, associated therapies should be considered, and research on innovative therapies continues. The management of affected patients by a multidisciplinary team with experience in MPS diseases is highly recommended.
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Affiliation(s)
- Filippo Vairo
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ; Clinical Research Group on Medical Genetics, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Andressa Federhen
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Clinical Research Group on Medical Genetics, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Post-Graduate Program in Child and Adolescent Health, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme Baldo
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ; Gene Therapy Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ; Department of Physiology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mariluce Riegel
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maira Burin
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Sandra Leistner-Segal
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Post-Graduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ; Clinical Research Group on Medical Genetics, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Post-Graduate Program in Child and Adolescent Health, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ; Gene Therapy Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil ; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ; Post-Graduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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18
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Retterer K, Scuffins J, Schmidt D, Lewis R, Pineda-Alvarez D, Stafford A, Schmidt L, Warren S, Gibellini F, Kondakova A, Blair A, Bale S, Matyakhina L, Meck J, Aradhya S, Haverfield E. Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. Genet Med 2014; 17:623-9. [PMID: 25356966 DOI: 10.1038/gim.2014.160] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/01/2014] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing. METHODS Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array. RESULTS In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons. CONCLUSION These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array.Genet Med 17 8, 623-629.
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19
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Smith AD, Roda D, Yap TA. Strategies for modern biomarker and drug development in oncology. J Hematol Oncol 2014; 7:70. [PMID: 25277503 PMCID: PMC4189730 DOI: 10.1186/s13045-014-0070-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/21/2014] [Indexed: 02/08/2023] Open
Abstract
Technological advancements in the molecular characterization of cancers have enabled researchers to identify an increasing number of key molecular drivers of cancer progression. These discoveries have led to multiple novel anticancer therapeutics, and clinical benefit in selected patient populations. Despite this, the identification of clinically relevant predictive biomarkers of response continues to lag behind. In this review, we discuss strategies for the molecular characterization of cancers and the importance of biomarkers for the development of novel antitumor therapeutics. We also review critical successes and failures in oncology, and detail the lessons learnt, which may aid in the acceleration of anticancer drug development and biomarker discovery.
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Affiliation(s)
- Alan D Smith
- Drug Development Unit, Royal Marsden NHS Foundation Trust, Division of Clinical Studies, The Institute of Cancer Research, Downs Road, Sutton, Surrey, SM2 5PT, UK.
| | - Desam Roda
- Drug Development Unit, Royal Marsden NHS Foundation Trust, Division of Clinical Studies, The Institute of Cancer Research, Downs Road, Sutton, Surrey, SM2 5PT, UK.
| | - Timothy A Yap
- Drug Development Unit, Royal Marsden NHS Foundation Trust, Division of Clinical Studies, The Institute of Cancer Research, Downs Road, Sutton, Surrey, SM2 5PT, UK.
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20
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Ankala A, Nallamilli BR, Rufibach LE, Hwang E, Hegde MR. Diagnostic overview of blood-based dysferlin protein assay for dysferlinopathies. Muscle Nerve 2014; 50:333-9. [PMID: 24488599 DOI: 10.1002/mus.24195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 01/13/2014] [Accepted: 01/29/2014] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Dysferlin deficiency causes dysferlinopathies. Among peripheral blood mononuclear cells (PBMCs), the dysferlin protein is expressed specifically in CD14(+) monocytes. METHODS We quantified dysferlin protein levels in PBMC lysates of 77 individuals suspected clinically of having a dysferlinopathy to screen for true positives. Subsequent molecular confirmation was done by Sanger sequencing and comparative genomic hybridization arrays to establish diagnosis. RESULTS Of the 44 individuals who had significantly reduced dysferlin levels (≤10%), 41 underwent molecular testing. We identified at least 1 mutation in 85% (35 of 41), and 2 mutations, establishing a dysferlinopathy diagnosis, in 61% (25 of 41) of these individuals. Among those with dysferlin protein levels of >10% (33 of 77), only 1 individual (of 14 who underwent molecular testing) had a detectable mutation. CONCLUSIONS Our results suggest that dysferlin protein levels of ≤10% in PBMCs, are highly indicative of primary dysferlinopathies. However, this assay may not distinguish carriers from those with secondary dysferlin reduction.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia, 30322, USA
