Browsing by Subject "Whole-exome sequencing"

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  • Johnson, Katherine; Bertoli, Marta; Phillips, Lauren; Topf, Ana; Van den Bergh, Peter; Vissing, John; Witting, Nanna; Nafissi, Shahriar; Jamal-Omidi, Shirin; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Potulska-Chromik, Anna; Deconinck, Nicolas; Wallgren-Pettersson, Carina; Strang-Karlsson, Sonja; Colomer, Jaume; Claeys, Kristl G.; De Ridder, Willem; Baets, Jonathan; von der Hagen, Maja; Fernandez-Torron, Roberto; Zulaica Ijurco, Miren; Espinal Valencia, Juan Bautista; Hahn, Andreas; Durmus, Hacer; Willis, Tracey; Xu, Liwen; Valkanas, Elise; Mullen, Thomas E.; Lek, Monkol; MacArthur, Daniel G.; Straub, Volker (2018)
    Background: Dystroglycanopathies are a clinically and genetically heterogeneous group of disorders that are typically characterised by limb-girdle muscle weakness. Mutations in 18 different genes have been associated with dystroglycanopathies, the encoded proteins of which typically modulate the binding of alpha-dystroglycan to extracellular matrix ligands by altering its glycosylation. This results in a disruption of the structural integrity of the myocyte, ultimately leading to muscle degeneration. Methods: Deep phenotypic information was gathered using the PhenoTips online software for 1001 patients with unexplained limb-girdle muscle weakness from 43 different centres across 21 European and Middle Eastern countries. Whole-exome sequencing with at least 250 ng DNA was completed using an Illumina exome capture and a 38 Mb baited target. Genes known to be associated with dystroglycanopathies were analysed for disease-causing variants. Results: Suspected pathogenic variants were detected in DPM3, ISPD, POMT1 and FKTN in one patient each, in POMK in two patients, in GMPPB in three patients, in FKRP in eight patients and in POMT2 in ten patients. This indicated a frequency of 2.7% for the disease group within the cohort of 1001 patients with unexplained limb-girdle muscle weakness. The phenotypes of the 27 patients were highly variable, yet with a fundamental presentation of proximal muscle weakness and elevated serum creatine kinase. Conclusions: Overall, we have identified 27 patients with suspected pathogenic variants in dystroglycanopathy-associated genes. We present evidence for the genetic and phenotypic diversity of the dystroglycanopathies as a disease group, while also highlighting the advantage of incorporating next-generation sequencing into the diagnostic pathway of rare diseases.
  • Johnson, Katherine; Bertoli, Marta; Phillips, Lauren; Töpf, Ana; Van den Bergh, Peter; Vissing, John; Witting, Nanna; Nafissi, Shahriar; Jamal-Omidi, Shirin; Łusakowska, Anna; Kostera-Pruszczyk, Anna; Potulska-Chromik, Anna; Deconinck, Nicolas; Wallgren-Pettersson, Carina; Strang-Karlsson, Sonja; Colomer, Jaume; Claeys, Kristl G; De Ridder, Willem; Baets, Jonathan; von der Hagen, Maja; Fernández-Torrón, Roberto; Zulaica Ijurco, Miren; Espinal Valencia, Juan B; Hahn, Andreas; Durmus, Hacer; Willis, Tracey; Xu, Liwen; Valkanas, Elise; Mullen, Thomas E; Lek, Monkol; MacArthur, Daniel G; Straub, Volker (BioMed Central, 2018)
    Abstract Background Dystroglycanopathies are a clinically and genetically heterogeneous group of disorders that are typically characterised by limb-girdle muscle weakness. Mutations in 18 different genes have been associated with dystroglycanopathies, the encoded proteins of which typically modulate the binding of α-dystroglycan to extracellular matrix ligands by altering its glycosylation. This results in a disruption of the structural integrity of the myocyte, ultimately leading to muscle degeneration. Methods Deep phenotypic information was gathered using the PhenoTips online software for 1001 patients with unexplained limb-girdle muscle weakness from 43 different centres across 21 European and Middle Eastern countries. Whole-exome sequencing with at least 250 ng DNA was completed using an Illumina exome capture and a 38 Mb baited target. Genes known to be associated with dystroglycanopathies were analysed for disease-causing variants. Results Suspected pathogenic variants were detected in DPM3, ISPD, POMT1 and FKTN in one patient each, in POMK in two patients, in GMPPB in three patients, in FKRP in eight patients and in POMT2 in ten patients. This indicated a frequency of 2.7% for the disease group within the cohort of 1001 patients with unexplained limb-girdle muscle weakness. The phenotypes of the 27 patients were highly variable, yet with a fundamental presentation of proximal muscle weakness and elevated serum creatine kinase. Conclusions Overall, we have identified 27 patients with suspected pathogenic variants in dystroglycanopathy-associated genes. We present evidence for the genetic and phenotypic diversity of the dystroglycanopathies as a disease group, while also highlighting the advantage of incorporating next-generation sequencing into the diagnostic pathway of rare diseases.
