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Szafranski P, Patrizi S, Gambin T, Afzal B, Schlotterbeck E, Karolak JA, Deutsch G, Roberts D, Stankiewicz P. Diminished TMEM100 Expression in a Newborn With Acinar Dysplasia and a Novel TBX4 Variant: A Case Report. Pediatr Dev Pathol 2024; 27:255-259. [PMID: 38044468 PMCID: PMC11087193 DOI: 10.1177/10935266231213464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Acinar dysplasia (AcDys) of the lung is a rare lethal developmental disorder in neonates characterized by severe respiratory failure and pulmonary arterial hypertension refractory to treatment. Recently, abnormalities of TBX4-FGF10-FGFR2-TMEM100 signaling regulating lung development have been reported in patients with AcDys due to heterozygous single-nucleotide variants or copy-number variant deletions involving TBX4, FGF10, or FGFR2. Here, we describe a female neonate who died at 4 hours of life due to severe respiratory distress related to AcDys diagnosed by postmortem histopathologic evaluation. Genomic analyses revealed a novel deleterious heterozygous missense variant c.728A>C (p.Asn243Thr) in TBX4 that arose de novo on paternal chromosome 17. We also identified 6 candidate hypomorphic rare variants in the TBX4 enhancer in trans to TBX4 coding variant. Gene expression analyses of proband's lung tissue showed a significant reduction of TMEM100 expression with near absence of TMEM100 within the endothelium of arteries and capillaries by immunohistochemistry. These results support the pathogenicity of the detected TBX4 variant and provide further evidence that disrupted signaling between TBX4 and TMEM100 may contribute to severe lung phenotypes in humans, including AcDys.
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Affiliation(s)
| | - Silvia Patrizi
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital and Newton-Wellesley Hospital, Harvard Medical School, Boston, MA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Bushra Afzal
- Division of Neonatology, Department of Pediatrics, Harvard University School of Medicine, Boston, MA
| | - Emily Schlotterbeck
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. WRN 219, Boston, MA
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Gail Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Drucilla Roberts
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. WRN 219, Boston, MA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
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2
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Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny D, Fatih JM, Yesil G, Elçioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res 2024; 52:e18. [PMID: 38153174 PMCID: PMC10899794 DOI: 10.1093/nar/gkad1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/18/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Homozygous duplications contribute to genetic disease by altering gene dosage or disrupting gene regulation and can be more deleterious to organismal biology than heterozygous duplications. Intragenic exonic duplications can result in loss-of-function (LoF) or gain-of-function (GoF) alleles that when homozygosed, i.e. brought to homozygous state at a locus by identity by descent or state, could potentially result in autosomal recessive (AR) rare disease traits. However, the detection and functional interpretation of homozygous duplications from exome sequencing data remains a challenge. We developed a framework algorithm, HMZDupFinder, that is designed to detect exonic homozygous duplications from exome sequencing (ES) data. The HMZDupFinder algorithm can efficiently process large datasets and accurately identifies small intragenic duplications, including those associated with rare disease traits. HMZDupFinder called 965 homozygous duplications with three or less exons from 8,707 ES with a recall rate of 70.9% and a precision of 16.1%. We experimentally confirmed 8/10 rare homozygous duplications. Pathogenicity assessment of these copy number variant alleles allowed clinical genomics contextualization for three homozygous duplications alleles, including two affecting known OMIM disease genes EDAR (MIM# 224900), TNNT1(MIM# 605355), and one variant in a novel candidate disease gene: PAAF1.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gozde Yesil
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul 34093, Turkey
| | - Nursel H Elçioglu
- Department of Pediatric Genetics, Marmara University Medical Faculty, Istanbul and Eastern Mediterranean University Faculty of Medicine, Mersin 10, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, 34480 Istanbul, Turkey
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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3
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia. Hum Genet 2023; 142:721-733. [PMID: 37031326 PMCID: PMC10996436 DOI: 10.1007/s00439-023-02550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Baylor Genetics, Houston, TX, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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4
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant - Fanconi anemia. Res Sq 2023:rs.3.rs-2628288. [PMID: 36909564 PMCID: PMC10002829 DOI: 10.21203/rs.3.rs-2628288/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C . Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5%-37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the rare phenomenon of hypermutation. Eight-hundred-thirty apparent dnSNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component with an average VAF of 25% (range: 18.7-37.41%) (n=446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range: 9.55-18.69%) (n=384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA, and pregnancy loss in general. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics, Houston, TX
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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5
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Wiewiórka M, Szmurło A, Stankiewicz P, Gambin T. Cloud-native distributed genomic pileup operations. Bioinformatics 2022; 39:6900922. [PMID: 36515465 PMCID: PMC9848050 DOI: 10.1093/bioinformatics/btac804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/16/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Pileup analysis is a building block of many bioinformatics pipelines, including variant calling and genotyping. This step tends to become a bottleneck of the entire assay since the straightforward pileup implementations involve processing of all base calls from all alignments sequentially. On the other hand, a distributed version of the algorithm faces the intrinsic challenge of splitting reads-oriented file formats into self-contained partitions to avoid costly data exchange between computational nodes. RESULTS Here, we present a scalable, distributed and efficient implementation of a pileup algorithm that is suitable for deploying in cloud computing environments. In particular, we implemented: (i) our custom data-partitioning algorithm optimized to work with the alignment reads, (ii) a novel and unique approach to process alignment events from sequencing reads using the MD tags, (iii) the source code micro-optimizations for recurrent operations, and (iv) a modular structure of the algorithm. We have proven that our novel approach consistently and significantly outperforms other state-of-the-art distributed tools in terms of execution time (up to 6.5× faster) and memory usage (up to 2× less), resulting in a substantial cloud cost reduction. SeQuiLa is a cloud-native solution that can be easily deployed using any managed Kubernetes and Hadoop services available in public clouds, like Microsoft Azure Cloud, Google Cloud Platform, or Amazon Web Services. Together with the already implemented distributed range join and coverage calculations, our package provides end-users with a unified SQL interface for convenient analyses of population-scale genomic data in an interactive way. AVAILABILITY AND IMPLEMENTATION https://biodatageeks.github.io/sequila/.
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Affiliation(s)
| | | | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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6
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Matsika A, McManus S, Scott HS, Arts P, Ha T, Barnett CP, Rodgers J, Stankiewicz P. Variable expressivity in a four-generation ACDMPV family with a non-coding hypermorphic SNV in trans to the frameshifting FOXF1 variant. Eur J Hum Genet 2022; 30:1182-1186. [PMID: 35902696 PMCID: PMC9554184 DOI: 10.1038/s41431-022-01159-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022] Open
Abstract
Heterozygous single nucleotide variants (SNVs) or copy-number variant deletions involving FOXF1 or its distant lung-specific enhancer on chromosome 16q24.1 have been identified in 80-90% of patients with Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe a four-generation family with a deceased ACDMPV neonate, her sibling from the electively terminated pregnancy, healthy mother with a history of pulmonary arterial hypertension (PAH), an unaffected aunt, an aunt deceased due to findings consistent with ACDMPV, and a reportedly unaffected grandmother, all with the frameshifting variant c.881_902dup (p.Gly302Profs*46) in FOXF1, and a deceased great-grandmother with a history of PAH. Genome sequencing analyses in the proband's unaffected mother revealed a non-coding putative regulatory SNV rs560517434-A within the lung-specific distant FOXF1 enhancer in trans to the FOXF1 frameshift mutation. Functional testing of this variant using an in vitro luciferase reporter assay showed that it increased FOXF1 promoter activity 10-fold. Our studies further demonstrate that non-coding SNVs in the FOXF1 enhancer region can rescue the lethal ACDMPV phenotype and support the compound inheritance gene dosage model.
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Affiliation(s)
- Esra Yıldız Bölükbaşı
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Admire Matsika
- Mater Pathology, Mater Hospital Brisbane, South Brisbane, QLD, Australia
| | - Sam McManus
- Mater Pathology, Mater Hospital Brisbane, South Brisbane, QLD, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, , SA Pathology, Adelaide, SA, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Christopher P Barnett
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Jonathan Rodgers
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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7
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Willard N, Abman SH, Galambos C, Kinsella JP, Stankiewicz P. High-level gonosomal mosaicism for a pathogenic non-coding CNV deletion of the lung-specific FOXF1 enhancer in an unaffected mother of an infant with ACDMPV. Mol Genet Genomic Med 2022; 10:e2062. [PMID: 36124617 PMCID: PMC9651602 DOI: 10.1002/mgg3.2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) results from haploinsufficiency of the mesenchymal transcription factor FOXF1 gene. To date, only one case of an ACDMPV-causative CNV deletion inherited from a very-low level somatic mosaic mother has been reported. METHODS Clinical, histopathological, and molecular studies, including whole genome sequencing, chromosomal microarray analysis, qPCR, and Sanger sequencing, followed by in vitro fertilization (IVF) with preimplantation genetic testing (PGT) were used to study a family with a deceased neonate with ACDMPV. RESULTS A pathogenic CNV deletion of the lung-specific FOXF1 enhancer in the proband was found to be inherited from an unaffected mother, 36% mosaic for this deletion in her peripheral blood cells. The qPCR analyses of saliva, buccal cells, urine, nail, and hair samples revealed 19%, 18%, 15%, 19%, and 27% variant allele fraction, respectively, indicating a high recurrence risk. Grandparental studies revealed that the deletion arose on the mother's paternal chromosome 16. PGT studies revealed 44% embryos with the deletion, reflecting high-level germline mosaicism. CONCLUSION Our data further demonstrate the importance of parental testing in ACDMPV families and reproductive usefulness of IVF with PGT in families with high-level parental gonosomal mosaicism.
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Affiliation(s)
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical MicrobiologyPoznan University of Medical SciencesPoznanPoland
| | | | - Tomasz Gambin
- Institute of Computer ScienceWarsaw University of TechnologyWarsawPoland
| | - Nicholas Willard
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Steven H. Abman
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Csaba Galambos
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA,Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - John P. Kinsella
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Paweł Stankiewicz
- Department of Molecular & Human GeneticsBaylor College of MedicineHoustonTexasUSA
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8
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Tóth A, Demcsák A, Zankl F, Oracz G, Unger LS, Bugert P, Laumen H, Párniczky A, Hegyi P, Rosendahl J, Gambin T, Płoski R, Koziel D, Gluszek S, Lindgren F, Löhr JM, Sahin-Tóth M, Witt H, Rygiel AM, Ewers M, Hegyi E. Loss-of-function variant in chymotrypsin like elastase 3B (CELA3B) is associated with non-alcoholic chronic pancreatitis. Pancreatology 2022; 22:713-718. [PMID: 35773178 PMCID: PMC9474678 DOI: 10.1016/j.pan.2022.06.258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/20/2022] [Accepted: 06/19/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genetic alterations in digestive enzymes have been associated with chronic pancreatitis (CP). Recently, chymotrypsin like elastase 3B (CELA3B) emerged as a novel risk gene. Thus, we evaluated CELA3B in two European cohorts with CP. METHODS We analyzed all 8 CELA3B exons in 550 German non-alcoholic CP (NACP) patients and in 241 German controls by targeted DNA sequencing. In addition, we analyzed exons 6 and 7 by Sanger sequencing and the c.129+1G>A variant by melting curve analysis in 1078 further German controls. As replication cohort, we investigated up to 243 non-German European NACP patients and up to 1665 controls originating from Poland, Hungary, and Sweden. We assessed the cellular secretion and the elastase activity of recombinant CELA3B variants. RESULTS In the German discovery cohort, we detected a splice-site variant in intron 2, c.129+1G>A, in 9/550 (1.64%) CP patients and in 5/1319 (0.38%) controls (P=0.007, OR=4.4, 95% CI=1.5-13.0). In the European replication cohort, this variant was also enriched in patients (9/178 [5.06%]) versus controls (13/1247 [1.04%]) (P=0.001, OR=5.1, 95% CI=2.1-12.0). We did not find the two previously reported codon 90 variants, p.R90C and p.R90L. CONCLUSIONS Our data indicate that CELA3B is a susceptibility gene for CP. In contrast to previous reports suggesting that increased CELA3B activity is associated with CP risk, the splice-site variant identified here is predicted to cause diminished CELA3B expression. How reduced CELA3B function predisposes to pancreatitis remains to be elucidated.