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21
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Hegde M, Ferber M, Mao R, Samowitz W, Ganguly A. ACMG technical standards and guidelines for genetic testing for inherited colorectal cancer (Lynch syndrome, familial adenomatous polyposis, and MYH-associated polyposis). Genet Med 2013; 16:101-16. [PMID: 24310308 DOI: 10.1038/gim.2013.166] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/28/2022] Open
Abstract
Lynch syndrome, familial adenomatous polyposis, and Mut Y homolog (MYH)-associated polyposis are three major known types of inherited colorectal cancer, which accounts for up to 5% of all colon cancer cases. Lynch syndrome is most frequently caused by mutations in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2 and is inherited in an autosomal dominant manner. Familial adenomatous polyposis is manifested as colonic polyposis caused by mutations in the APC gene and is also inherited in an autosomal dominant manner. Finally, MYH-associated polyposis is caused by mutations in the MUTYH gene and is inherited in an autosomal recessive manner but may or may not be associated with polyps. There are variants of both familial adenomatous polyposis (Gardner syndrome--with extracolonic features--and Turcot syndrome, which features medulloblastoma) and Lynch syndrome (Muir-Torre syndrome features sebaceous skin carcinomas, and Turcot syndrome features glioblastomas). Although a clinical diagnosis of familial adenomatous polyposis can be made using colonoscopy, genetic testing is needed to inform at-risk relatives. Because of the overlapping phenotypes between attenuated familial adenomatous polyposis, MYH-associated polyposis, and Lynch syndrome, genetic testing is needed to distinguish among these conditions. This distinction is important, especially for women with Lynch syndrome, who are at increased risk for gynecological cancers. Clinical testing for these genes has progressed rapidly in the past few years with advances in technologies and the lower cost of reagents, especially for sequencing. To assist clinical laboratories in developing and validating testing for this group of inherited colorectal cancers, the American College of Medical Genetics and Genomics has developed the following technical standards and guidelines. An algorithm for testing is also proposed.
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Affiliation(s)
- Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Rong Mao
- Mayo Clinic, Salt Lake City, Utah, USA
| | | | - Arupa Ganguly
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
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22
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Askree SH, Chin ELH, Bean LH, Coffee B, Tanner A, Hegde M. Detection limit of intragenic deletions with targeted array comparative genomic hybridization. BMC Genet 2013; 14:116. [PMID: 24304607 PMCID: PMC4235222 DOI: 10.1186/1471-2156-14-116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/12/2013] [Indexed: 11/24/2022] Open
Abstract
Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered.
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Affiliation(s)
| | | | | | | | | | - Madhuri Hegde
- Emory Genetics Laboratory, Department of Human Genetics, Emory University, 2165 N Decatur Road, Decatur, GA 30033, USA.
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23
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Single exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes. Eur J Hum Genet 2013; 22:792-800. [PMID: 24253858 DOI: 10.1038/ejhg.2013.248] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 09/05/2013] [Accepted: 09/27/2013] [Indexed: 02/07/2023] Open
Abstract
Intellectual disability affects about 3% of individuals globally, with∼50% idiopathic. We designed an exonic-resolution array targeting all known submicroscopic chromosomal intellectual disability syndrome loci, causative genes for intellectual disability, and potential candidate genes, all genes encoding glutamate receptors and epigenetic regulators. Using this platform, we performed chromosomal microarray analysis on 165 intellectual disability trios (affected child and both normal parents). We identified and independently validated 36 de novo copy-number changes in 32 trios. In all, 67% of the validated events were intragenic, involving only exon 1 (which includes the promoter sequence according to our design), exon 1 and adjacent exons, or one or more exons excluding exon 1. Seventeen of the 36 copy-number variants involve genes known to cause intellectual disability. Eleven of these, including seven intragenic variants, are clearly pathogenic (involving STXBP1, SHANK3 (3 patients), IL1RAPL1, UBE2A, NRXN1, MEF2C, CHD7, 15q24 and 9p24 microdeletion), two are likely pathogenic (PI4KA, DCX), two are unlikely to be pathogenic (GRIK2, FREM2), and two are unclear (ARID1B, 15q22 microdeletion). Twelve individuals with genomic imbalances identified by our array were tested with a clinical microarray, and six had a normal result. We identified de novo copy-number variants within genes not previously implicated in intellectual disability and uncovered pathogenic variation of known intellectual disability genes below the detection limit of standard clinical diagnostic chromosomal microarray analysis.