  • Trotta, Luca; Norberg, Anna; Taskinen, Mervi; Beziat, Vivien; Degerman, Sofie; Wartiovaara-Kautto, Ulla; Välimaa, Hannamari; Jahnukainen, Kirsi; Casanova, Jean-Laurent; Seppänen, Mikko; Saarela, Janna; Koskenvuo, Minna; Martelius, Timi (2018)
    Background: The telomere biology disorders (TBDs) include a range of multisystem diseases characterized by mucocutaneous symptoms and bone marrow failure. In dyskeratosis congenita (DKQ, the clinical features of TBDs stem from the depletion of crucial stem cell populations in highly proliferative tissues, resulting from abnormal telomerase function. Due to the wide spectrum of clinical presentations and lack of a conclusive laboratory test it may be challenging to reach a clinical diagnosis, especially if patients lack the pathognomonic clinical features of TBDs. Methods: Clinical sequencing was performed on a cohort of patients presenting with variable immune phenotypes lacking molecular diagnoses. Hypothesis-free whole-exome sequencing (WES) was selected in the absence of compelling diagnostic hints in patients with variable immunological and haematological conditions. Results: In four patients belonging to three families, we have detected five novel variants in known TBD-causing genes (DKC1, TERT and RTEL1). In addition to the molecular findings, they all presented shortened blood cell telomeres. These findings are consistent with the displayed TBD phenotypes, addressing towards the molecular diagnosis and subsequent clinical follow-up of the patients. Conclusions: Our results strongly support the utility of WES-based approaches for routine genetic diagnostics of TBD patients with heterogeneous or atypical clinical presentation who otherwise might remain undiagnosed.
  • Trotta, Luca; Norberg, Anna; Taskinen, Mervi; Béziat, Vivien; Degerman, Sofie; Wartiovaara-Kautto, Ulla; Välimaa, Hannamari; Jahnukainen, Kirsi; Casanova, Jean-Laurent; Seppänen, Mikko; Saarela, Janna; Koskenvuo, Minna; Martelius, Timi (BioMed Central, 2018)
    Abstract Background The telomere biology disorders (TBDs) include a range of multisystem diseases characterized by mucocutaneous symptoms and bone marrow failure. In dyskeratosis congenita (DKC), the clinical features of TBDs stem from the depletion of crucial stem cell populations in highly proliferative tissues, resulting from abnormal telomerase function. Due to the wide spectrum of clinical presentations and lack of a conclusive laboratory test it may be challenging to reach a clinical diagnosis, especially if patients lack the pathognomonic clinical features of TBDs. Methods Clinical sequencing was performed on a cohort of patients presenting with variable immune phenotypes lacking molecular diagnoses. Hypothesis-free whole-exome sequencing (WES) was selected in the absence of compelling diagnostic hints in patients with variable immunological and haematological conditions. Results In four patients belonging to three families, we have detected five novel variants in known TBD-causing genes (DKC1, TERT and RTEL1). In addition to the molecular findings, they all presented shortened blood cell telomeres. These findings are consistent with the displayed TBD phenotypes, addressing towards the molecular diagnosis and subsequent clinical follow-up of the patients. Conclusions Our results strongly support the utility of WES-based approaches for routine genetic diagnostics of TBD patients with heterogeneous or atypical clinical presentation who otherwise might remain undiagnosed.
