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Winberg J, Gustavsson P, Sahlin E, Larsson M, Ehrén H, Fossum M, Wester T, Nordgren A, Nordenskjöld A. Pathogenic copy number variants are detected in a subset of patients with gastrointestinal malformations. Mol Genet Genomic Med 2019; 8:e1084. [PMID: 31837127 PMCID: PMC7005659 DOI: 10.1002/mgg3.1084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 12/14/2022] Open
Abstract
Background Gastrointestinal atresias and urological defects are main causes of pediatric surgery in infants. As copy number variants (CNVs) have been shown to be involved in the development of congenital malformations, the aim of our study was to investigate the presence of CNVs in patients with gastrointestinal and urological malformations as well as the possibility of tissue‐specific mosaicism for CNVs in the cohort. Methods We have collected tissue and/or blood samples from 25 patients with anorectal malformations, esophageal atresia, or hydronephrosis, and screened for pathogenic CNVs using array comparative genomic hybridization (array‐CGH). Results We detected pathogenic aberrations in 2/25 patients (8%) and report a novel possible susceptibility region for esophageal atresia on 15q26.3. CNV analysis in different tissues from the same patients did not reveal evidence of tissue‐specific mosaicism. Conclusion Our study shows that it is important to perform clinical genetic investigations, including CNV analysis, in patients with congenital gastrointestinal malformations since this leads to improved information to families as well as an increased understanding of the pathogenesis.
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Affiliation(s)
- Johanna Winberg
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Larsson
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Ehrén
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena Fossum
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Wester
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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Salehi Karlslätt K, Pettersson M, Jäntti N, Szafranski P, Wester T, Husberg B, Ullberg U, Stankiewicz P, Nordgren A, Lundin J, Lindstrand A, Nordenskjöld A. Rare copy number variants contribute pathogenic alleles in patients with intestinal malrotation. Mol Genet Genomic Med 2019; 7:e549. [PMID: 30632303 PMCID: PMC6418355 DOI: 10.1002/mgg3.549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Intestinal malrotation is a potentially life-threatening congenital anomaly due to the risk of developing midgut volvulus. The reported incidence is 0.2%-1% and both apparently hereditary and sporadic cases have been reported. Intestinal malrotation is associated with a few syndromes with known genotype but the genetic contribution in isolated intestinal malrotation has not yet been reported. Rare copy number variants (CNVs) have been implicated in many congenital anomalies, and hence we sought to investigate the potential contribution of rare CNVs in intestinal malrotation. METHODS Analysis of array comparative genomic hybridization (aCGH) data from 47 patients with symptomatic intestinal malrotation was performed. RESULTS We identified six rare CNVs in five patients. Five CNVs involved syndrome loci: 7q11.23 microduplication, 16p13.11 microduplication, 18q terminal deletion, HDAC8 (Cornelia de Lange syndrome type 5 and FOXF1) as well as one intragenic deletion in GALNT14, not previously implicated in human disease. CONCLUSION In the present study, we identified rare CNVs contributing pathogenic or potentially pathogenic alleles in five patients with syndromic intestinal malrotation, suggesting that CNV screening is indicated in intestinal malrotation with associated malformations or neurological involvements. In addition, we identified intestinal malrotation in two known syndromes (Cornelia de Lange type 5 and 18q terminal deletion syndrome) that has not previously been associated with gastrointestinal malformations.
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Affiliation(s)
- Karin Salehi Karlslätt
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Tomas Wester
- Department of Pediatric Surgery, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Britt Husberg
- Department of General Surgery, Ersta Hospital, Stockholm, Sweden
| | - Ulla Ullberg
- Department of Pediatric Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Surgery, Karolinska University Hospital, Stockholm, Sweden
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Manheimer KB, Richter F, Edelmann LJ, D'Souza SL, Shi L, Shen Y, Homsy J, Boskovski MT, Tai AC, Gorham J, Yasso C, Goldmuntz E, Brueckner M, Lifton RP, Chung WK, Seidman CE, Seidman JG, Gelb BD. Robust identification of mosaic variants in congenital heart disease. Hum Genet 2018; 137:183-193. [PMID: 29417219 PMCID: PMC5997246 DOI: 10.1007/s00439-018-1871-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been developed to identify low-frequency variants, specifically from matched tumor-normal tissues in cancer studies. To investigate whether mosaic variants are implicated in congenital heart disease (CHD), we developed a pipeline using the cancer somatic variant caller MuTect to identify mosaic variants in whole-exome sequencing (WES) data from a cohort of parent/affected child trios (n = 715) and a cohort of healthy individuals (n = 416). This is a novel application of the somatic variant caller designed for cancer to WES trio data. We identified two cases with mosaic KMT2D mutations that are likely pathogenic for CHD, but conclude that, overall, mosaicism detectable in peripheral blood or saliva does not account for a significant portion of CHD etiology.
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Affiliation(s)
- Kathryn B Manheimer
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Felix Richter
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa J Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sunita L D'Souza
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Cardiovscular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Marko T Boskovski
- Division of Cardiac Surgery, The Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela C Tai
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiology, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
- Yale Center for Mendelian Genomics, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine (Cardiology), Brigham and Women's Hospital, Boston, MA, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Zaidi S, Brueckner M. Genetics and Genomics of Congenital Heart Disease. Circ Res 2017; 120:923-940. [PMID: 28302740 DOI: 10.1161/circresaha.116.309140] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
Abstract
Congenital heart disease is the most common birth defect, and because of major advances in medical and surgical management, there are now more adults living with congenital heart disease (CHD) than children. Until recently, the cause of the majority of CHD was unknown. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. This review will focus on the evidence for genetic causes underlying CHD and discuss data supporting both monogenic and complex genetic mechanisms underlying CHD. The discoveries from CHD genetic studies draw attention to biological pathways that simultaneously open the door to a better understanding of cardiac development and affect clinical care of patients with CHD. Finally, we address clinical genetic evaluation of patients and families affected by CHD.
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Affiliation(s)
- Samir Zaidi
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT
| | - Martina Brueckner
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT.
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