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Gong X, Wu X, Ma X, Wu D, Zhang T, He L, Qin S, Li X. Microdeletion and microduplication analysis of chinese conotruncal defects patients with targeted array comparative genomic hybridization. PLoS One 2013; 8:e76314. [PMID: 24098474 PMCID: PMC3788710 DOI: 10.1371/journal.pone.0076314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/23/2013] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE The current study aimed to develop a reliable targeted array comparative genomic hybridization (aCGH) to detect microdeletions and microduplications in congenital conotruncal defects (CTDs), especially on 22q11.2 region, and for some other chromosomal aberrations, such as 5p15-5p, 7q11.23 and 4p16.3. METHODS Twenty-seven patients with CTDs, including 12 pulmonary atresia (PA), 10 double-outlet right ventricle (DORV), 3 transposition of great arteries (TGA), 1 tetralogy of Fallot (TOF) and one ventricular septal defect (VSD), were enrolled in this study and screened for pathogenic copy number variations (CNVs), using Agilent 8 x 15K targeted aCGH. Real-time quantitative polymerase chain reaction (qPCR) was performed to test the molecular results of targeted aCGH. RESULTS Four of 27 patients (14.8%) had 22q11.2 CNVs, 1 microdeletion and 3 microduplications. qPCR test confirmed the microdeletion and microduplication detected by the targeted aCGH. CONCLUSION Chromosomal abnormalities were a well-known cause of multiple congenital anomalies (MCA). This aCGH using arrays with high-density coverage in the targeted regions can detect genomic imbalances including 22q11.2 and other 10 kinds CNVs effectively and quickly. This approach has the potential to be applied to detect aneuploidy and common microdeletion/microduplication syndromes on a single microarray.
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Affiliation(s)
- Xiaohui Gong
- Obstetrics and Gynecology Hospital of Shanghai Fudan University, the Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojing Ma
- Pediatric Hospital, Shanghai Fudan University, Shanghai, China
| | - Dandan Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, Chaoyang District, Beijing , China
| | - Li He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Shanghai Fudan University, the Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
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Coughlin CR, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med 2012; 4:80. [PMID: 23114084 PMCID: PMC3580449 DOI: 10.1186/gm381] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Copy number variation (CNV) analysis has had a major impact on the field of medical genetics, providing a mechanism to identify disease-causing genomic alterations in an unprecedented number of diseases and phenotypes. CNV analysis is now routinely used in the clinical diagnostic laboratory, and has led to a significant increase in the detection of chromosomal abnormalities. These findings are used for prenatal decision making, clinical management and genetic counseling. Although a powerful tool to identify genomic alterations, CNV analysis may also result in the detection of genomic alterations that have unknown clinical significance or reveal unintended information. This highlights the importance of informed consent and genetic counseling for clinical CNV analysis. This review examines the advantages and limitations of CNV discovery in the clinical diagnostic laboratory, as well as the impact on the clinician and family.