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Affiliation(s)
- Andrea Tóth
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Alexandra Demcsák
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, United States
| | - Florence Zankl
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Grzegorz Oracz
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Lara Sophie Unger
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service of Baden-Württemberg, Mannheim, Germany
| | - Helmut Laumen
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany; Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Párniczky
- Heim Pál National Pediatric Institute, Budapest, Hungary; Institute for Translational Medicine, Medical School, Szentágothai Research Center, University of Pécs, Pécs, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, Szentágothai Research Center, University of Pécs, Pécs, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Koziel
- Collegium Medicum, Jan Kochanowski University of Kielce, Poland
| | | | - Fredrik Lindgren
- Department of Pediatric, Karolinska University Hospital, Stockholm, Sweden
| | - J Matthias Löhr
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Miklós Sahin-Tóth
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, United States
| | - Heiko Witt
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | | | - Maren Ewers
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany.
| | - Eszter Hegyi
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Institute for Translational Medicine, Medical School, Szentágothai Research Center, University of Pécs, Pécs, Hungary.
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9
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. Mutat Res Rev Mutat Res 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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10
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Karolak JA, Deutsch G, Gambin T, Szafranski P, Popek E, Stankiewicz P. Transcriptome and Immunohistochemical Analyses in TBX4- and FGF10-Deficient Lungs Imply TMEM100 as a Mediator of Human Lung Development. Am J Respir Cell Mol Biol 2022; 66:694-697. [PMID: 35648090 PMCID: PMC9163642 DOI: 10.1165/rcmb.2021-0470le] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Gail Deutsch
- University of Washington School of MedicineSeattle, Washington
| | - Tomasz Gambin
- Baylor College of MedicineHouston, Texas
- Warsaw University of TechnologyWarsaw, Poland
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11
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Rygiel AM, Unger LS, Sörgel FL, Masson E, Matsumoto R, Ewers M, Chen JM, Bugert P, Buscail L, Gambin T, Oracz G, Winiewska-Szajewska M, Mianowska A, Poznanski J, Kosińska J, Stawinski P, Płoski R, Koziel D, Gluszek S, Laumen H, Lindgren F, Löhr JM, Orekhova A, Rebours V, Rosendahl J, Párniczky A, Hegyi P, Sasaki A, Kataoka F, Tanaka Y, Hamada S, Sahin-Tóth M, Hegyi E, Férec C, Masamune A, Witt H. Variants in the pancreatic CUB and zona pellucida-like domains 1 (CUZD1) gene in early-onset chronic pancreatitis - A possible new susceptibility gene. Pancreatology 2022; 22:564-571. [PMID: 35589511 PMCID: PMC9250292 DOI: 10.1016/j.pan.2022.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Non-alcoholic chronic pancreatitis (NACP) frequently develops in the setting of genetic susceptibility associated with alterations in genes that are highly expressed in the pancreas. However, the genetic basis of NACP remains unresolved in a significant number of patients warranting a search for further risk genes. DESIGN We analyzed CUZD1, which encodes the CUB and zona pellucida-like domains 1 protein that is found in high levels in pancreatic acinar cells. We sequenced the coding region in 1163 European patients and 2018 European controls. In addition, we analyzed 297 patients and 1070 controls from Japan. We analyzed secretion of wild-type and mutant CUZD1 from transfected cells using Western blotting. RESULTS In the European cohort, we detected 30 non-synonymous variants. Using different prediction tools (SIFT, CADD, PROVEAN, PredictSNP) or the combination of these tools, we found accumulation of predicted deleterious variants in patients (p-value range 0.002-0.013; OR range 3.1-5.2). No association was found in the Japanese cohort, in which 13 non-synonymous variants were detected. Functional studies revealed >50% reduced secretion of 7 variants, however, these variants were not significantly enriched in European CP patients. CONCLUSION Our data indicate that CUZD1 might be a novel susceptibility gene for NACP. How these variants predispose to pancreatitis remains to be elucidated.
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Affiliation(s)
| | - Lara Sophie Unger
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine EKFZ, Technical University Munich TUM, Freising, Germany
| | - Franziska Lena Sörgel
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine EKFZ, Technical University Munich TUM, Freising, Germany
| | - Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Ryotaro Matsumoto
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Maren Ewers
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine EKFZ, Technical University Munich TUM, Freising, Germany
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service of Baden-Württemberg, Mannheim, Germany
| | - Louis Buscail
- Department of Gastroenterology and Pancreatology, CHU Rangueil and University of Toulouse, Toulouse, France
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Grzegorz Oracz
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Maria Winiewska-Szajewska
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Mianowska
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Jarosław Poznanski
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Koziel
- Collegium Medicum, Jan Kochanowski University of Kielce, Poland
| | | | - Helmut Laumen
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine EKFZ, Technical University Munich TUM, Freising, Germany; Department of Internal Medicine I, Martin Luther University, Halle, Germany
| | - Fredrik Lindgren
- Department of Pediatric, Karolinska University Hospital, Stockholm, Sweden
| | - J Matthias Löhr
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Orekhova
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States
| | - Vinciane Rebours
- Pancreatology and Digestive Oncology Department, Beaujon Hospital, Clichy, APHP, Université de Paris, Paris, France
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin Luther University, Halle, Germany
| | - Andrea Párniczky
- Heim Pál National Pediatric Institute, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Akira Sasaki
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiya Kataoka
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yu Tanaka
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Miklós Sahin-Tóth
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, United States
| | - Eszter Hegyi
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Heiko Witt
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine EKFZ, Technical University Munich TUM, Freising, Germany.
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12
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Yıldız Bölükbaşı E, Karolak JA, Gambin T, Szafranski P, Deutsch GH, Stankiewicz P. Do paternal deletions involving the FOXF1 locus on chromosome 16q24.1 manifest with more severe non-lung anomalies? Eur J Med Genet 2022; 65:104519. [PMID: 35533956 PMCID: PMC10022888 DOI: 10.1016/j.ejmg.2022.104519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 12/31/2022]
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal lung developmental disorder in neonates due to heterozygous loss-of-function of the mesenchymal transcription factor gene, FOXF1. Interestingly, unlike ACDMPV-causing point mutations in FOXF1 that can be inherited from the mother or father, causative copy-number variant (CNV) deletions arise de novo and almost exclusively on chromosome 16 inherited from the mother (n = 50 vs. n = 3). Here, we describe a fourth case of a de novo paternal CNV deletion encompassing FOXF1, its neighboring long non-coding RNA gene FENDRR, and their distant lung-specific enhancer, identified in a 21-week-old fetus with tetralogy of Fallot, gastrointestinal and genitourinary abnormalities, a single umbilical artery, and patchy histopathological findings of ACDMPV in autopsy lung. We also review the ACDMPV-causative CNV deletions detected prenatally and propose that the majority of paternal deletions manifest with more severe additional non-lung abnormalities.
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Affiliation(s)
- Esra Yıldız Bölükbaşı
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gail H Deutsch
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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13
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Murik O, Zeevi DA, Altarescu G, Stankiewicz P. Exacerbation of mild lung disorders to lethal pulmonary hypoplasia by a noncoding hypomorphic SNV in a lung-specific enhancer in trans to the frameshifting TBX4 variant. Am J Med Genet A 2022; 188:1420-1425. [PMID: 35075769 PMCID: PMC8995354 DOI: 10.1002/ajmg.a.62656] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022]
Abstract
Variants involving TBX4 are associated with a wide variety of disorders, including pulmonary arterial hypertension, ischiocoxopodopatellar syndrome (ICPPS)/small patella syndrome (SPS), lethal lung developmental disorders (LLDDs) in neonates, heart defects, and prenatally lethal posterior amelia with pelvic and pulmonary hypoplasia syndrome. The objective of our study was to elucidate the wide variable phenotypic expressivity and incomplete penetrance in a three-generation family with a truncating variant in TBX4. In addition to exome and genome sequencing analyses, a candidate noncoding regulatory single nucleotide variant (SNV) within the lung-specific TBX4 enhancer was functionally tested using an in vitro luciferase reporter assay. A heterozygous frameshift variant c.1112dup (p.Pro372Serfs*14) in TBX4 was identified in patients with mild interstitial lung disease (1), bronchiolitis obliterans (1), recurrent pneumothorax (1), ICPPS/SPS (1), LLDD (2), and in unaffected individuals (4). In two deceased neonates with LLDD, we identified a noncoding SNV rs62069651-C located in trans to the mutated TBX4 allele that reduced the TBX4 promoter activity by 63% in the reporter assay. Our findings provide a functional evidence for the recently reported model of complex compound inheritance in which both TBX4 coding and in trans noncoding hypomorphic variants in the lung-specific enhancer of TBX4 contribute to LLDD.
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Affiliation(s)
- Esra Yıldız Bölükbaşı
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Omer Murik
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - David A Zeevi
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Gheona Altarescu
- Preimplantation Genetic Unit, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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14
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Domogala DD, Gambin T, Zemet R, Wu CW, Schulze KV, Yang Y, Wilson TA, Machol I, Liu P, Stankiewicz P. Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset. Hum Genomics 2021; 15:72. [PMID: 34930489 PMCID: PMC8686574 DOI: 10.1186/s40246-021-00369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. METHODS Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). RESULTS In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. CONCLUSIONS Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.
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Affiliation(s)
- Daniel D Domogala
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas at MD Anderson, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chung Wah Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- AiLife Diagnostics, 1920 Country Place Pkwy Suite 100, Pearland, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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15
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Oracz G, Zaród M, Ewers M, Laumen H, Gambin T, Kamiński P, Grabowska I, Drożak A, Kwiatkowski S, Wertheim-Tysarowska K, Kołodziejczyk E, Domaszewicz A, Dorożko B, Kosińska J, Głuszek S, Kozieł D, Płoski R, Rosendahl J, Witt H, Drożak J, Rygiel AM. Loss of function TRPV6 variants are associated with chronic pancreatitis in nonalcoholic early-onset Polish and German patients. Pancreatology 2021; 21:1434-1442. [PMID: 34538581 DOI: 10.1016/j.pan.2021.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 12/11/2022]
Abstract
PURPOSE Loss of function variants of the transient receptor potential cation channel, subfamily V, member 6 (TRPV6) have been recently associated with chronic pancreatitis (CP) in Japanese, German and French patients. Here, we investigated the association of TRPV6 variants with CP in independent European cohorts of early-onset CP patients from Poland and Germany. PATIENTS AND METHODS We enrolled 152 pediatric CP patients (median age 8.6 yrs) with no history of alcohol/smoking abuse and 472 controls from Poland as well as 157 nonalcoholic young CP patients (median age 20 yrs) and 750 controls from Germany. Coding regions of TRPV6 were screened by Sanger and next generation sequencing. Selected, potentially pathogenic TRPV6 variants were expressed in HEK293T cells and TRPV6 activity was analyzed using ratiometric Ca2+ measurements. RESULTS Overall, we identified 10 novel (3 nonsense and 7 missenses) TRPV6 variants in CP patients. TRPV6 p.V239SfsX53 nonsense variant and the variants showing significant decrease in intracellular Ca2+ concentration in HEK293T cells (p.R174X, p.L576R, p.R342Q), were significantly overrepresented in Polish patients as compared to controls (6/152, 3.9% vs. 0/358, 0%; P = 0,0007). Nonsense TRPV6 variants predicted as loss of function (p.V239SfsX53 and p.R624X) were also significantly overrepresented in German patients (3/157; 2.0% vs 0/750; 0%, P = 0.005). CONCLUSIONS We showed that TRPV6 loss of function variants are associated with elevated CP risk in early-onset Polish and German patients confirming that TRPV6 is a novel CP susceptibility gene.
