scholarly journals Beyond Homozygosity Mapping: Family-Control analysis based on Hamming distance for prioritizing variants in exome sequencing

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Atsuko Imai ◽  
Akihiro Nakaya ◽  
Somayyeh Fahiminiya ◽  
Martine Tétreault ◽  
Jacek Majewski ◽  
...  

2016 ◽  
Vol 98 ◽  
Author(s):  
LIOR COHEN ◽  
SHAY TZUR ◽  
NITZA GOLDENBERG-COHEN ◽  
CONCETTA BORMANS ◽  
DORON M. BEHAR ◽  
...  

SummaryInherited optic neuropathies are a heterogeneous group of disorders characterized by mild to severe visual loss, colour vision deficit, central or paracentral visual field defects and optic disc pallor. Optic atrophies can be classified into isolated or non-syndromic and syndromic forms. While multiple modes of inheritance have been reported, autosomal dominant optic atrophy and mitochondrial inherited Leber's hereditary optic neuropathy are the most common forms. Optic atrophy type 1, caused by mutations in theOPA1gene is believed to be the most common hereditary optic neuropathy, and most patients inherit a mutation from an affected parent. In this study we used whole-exome sequencing to investigate the genetic aetiology in a patient affected with isolated optic atrophy. Since the proband was the only affected individual in his extended family, and was a product of consanguineous marriage, homozygosity mapping followed by whole-exome sequencing were pursued. Exome results identified a novelde novo OPA1mutation in the proband. We conclude, that thoughde novo OPA1mutations are uncommon, testing of common optic atrophy-associated genes such as mitochondrial mutations andOPA1gene sequencing should be performed first in single individuals presenting with optic neuropathy, even when dominant inheritance is not apparent.



2020 ◽  
Vol 42 (8) ◽  
pp. 587-593
Author(s):  
Jamil A. Hashmi ◽  
Fatima Fadhli ◽  
Ahmed Almatrafi ◽  
Sibtain Afzal ◽  
Khushnooda Ramzan ◽  
...  


PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e112747 ◽  
Author(s):  
Alireza Haghighi ◽  
Amit Tiwari ◽  
Niloofar Piri ◽  
Gudrun Nürnberg ◽  
Nasrollah Saleh-Gohari ◽  
...  


2011 ◽  
Vol 89 (6) ◽  
pp. 773-781 ◽  
Author(s):  
Agnès Bloch-Zupan ◽  
Xavier Jamet ◽  
Christelle Etard ◽  
Virginie Laugel ◽  
Jean Muller ◽  
...  


2017 ◽  
Vol 38 (12) ◽  
pp. 1796-1800 ◽  
Author(s):  
Atsuko Imai-Okazaki ◽  
Masakazu Kohda ◽  
Kaori Kobayashi ◽  
Tomoko Hirata ◽  
Yasushi Sakata ◽  
...  


F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 207
Author(s):  
Intisar Al Alawi ◽  
Mohammed Al Riyami ◽  
Miguel Barroso-Gil ◽  
Laura Powell ◽  
Eric Olinger ◽  
...  

Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, (TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.



Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Johanna C Herkert ◽  
Rowida Almomani ◽  
Judith M Verhagen ◽  
Marja W Wessels ◽  
Aida M Bertoli-Avella ◽  
...  

Cardiomyopathies (CMP) in children are heterogeneous disorders of cardiac muscle with a relatively high incidence in infancy (8/100.000) as compared to older children (0.7/100.000). Beyond infancy, CMP is the most important indication for heart transplantation and transplantation free survival at 5 years after initial diagnosis is only 54%. Mutations in over 65 genes encoding sarcomeric, cytoskeletal and calcium-metabolizing proteins, cell-signaling molecules, and mitochondrial enzymes have been shown to cause CMPs. This has led to new recommendations for diagnostic evaluation and family screening incorporating genetic testing. However, present (targeted/custom based) diagnostic tests do not represent the whole spectrum of genetic etiologies and are leading to a correct diagnosis in just a subset of pediatric CMP patients. We present four children from two consanguineous families of Dutch and Moroccan descent with severe neonatal onset of CMP, ranging from lethal cardiomegaly with reduced contractility in three to severe left ventricular hypertrophy that remained stable in one child. A combined approach using homozygosity mapping and exome sequencing in both families identified a homozygous splice site variant resulting in exon skipping in the Dutch family, and a homozygous nonsense mutation in the Moroccan family within the same gene. This novel disease causing gene is implicated in the early differentiation of cardiomyocytes. Both variants were confirmed with Sanger sequencing and absent in large control populations. Previously published studies in a knockout mouse model demonstrated the functional role of this gene in CMPs. Additionally, we investigated the effect of the homozygous splice site mutation on the expression of different proteins at myocardial cell-cell junctions and myofibrils. These results point towards a role in intercalated disk remodeling. Electron microscopy- and protein expression studies on heart tissue of the patients are ongoing. Our findings add a new autosomal recessive gene to the list of genes already implicated in pediatric CMP, underscoring its genetic heterogeneity. Furthermore, our study indicates that the application of exome sequencing can improve the diagnostic yield in pediatric CMP.



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