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Affiliation(s)
- Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA
| | - Gunter H Scharer
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA ; Intellectual and Developmental Disabilities Research Center, University of Colorado Denver, Aurora, CO 80045, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA ; Intellectual and Developmental Disabilities Research Center, University of Colorado Denver, Aurora, CO 80045, USA
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Quirk ME, Dobrowolski SF, Nelson BE, Coffee B, Singh RH. Utility of phenylalanine hydroxylase genotype for tetrahydrobiopterin responsiveness classification in patients with phenylketonuria. Mol Genet Metab 2012; 107:31-6. [PMID: 22841515 PMCID: PMC4029439 DOI: 10.1016/j.ymgme.2012.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND A need exists to expand the characterization of tetrahydrobiopterin (BH(4)) responsiveness in patients with phenylketonuria (PKU), beyond simply evaluating change in blood phenylalanine concentrations. The clinical interpretation of BH(4) responsiveness should be evaluated within the context of phenylalanine hydroxylase (PAH) genotype. AIM This investigation seeks to use a modified version of a previously developed PAH genotype severity tool, the assigned value (AV) sum, to assess the molecular basis of responsiveness in a clinical cohort and to explore the tool's ability to differentiate BH(4) responsive groups. METHODS BH(4) response was previously clinically classified in 58 patients with PKU, with three response groups emerging: definitive responders, provisional responders, and non-responders. Provisional responders represented a clinically ambiguous group, with an initial decrease in plasma phenylalanine concentrations, but limited ability to improve dietary phenylalanine tolerance. In this retrospective analysis, mutations in the PAH gene were identified in each patient. PAH genotype was characterized through the AV sum approach, in which each mutation is given an AV of 1, 2, 4, or 8; the sum of both mutations' AV corresponds to genotype severity, with a lower number representing a more severe phenotype. An AV sum cutoff of 2 (indicative of the most severe genotypes) was used to dichotomize patients and predict BH(4) responsiveness. Provisional responders were classified with the definitive responders then the non-responders to see with which group they best aligned. RESULTS In 17/19 definitive responders, at least one mutation was mild or moderate in severity (AV sum>2). In contrast, 7/9 provisional responders carried two severe or null mutations (AV sum=2), suggesting little molecular basis for responsiveness. Non-responders represent a heterogeneous group with 15/25 patients carrying two severe mutations (AV sum=2), 5/25 patients carrying one moderate or mild mutation in combination with a severe or null mutation (AV sum>2), and the remaining five patients carrying an uncharacterized mutation in combination with a severe mutation. Predictive sensitivity of the AV sum was maximized (89.5% vs. 67.9%) with limited detriment to specificity (79.4% vs. 80.0%), by classifying provisional responders with the non-responders rather than with the definitive responders. CONCLUSIONS In our clinical cohort, the AV sum tool was able to identify definitive responders with a high degree of sensitivity. As demonstrated by both the provisional responder group and the substantial number of non-responders with AV sums>2, a potential exists for misclassification when BH(4) response is determined by relying solely on change in plasma phenylalanine concentrations. PAH genotype should be incorporated in the clinical evaluation of BH(4) responsiveness.
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Affiliation(s)
- Meghan E. Quirk
- Division of Biological and Biomedical Sciences, Nutrition and Health Sciences, Emory University, Atlanta, GA, USA
| | - Steven F. Dobrowolski
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Bradford Coffee
- Department of Human Genetics, Emory University School of Medicine, Decatur, GA, USA
| | - Rani H. Singh
- Division of Biological and Biomedical Sciences, Nutrition and Health Sciences, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Decatur, GA, USA
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Tanner AK, Chin ELH, Duffner PK, Hegde M. Array CGH improves detection of mutations in the GALC gene associated with Krabbe disease. Orphanet J Rare Dis 2012; 7:38. [PMID: 22704718 PMCID: PMC3404939 DOI: 10.1186/1750-1172-7-38] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 06/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Krabbe disease is an autosomal recessive lysosomal storage disorder caused by mutations in the GALC gene. The most common mutation in the Caucasian population is a 30-kb deletion of exons 11 through 17. There are few other reports of intragenic GALC deletions or duplications, due in part to difficulties detecting them. METHODS AND RESULTS We used gene-targeted array comparative genomic hybridization (CGH) to analyze the GALC gene in individuals with Krabbe disease in whom sequence analysis with 30-kb deletion analysis identified only one mutation. In our sample of 33 cases, traditional approaches failed to identify two pathogenic mutations in five (15.2%) individuals with confirmed Krabbe disease. The addition of array CGH deletion/duplication analysis to the genetic testing strategy led to the identification of a second pathogenic mutation in three (9.1%) of these five individuals. In all three cases, the deletion or duplication identified through array CGH was a novel GALC mutation, including the only reported duplication in the GALC gene, which would have been missed by traditional testing methodologies. We report these three cases in detail. The second mutation remains unknown in the remaining two individuals (6.1%), despite our full battery of testing. CONCLUSIONS Analysis of the GALC gene using array CGH deletion/duplication testing increased the two-mutation detection rate from 84.8% to 93.9% in affected individuals. Better mutation detection rates are important for improving molecular diagnosis of Krabbe disease, as well as for providing prenatal and carrier testing in family members.