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Affiliation(s)
- Grzegorz Oracz
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Michał Zaród
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maren Ewers
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Munich, Germany
| | - Helmut Laumen
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Munich, Germany; Department of Internal Medicine I, Martin Luther University, Halle, Germany
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Paweł Kamiński
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Drożak
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Sebastian Kwiatkowski
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Elwira Kołodziejczyk
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Alicja Domaszewicz
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Barbara Dorożko
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Dorota Kozieł
- Collegium Medicum Jan Kochanowski University, Kielce, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin Luther University, Halle, Germany
| | - Heiko Witt
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Munich, Germany
| | - Jakub Drożak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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16
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Karolak JA, Gambin T, Szafranski P, Maywald RL, Popek E, Heaney JD, Stankiewicz P. Perturbation of semaphorin and VEGF signaling in ACDMPV lungs due to FOXF1 deficiency. Respir Res 2021; 22:212. [PMID: 34315444 PMCID: PMC8314029 DOI: 10.1186/s12931-021-01797-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal congenital lung disorder in neonates characterized by severe progressive respiratory failure and refractory pulmonary hypertension, resulting from underdevelopment of the peripheral pulmonary tree. Causative heterozygous single nucleotide variants (SNVs) or copy-number variant (CNV) deletions involving FOXF1 or its distant lung-specific enhancer on chromosome 16q24.1 have been identified in 80-90% of ACDMPV patients. FOXF1 maps closely to and regulates the oppositely oriented FENDRR, with which it also shares regulatory elements. METHODS To better understand the transcriptional networks downstream of FOXF1 that are relevant for lung organogenesis, using RNA-seq, we have examined lung transcriptomes in 12 histopathologically verified ACDMPV patients with or without pathogenic variants in the FOXF1 locus and analyzed gene expression profile in FENDRR-depleted fetal lung fibroblasts, IMR-90. RESULTS RNA-seq analyses in ACDMPV neonates revealed changes in the expression of several genes, including semaphorins (SEMAs), neuropilin 1 (NRP1), and plexins (PLXNs), essential for both epithelial branching and vascular patterning. In addition, we have found deregulation of the vascular endothelial growth factor (VEGF) signaling that also controls pulmonary vasculogenesis and a lung-specific endothelial gene TMEM100 known to be essential in vascular morphogenesis. Interestingly, we have observed a substantial difference in gene expression profiles between the ACDMPV samples with different types of FOXF1 defect. Moreover, partial overlap between transcriptome profiles of ACDMPV lungs with FOXF1 SNVs and FENDRR-depleted IMR-90 cells suggests contribution of FENDRR to ACDMPV etiology. CONCLUSIONS Our transcriptomic data imply potential crosstalk between several lung developmental pathways, including interactions between FOXF1-SHH and SEMA-NRP or VEGF/VEGFR2 signaling, and provide further insight into complexity of lung organogenesis in humans.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznań, Poland
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Rebecca L Maywald
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.
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17
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Jędrzejowska M, Potulska-Chromik A, Gos M, Gambin T, Dębek E, Rosiak E, Stępień A, Szymańczak R, Wojtaś B, Gielniewski B, Ciara E, Sobczyńska A, Chrzanowska K, Kostera-Pruszczyk A, Madej-Pilarczyk A. Floppy infant syndrome as a first manifestation of LMNA-related congenital muscular dystrophy. Eur J Paediatr Neurol 2021; 32:115-121. [PMID: 33940562 DOI: 10.1016/j.ejpn.2021.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 10/21/2022]
Abstract
LMNA-related congenital muscular dystrophy (L-CMD) is the most severe phenotypic form of skeletal muscle laminopathies. This paper reports clinical presentation of the disease in 15 Polish patients from 13 families with genetically confirmed skeletal muscle laminopathy. In all these patients floppy infant syndrome was the first manifestation of the disease. The genetic diagnosis was established by next generation sequencing (targeted panel or exome; 11 patients) or classic Sanger sequencing (4 patients). In addition to known pathogenic LMNA variants: c.116A > G (p.Asn39Ser), c.745C > T (p.Arg249Trp), c.746G > A (p.Arg249Gln), c.1072G > A (p.Glu358Lys), c.1147G > A (p.Glu383Lys), c.1163G > C (p.Arg388Pro), c.1357C > T (p.Arg453Trp), c.1583C > G (p.Thr528Arg), we have identified three novel ones: c.121C > G (p.Arg41Gly), c.1127A > G (p.Tyr376Cys) and c.1160T > C (p.Leu387Pro). Eleven patients had de novo mutations, 4 - familial. In one family we observed intrafamilial variability of clinical course: severe L-CMD in the male proband, intermediate form in his sister and asymptomatic in their mother. One asymptomatic father had somatic mosaicism. L-CMD should be suspected in children with hypotonia in infancy and delayed motor development, who have poor head control, severe hyperlordosis and unstable and awkward gait. Serum creatine kinase may be high (~1000IU/l). Progression of muscle weakness is fast, leading to early immobilization. In some patients with L-CMD joint contractures can develop with time. MRI shows that the most frequently affected muscles are the serratus anterior, lumbar paraspinal, gluteus, vastus, adductor magnus, hamstrings, medial head of gastrocnemius and soleus. Ultra-rare laminopathies can be a relatively common cause of generalized hypotonia in children. Introduction of wide genome sequencing methods was a breakthrough in diagnostics of diseases with great clinical and genetic variability and allowed approach "from genotype do phenotype". However target sequencing of LMNA gene could be considered in selected patients with clinical picture suggestive for laminopathy.
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Affiliation(s)
- Maria Jędrzejowska
- Rare Diseases Research Platform, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland; Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland.
| | | | - Monika Gos
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Emilia Dębek
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Edyta Rosiak
- 2nd Department of Radiology, Medical University of Warsaw, Poland
| | - Agnieszka Stępień
- Faculty of Rehabilitation, Józef Piłsudski University of Physical Education, Warsaw, Poland
| | | | - Bartosz Wojtaś
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartłomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Elżbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
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18
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Szafranski P, Gambin T, Karolak JA, Popek E, Stankiewicz P. Lung-specific distant enhancer cis regulates expression of FOXF1 and lncRNA FENDRR. Hum Mutat 2021; 42:694-698. [PMID: 33739555 DOI: 10.1002/humu.24198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/22/2021] [Accepted: 03/14/2021] [Indexed: 12/21/2022]
Abstract
The FOXF1 gene, causative for a neonatal lethal lung developmental disorder alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), maps 1.7 kb away from the long noncoding RNA gene FENDRR on the opposite strand, suggesting they may be coregulated. Using RNA sequencing in lung tissue from ACDMPV patients with heterozygous deletions of the FOXF1 distant enhancer located 286 kb upstream, leaving FOXF1 and FENDRR intact, we have found that the FENDRR and FOXF1 expressions were reduced by approximately 75% and 50%, respectively, and were monoallelic from the intact chromosome 16q24.1. In contrast, ACDMPV patients with FOXF1 SNVs had biallelic FENDRR expression reduced by 66%-82%. Corroboratively, depletion of FOXF1 by small interfering RNA in lung fibroblasts resulted in a 50% decrease of FENDRR expression. These data indicate that FENDRR expression in the lungs is regulated both in cis by the FOXF1 distant enhancer and in trans by FOXF1. Our findings are compatible with the involvement of FENDRR in FOXF1-related disorders, including ACDMPV.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznań University of Medical Sciences, Poznań, Poland
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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19
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Karolak JA, Gambin T, Szafranski P, Stankiewicz P. Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq. Respir Res 2021; 22:26. [PMID: 33478486 PMCID: PMC7818749 DOI: 10.1186/s12931-021-01617-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Background The epithelial-mesenchymal signaling involving SHH-FOXF1, TBX4-FGF10, and TBX2 pathways is an essential transcriptional network operating during early lung organogenesis. However, precise regulatory interactions between different genes and proteins in this pathway are incompletely understood. Methods To identify TBX2 and TBX4 genome-wide binding sites, we performed chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) in human fetal lung fibroblasts IMR-90. Results We identified 14,322 and 1,862 sites strongly-enriched for binding of TBX2 and TBX4, respectively, 43.95% and 18.79% of which are located in the gene promoter regions. Gene Ontology, pathway enrichment, and DNA binding motif analyses revealed a number of overrepresented cues and transcription factor binding motifs relevant for lung branching that can be transcriptionally regulated by TBX2 and/or TBX4. In addition, TBX2 and TBX4 binding sites were found enriched around and within FOXF1 and its antisense long noncoding RNA FENDRR, indicating that the TBX4-FGF10 cascade may directly interact with the SHH-FOXF1 signaling. Conclusions We highlight the complexity of transcriptional network driven by TBX2 and TBX4 and show that disruption of this crosstalk during morphogenesis can play a substantial role in etiology of lung developmental disorders.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.
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20
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Robak LA, Du R, Yuan B, Gu S, Alfradique-Dunham I, Kondapalli V, Hinojosa E, Stillwell A, Young E, Zhang C, Song X, Du H, Gambin T, Jhangiani SN, Coban Akdemir Z, Muzny DM, Tejomurtula A, Ross OA, Shaw C, Jankovic J, Bi W, Posey JE, Lupski JR, Shulman JM. Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. Neurol Genet 2020; 6:e498. [PMID: 32802956 PMCID: PMC7413630 DOI: 10.1212/nxg.0000000000000498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
Abstract
Objective To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms. Methods We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. Results Using ES, we discovered individuals with known pathogenic SNVs in GBA (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and LRRK2 (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the PRKN locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. Conclusions Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PRKN CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.
