1
|
Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
Collapse
Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
| |
Collapse
|
2
|
Kucińska A, Hawuła W, Rutkowska L, Wysocka U, Kępczyński Ł, Piotrowicz M, Chilarska T, Wieczorek-Cichecka N, Połatyńska K, Przysło Ł, Gach A. The Use of CGH Arrays for Identifying Copy Number Variations in Children with Autism Spectrum Disorder. Brain Sci 2024; 14:273. [PMID: 38539661 PMCID: PMC10968557 DOI: 10.3390/brainsci14030273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
Autism spectrum disorders (ASDs) encompass a broad group of neurodevelopmental disorders with varied clinical symptoms, all being characterized by deficits in social communication and repetitive behavior. Although the etiology of ASD is heterogeneous, with many genes involved, a crucial role is believed to be played by copy number variants (CNVs). The present study examines the role of copy number variation in the development of isolated ASD, or ASD with additional clinical features, among a group of 180 patients ranging in age from two years and four months to 17 years and nine months. Samples were taken and subjected to array-based comparative genomic hybridization (aCGH), the gold standard in detecting gains or losses in the genome, using a 4 × 180 CytoSure Autism Research Array, with a resolution of around 75 kb. The results indicated the presence of nine pathogenic and six likely pathogenic imbalances, and 20 variants of uncertain significance (VUSs) among the group. Relevant variants were more prevalent in patients with ASD and additional clinical features. Twelve of the detected variants, four of which were probably pathogenic, would not have been identified using the routine 8 × 60 k microarray. These results confirm the value of microarrays in ASD diagnostics and highlight the need for dedicated tools.
Collapse
Affiliation(s)
- Agata Kucińska
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Wanda Hawuła
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Lena Rutkowska
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Urszula Wysocka
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Łukasz Kępczyński
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Małgorzata Piotrowicz
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Tatiana Chilarska
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Nina Wieczorek-Cichecka
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| | - Katarzyna Połatyńska
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (K.P.); (Ł.P.)
| | - Łukasz Przysło
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (K.P.); (Ł.P.)
| | - Agnieszka Gach
- Department of Genetics, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland; (W.H.); (L.R.); (U.W.); (Ł.K.); (M.P.); (T.C.); (N.W.-C.); (A.G.)
| |
Collapse
|
3
|
Maya I, Kahana S, Agmon-Fishman I, Klein C, Matar R, Berger R, Josefsberg SBY, Shohat M, Marom D, Basel-Salmon L, Sagi-Dain L. The phenotype of 15 cases with rare 8q24.13-q24.3 deletions-A new syndrome or still an enigma? Am J Med Genet A 2021; 185:1461-1467. [PMID: 33619900 DOI: 10.1002/ajmg.a.62131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/26/2021] [Accepted: 02/06/2021] [Indexed: 11/10/2022]
Abstract
Diagnosis of rare copy number variants (CNVs) with scarce literature evidence poses a major challenge for interpretation of the clinical significance of chromosomal microarray analysis (CMA) results, especially in the prenatal setting. Bioinformatic tools can be used to assist in this issue; however, this prediction can be imprecise. Our objective was to describe the phenotype of the rare copy number losses encompassing the 8q24.13-q24.3 locus, and to find common features in terms of genomic coordinates, gene content, and clinical phenotypic characteristics. Appropriate cases were retrieved using local databases of two largest Israeli centers performing CMA analysis. In addition, literature and public databases search was performed. Local database search yielded seven new patients with del (8)(q24.13q24.3) (one of these with an additional copy number variant). Literature and public databases search yielded eight additional patients. The cases showed high phenotypic variability, ranging from asymptomatic adults and fetuses with normal ultrasound to patients with autism/developmental delay (6/11 postnatal cases, 54.5%). No clear association was noted between the specific disease-causing/high-pLI gene content of the described del (8)(q24.13q24.3) to neurodevelopmental disorders, except for a possibly relevant locus encompassing the KCNQ3 gene. We present the challenges in classification of rare variants with limited clinical information. In such cases, genotype-phenotype correlation must be assessed with extra-caution and possibly using additional methods to assist the classification, especially in the prenatal setting.
Collapse
Affiliation(s)
- Idit Maya
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarit Kahana
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Ifaat Agmon-Fishman
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Cochava Klein
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Reut Matar
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Racheli Berger
- Genetics Laboratory, Maccabi Health Services, Rehovot, Israel
| | | | - Mordechai Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Genetics Laboratory, Maccabi Health Services, Rehovot, Israel.,Bioinformatics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Daphna Marom
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Lina Basel-Salmon
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, affiliated to the Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| |
Collapse
|