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Affiliation(s)
- Alice K Tanner
- Emory Genetics Laboratory, Department of Human Genetics, Emory University, Atlanta, GA, USA
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Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet Med 2012; 13:921-32. [PMID: 21811164 DOI: 10.1097/gim.0b013e318226fbf2] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Congenital disorders of glycosylation are a heterogeneous group of disorders caused by deficient glycosylation, primarily affecting the N-linked pathway. It is estimated that more than 40% of congenital disorders of glycosylation patients lack a confirmatory molecular diagnosis. The purpose of this study was to improve molecular diagnosis for congenital disorders of glycosylation by developing and validating a next generation sequencing panel for comprehensive mutation detection in 24 genes known to cause congenital disorders of glycosylation. METHODS Next generation sequencing validation was performed on 12 positive control congenital disorders of glycosylation patients. These samples were blinded as to the disease-causing mutations. Both RainDance and Fluidigm platforms were used for sequence enrichment and targeted amplification. The SOLiD platform was used for sequencing the amplified products. Bioinformatic analysis was performed using NextGENe® software. RESULTS The disease-causing mutations were identified by next generation sequencing for all 12 positive controls. Additional variants were also detected in three controls that are known or predicted to impair gene function and may contribute to the clinical phenotype. CONCLUSIONS We conclude that development of next generation sequencing panels in the diagnostic laboratory where multiple genes are implicated in a disorder is more cost-effective and will result in improved and faster patient diagnosis compared with a gene-by-gene approach. Recommendations are also provided for data analysis from the next generation sequencing-derived data in the clinical laboratory, which will be important for the widespread use of this technology.
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Bayat V, Thiffault I, Jaiswal M, Tétreault M, Donti T, Sasarman F, Bernard G, Demers-Lamarche J, Dicaire MJ, Mathieu J, Vanasse M, Bouchard JP, Rioux MF, Lourenco CM, Li Z, Haueter C, Shoubridge EA, Graham BH, Brais B, Bellen HJ. Mutations in the mitochondrial methionyl-tRNA synthetase cause a neurodegenerative phenotype in flies and a recessive ataxia (ARSAL) in humans. PLoS Biol 2012; 10:e1001288. [PMID: 22448145 PMCID: PMC3308940 DOI: 10.1371/journal.pbio.1001288] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 02/08/2012] [Indexed: 11/23/2022] Open
Abstract
The study of Drosophila neurodegenerative mutants combined with genetic and biochemical analyses lead to the identification of multiple complex mutations in 60 patients with a novel form of ataxia/leukoencephalopathy. An increasing number of genes required for mitochondrial biogenesis, dynamics, or function have been found to be mutated in metabolic disorders and neurological diseases such as Leigh Syndrome. In a forward genetic screen to identify genes required for neuronal function and survival in Drosophila photoreceptor neurons, we have identified mutations in the mitochondrial methionyl-tRNA synthetase, Aats-met, the homologue of human MARS2. The fly mutants exhibit age-dependent degeneration of photoreceptors, shortened lifespan, and reduced cell proliferation in epithelial tissues. We further observed that these mutants display defects in oxidative phosphorylation, increased Reactive Oxygen Species (ROS), and an upregulated mitochondrial Unfolded Protein Response. With the aid of this knowledge, we identified MARS2 to be mutated in Autosomal Recessive Spastic Ataxia with Leukoencephalopathy (ARSAL) patients. We uncovered complex rearrangements in the MARS2 gene in all ARSAL patients. Analysis of patient cells revealed decreased levels of MARS2 protein and a reduced rate of mitochondrial protein synthesis. Patient cells also exhibited reduced Complex I activity, increased ROS, and a slower cell proliferation rate, similar to Drosophila Aats-met mutants. Neurodegenerative diseases, as a group, are relatively common and often devastating to those who suffer from them. Key insights are emerging from the study of homologues of identified human disease-causing genes in model organisms such as fruit flies, worms, and mice. In this study, we used the fruit fly to identify novel neurodegeneration-causing mutations and identified the Aats-met gene, whose protein product is involved in mitochondrial translation. We found that mutations in this gene cause neurodegeneration, impaired mitochondrial activity, and elevated oxidative stress. We were able to attenuate these defects with antioxidants like Vitamin E. We also determined that unusual duplications in the homologous human gene, MARS2, were responsible for a novel type of progressive ataxia found in some French Canadian families. Cells taken from these patients have many of the characteristic defects observed in flies, showing that the fly mutants can be used to further explore disease mechanisms and test potential treatments.
