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La Cognata V, Cavallaro S. Detection of Structural Variants by NGS: Revealing Missing Alleles in Lysosomal Storage Diseases. Biomedicines 2022; 10:biomedicines10081836. [PMID: 36009380 PMCID: PMC9405548 DOI: 10.3390/biomedicines10081836] [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: 06/17/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells. Although biochemical enzymatic assays are considered the gold standard for diagnosis of symptomatic patients, genotyping is a requirement for inclusion in enzyme replacement programs and is a prerequisite for carrier tests in relatives and DNA-based prenatal diagnosis. The emerging next-generation sequencing (NGS) technologies are now offering a powerful diagnostic tool for genotyping LSDs patients by providing faster, cheaper, and higher-resolution testing options, and are allowing to unravel, in a single integrated workflow SNVs, small insertions and deletions (indels), as well as major structural variations (SVs) responsible for the pathology. Here, we summarize the current knowledge about the most recurrent and private SVs involving LSDs-related genes, review advantages and drawbacks related to the use of the NGS in the SVs detection, and discuss the challenges to bring this type of analysis in clinical diagnostics.
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Development and validation of a TTR-specific copy number screening tool, and application to potentially relevant patient cohorts. Mol Cell Probes 2018; 41:61-63. [PMID: 30142390 DOI: 10.1016/j.mcp.2018.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/22/2022]
Abstract
TTR amyloidosis (ATTR) is a fatal condition caused by extracellular deposits of misfolded transthyretin. Patients often present with cardiac disease, but manifestations may also involve other organs including the peripheral nervous system. ATTR is considered familial when heterozygous mutations in the TTR gene are present (ATTRmutant or ATTRm), or acquired when no TTR aberrations are detected (ATTRwildtype or ATTRwt). We hypothesized that TTR copy number variants (CNVs), which would escape the standard diagnostic approaches, contribute to ATTR-related phenotypes, and developed a multiplex ligation-dependent probe amplification-based (MLPA-based), TTR-specific copy number screening tool. High inter-sample and intra-sample homogeneity of MLPA signals and the expected drop in signal intensity for restriction digest-based positive controls validated this tool. Subsequent application to 13 patients diagnosed with ATTRwt, and to 93 patients presenting with late onset and presumably inherited polyneuropathy did not identify TTR CNVs. We discuss insufficient sensitivity of the assay as well as non-existence and non-pathogenicity of TTR CNVs as potentially underlying our negative finding, but suggest size and composition of our cohorts as more likely explanations. Our CNV-screening tool will be made available to initiatives interested in screening additional and potentially more appropriate patient samples.
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Jávorszky E, Morinière V, Kerti A, Balogh E, Pikó H, Saunier S, Karcagi V, Antignac C, Tory K. QMPSF is sensitive and specific in the detection of NPHP1 heterozygous deletions. ACTA ACUST UNITED AC 2017; 55:809-816. [DOI: 10.1515/cclm-2016-0819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Background:
Nephronophthisis, an autosomal recessive nephropathy, is responsible for 10% of childhood chronic renal failure. The deletion of its major gene, NPHP1, with a minor allele frequency of 0.24% in the general population, is the most common mutation leading to a monogenic form of childhood chronic renal failure. It is challenging to detect it in the heterozygous state. We aimed to evaluate the sensitivity and the specificity of the quantitative multiplex PCR of short fluorescent fragments (QMPSF) in its detection.
Methods:
After setting up the protocol of QMPSF, we validated it on 39 individuals diagnosed by multiplex ligation-dependent probe amplification (MLPA) with normal NPHP1 copy number (n=17), with heterozygous deletion (n=13, seven parents and six patients), or with homozygous deletion (n=9). To assess the rate of the deletions that arise from independent events, deleted alleles were haplotyped.
Results:
The results of QMPSF and MLPA correlated perfectly in the identification of 76 heterozygously deleted and 56 homozygously deleted exons. The inter-experimental variability of the dosage quotient obtained by QMPSF was low: control, 1.05 (median; range, 0.86−1.33, n = 102 exons); heterozygous deletion, 0.51 (0.42−0.67, n = 76 exons); homozygous deletion, 0 (0−0, n = 56 exons). All patients harboring a heterozygous deletion were found to carry a hemizygous mutation. At least 15 out of 18 deletions appeared on different haplotypes and one deletion appeared de novo.
Conclusions:
The cost- and time-effective QMPSF has a 100% sensitivity and specificity in the detection of NPHP1 deletion. The potential de novo appearance of NPHP1 deletions makes its segregation analysis highly recommended in clinical practice.