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Affiliation(s)
- Laurie A Robak
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Renqian Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Bo Yuan
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shen Gu
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Isabel Alfradique-Dunham
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Vismaya Kondapalli
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Evelyn Hinojosa
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Amanda Stillwell
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Emily Young
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chaofan Zhang
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Xiaofei Song
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Haowei Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Tomasz Gambin
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Donna M Muzny
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Anusha Tejomurtula
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Owen A Ross
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chad Shaw
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joseph Jankovic
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Weimin Bi
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Jennifer E Posey
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - James R Lupski
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joshua M Shulman
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
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21
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Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YH, Cao Y, Coban Akdemir ZH, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny D, Posey JE, Yang Y, Zhang DY, Shaw C, Liu P, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med 2020; 22:1768-1776. [PMID: 32655138 PMCID: PMC7606563 DOI: 10.1038/s41436-020-0897-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose: The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases. Methods: We analyzed approximately 2000 family trio ES datasets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single nucleotide variants (SNVs) identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30-70% in the probands and lower than 10% in one of the parents. Results: Out of 102 candidate mosaic variants validated using amplicon-based NGS, droplet digital PCR, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1-10%) or very low- (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples. Conclusion: Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Nina G Xie
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ed Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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22
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Wiewiórka M, Leśniewska A, Szmurło A, Stępień K, Borowiak M, Okoniewski M, Gambin T. SeQuiLa: an elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals. Bioinformatics 2020; 35:2156-2158. [PMID: 30428005 DOI: 10.1093/bioinformatics/bty940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/23/2018] [Accepted: 11/13/2018] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Efficient processing of large-scale genomic datasets has recently become possible due to the application of 'big data' technologies in bioinformatics pipelines. We present SeQuiLa-a distributed, ANSI SQL-compliant solution for speedy querying and processing of genomic intervals that is available as an Apache Spark package. Proposed range join strategy is significantly (∼22×) faster than the default Apache Spark implementation and outperforms other state-of-the-art tools for genomic intervals processing. AVAILABILITY AND IMPLEMENTATION The project is available at http://biodatageeks.org/sequila/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marek Wiewiórka
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Anna Leśniewska
- Department of Computer Science, Poznan University of Technology, Poznań, Poland
| | - Agnieszka Szmurło
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Kacper Stępień
- Department of Computer Science, Poznan University of Technology, Poznań, Poland
| | - Mateusz Borowiak
- Department of Computer Science, Poznan University of Technology, Poznań, Poland
| | | | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
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23
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Coban-Akdemir ZH, Charng WL, Azamian M, Paine IS, Punetha J, Grochowski CM, Gambin T, Valdes S, Cannon B, Zapata G, Hernandez PP, Jhangiani S, Doddapaneni H, Hu J, Boricha F, Muzny DM, Boerwinkle E, Yang Y, Gibbs RA, Posey JE, Wehrens XH, Belmont JW, Kim JJ, Miyake CY, Lupski JR, Lalani SR. Wolff-Parkinson-White syndrome: De novo variants and evidence for mutational burden in genes associated with atrial fibrillation. Am J Med Genet A 2020; 182:1387-1399. [PMID: 32233023 PMCID: PMC7275694 DOI: 10.1002/ajmg.a.61571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/17/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Wolff-Parkinson-White (WPW) syndrome is a relatively common arrhythmia affecting ~1-3/1,000 individuals. Mutations in PRKAG2 have been described in rare patients in association with cardiomyopathy. However, the genetic basis of WPW in individuals with a structurally normal heart remains poorly understood. Sudden death due to atrial fibrillation (AF) can also occur in these individuals. Several studies have indicated that despite ablation of an accessory pathway, the risk of AF remains high in patients compared to general population. METHODS We applied exome sequencing in 305 subjects, including 65 trios, 80 singletons, and 6 multiple affected families. We used de novo analysis, candidate gene approach, and burden testing to explore the genetic contributions to WPW. RESULTS A heterozygous deleterious variant in PRKAG2 was identified in one subject, accounting for 0.6% (1/151) of the genetic basis of WPW in this study. Another individual with WPW and left ventricular hypertrophy carried a known pathogenic variant in MYH7. We found rare de novo variants in genes associated with arrhythmia and cardiomyopathy (ANK2, NEBL, PITX2, and PRDM16) in this cohort. There was an increased burden of rare deleterious variants (MAF ≤ 0.005) with CADD score ≥ 25 in genes linked to AF in cases compared to controls (P = .0023). CONCLUSIONS Our findings show an increased burden of rare deleterious variants in genes linked to AF in WPW syndrome, suggesting that genetic factors that determine the development of accessory pathways may be linked to an increased susceptibility of atrial muscle to AF in a subset of patients.
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Affiliation(s)
- Zeynep H. Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- These authors contributed equally to the work
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Current affiliation: Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
- These authors contributed equally to the work
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ingrid Sophie Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Current affiliation: Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Santiago Valdes
- Department of Pediatrics, Division of Cardiology, Texas Children’s Hospital, Houston, Texas
| | - Bryan Cannon
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
| | - Gladys Zapata
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Patricia P. Hernandez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Fatima Boricha
- Department of Pediatrics, the University of Texas Health Science Center at Houston, Houston, Texas
| | - Donna M. Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratories, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xander H.T. Wehrens
- Department of Pediatrics, Division of Cardiology, Texas Children’s Hospital, Houston, Texas
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Division of Cardiology, Texas Children’s Hospital, Houston, Texas
| | - Jeffrey J. Kim
- Department of Pediatrics, Division of Cardiology, Texas Children’s Hospital, Houston, Texas
| | - Christina Y. Miyake
- Department of Pediatrics, Division of Cardiology, Texas Children’s Hospital, Houston, Texas
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Texas Children’s Hospital, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
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24
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Karolak JA, Gambin T, Rydzanicz M, Polakowski P, Ploski R, Szaflik JP, Gajecka M. Accumulation of sequence variants in genes of Wnt signaling and focal adhesion pathways in human corneas further explains their involvement in keratoconus. PeerJ 2020; 8:e8982. [PMID: 32328353 PMCID: PMC7164425 DOI: 10.7717/peerj.8982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Background Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in loss of visual acuity. The etiology of KTCN remains unclear. The purpose of this study was to assess the potential involvement of new genetic variants in KTCN etiology based on both the genomic and transcriptomic findings recognized in the same corneal tissues. Methods Corneal tissues derived from five unrelated Polish individuals with KTCN were examined using exome sequencing (ES), followed by enrichment analyses. For comparison purposes, the datasets comprising ES data of five randomly selected Polish individuals without ocular abnormalities and five Polish patients with high myopia were used. Expression levels of selected genes from the overrepresented pathways were obtained from the previous RNA-Seq study. Results Exome capture discovered 117 potentially relevant variants that were further narrowed by gene overrepresentation analyses. In each of five patients, the assessment of functional interactions revealed rare (MAF ≤ 0.01) DNA variants in at least one gene from Wnt signaling (VANGL1, WNT1, PPP3CC, LRP6, FZD2) and focal adhesion (BIRC2, PAK6, COL4A4, PPP1R12A, PTK6) pathways. No genes involved in pathways enriched in KTCN corneas were overrepresented in our control sample sets. Conclusions The results of this first pilot ES profiling of human KTCN corneas emphasized that accumulation of sequence variants in several genes from Wnt signaling and/or focal adhesion pathways might cause the phenotypic effect and further points to a complex etiology of KTCN.
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Affiliation(s)
- Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Piotr Polakowski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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25
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Vincent M, Karolak JA, Deutsch G, Gambin T, Popek E, Isidor B, Szafranski P, Le Caignec C, Stankiewicz P. Clinical, Histopathological, and Molecular Diagnostics in Lethal Lung Developmental Disorders. Am J Respir Crit Care Med 2020; 200:1093-1101. [PMID: 31189067 DOI: 10.1164/rccm.201903-0495tr] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lethal lung developmental disorders are a rare but important group of pediatric diffuse lung diseases presenting with neonatal respiratory failure. On the basis of histopathological appearance at lung biopsy or autopsy, they have been termed: alveolar capillary dysplasia with misalignment of the pulmonary veins, acinar dysplasia, congenital alveolar dysplasia, and other unspecified primary pulmonary hypoplasias. However, the histopathological continuum in these lethal developmental disorders has made accurate diagnosis challenging, which has implications for recurrence risk. Over the past decade, genetic studies in infants with alveolar capillary dysplasia with misalignment of the pulmonary veins have revealed the causative role of the dosage-sensitive FOXF1 gene and its noncoding regulatory variants in the distant lung-specific enhancer at chromosome 16q24.1. In contrast, the molecular bases of acinar dysplasia and congenital alveolar dysplasia have remained poorly understood. Most recently, disruption of the TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling pathway has been reported in patients with these lethal pulmonary dysplasias. Application of next-generation sequencing techniques, including exome sequencing and whole-genome sequencing, has demonstrated their complex compound inheritance. These data indicate that noncoding regulatory elements play a critical role in lung development in humans. We propose that for more precise lethal lung developmental disorder diagnosis, a diagnostic pathway including whole-genome sequencing should be implemented.
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Affiliation(s)
- Marie Vincent
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France.,Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, L'institut du Thorax, Nantes, France
| | - Justyna A Karolak
- Department of Molecular and Human Genetics and.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington
| | - Tomasz Gambin
- Department of Molecular and Human Genetics and.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; and.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Bertrand Isidor
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France.,Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, L'institut du Thorax, Nantes, France
| | | | - Cedric Le Caignec
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
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26
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Karolak JA, Gambin T, Honey EM, Slavik T, Popek E, Stankiewicz P. A de novo 2.2 Mb recurrent 17q23.1q23.2 deletion unmasks novel putative regulatory non-coding SNVs associated with lethal lung hypoplasia and pulmonary hypertension: a case report. BMC Med Genomics 2020; 13:34. [PMID: 32143628 PMCID: PMC7060516 DOI: 10.1186/s12920-020-0701-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single nucleotide variants (SNVs) have been reported in patients with lethal lung developmental disorders (LLDDs) or congenital scoliosis with recurrent copy-number variant (CNV) deletions at 17q23.1q23.2 or 16p11.2, respectively. CASE PRESENTATION Here, we report a deceased newborn with pulmonary hypertension and pulmonary interstitial emphysema with features suggestive of pulmonary hypoplasia, resulting in respiratory failure and neonatal death soon after birth. Using the array comparative genomic hybridization and WGS, two heterozygous recurrent CNV deletions: ~ 2.2 Mb on 17q23.1q23.2, involving TBX4, and ~ 600 kb on 16p11.2, involving TBX6, that both arose de novo on maternal chromosomes were identified. In the predicted lung-specific enhancer upstream to TBX4, we have detected seven novel putative regulatory non-coding SNVs that were absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. CONCLUSIONS Our findings further support a recently reported model of complex compound inheritance of LLDD in which both non-coding and coding heterozygous TBX4 variants contribute to the lung phenotype. In addition, this is the first report of a patient with combined de novo heterozygous recurrent 17q23.1q23.2 and 16p11.2 CNV deletions.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
| | - Tomas Slavik
- Ampath Pathology Laboratories, and Department of Anatomical Pathology, University of Pretoria, Pretoria, South Africa
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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27
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Mitani T, Punetha J, Akalin I, Pehlivan D, Dawidziuk M, Coban Akdemir Z, Yilmaz S, Aslan E, Hunter JV, Hijazi H, Grochowski CM, Jhangiani SN, Karaca E, Fatih JM, Iwanowski P, Gambin T, Wlasienko P, Goszczanska-Ciuchta A, Bekiesinska-Figatowska M, Hosseini M, Arzhangi S, Najmabadi H, Rosenfeld JA, Du H, Marafi D, Blaser S, Teitelbaum R, Silver R, Posey JE, Ropers HH, Gibbs RA, Wiszniewski W, Lupski JR, Chitayat D, Kahrizi K, Gawlinski P, Gawlinski P. Bi-allelic Pathogenic Variants in TUBGCP2 Cause Microcephaly and Lissencephaly Spectrum Disorders. Am J Hum Genet 2019; 105:1005-1015. [PMID: 31630790 DOI: 10.1016/j.ajhg.2019.09.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/13/2019] [Indexed: 10/25/2022] Open
Abstract
Lissencephaly comprises a spectrum of malformations of cortical development. This spectrum includes agyria, pachygyria, and subcortical band heterotopia; each represents anatomical malformations of brain cortical development caused by neuronal migration defects. The molecular etiologies of neuronal migration anomalies are highly enriched for genes encoding microtubules and microtubule-associated proteins, and this enrichment highlights the critical role for these genes in cortical growth and gyrification. Using exome sequencing and family based rare variant analyses, we identified a homozygous variant (c.997C>T [p.Arg333Cys]) in TUBGCP2, encoding gamma-tubulin complex protein 2 (GCP2), in two individuals from a consanguineous family; both individuals presented with microcephaly and developmental delay. GCP2 forms the multiprotein γ-tubulin ring complex (γ-TuRC) together with γ-tubulin and other GCPs to regulate the assembly of microtubules. By querying clinical exome sequencing cases and through GeneMatcher-facilitated collaborations, we found three additional families with bi-allelic variation and similarly affected phenotypes including a homozygous variant (c.1843G>C [p.Ala615Pro]) in two families and compound heterozygous variants consisting of one missense variant (c.889C>T [p.Arg297Cys]) and one splice variant (c.2025-2A>G) in another family. Brain imaging from all five affected individuals revealed varying degrees of cortical malformations including pachygyria and subcortical band heterotopia, presumably caused by disruption of neuronal migration. Our data demonstrate that pathogenic variants in TUBGCP2 cause an autosomal recessive neurodevelopmental trait consisting of a neuronal migration disorder, and our data implicate GCP2 as a core component of γ-TuRC in neuronal migrating cells.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pawel Gawlinski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland.