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Affiliation(s)
- Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, United States of America
| | - Isabelle Thiffault
- Laboratoire de Neurogénétique de la Motricité, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
- Department of Human Genetics, Montreal Neurological Institute–McGill University, Montréal, Québec, Canada
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Martine Tétreault
- Laboratoire de Neurogénétique de la Motricité, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Taraka Donti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Florin Sasarman
- Department of Human Genetics, Montreal Neurological Institute–McGill University, Montréal, Québec, Canada
| | - Geneviève Bernard
- Laboratoire de Neurogénétique de la Motricité, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Julie Demers-Lamarche
- Laboratoire de Neurogénétique de la Motricité, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Marie-Josée Dicaire
- Laboratoire de Neurogénétique de la Motricité, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Jean Mathieu
- Clinique des Maladies Neuromusculaires, Centre de Santé et de Services Sociaux de Jonquière, Saguenay, Québec, Canada
| | - Michel Vanasse
- Clinique des Maladies Neuromusculaires, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
| | - Jean-Pierre Bouchard
- Service de Neurologie, Centre Hospitalier Affilié Universitaire de Québec–Hôpital de l'Enfant-Jésus, Université Laval, Québec, Québec, Canada
| | - Marie-France Rioux
- Service de Neurologie, Centre hospitalier de l'Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Charles M. Lourenco
- Department of Medical Genetics, University of São Paulo, Ribeirao Preto–São Paulo, Brazil
| | - Zhihong Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Claire Haueter
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
| | - Eric A. Shoubridge
- Department of Human Genetics, Montreal Neurological Institute–McGill University, Montréal, Québec, Canada
| | - Brett H. Graham
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Bernard Brais
- Laboratoire de Neurogénétique de la Motricité, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
- Department of Human Genetics, Montreal Neurological Institute–McGill University, Montréal, Québec, Canada
- Clinique des Maladies Neuromusculaires, Centre de Santé et de Services Sociaux de Jonquière, Saguenay, Québec, Canada
- Clinique des Maladies Neuromusculaires, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- * E-mail: (BB); (HJB)
| | - Hugo J. Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (BB); (HJB)
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Aradhya S, Lewis R, Bonaga T, Nwokekeh N, Stafford A, Boggs B, Hruska K, Smaoui N, Compton JG, Richard G, Suchy S. Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders. Genet Med 2012; 14:594-603. [PMID: 22382802 DOI: 10.1038/gim.2011.65] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Mendelian disorders are most commonly caused by mutations identifiable by DNA sequencing. Exonic deletions and duplications can go undetected by sequencing, and their frequency in most Mendelian disorders is unknown. METHODS We designed an array comparative genomic hybridization (CGH) test with probes in exonic regions of 589 genes. Targeted testing was performed for 219 genes in 3,018 patients. We demonstrate for the first time the utility of exon-level array CGH in a large clinical cohort by testing for 136 autosomal dominant, 53 autosomal recessive, and 30 X-linked disorders. RESULTS Overall, 98 deletions and two duplications were identified in 53 genes, corresponding to a detection rate of 3.3%. Approximately 40% of positive findings were deletions of only one or two exons. A high frequency of deletions was observed for several autosomal dominant disorders, with a detection rate of 2.9%. For autosomal recessive disorders, array CGH was usually performed after a single mutation was identified by sequencing. Among 138 individuals tested for recessive disorders, 10.1% had intragenic deletions. For X-linked disorders, 3.5% of 313 patients carried a deletion or duplication. CONCLUSION Our results demonstrate that exon-level array CGH provides a robust option for intragenic copy number analysis and should routinely supplement sequence analysis for Mendelian disorders.
