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Vaseghi H, Akrami SM, Rashidi‐Nezhad A. The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies. J Clin Lab Anal 2023; 37:e24967. [PMID: 37823350 PMCID: PMC10623530 DOI: 10.1002/jcla.24967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/28/2023] [Accepted: 09/16/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Despite the efforts that have been made to standardize the interpretation of variants, in some cases, their pathogenicity remains vague and confusing, and sometimes their interpretation does not help clinicians to establish clinical correlation using genetic test results. This study aims to shed more lights on these challenging variants. METHODS In a clinical setting, the variants found from 81 array CGH and 79 whole exome sequencing (WES) in patients with congenital anomalies were interpreted based on American College of Medical Genetics and Genomics guidelines. RESULTS In this study, the interpretation of the disease-causing variants and the variants with uncertain clinical significance detected by WES was far more challenging than the variants detected by array CGH. The presence of unreported clinical symptoms, incomplete penetrance, variable expressivity, parents' reluctance to analyze segregation in the family, and the limitations of prenatal tests, were among the challenging factors in the interpretation of variants in this study. CONCLUSION A careful study of the pedigree and disease mode of inheritance, as well as a careful clinical examination of the carrier parents in diseases with autosomal dominant inheritance, are among the primary strategies for determining the clinical significance of the variants. Continued efforts to mitigate these challenges are needed to improve the interpretation of variants.
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Affiliation(s)
- Hajar Vaseghi
- Department of Medical Genetics, School of MedicineTehran University of Medical SciencesTehranIran
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of MedicineTehran University of Medical SciencesTehranIran
| | - Ali Rashidi‐Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research InstituteTehran University of Medical SciencesTehranIran
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Mussa A, Turchiano A, Cardaropoli S, Coppo P, Pantaleo A, Bagnulo R, Ranieri C, Iacoviello M, Garganese A, Stella A, Vallero SG, Bertin D, Santoro F, Carli D, Ferrero GB, Resta N. Lateralized overgrowth with vascular malformation caused by a somatic PTPN11 pathogenic variant: another piece added to the puzzle of mosaic RASopathies. Genes Chromosomes Cancer 2022; 61:689-695. [PMID: 35778969 PMCID: PMC9542063 DOI: 10.1002/gcc.23086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
Lateralized/segmental overgrowth disorders (LOs) encompass a heterogeneous group of congenital conditions with excessive body tissue growth. Documented molecular alterations in LOs mostly consist of somatic variants in genes of the PI3KCA/AKT/mTOR pathway or of chromosome band 11p15.5 imprinted region anomalies. In some cases, somatic pathogenic variants in genes of the RAS/MAPK pathway have been reported. We present the first case of a somatic pathogenic variant (T507K) in PTPN11 causing a LO phenotype characterized by severe lateralized overgrowth, vascular proliferation, and cerebral astrocytoma. The T507K variant was detected in DNA from overgrown tissue in a leg with capillary malformation. The astrocytoma tissue showed a higher PTPN11 variant allele frequency. A pathogenic variant in FGFR1 was also found in tumor tissue, representing a second hit on the RAS/MAPK pathway. These findings indicate that RAS/MAPK cascade overactivation can cause mosaic overgrowth phenotypes resembling PIK3CA‐related overgrowth disorders (PROS) with cancer predisposition and are consistent with the hypothesis that RAS/MAPK hyperactivation can be involved in the pathogenesis of astrocytoma. This observation raises the issue of cancer predisposition in patients with RAS/MAPK pathway gene variants and expands genotype spectrum of LOs and the treatment options for similar cases through inhibition of the RAS/MAPK oversignaling.
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Affiliation(s)
- Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy.,Pediatric Clinical Genetics Unit, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Torino, Italy
| | - Antonella Turchiano
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy
| | - Paola Coppo
- Pediatric Dermatology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Antonino Pantaleo
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
| | - Rosanna Bagnulo
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
| | - Carlotta Ranieri
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
| | - Matteo Iacoviello
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
| | - Antonella Garganese
- Unit of Medical Genetics, Ospedale Consorziale Policlinico di Bari, Bari, Italy
| | - Alessandro Stella
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Gabriele Vallero
- Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Daniele Bertin
- Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Federica Santoro
- Pathology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Diana Carli
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy.,Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | | | - Nicoletta Resta
- Department of Biomedical Sciences and Human Oncology (DIMO), Division of Medical Genetics, University of Bari "Aldo Moro", Bari, Italy
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Ongoing Challenges in the Diagnosis of 11p15.5-Associated Imprinting Disorders. Mol Diagn Ther 2022; 26:263-272. [PMID: 35522427 DOI: 10.1007/s40291-022-00587-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
Abstract
The overgrowth disorder Beckwith-Wiedemann syndrome and the growth restriction disorder Silver-Russell syndrome have been described as 'mirror' syndromes, in both their clinical features and molecular causes. Clinically, their nonspecific features, focused around continuous variables of atypical growth, make it hard to set diagnostic thresholds that are pragmatic without potentially excluding some cases. Molecularly, both are imprinting disorders, classically associated with 'opposite' genetic and epigenetic changes to genes on chromosome 11p15, but both are associated with somatic mosaicism as well as an increasing range of alternative (epi)genetic changes to other genes, which make molecular diagnosis an increasingly complex process. In this Current Opinion, we explore how the understanding of Beckwith-Wiedemann syndrome and Silver-Russell syndrome has evolved in recent years, stretching the canonical 'mirror' designations in different ways for the two disorders and how this is changing clinical and molecular diagnosis. We suggest some possible directions of travel toward more timely and stratified diagnosis, so that patients can access the early interventions that are so critical for good outcome.
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