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28
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Oswiecimska J, Dawidziuk M, Gambin T, Ziora K, Marek M, Rzonca S, Guilbride DL, Jhangiani SN, Obuchowicz A, Sikora A, Lupski JR, Wiszniewski W, Gawlinski P. A Patient with Berardinelli-Seip Syndrome, Novel AGPAT2 Splicesite Mutation and Concomitant Development of Non-diabetic Polyneuropathy. J Clin Res Pediatr Endocrinol 2019; 11:319-326. [PMID: 30563316 PMCID: PMC6745459 DOI: 10.4274/jcrpe.galenos.2018.2018.0227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/17/2018] [Indexed: 12/01/2022] Open
Abstract
Primary polyneuropathy in the context of Seip-Berardinelli type 1 seipinopathy, or congenital generalized lipodystrophy type 1 (CGL1) has not been previously reported. We report the case history of a 27 year old female CGL1 patient presenting with an unusual additional development of non-diabetic peripheral neuropathy and learning disabilities in early adolescence. Whole exome sequencing (WES) of the patient genome identified a novel variant, homozygous for a 52 bp intronic deletion in the AGPAT2 locus, coding for 1-acylglycerol-3-phosphate O-acyltransferase 2, which is uniquely associated with CGL1 seipinopathies, with no molecular evidence for dual diagnosis. Functional studies using RNA isolated from patient peripheral blood leucocytes showed abnormal RNA splicing resulting in the loss of 25 amino acids from the patient AGPAT2 protein coding sequence. Stability and transcription levels for the misspliced AGPAT2 mRNA in our patient nonetheless remained normal. Any AGPAT2 protein produced in our patient is therefore likely to be dysfunctional. However, formal linkage of this deletion to the neuropathy observed remains to be shown. The classical clinical presentation of a patient with AGPAT2-associated lipodystrophy shows normal cognition and no development of polyneuropathy. Cognitive disabilities and polyneuropathy are features associated exclusively with clinical CGL type 2 arising from seipin (BSCL2) gene mutations. This case study suggests that in some genetic contexts, AGPAT2 mutations can also produce phenotypes with primary polyneuropathy.
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Affiliation(s)
- Joanna Oswiecimska
- Medical University of Silesia in Katowice, Department of Pediatrics in Zabrze, Silesia, Poland
| | - Mateusz Dawidziuk
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
| | - Tomasz Gambin
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
- Warsaw University of Technology, Institute of Computer Science, Warsaw, Poland
- Baylor College of Medicine, Department of Molecular and Human Genetics, Texas, USA
| | - Katarzyna Ziora
- Medical University of Silesia in Katowice, Department of Pediatrics in Zabrze, Silesia, Poland
| | - Marta Marek
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - Sylwia Rzonca
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
| | | | | | - Anna Obuchowicz
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - Alicja Sikora
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - James R. Lupski
- Baylor College of Medicine, Department of Molecular and Human Genetics, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Texas, USA
- Baylor College of Medicine, Department of Pediatrics, Texas, USA
- Texas Children’s Hospital, Texas, USA
| | - Wojciech Wiszniewski
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
- Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, USA
| | - Pawel Gawlinski
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
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29
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Wiewiórka M, Szmurło A, Kuśmirek W, Gambin T. SeQuiLa-cov: A fast and scalable library for depth of coverage calculations. Gigascience 2019; 8:giz094. [PMID: 31378808 PMCID: PMC6680061 DOI: 10.1093/gigascience/giz094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Depth of coverage calculation is an important and computationally intensive preprocessing step in a variety of next-generation sequencing pipelines, including the analysis of RNA-sequencing data, detection of copy number variants, or quality control procedures. RESULTS Building upon big data technologies, we have developed SeQuiLa-cov, an extension to the recently released SeQuiLa platform, which provides efficient depth of coverage calculations, reaching >100× speedup over the state-of-the-art tools. The performance and scalability of our solution allow for exome and genome-wide calculations running locally or on a cluster while hiding the complexity of the distributed computing with Structured Query Language Application Programming Interface. CONCLUSIONS SeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.
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Affiliation(s)
- Marek Wiewiórka
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Agnieszka Szmurło
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Wiktor Kuśmirek
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
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30
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Cao Y, Tokita MJ, Chen ES, Ghosh R, Chen T, Feng Y, Gorman E, Gibellini F, Ward PA, Braxton A, Wang X, Meng L, Xiao R, Bi W, Xia F, Eng CM, Yang Y, Gambin T, Shaw C, Liu P, Stankiewicz P. A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Genome Med 2019; 11:48. [PMID: 31349857 PMCID: PMC6660700 DOI: 10.1186/s13073-019-0658-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/11/2019] [Indexed: 12/23/2022] Open
Abstract
Background Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed. Methods To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~ 12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics. Results We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes. Conclusions In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort. Electronic supplementary material The online version of this article (10.1186/s13073-019-0658-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mari J Tokita
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Rajarshi Ghosh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | | | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 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, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 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, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Statistics, Rice University, Houston, TX, 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, USA.
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, USA.
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31
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Kuśmirek W, Szmurło A, Wiewiórka M, Nowak R, Gambin T. Comparison of kNN and k-means optimization methods of reference set selection for improved CNV callers performance. BMC Bioinformatics 2019; 20:266. [PMID: 31138108 PMCID: PMC6537193 DOI: 10.1186/s12859-019-2889-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 05/09/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are over 25 tools dedicated for the detection of Copy Number Variants (CNVs) using Whole Exome Sequencing (WES) data based on read depth analysis. The tools reported consist of several steps, including: (i) calculation of read depth for each sequencing target, (ii) normalization, (iii) segmentation and (iv) actual CNV calling. The essential aspect of the entire process is the normalization stage, in which systematic errors and biases are removed and the reference sample set is used to increase the signal-to-noise ratio. Although some CNV calling tools use dedicated algorithms to obtain the optimal reference sample set, most of the advanced CNV callers do not include this feature. To our knowledge, this work is the first attempt to assess the impact of reference sample set selection on CNV detection performance. METHODS We used WES data from the 1000 Genomes project to evaluate the impact of various methods of reference sample set selection on CNV calling performance of three chosen state-of-the-art tools: CODEX, CNVkit and exomeCopy. Two naive solutions (all samples as reference set and random selection) as well as two clustering methods (k-means and k nearest neighbours (kNN) with a variable number of clusters or group sizes) have been evaluated to discover the best performing sample selection method. RESULTS AND CONCLUSIONS The performed experiments have shown that the appropriate selection of the reference sample set may greatly improve the CNV detection rate. In particular, we found that smart reduction of reference sample size may significantly increase the algorithms' precision while having negligible negative effect on sensitivity. We observed that a complete CNV calling process with the k-means algorithm as the selection method has significantly better time complexity than kNN-based solution.
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Affiliation(s)
- Wiktor Kuśmirek
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, Warsaw, 00-665, Poland
| | - Agnieszka Szmurło
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, Warsaw, 00-665, Poland
| | - Marek Wiewiórka
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, Warsaw, 00-665, Poland
| | - Robert Nowak
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, Warsaw, 00-665, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, Warsaw, 00-665, Poland.
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32
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Jordan VK, Beck TF, Hernandez-Garcia A, Kundert PN, Kim BJ, Jhangiani SN, Gambin T, Starkovich M, Punetha J, Paine IS, Posey JE, Li AH, Muzny D, Hsu CW, Lashua AJ, Sun X, Fernandes CJ, Dickinson ME, Lally KP, Gibbs RA, Boerwinkle E, Lupski JR, Scott DA. The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. Hum Mol Genet 2019; 27:2064-2075. [PMID: 29618029 DOI: 10.1093/hmg/ddy110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/26/2018] [Indexed: 11/13/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) has been reported twice in individuals with a clinical diagnosis of Fraser syndrome, a genetic disorder that can be caused by recessive mutations affecting FREM2 and FRAS1. In the extracellular matrix, FREM2 and FRAS1 form a self-stabilizing complex with FREM1, a protein whose deficiency causes sac CDH in humans and mice. By sequencing FREM2 and FRAS1 in a CDH cohort, and searching online databases, we identified five individuals who carried recessive or double heterozygous, putatively deleterious variants in these genes which may represent susceptibility alleles. Three of these alleles were significantly enriched in our CDH cohort compared with ethnically matched controls. We subsequently demonstrated that 8% of Frem2ne/ne and 1% of Fras1Q1263*/Q1263* mice develop the same type of anterior sac CDH seen in FREM1-deficient mice. We went on to show that development of sac hernias in FREM1-deficient mice is preceded by failure of anterior mesothelial fold progression resulting in the persistence of an amuscular, poorly vascularized anterior diaphragm that is abnormally adherent to the underlying liver. Herniation occurs in the perinatal period when the expanding liver protrudes through this amuscular region of the anterior diaphragm that is juxtaposed to areas of muscular diaphragm. Based on these data, we conclude that deficiency of FREM2, and possibly FRAS1, are associated with an increased risk of developing CDH and that loss of the FREM1/FREM2/FRAS1 complex, or its function, leads to anterior sac CDH development through its effects on mesothelial fold progression.