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Granberg CF, Harrison SM, Dajusta D, Zhang S, Hajarnis S, Igarashi P, Baker LA. Genetic basis of prune belly syndrome: screening for HNF1β gene. J Urol 2012; 187:272-8. [PMID: 22114815 PMCID: PMC3399512 DOI: 10.1016/j.juro.2011.09.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Indexed: 11/21/2022]
Abstract
PURPOSE Although the cause of prune belly syndrome is unknown, familial evidence suggests a genetic component. Recently 2 nonfamilial cases of prune belly syndrome with chromosome 17q12 deletions encompassing the HNF1β gene have made this a candidate gene for prune belly syndrome. To date, there has been no large-scale screening of patients with prune belly syndrome for HNF1β mutations. We assessed the role of HNF1β in prune belly syndrome by screening for genomic mutations with functional characterization of any detected mutations. MATERIALS AND METHODS We studied patients with prune belly syndrome who were prospectively enrolled in our Pediatric Genitourinary DNA Repository since 2001. DNA from patient samples was amplified by polymerase chain reaction, sequenced for coding and splice regions of the HNF1β gene, and compared to control databases. We performed functional assay testing of the ability of mutant HNF1β to activate a luciferase construct with an HNF1β DNA binding site. RESULTS From 32 prune belly syndrome probands (30 males, 2 females) HNF1β sequencing detected a missense mutation (V61G) in 1 child with prune belly syndrome. Absent in control databases, V61G was previously reported in 2 patients without prune belly syndrome who had congenital genitourinary anomalies. Functional testing showed similar luciferase activity compared to wild-type HNF1β, suggesting the V61G substitution does not disturb HNF1β function. CONCLUSIONS One genomic HNF1β mutation was detected in 3% of patients with prune belly syndrome but found to be functionally normal. Thus, functionally significant HNF1β mutations are uncommon in prune belly syndrome, despite case reports of HNF1β deletions. Further genetic study is necessary, as identification of the genetic basis of prune belly syndrome may ultimately lead to prevention and improved treatments for this rare but severe syndrome.
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Affiliation(s)
| | | | - Daniel Dajusta
- Department of Urology (CFG, SMH, DD, SZ, LAB) and Department of Internal Medicine (SH, PI), University of Texas Southwestern, Dallas, Texas
| | - Shaohua Zhang
- Department of Urology (CFG, SMH, DD, SZ, LAB) and Department of Internal Medicine (SH, PI), University of Texas Southwestern, Dallas, Texas
| | - Sachin Hajarnis
- Department of Urology (CFG, SMH, DD, SZ, LAB) and Department of Internal Medicine (SH, PI), University of Texas Southwestern, Dallas, Texas
| | - Peter Igarashi
- Department of Urology (CFG, SMH, DD, SZ, LAB) and Department of Internal Medicine (SH, PI), University of Texas Southwestern, Dallas, Texas
| | - Linda A. Baker
- Department of Urology (CFG, SMH, DD, SZ, LAB) and Department of Internal Medicine (SH, PI), University of Texas Southwestern, Dallas, Texas
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Pong AW, Pal DK, Chung WK. Developments in molecular genetic diagnostics: an update for the pediatric epilepsy specialist. Pediatr Neurol 2011; 44:317-27. [PMID: 21481738 DOI: 10.1016/j.pediatrneurol.2011.01.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 08/31/2010] [Accepted: 01/31/2011] [Indexed: 02/02/2023]
Abstract
The contributions of genetic influences in both rare and common epilepsies are rapidly being elucidated, and neurologists routinely consider genetic testing in the workup of numerous epilepsy syndromes. Trends in patient attitudes and developments in clinical molecular diagnostics will increase interest in, and the availability of genetic tests for, genetic evaluations of epilepsies. We review recent and planned developments in clinical genetic testing platforms, including their indications, strengths, and limitations. We discuss genome-wide microarray methods (i.e., methods to detect copy number variations), karyotypes, and sequence-based testing. We outline the general approach to genetic evaluations of epilepsy, emphasizing the importance of clinical evaluations, and provide online clinical resources. Finally, we present potential social, legal, and financial barriers to genetic evaluations, and discuss concerns regarding clinical utility and recurrence risk. This review provides a practical overview of molecular diagnostics for the neurologist in the genetic evaluation of epilepsies in 2011.