  • Kausar, Mehran; Siddiqi, Saima; Yaqoob, Muhammad; Mansoor, Sajid; Makitie, Outi; Mir, Asif; Khor, Chiea Chuen; Foo, Jia Nee; Anees, Mariam (2018)
    IntroductionOsteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disease with skeletal fragility and variable extra-skeletal manifestations. To date several point mutations in 18 different genes causing different types of OI have been identified. Mutations in WNT1 compromise activity of the osteoblasts leading to disturbed bone mass accrual, fragility fractures and progressive skeletal abnormalities. The present study was conducted to determine the underlying genetic cause of an autosomal recessive skeletal dysplasia in a large consanguineous family from Chinute, Pakistan.Materials and methodsBlood was collected from 24 individuals of affected family along with clinical data. Homozygosity mapping was performed to confirm consanguinity. SNPs were identified, followed by whole exome and Sanger sequencing. In silico characterization of WNT1 mutation was performed using multiple platforms.ResultsNine affected family members exhibited severe bone deformities, recurrent fractures, short stature and low bone mineral density. SNP array data revealed homozygous segments >1Mb in length accounting for 2.1-12.7% of the genome in affected individuals and their siblings and a single 6,344,821bp homozygous region in all affected individuals on chromosome 12q12-q13. This region includes two potential OI candidate genes WNT1 and VDR. We did whole-exome sequencing for both genes in two patients and identified a novel damaging missense mutation in exon 4 of WNT1: c.1168G>T (NM_005430) resulting in p.G324C. Sanger sequencing confirmed segregation of mutation with the disease in family.ConclusionWe report a novel mutation responsible for OI and our investigation expands the spectrum of disease-causing WNT1 mutations and the resulting OI phenotypes.
  • Kausar, Mehran; Siddiqi, Saima; Yaqoob, Muhammad; Mansoor, Sajid; Makitie, Outi; Mir, Asif; Khor, Chiea C; Foo, Jia N; Anees, Mariam (BioMed Central, 2018)
    Abstract Introduction Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disease with skeletal fragility and variable extra-skeletal manifestations. To date several point mutations in 18 different genes causing different types of OI have been identified. Mutations in WNT1 compromise activity of the osteoblasts leading to disturbed bone mass accrual, fragility fractures and progressive skeletal abnormalities. The present study was conducted to determine the underlying genetic cause of an autosomal recessive skeletal dysplasia in a large consanguineous family from Chinute, Pakistan. Materials and methods Blood was collected from 24 individuals of affected family along with clinical data. Homozygosity mapping was performed to confirm consanguinity. SNPs were identified, followed by whole exome and Sanger sequencing. In silico characterization of WNT1 mutation was performed using multiple platforms. Results Nine affected family members exhibited severe bone deformities, recurrent fractures, short stature and low bone mineral density. SNP array data revealed homozygous segments > 1 Mb in length accounting for 2.1–12.7% of the genome in affected individuals and their siblings and a single 6,344,821 bp homozygous region in all affected individuals on chromosome 12q12-q13. This region includes two potential OI candidate genes WNT1 and VDR. We did whole-exome sequencing for both genes in two patients and identified a novel damaging missense mutation in exon 4 of WNT1: c.1168G > T (NM_005430) resulting in p.G324C. Sanger sequencing confirmed segregation of mutation with the disease in family. Conclusion We report a novel mutation responsible for OI and our investigation expands the spectrum of disease-causing WNT1 mutations and the resulting OI phenotypes.