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Affiliation(s)
- Valerie K Jordan
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tyler F Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter N Kundert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bum-Jun Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Molly Starkovich
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander H Li
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amber J Lashua
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xin Sun
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin P Lally
- Department of Pediatric Surgery, McGovern Medical School at UT Health, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daryl A Scott
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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33
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Volpi S, Cicalese MP, Tuijnenburg P, Tool ATJ, Cuadrado E, Abu-Halaweh M, Ahanchian H, Alzyoud R, Akdemir ZC, Barzaghi F, Blank A, Boisson B, Bottino C, Brigida I, Caorsi R, Casanova JL, Chiesa S, Chinn IK, Dückers G, Enders A, Erichsen HC, Forbes LR, Gambin T, Gattorno M, Karimiani EG, Giliani S, Gold MS, Jacobsen EM, Jansen MH, King JR, Laxer RM, Lupski JR, Mace E, Marcenaro S, Maroofian R, Meijer AB, Niehues T, Notarangelo LD, Orange J, Pannicke U, Pearson C, Picco P, Quinn PJ, Schulz A, Seeborg F, Stray-Pedersen A, Tawamie H, van Leeuwen EMM, Aiuti A, Yeung R, Schwarz K, Kuijpers TW. A combined immunodeficiency with severe infections, inflammation, and allergy caused by ARPC1B deficiency. J Allergy Clin Immunol 2019; 143:2296-2299. [PMID: 30771411 DOI: 10.1016/j.jaci.2019.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Stefano Volpi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto Giannina Gaslini, Genova, Italy; DINOGMI, Università degli Studi di Genova, Genova, Italy.
| | - Maria Pia Cicalese
- Pediatric Immunohematology, San Raffaele Hospital and San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Milan, Italy
| | - Paul Tuijnenburg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anton T J Tool
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eloy Cuadrado
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marwan Abu-Halaweh
- Department of Biotechnology and Genetics Engineering in Philadelphia University, Amman, Jordan
| | - Hamid Ahanchian
- Department of Allergy and Immunology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Raed Alzyoud
- Queen Rania Children's Hospital, Immunology, Allergy and Rheumatology Section, Bone Marrow Transplantation for Primary Immunodeficiency Disorders, Amman, Jordan
| | - Zeynep Coban Akdemir
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Federica Barzaghi
- Pediatric Immunohematology, San Raffaele Hospital and San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Milan, Italy
| | - Alexander Blank
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris, France; Imagine Institute, Paris Descartes University, Paris, France
| | - Cristina Bottino
- Department of Experimental Medicine (DIMES), University of Genoa, Genova, Italy; Istituto Giannina Gaslini, Genova, Italy
| | - Immacolata Brigida
- Pediatric Immunohematology, San Raffaele Hospital and San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Milan, Italy
| | - Roberta Caorsi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto Giannina Gaslini, Genova, Italy
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris, France; Imagine Institute, Paris Descartes University, Paris, France; Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, APHP, Paris, France; Howard Hughes Medical Institute, New York, NY
| | - Sabrina Chiesa
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto Giannina Gaslini, Genova, Italy
| | - Ivan Kingyue Chinn
- Department of Pediatrics, Section of Allergy, Immunology, and Rheumatology & Center for Human Immunobiology, Texas Children's Hospital, Houston, Texas
| | - Gregor Dückers
- Center for Child and Adolescent Medicine, Helios-Clinic, Krefeld, Germany
| | - Anselm Enders
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research and Centre for Personalised Immunology, Australian National University, Canberra, ACT, Australia
| | - Hans Christian Erichsen
- Section of Paediatric Medicine and Transplantation, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Lisa R Forbes
- Department of Pediatrics, Section of Allergy, Immunology, and Rheumatology & Center for Human Immunobiology, Texas Children's Hospital, Houston, Texas
| | - Tomasz Gambin
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Marco Gattorno
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto Giannina Gaslini, Genova, Italy
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St George's, University of London, Cranmer Terrace, London, United Kingdom; Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Silvia Giliani
- Medical Genetics Unit and "A. Nocivelli" Institute for Molecular Medicine, Spedali Civili Hospital, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Michael S Gold
- Discipline of Pediatrics, School of Medicine, University of Adelaide and Department of Allergy and Clinical Immunology, Women's and Children's Health Network, Adelaide, South Australia, Australia
| | | | - Machiel H Jansen
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jovanka R King
- Discipline of Pediatrics, School of Medicine, University of Adelaide and Department of Allergy and Clinical Immunology, Women's and Children's Health Network, Adelaide, South Australia, Australia
| | - Ronald M Laxer
- Division of Rheumatology, Department of Paediatrics and Department of Medicine, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Texas Children's Hospital, Houston, Texas
| | - Emily Mace
- Department of Pediatrics, Section of Allergy, Immunology, and Rheumatology & Center for Human Immunobiology, Texas Children's Hospital, Houston, Texas
| | | | - Reza Maroofian
- Medical Research, RILD Welcome Wolfson Centre, Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter and Genetics and Molecular Cell Sciences Research Centre, St George's University of London, London, United Kingdom
| | - Alexander B Meijer
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tim Niehues
- Center for Child and Adolescent Medicine, Helios-Clinic, Krefeld, Germany
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Md
| | - Jordan Orange
- Department of Pediatrics, Section of Allergy, Immunology, and Rheumatology & Center for Human Immunobiology, Texas Children's Hospital, Houston, Texas
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany
| | - Chris Pearson
- Department of General Medicine, Women's and Children's Health Network, Adelaide, South Australia, Australia
| | - Paolo Picco
- Clinica Pediatrica e Reumatologia, Istituto Giannina Gaslini, Genova, Italy
| | - Patrick J Quinn
- Discipline of Pediatrics, School of Medicine, University of Adelaide and Department of Allergy and Clinical Immunology, Women's and Children's Health Network, Adelaide, South Australia, Australia
| | - Ansgar Schulz
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Filiz Seeborg
- Department of Pediatrics, Section of Allergy, Immunology, and Rheumatology & Center for Human Immunobiology, Texas Children's Hospital, Houston, Texas
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Hasan Tawamie
- Institute of Human Genetics of Leipzig, Leipzig, Germany
| | - Ester M M van Leeuwen
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alessandro Aiuti
- Pediatric Immunohematology, San Raffaele Hospital and San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Milan, Italy
| | - Rae Yeung
- Division of Rheumatology, Department of Paediatrics and Department of Medicine, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Paediatrics, Institute of Medical Science, University of Toronto, Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Immunology, Institute of Medical Science, University of Toronto, Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany; the Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg - Hessen, Ulm, Germany
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory AMC, University of Amsterdam, Amsterdam, the Netherlands.
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34
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Karolak JA, Vincent M, Deutsch G, Gambin T, Cogné B, Pichon O, Vetrini F, Mefford HC, Dines JN, Golden-Grant K, Dipple K, Freed AS, Leppig KA, Dishop M, Mowat D, Bennetts B, Gifford AJ, Weber MA, Lee AF, Boerkoel CF, Bartell TM, Ward-Melver C, Besnard T, Petit F, Bache I, Tümer Z, Denis-Musquer M, Joubert M, Martinovic J, Bénéteau C, Molin A, Carles D, André G, Bieth E, Chassaing N, Devisme L, Chalabreysse L, Pasquier L, Secq V, Don M, Orsaria M, Missirian C, Mortreux J, Sanlaville D, Pons L, Küry S, Bézieau S, Liet JM, Joram N, Bihouée T, Scott DA, Brown CW, Scaglia F, Tsai ACH, Grange DK, Phillips JA, Pfotenhauer JP, Jhangiani SN, Gonzaga-Jauregui CG, Chung WK, Schauer GM, Lipson MH, Mercer CL, van Haeringen A, Liu Q, Popek E, Coban Akdemir ZH, Lupski JR, Szafranski P, Isidor B, Le Caignec C, Stankiewicz P. Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. Am J Hum Genet 2019; 104:213-228. [PMID: 30639323 DOI: 10.1016/j.ajhg.2018.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.
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MESH Headings
- DNA Copy Number Variations/genetics
- Female
- Fibroblast Growth Factor 10/genetics
- Fibroblast Growth Factor 10/metabolism
- Gene Expression Regulation
- Gestational Age
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/genetics
- Infant, Newborn, Diseases/metabolism
- Infant, Newborn, Diseases/mortality
- Infant, Newborn, Diseases/pathology
- Lung/embryology
- Lung/growth & development
- Lung Diseases/genetics
- Lung Diseases/metabolism
- Lung Diseases/mortality
- Lung Diseases/pathology
- Male
- Maternal Inheritance
- Organogenesis
- Paternal Inheritance
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Signal Transduction/genetics
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Marie Vincent
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Olivier Pichon
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer N Dines
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Amanda S Freed
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen A Leppig
- Genetic Services Kaiser Permanente of Washington, Seattle, WA 98112, USA
| | - Megan Dishop
- Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick Sydney, NSW 2031 Australia; School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Bruce Bennetts
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew J Gifford
- School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Martin A Weber
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Tina M Bartell
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | | | - Thomas Besnard
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, 59000 Lille, France
| | - Iben Bache
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 N Copenhagen, Denmark; Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Ø Copenhagen, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Copenhagen, Denmark; Deparment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N, Copenhagen, Denmark
| | | | | | - Jelena Martinovic
- Unit of Fetal Pathology, AP-HP, Antoine Beclere Hospital, 75000 Paris, France
| | - Claire Bénéteau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Arnaud Molin
- Service de Génétique Médicale, CHU Caen, 14000 Caen, France
| | - Dominique Carles
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Gwenaelle André
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Eric Bieth
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | - Nicolas Chassaing
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | | | | | | | - Véronique Secq
- Aix Marseille Univ, APHM, Hôpital Nord, Service d'anatomo-pathologie, 13000 Marseille, France
| | - Massimiliano Don
- Sant'Antonio General Hospital, Pediatric Care Unit, San Daniele del Friuli, 33100 Udine, Italy
| | - Maria Orsaria
- Department of Medical and Biological Sciences, Pathology Unit, University of Udine, Udine, Italy
| | - Chantal Missirian
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Jérémie Mortreux
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Linda Pons
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Jean-Michel Liet
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | - Nicolas Joram
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | | | - Daryl A Scott
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fernando Scaglia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, New Territories, Hong Kong SAR
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dorothy K Grange
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Galen M Schauer
- Department of Pathology, Kaiser Permanente Oakland Medical Center, Oakland, CA 94611, USA
| | - Mark H Lipson
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | - Catherine L Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Qian Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | | | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Institute of Mother and Child, 01-211 Warsaw, Poland.