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Affiliation(s)
- Amanda W Pong
- Department of Neurology, Neurological Institute, Columbia University Medical Center, Columbia University, New York, New York 10032, USA.
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Boone PM, Bacino CA, Shaw CA, Eng PA, Hixson PM, Pursley AN, Kang SHL, Yang Y, Wiszniewska J, Nowakowska BA, del Gaudio D, Xia Z, Simpson-Patel G, Immken LL, Gibson JB, Tsai ACH, Bowers JA, Reimschisel TE, Schaaf CP, Potocki L, Scaglia F, Gambin T, Sykulski M, Bartnik M, Derwinska K, Wisniowiecka-Kowalnik B, Lalani SR, Probst FJ, Bi W, Beaudet AL, Patel A, Lupski JR, Cheung SW, Stankiewicz P. Detection of clinically relevant exonic copy-number changes by array CGH. Hum Mutat 2010; 31:1326-42. [PMID: 20848651 DOI: 10.1002/humu.21360] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/02/2010] [Indexed: 12/22/2022]
Abstract
Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications--those including genomic intervals of a size smaller than a gene--have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.
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Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Genetic screening for OPA1 and OPA3 mutations in patients with suspected inherited optic neuropathies. Ophthalmology 2010; 118:558-63. [PMID: 21036400 DOI: 10.1016/j.ophtha.2010.07.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 06/11/2010] [Accepted: 07/29/2010] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Autosomal-dominant optic atrophy (DOA) is one of the most common inherited optic neuropathies, and it is genetically heterogeneous, with mutations in both OPA1 and OPA3 known to cause disease. Approximately 60% of cases harbor OPA1 mutations, whereas OPA3 mutations have been reported in only 2 pedigrees with DOA and premature cataracts. The aim of this study was to determine the yield of OPA1 and OPA3 screening in a cohort of presumed DOA cases referred to a tertiary diagnostic laboratory. DESIGN Retrospective case series. PARTICIPANTS One hundred eighty-eight probands with bilateral optic atrophy referred for molecular genetic investigations at a tertiary diagnostic facility: 38 patients with an autosomal-dominant pattern of inheritance and 150 sporadic cases. METHODS OPA1 and OPA3 genetic testing was initially performed using polymerase chain reaction-based sequencing methods. The presence of large-scale OPA1 and OPA3 genomic rearrangements was assessed further with a targeted comparative genomic hybridization microarray platform. The 3 primary Leber hereditary optic neuropathy (LHON) mutations, m.3460G→>A, m.11778G→A, and m.14484T→C, also were screened in all patients. MAIN OUTCOME MEASURES The proportion of patients with OPA1 and OPA3 pathogenic mutations. The clinical profile observed in molecularly confirmed DOA cases. RESULTS Twenty-one different OPA1 mutations were found in 27 (14.4%) of the 188 probands screened. The mutations included 6 novel pathogenic variants and the first reported OPA1 initiation codon mutation at c.1A→T. An OPA1 missense mutation, c.239A→G (p.Y80C), was identified in an 11-year-old black girl with optic atrophy and peripheral sensorimotor neuropathy in her lower limbs. The OPA1 detection rate was significantly higher among individuals with a positive family history of visual failure (50.0%) compared with sporadic cases (5.3%). The primary LHON screen was negative in the patient cohort, and additional molecular investigations did not reveal any large-scale OPA1 rearrangements or OPA3 genetic defects. The mean baseline visual acuity for the OPA1-positive group was 0.48 logarithm of the minimum angle of resolution (units mean Snellen equivalent, 20/61; range, 20/20-20/400; 95% confidence interval, 20/52-20/71), and visual deterioration occurred in 54.2% of patients during follow-up. CONCLUSIONS OPA1 mutations are the most common genetic defects identified in patients with suspected DOA, whereas OPA3 mutations are very rare in isolated optic atrophy cases.
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