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Murtazina A, Borovikov A, Kuchina A, Ovsova O, Bulakh M, Chukhrova A, Braslavskaya S, Ryzhkova O, Skryabin N, Kutsev S, Dadali E. Expanding the Phenotype of Hereditary Congenital Facial Paresis Type 3. Int J Mol Sci 2023; 25:129. [PMID: 38203298 PMCID: PMC10779017 DOI: 10.3390/ijms25010129] [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: 11/26/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The HOXB1 gene encodes a homeobox transcription factor pivotal in the development of rhombomere 4. Biallelic pathogenic variants in this gene are associated with congenital facial paresis type 3 (HCFP3). Only seven single nucleotide variants have been reported in the literature to date. Here, we report a 27-year-old female with a unique presentation of HCFP3 with two novel compound-heterozygous missense variants: c.763C>G, p.(Arg255Gly), which arose de novo and an inherited c.781C>T, p.(Arg261Cys) variant. The patient exhibited HCFP3 symptoms with mild upward esodeviation and lacked the documented ear malformations common in HCFP. For many years, she was misdiagnosed with facio-scapulo-humeral muscular dystrophy, due to complaints of shoulder girdle and neck muscle weakness. No alternative genetic or acquired causes of neck and shoulder girdle weakness were found, suggesting its potential inclusion in the phenotypic spectrum.
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Affiliation(s)
- Aysylu Murtazina
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Artem Borovikov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Anna Kuchina
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Olga Ovsova
- Department of Neurology, Neurosurgery and Medical Genetics, Ural State Medical University, 620028 Ekaterinburg, Russia;
| | - Maria Bulakh
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Alena Chukhrova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Svetlana Braslavskaya
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Oksana Ryzhkova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Nikolay Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia;
| | - Sergey Kutsev
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Elena Dadali
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
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Guruju NM, Jump V, Lemmers R, Van Der Maarel S, Liu R, Nallamilli BR, Shenoy S, Chaubey A, Koppikar P, Rose R, Khadilkar S, Hegde M. Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy in Patients Clinically Suspected of FSHD Using Optical Genome Mapping. Neurol Genet 2023; 9:e200107. [PMID: 38021397 PMCID: PMC10664978 DOI: 10.1212/nxg.0000000000200107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 12/01/2023]
Abstract
Background and Objectives Facioscapulohumeral muscular dystrophy (FSHD) represents the third most common muscular dystrophy in the general population and is characterized by progressive and often asymmetric muscle weakness of the face, upper extremities, arms, lower leg, and hip girdle. In FSHD type 1, contraction of the number of D4Z4 repeats to 1-10 on the chromosome 4-permissive allele (4qA) results in abnormal epigenetic derepression of the DUX4 gene in skeletal muscle. In FSHD type 2, epigenetic derepression of the DUX4 gene on the permissive allele (4qA) with normal-sized D4Z4 repeats (mostly 8-20) is caused by heterozygous pathogenic variants in chromatin modifier genes such as SMCHD1, DNMT3B, or LRIF1. We present validation of the optical genome mapping (OGM) platform for accurate mapping of the D4Z4 repeat size, followed by diagnostic testing of 547 cases with a suspected clinical diagnosis of FSHD and next-generation sequencing (NGS) of the SMCHD1 gene to identify cases with FSHD2. Methods OGM with Bionano Genomics Saphyr and EnFocus FSHD analysis software was used to identify FSHD haplotypes and D4Z4 repeat number and compared with the gold standard of Southern blot-based diagnosis. A custom Agilent SureSelect enrichment kit was used to enrich SMCHD1, followed by NGS on an Illumina system with 100-bp paired-end reads. Copy number variants were assessed using NxClinical software. Results We performed OGM for the diagnosis of FSHD in 547 patients suspected of FSHD between December 2019 and December 2022, including 301 male (55%) and 246 female patients (45%). Overall, 308 of the referred patients were positive for D4Z4 contraction on a permissive haplotype, resulting in a diagnosis of FSHD1. A total of 252 of 547 patients were referred for concurrent testing for FSHD1 and FSHD2. This resulted in the identification of FSHD2 in 9/252 (3.6%) patients. In our FSHD2 cohort, the 4qA allele size ranged from 8 to 18 repeats. Among FSHD1-positive cases, 2 patients had biallelic contraction and 4 patients had homozygous contraction and showed early onset of clinical features. Nine of the 308 patients (3%) positive for 4qA contraction had mosaic 4q alleles with contraction on at least one 4qA allele. The overall diagnostic yield in our cohort was 58%. Discussion A combination of OGM to identify the FSHD haplotype and D4Z4 repeat number and NGS to identify sequence and copy number variants in the SMCHD1 gene is a practical and cost-effective option with increased precision for accurate diagnosis of FSHD types 1 and 2.
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Affiliation(s)
- Naga M Guruju
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Vanessa Jump
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Richard Lemmers
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Silvere Van Der Maarel
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Ruby Liu
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Babi R Nallamilli
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Suresh Shenoy
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Alka Chaubey
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Pratik Koppikar
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Rajiv Rose
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Satish Khadilkar
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Madhuri Hegde
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
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Kovanda A, Lovrečić L, Rudolf G, Babic Bozovic I, Jaklič H, Leonardis L, Peterlin B. Evaluation of Optical Genome Mapping in Clinical Genetic Testing of Facioscapulohumeral Muscular Dystrophy. Genes (Basel) 2023; 14:2166. [PMID: 38136988 PMCID: PMC10743191 DOI: 10.3390/genes14122166] [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: 10/18/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common hereditary muscular dystrophy, caused by the contraction of the D4Z4 repeats on the permissive 4qA haplotype on chromosome 4, resulting in the faulty expression of the DUX4 gene. Traditional diagnostics are based on Southern blotting, a time- and effort-intensive method that can be affected by single nucleotide variants (SNV) and copy number variants (CNV), as well as by the similarity of the D4Z4 repeats located on chromosome 10. We aimed to evaluate optical genome mapping (OGM) as an alternative molecular diagnostic method for the detection of FSHD. We first performed optical genome mapping with EnFocus™ FSHD analysis using DLE-1 labeling and the Saphyr instrument in patients with inconclusive diagnostic Southern blot results, negative FSHD2 results, and clinically evident FSHD. Second, we performed OGM in parallel with the classical Southern blot analysis for our prospectively collected new FSHD cases. Finally, panel exome sequencing was performed to confirm the presence of FSHD2. In two patients with diagnostically inconclusive Southern blot results, OGM was able to identify shortened D4Z4 repeats on the permissive 4qA alleles, consistent with the clinical presentation. The results of the prospectively collected patients tested in parallel using Southern blotting and OGM showed full concordance, indicating that OGM is a useful alternative to the classical Southern blotting method for detecting FSHD1. In a patient showing clinical FSHD but no shortened D4Z4 repeats in the 4qA allele using OGM or Southern blotting, a likely pathogenic variant in SMCHD1 was detected using exome sequencing, confirming FSHD2. OGM and panel exome sequencing can be used consecutively to detect FSHD2.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Gorazd Rudolf
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ivana Babic Bozovic
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
| | - Lea Leonardis
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Clinical Neurophysiology, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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