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35
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Leńska-Mieciek M, Charzewska A, Królicki L, Hoffman-Zacharska D, Chen ZS, Lau KF, Chan HYE, Gambin T, Fiszer U. Familial ataxia, tremor, and dementia in a polish family with a novel mutation in the CCDC88C gene. Mov Disord 2018; 34:142-144. [PMID: 30398676 DOI: 10.1002/mds.27536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 09/20/2018] [Accepted: 09/23/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marta Leńska-Mieciek
- Department of Neurology and Epileptology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | | | - Leszek Królicki
- Department of Nuclear Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Zhefan Stephen Chen
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kwok-Fai Lau
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Urszula Fiszer
- Department of Neurology and Epileptology, Centre of Postgraduate Medical Education, Warsaw, Poland
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36
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Coban-Akdemir Z, White JJ, Song X, Jhangiani SN, Fatih JM, Gambin T, Bayram Y, Chinn IK, Karaca E, Punetha J, Poli C, Boerwinkle E, Shaw CA, Orange JS, Gibbs RA, Lappalainen T, Lupski JR, Carvalho CM, Carvalho CMB. Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. Am J Hum Genet 2018; 103:171-187. [PMID: 30032986 DOI: 10.1016/j.ajhg.2018.06.009] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022] Open
Abstract
Premature termination codon (PTC)-bearing transcripts are often degraded by nonsense-mediated decay (NMD) resulting in loss-of-function (LoF) alleles. However, not all PTCs result in LoF mutations, i.e., some such transcripts escape NMD and are translated to truncated peptide products that result in disease due to gain-of-function (GoF) effects. Since the location of the PTC is a major factor determining transcript fate, we hypothesized that depletion of protein-truncating variants (PTVs) within the gene region predicted to escape NMD in control databases could provide a rank for genic susceptibility for disease through GoF versus LoF. We developed an NMD escape intolerance score to rank genes based on the depletion of PTVs that would render them able to escape NMD using the Atherosclerosis Risk in Communities Study (ARIC) and the Exome Aggregation Consortium (ExAC) control databases, which was further used to screen the Baylor-Center for Mendelian Genomics disease database. This analysis revealed 1,996 genes significantly depleted for PTVs that are predicted to escape from NMD, i.e., PTVesc; further studies provided evidence that revealed a subset as candidate genes underlying Mendelian phenotypes. Importantly, these genes have characteristically low pLI scores, which can cause them to be overlooked as candidates for dominant diseases. Collectively, we demonstrate that this NMD escape intolerance score is an effective and efficient tool for gene discovery in Mendelian diseases due to production of truncated or altered proteins. More importantly, we provide a complementary analytical tool to aid identification of genes associated with dominant traits through a mechanism distinct from LoF.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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37
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Wiszniewski W, Gawlinski P, Gambin T, Bekiesinska-Figatowska M, Obersztyn E, Antczak-Marach D, Akdemir ZHC, Harel T, Karaca E, Jurek M, Sobecka K, Nowakowska B, Kruk M, Terczynska I, Goszczanska-Ciuchta A, Rudzka-Dybala M, Jamroz E, Pyrkosz A, Jakubiuk-Tomaszuk A, Iwanowski P, Gieruszczak-Bialek D, Piotrowicz M, Sasiadek M, Kochanowska I, Gurda B, Steinborn B, Dawidziuk M, Castaneda J, Wlasienko P, Bezniakow N, Jhangiani SN, Hoffman-Zacharska D, Bal J, Szczepanik E, Boerwinkle E, Gibbs RA, Lupski JR. Comprehensive genomic analysis of patients with disorders of cerebral cortical development. Eur J Hum Genet 2018; 26:1121-1131. [PMID: 29706646 DOI: 10.1038/s41431-018-0137-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 11/09/2022] Open
Abstract
Malformations of cortical development (MCDs) manifest with structural brain anomalies that lead to neurologic sequelae, including epilepsy, cerebral palsy, developmental delay, and intellectual disability. To investigate the underlying genetic architecture of patients with disorders of cerebral cortical development, a cohort of 54 patients demonstrating neuroradiologic signs of MCDs was investigated. Individual genomes were interrogated for single-nucleotide variants (SNV) and copy number variants (CNV) with whole-exome sequencing and chromosomal microarray studies. Variation affecting known MCDs-associated genes was found in 16/54 cases, including 11 patients with SNV, 2 patients with CNV, and 3 patients with both CNV and SNV, at distinct loci. Diagnostic pathogenic SNV and potentially damaging variants of unknown significance (VUS) were identified in two groups of seven individuals each. We demonstrated that de novo variants are important among patients with MCDs as they were identified in 10/16 individuals with a molecular diagnosis. Three patients showed changes in known MCDs genes and a clinical phenotype beyond the usual characteristics observed, i.e., phenotypic expansion, for a particular known disease gene clinical entity. We also discovered 2 likely candidate genes, CDH4, and ASTN1, with human and animal studies supporting their roles in brain development, and 5 potential candidate genes. Our findings emphasize genetic heterogeneity of MCDs disorders and postulate potential novel candidate genes involved in cerebral cortical development.
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Affiliation(s)
- Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland. .,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
| | - Pawel Gawlinski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Dorota Antczak-Marach
- Clinic of Neurology of Children and Adolescents, Institute of Mother and Child, Warsaw, Poland
| | | | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Marta Jurek
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Katarzyna Sobecka
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Beata Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Malgorzata Kruk
- Clinic of Neurology of Children and Adolescents, Institute of Mother and Child, Warsaw, Poland
| | - Iwona Terczynska
- Clinic of Neurology of Children and Adolescents, Institute of Mother and Child, Warsaw, Poland
| | | | - Mariola Rudzka-Dybala
- Clinic of Neurology of Children and Adolescents, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Jamroz
- School of Medicine in Katowice, Department of Pediatrics and Developmental Age Neurology, Medical University of Silesia, Katowice, Poland
| | - Antoni Pyrkosz
- Department of Medical Genetics, University of Rzeszow, Rzeszow, Poland
| | - Anna Jakubiuk-Tomaszuk
- Department of Pediatric Neurology and Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Iwanowski
- Department of Medical Genetics, Children's Memorial Health Institute, Warsaw, Poland
| | - Dorota Gieruszczak-Bialek
- Department of Medical Genetics, Children's Memorial Health Institute, Warsaw, Poland.,Department of Pediatrics, Medical University of Warsaw, Warsaw, Poland
| | - Malgorzata Piotrowicz
- Department of Genetics, Polish Mother's Memorial Hospital - Research Institute, Lodz, Poland
| | - Maria Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Iwona Kochanowska
- Individual Medical Practice in Pediatric Neurology, Szczecin, Poland
| | - Barbara Gurda
- Department of Developmental Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Barbara Steinborn
- Department of Developmental Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Mateusz Dawidziuk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Jennifer Castaneda
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Pawel Wlasienko
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Natalia Bezniakow
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Jerzy Bal
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elzbieta Szczepanik
- Clinic of Neurology of Children and Adolescents, Institute of Mother and Child, Warsaw, Poland
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Human Genetics Center and Institute of Molecular Medicine, University of Texas-Houston Health Science Center, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
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38
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Gawliński P, Pelc M, Ciara E, Jhangiani S, Jurkiewicz E, Gambin T, Różdżyńska-Świątkowska A, Dawidziuk M, Coban-Akdemir Z, Guilbride D, Muzny D, Lupski J, Krajewska-Walasek M. Phenotype expansion and development in Kosaki overgrowth syndrome. Clin Genet 2018; 93:919-924. [DOI: 10.1111/cge.13192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
Affiliation(s)
- P. Gawliński
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | - M. Pelc
- Department of Medical Genetics; The Children's Memorial Health Institute; Warsaw Poland
| | - E. Ciara
- Department of Medical Genetics; The Children's Memorial Health Institute; Warsaw Poland
| | - S. Jhangiani
- Human Genome Sequencing Center; Baylor College of Medicine; Houston Texas
| | - E. Jurkiewicz
- Department of Diagnostic Imaging; The Children's Memorial Health Institute; Warsaw Poland
| | - T. Gambin
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
- Institute of Computer Science; Warsaw University of Technology; Warsaw Texas
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | | | - M. Dawidziuk
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | - Z.H. Coban-Akdemir
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | | | - D. Muzny
- Human Genome Sequencing Center; Baylor College of Medicine; Houston Texas
| | - J.R. Lupski
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Human Genome Sequencing Center; Baylor College of Medicine; Houston Texas
- Texas Children's Hospital; Houston Texas
| | - M. Krajewska-Walasek
- Department of Medical Genetics; The Children's Memorial Health Institute; Warsaw Poland
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39
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Spólnicka M, Zbieć-Piekarska R, Karp M, Machnicki MM, Własiuk P, Makowska Ż, Pięta A, Gambin T, Gasperowicz P, Branicki W, Giannopoulos K, Stokłosa T, Płoski R. DNA methylation signature in blood does not predict calendar age in patients with chronic lymphocytic leukemia but may alert to the presence of disease. Forensic Sci Int Genet 2018; 34:e15-e17. [PMID: 29472117 DOI: 10.1016/j.fsigen.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/02/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Magdalena Spólnicka
- Biology Department, Central Forensic Laboratory of the Police, Warsaw, 00-735, Poland
| | | | - Marta Karp
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Marcin M Machnicki
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Paulina Własiuk
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Żanetta Makowska
- Biology Department, Central Forensic Laboratory of the Police, Warsaw, 00-735, Poland
| | - Agnieszka Pięta
- Biology Department, Central Forensic Laboratory of the Police, Warsaw, 00-735, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland
| | - Piotr Gasperowicz
- Department of Medical Genetics, Warsaw Medical University, 02-106 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | | | - Tomasz Stokłosa
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland.
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, 02-106 Warsaw, Poland.
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40
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Wiewiórka MS, Wysakowicz DP, Okoniewski MJ, Gambin T. Benchmarking distributed data warehouse solutions for storing genomic variant information. Database (Oxford) 2018; 2017:3953981. [PMID: 29220442 PMCID: PMC5504537 DOI: 10.1093/database/bax049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 05/29/2017] [Indexed: 01/25/2023]
Abstract
Database URL https://github.com/ZSI-Bio/variantsdwh.
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Affiliation(s)
- Marek S Wiewiórka
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, Warsaw 00-665, Poland
| | - Dawid P Wysakowicz
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, Warsaw 00-665, Poland
| | - Michal J Okoniewski
- Scientific IT Services, ETH Zurich, Weinbergstrasse 11, Zurich 8092, Switzerland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, Warsaw 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, Warsaw 01-211, Poland
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41
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Gambin T, Akdemir ZC, Yuan B, Gu S, Chiang T, Carvalho CMB, Shaw C, Jhangiani S, Boone PM, Eldomery MK, Karaca E, Bayram Y, Stray-Pedersen A, Muzny D, Charng WL, Bahrambeigi V, Belmont JW, Boerwinkle E, Beaudet AL, Gibbs RA, Lupski JR. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. Nucleic Acids Res 2017; 45:1633-1648. [PMID: 27980096 PMCID: PMC5389578 DOI: 10.1093/nar/gkw1237] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/29/2016] [Indexed: 11/14/2022] Open
Abstract
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor–Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17–50% of pathogenic CNVs in different disease cohorts where 7.1–11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Warsaw, Poland
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, Norway
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vahid Bahrambeigi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA
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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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43
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Zhang J, Gambin T, Yuan B, Szafranski P, Rosenfeld JA, Balwi MA, Alswaid A, Al-Gazali L, Shamsi AMA, Komara M, Ali BR, Roeder E, McAuley L, Roy DS, Manchester DK, Magoulas P, King LE, Hannig V, Bonneau D, Denommé-Pichon AS, Charif M, Besnard T, Bézieau S, Cogné B, Andrieux J, Zhu W, He W, Vetrini F, Ward PA, Cheung SW, Bi W, Eng CM, Lupski JR, Yang Y, Patel A, Lalani SR, Xia F, Stankiewicz P. Erratum to: Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. Hum Genet 2017; 136:1009-1011. [PMID: 28660352 DOI: 10.1007/s00439-017-1828-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 02-038, 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, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mohammed Al Balwi
- Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, 11246, Saudi Arabia
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aisha M Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Makanko Komara
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, 78230, USA
| | - Laura McAuley
- UT Southwestern Medical Center, Children's Health Children's Medical Center, Dallas, TX, 75235, USA
| | - Daniel S Roy
- Tripler Army Medical Center, Honolulu, 96859, USA
| | | | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Lauren E King
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Vickie Hannig
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France.,UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Anne-Sophie Denommé-Pichon
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France.,UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Majida Charif
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Stéphane Bézieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Joris Andrieux
- Institute of Medical Genetics, Jeanne de Flandre Hospital, Lille University Hospital, Lille, 59800, France
| | - Wenmiao Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Francesco Vetrini
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, 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, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell 2017; 168:830-842.e7. [PMID: 28235197 DOI: 10.1016/j.cell.2017.01.037] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 10/13/2016] [Accepted: 01/27/2017] [Indexed: 01/07/2023]
Abstract
De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities. We describe a multiple dnCNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional dnCNVs. These CNVs originate from independent formation incidences, are predominantly tandem duplications or complex gains, exhibit breakpoint junction features reminiscent of replicative repair, and show increased de novo point mutations flanking the rearrangement junctions. The active CNV mutation shower appears to be restricted to a transient perizygotic period. We propose that a defect in the CNV formation process is responsible for the "CNV-mutator state," and this state is dampened after early embryogenesis. The constitutional MdnCNV phenomenon resembles chromosomal instability in various cancers. Investigations of this phenomenon may provide unique access to understanding genomic disorders, structural variant mutagenesis, human evolution, and cancer biology.
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Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA.