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Amico G, Grossi S, Vijzelaar R, Lanza F, Mazzotti R, Corsolini F, Ketema M, Filocamo M. MLPA-based approach for initial and simultaneous detection of GBA deletions and recombinant alleles in patients affected by Gaucher Disease. Mol Genet Metab 2016; 119:329-337. [PMID: 27802905 DOI: 10.1016/j.ymgme.2016.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 11/23/2022]
Abstract
The chromosomal region, in which the GBA gene is located, is structurally subject to misalignments, reciprocal and nonreciprocal homologous recombination events, leading to structural defects such as deletions, duplications and gene-pseudogene complex rearrangements causing Gaucher Disease (GD). Interestingly deletions and duplications, belonging to the heterogeneous group of structural defects collectively termed Copy Number Variations (CNVs), together with gene-pseudogene complex rearrangements represent the main cause of pitfalls in GD mutational analysis. In the present study, we set up and validate a Multiplex Ligation-dependent Probe Amplification (MLPA)-based approach to simultaneously investigate the potential occurrence of CNVs and complex rearrangements in 8 unrelated GD patients who had still not-well-characterized or uncharacterized alleles. The findings allowed us to complete the mutational analysis in 4 patients, identifying a rare deletion (g.-3100_+834del3934) and 2 novel recombinant alleles (g.4356_7031conJ03060.1:g.2544_4568; g.1942_7319conJ03060.1:g.1092_4856). These results demonstrate the diagnostic usefulness of MLPA in the detection of GBA deletions and recombinations. In addition, MLPA findings have also served as a basis for developing molecular approaches to precisely pinpoint the breakpoints and characterize the underlying mechanism of copy number variations.
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Affiliation(s)
- Giulia Amico
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Serena Grossi
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Raymon Vijzelaar
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands.
| | - Federica Lanza
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Raffaella Mazzotti
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Fabio Corsolini
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Mirjam Ketema
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands.
| | - Mirella Filocamo
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
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Elmonem MA, Veys KR, Soliman NA, van Dyck M, van den Heuvel LP, Levtchenko E. Cystinosis: a review. Orphanet J Rare Dis 2016; 11:47. [PMID: 27102039 PMCID: PMC4841061 DOI: 10.1186/s13023-016-0426-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/15/2016] [Indexed: 01/01/2023] Open
Abstract
Cystinosis is the most common hereditary cause of renal Fanconi syndrome in children. It is an autosomal recessive lysosomal storage disorder caused by mutations in the CTNS gene encoding for the carrier protein cystinosin, transporting cystine out of the lysosomal compartment. Defective cystinosin function leads to intra-lysosomal cystine accumulation in all body cells and organs. The kidneys are initially affected during the first year of life through proximal tubular damage followed by progressive glomerular damage and end stage renal failure during mid-childhood if not treated. Other affected organs include eyes, thyroid, pancreas, gonads, muscles and CNS. Leucocyte cystine assay is the cornerstone for both diagnosis and therapeutic monitoring of the disease. Several lines of treatment are available for cystinosis including the cystine depleting agent cysteamine, renal replacement therapy, hormonal therapy and others; however, no curative treatment is yet available. In the current review we will discuss the most important clinical features of the disease, advantages and disadvantages of the current diagnostic and therapeutic options and the main topics of future research in cystinosis.
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Affiliation(s)
- Mohamed A Elmonem
- Department of Pediatric Nephrology & Growth and Regeneration, University Hospitals Leuven & KU Leuven, UZ Herestraat 49-3000, Leuven, Belgium.,Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Koenraad R Veys
- Department of Pediatric Nephrology & Growth and Regeneration, University Hospitals Leuven & KU Leuven, UZ Herestraat 49-3000, Leuven, Belgium
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation (CPNT), Faculty of Medicine, Cairo University, Cairo, Egypt.,EGORD, Egyptian group of orphan renal diseases, Cairo, Egypt
| | - Maria van Dyck
- Department of Pediatric Nephrology & Growth and Regeneration, University Hospitals Leuven & KU Leuven, UZ Herestraat 49-3000, Leuven, Belgium
| | - Lambertus P van den Heuvel
- Department of Pediatric Nephrology & Growth and Regeneration, University Hospitals Leuven & KU Leuven, UZ Herestraat 49-3000, Leuven, Belgium.,Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elena Levtchenko
- Department of Pediatric Nephrology & Growth and Regeneration, University Hospitals Leuven & KU Leuven, UZ Herestraat 49-3000, Leuven, Belgium.
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