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur Wuster
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Ling Zhang
- Collaborative Innovation Center of Genetics and Development, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zechen Chong
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Violet Gelowani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karin Writzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Marjorie Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Scull
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Zhang
- Collaborative Innovation Center of Genetics and Development, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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45
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Lechowicz U, Gambin T, Pollak A, Podgorska A, Stawinski P, Franke A, Petersen BS, Firczuk M, Oldak M, Skarzynski H, Ploski R. Iterative Sequencing and Variant Screening (ISVS) as a novel pathogenic mutations search strategy - application for TMPRSS3 mutations screen. Sci Rep 2017; 7:2543. [PMID: 28566687 PMCID: PMC5451398 DOI: 10.1038/s41598-017-02315-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/10/2017] [Indexed: 01/03/2023] Open
Abstract
Autosomal recessive diseases (ARD) are typically caused by a limited number of mutations whose identification is challenged by their low prevalence. Our purpose was to develop a novel approach allowing an efficient search for mutations causing ARD and evaluation of their pathogenicity without a control group. We developed Iterative Sequencing and Variant Screening (ISVS) approach based on iterative cycles of gene sequencing and mutation screening, and ISVS Simulator software ( http://zsibio.ii.pw.edu.pl/shiny/isvs/ ) for assessment of detected variants' significance. As shown by simulations, ISVS efficiently identifies and correctly classifies pathogenic mutations except for cases where the gene of interest has extremely high number of low frequency nonpathogenic variants. By applying ISVS, we found 4 known and 9 novel (p.C73Y, p.S124L, p.C194Mfs*17, c.782 + 2 T > A, c.953-5 A > G, p.L325Q, p.D334Mfs*24, p.R436G, p.M448T) TMPRSS3 variants among deaf patients. For 3 known and 5 novel variants the disease association was supported by ISVS Simulator odds >90:1. Pathogenicity of 6 novel mutations has been supported by in-silico predictions of variants' deleteriousness. By directly comparing variant prevalence in patients and controls, disease association was demonstrated only for two variants and it was relatively weak (P < 0.05). Summarizing, ISVS strategy and ISVS Simulator are useful for detection of genetic variants causing AR diseases.
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Affiliation(s)
- Urszula Lechowicz
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child at Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Anna Podgorska
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Piotr Stawinski
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | | | - Malgorzata Firczuk
- Department of Immunology, Center of Biostructure Research, Medical University of Warsaw, Warsaw, Poland
| | - Monika Oldak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Henryk Skarzynski
- Oto-Rhino-Laryngology Surgery Clinic, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Center of Biostructure, Medical University of Warsaw, Warsaw, Poland.
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46
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Küry S, Besnard T, Ebstein F, Khan TN, Gambin T, Douglas J, Bacino CA, Craigen WJ, Sanders SJ, Lehmann A, Latypova X, Khan K, Pacault M, Sacharow S, Glaser K, Bieth E, Perrin-Sabourin L, Jacquemont ML, Cho MT, Roeder E, Denommé-Pichon AS, Monaghan KG, Yuan B, Xia F, Simon S, Bonneau D, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Pasquier L, Barbouth D, Shaw CA, Patel A, Smith JL, Bi W, Schmitt S, Deb W, Nizon M, Mercier S, Vincent M, Rooryck C, Malan V, Briceño I, Gómez A, Nugent KM, Gibson JB, Cogné B, Lupski JR, Stessman HAF, Eichler EE, Retterer K, Yang Y, Redon R, Katsanis N, Rosenfeld JA, Kloetzel PM, Golzio C, Bézieau S, Stankiewicz P, Isidor B. De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder. Am J Hum Genet 2017; 100:689. [PMID: 28388435 DOI: 10.1016/j.ajhg.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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47
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Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, Sutton VR, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 2017; 9:26. [PMID: 28327206 PMCID: PMC5361813 DOI: 10.1186/s13073-017-0412-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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Affiliation(s)
- Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN 46202 USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Women and Children’s Division, Oslo University Hospital, 0424 Oslo, Norway
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
- Atlantic Gene Therapies, UMR1089, Nantes, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Jordan S. Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital Center for Human Immuno-Biology, Houston, TX USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX 7703 USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030-3498 USA
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48
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Zhang J, Gambin T, Yuan B, Szafranski P, Rosenfeld JA, Balwi MA, Alswaid A, Al-Gazali L, Shamsi AMA, Komara M, Ali BR, Roeder E, McAuley L, Roy DS, Manchester DK, Magoulas P, King LE, Hannig V, Bonneau D, Denommé-Pichon AS, Charif M, Besnard T, Bézieau S, Cogné B, Andrieux J, Zhu W, He W, Vetrini F, Ward PA, Cheung SW, Bi W, Eng CM, Lupski JR, Yang Y, Patel A, Lalani SR, Xia F, Stankiewicz P. Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. Hum Genet 2017; 136:377-386. [PMID: 28251352 DOI: 10.1007/s00439-017-1763-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/08/2017] [Indexed: 02/05/2023]
Abstract
Impairment of ubiquitin-proteasome system activity involving ubiquitin ligase genes UBE3A, UBE3B, and HUWE1 and deubiquitinating enzyme genes USP7 and USP9X has been reported in patients with neurodevelopmental delays. To date, only a handful of single-nucleotide variants (SNVs) and copy-number variants (CNVs) involving TRIP12, encoding a member of the HECT domain E3 ubiquitin ligases family on chromosome 2q36.3 have been reported. Using chromosomal microarray analysis and whole-exome sequencing (WES), we have identified, respectively, five deletion CNVs and four inactivating SNVs (two frameshifts, one missense, and one splicing) in TRIP12. Seven of these variants were found to be de novo; parental studies could not be completed in two families. Quantitative PCR analyses of the splicing mutation showed a dramatically decreased level of TRIP12 mRNA in the proband compared to the family controls, indicating a loss-of-function mechanism. The shared clinical features include intellectual disability with or without autistic spectrum disorders, speech delay, and facial dysmorphism. Our findings demonstrate that E3 ubiquitin ligase TRIP12 plays an important role in nervous system development and function. The nine presented pathogenic variants further document that TRIP12 haploinsufficiency causes a childhood-onset neurodevelopmental disorder. Finally, our data enable expansion of the phenotypic spectrum of ubiquitin-proteasome dependent disorders.
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Affiliation(s)
- Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 02-038, 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, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mohammed Al Balwi
- Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, 11246, Saudi Arabia
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aisha M Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Makanko Komara
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, 78230, USA
| | - Laura McAuley
- UT Southwestern Medical Center, Children's Health Children's Medical Center, Dallas, TX, 75235, USA
| | - Daniel S Roy
- Tripler Army Medical Center, Honolulu, 96859, USA
| | | | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Lauren E King
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Vickie Hannig
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France.,UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Anne-Sophie Denommé-Pichon
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France.,UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Majida Charif
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Stéphane Bézieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Joris Andrieux
- Institute of Medical Genetics, Jeanne de Flandre Hospital, Lille University Hospital, Lille, 59800, France
| | - Wenmiao Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Francesco Vetrini
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, 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, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, 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, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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49
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Küry S, Besnard T, Ebstein F, Khan TN, Gambin T, Douglas J, Bacino CA, Craigen WJ, Sanders SJ, Lehmann A, Latypova X, Khan K, Pacault M, Sacharow S, Glaser K, Bieth E, Perrin-Sabourin L, Jacquemont ML, Cho MT, Roeder E, Denommé-Pichon AS, Monaghan KG, Yuan B, Xia F, Simon S, Bonneau D, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Pasquier L, Barbouth D, Shaw CA, Patel A, Smith JL, Bi W, Schmitt S, Deb W, Nizon M, Mercier S, Vincent M, Rooryck C, Malan V, Briceño I, Gómez A, Nugent KM, Gibson JB, Cogné B, Lupski JR, Stessman HA, Eichler EE, Retterer K, Yang Y, Redon R, Katsanis N, Rosenfeld JA, Kloetzel PM, Golzio C, Bézieau S, Stankiewicz P, Isidor B. De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder. Am J Hum Genet 2017; 100:352-363. [PMID: 28132691 DOI: 10.1016/j.ajhg.2017.01.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/04/2017] [Indexed: 10/25/2022] Open
Abstract
Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.
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50
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Stray-Pedersen A, Sorte HS, Samarakoon P, Gambin T, Chinn IK, Coban Akdemir ZH, Erichsen HC, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OK, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AG, Skogen V, Osnes LTN, Kulseth MA, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MS, Bezrodnik L, Lugo Reyes SO, Espinosa Rosales FJ, Guerrero-Cursaru ND, Pedroza LA, Poli CM, Franco JL, Trujillo Vargas CM, Aldave Becerra JC, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MM, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, Hanson IC, Zhang VW, Wong LJ, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 2017; 139:232-245. [PMID: 27577878 PMCID: PMC5222743 DOI: 10.1016/j.jaci.2016.05.042] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/10/2016] [Accepted: 05/13/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.
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Affiliation(s)
- Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway; Department of Pediatrics, Oslo University Hospital, Oslo, Norway.
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomasz Gambin
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Ivan K Chinn
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Zeynep H Coban Akdemir
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | | | - Lisa R Forbes
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Shen Gu
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Bo Yuan
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sarah K Nicholas
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Lenora M Noroski
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Filiz O Seeborg
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carla M Davis
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Debra L Canter
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Emily M Mace
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Timothy J Vece
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Harshal A Abhyankar
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Philip M Boone
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine R Beck
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Wojciech Wiszniewski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Børre Fevang
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Geir E Tjønnfjord
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Henrik Hjorth-Hansen
- Department of Hematology, St Olavs Hospital, Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Ingvild Nordøy
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Silje F Jørgensen
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vegard Skogen
- Department of Infectious Diseases, Medical Clinic, University Hospital of North-Norway, Tromsø, Norway
| | - Liv T N Osnes
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Mari Ann Kulseth
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine E Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil R Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Nicholas L Rider
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Javier Chinen
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Tram N Cao
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Eric A Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Tex
| | - Maria Soledad Caldirola
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Bezrodnik
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Saul Oswaldo Lugo Reyes
- Immunodeficiencies Research Unit, National Institute of Pediatrics, Coyoacan, Mexico City, Mexico
| | | | | | | | - Cecilia M Poli
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Hospital Roberto del Rio, Universidad de Chile, Santiago, Chile
| | - Jose L Franco
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Claudia M Trujillo Vargas
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Nicola Wright
- Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Thomas B Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Andrew C Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Jordan Abbott
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergic and Immunological Diseases, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC
| | - Diana K Bayer
- Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Alice Y Chan
- Department of Pediatrics, University of California, San Francisco, Calif
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), and Vita-Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- University Department of Pediatrics, DPUO, Bambino Gesù Children's Hospital, and Tor Vergata University, Rome, Italy
| | - Eva Holmberg
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Christina West
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Magnus Burstedt
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Ender Karaca
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Gözde Yesil
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul, Turkey
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Selcuk University Medical Faculty, Alaeddin Keykubat Kampusu, Konya, Turkey
| | - Yavuz Bayram
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mehmed Musa Atik
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad K Eldomery
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad S Ehlayel
- Department of Pediatrics, Section of Pediatric Allergy and Immunology, Hamad Medical Corporation, Doha, Department of Paediatrics, Weill Cornell Medical College, Ar-Rayyan, Qatar
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Alison A Bertuch
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex
| | - I Celine Hanson
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Victor W Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Eric Boerwinkle
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Human Genetics Center, University of Texas School of Public Health, Houston, Tex
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - William T Shearer
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jordan S Orange
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex.
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex.
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