Gene identification in the congenital disorders of glycosylation type I by whole-exome sequencing.

Congenital disorders of glycosylation type I (CDG-I) form a growing group of recessive neurometabolic diseases. Identification of disease genes is compromised by the enormous heterogeneity in clinical symptoms and the large number of potential genes involved. Until now, gene identification included the sequential application of biochemical methods in blood samples and fibroblasts. In genetically unsolved cases, homozygosity mapping has been applied in consanguineous families. Altogether, this time-consuming diagnostic strategy led to the identification of defects in 17 different CDG-I genes. Here, we applied whole-exome sequencing (WES) in combination with the knowledge of the protein N-glycosylation pathway for gene identification in our remaining group of six unsolved CDG-I patients from unrelated non-consanguineous families. Exome variants were prioritized based on a list of 76 potential CDG-I candidate genes, leading to the rapid identification of one known and two novel CDG-I gene defects. These included the first X-linked CDG-I due to a de novo mutation in ALG13, and compound heterozygous mutations in DPAGT1, together the first two steps in dolichol-PP-glycan assembly, and mutations in PGM1 in two cases, involved in nucleotide sugar biosynthesis. The pathogenicity of the mutations was confirmed by showing the deficient activity of the corresponding enzymes in patient fibroblasts. Combined with these results, the gene defect has been identified in 98% of our CDG-I patients. Our results implicate the potential of WES to unravel disease genes in the CDG-I in newly diagnosed singleton families.

[1]  G. Matthijs,et al.  Improved diagnostics lead to identification of three new patients with congenital disorder of glycosylation‐Ip , 2012, Human mutation.

[2]  J. Schuurs-Hoeijmakers,et al.  Autosomal Recessive Dilated Cardiomyopathy due to DOLK Mutations Results from Abnormal Dystroglycan O-Mannosylation , 2011, PLoS genetics.

[3]  J. Shendure,et al.  Exome sequencing as a tool for Mendelian disease gene discovery , 2011, Nature Reviews Genetics.

[4]  Madhuri R Hegde,et al.  Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation , 2011, Genetics in Medicine.

[5]  Andrew B Singleton,et al.  Exome sequencing: a transformative technology , 2011, The Lancet Neurology.

[6]  Christian Gilissen,et al.  Unlocking Mendelian disease using exome sequencing , 2011, Genome Biology.

[7]  E. Morava,et al.  How to find and diagnose a CDG due to defective N-glycosylation , 2011, Journal of Inherited Metabolic Disease.

[8]  Barbara Imperiali,et al.  The expanding horizons of asparagine-linked glycosylation. , 2011, Biochemistry.

[9]  S. Robertson,et al.  Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss , 2011, Nature Genetics.

[10]  L. Braiterman,et al.  Critical roles for the COOH terminus of the Cu-ATPase ATP7B in protein stability, trans-Golgi network retention, copper sensing, and retrograde trafficking. , 2011, American journal of physiology. Gastrointestinal and liver physiology.

[11]  Stephan Züchner,et al.  Exome sequencing allows for rapid gene identification in a Charcot‐Marie‐Tooth family , 2011, Annals of neurology.

[12]  G. Kuhlenbäumer,et al.  Novel genomic techniques open new avenues in the analysis of monogenic disorders , 2011, Human mutation.

[13]  J. Jaeken,et al.  Congenital disorders of glycosylation , 2010, Annals of the New York Academy of Sciences.

[14]  Christian Gilissen,et al.  A de novo paradigm for mental retardation , 2010, Nature Genetics.

[15]  J. van Reeuwijk,et al.  A novel cerebello-ocular syndrome with abnormal glycosylation due to abnormalities in dolichol metabolism. , 2010, Brain : a journal of neurology.

[16]  Christian Gilissen,et al.  Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. , 2010, American journal of human genetics.

[17]  T. Walsh,et al.  Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. , 2010, American journal of human genetics.

[18]  A. Afenjar,et al.  Guanosine diphosphate-mannose:GlcNAc2-PP-dolichol mannosyltransferase deficiency (congenital disorders of glycosylation type Ik): five new patients and seven novel mutations , 2010, Journal of Medical Genetics.

[19]  H. Freeze,et al.  SRD5A3 Is Required for Converting Polyprenol to Dolichol and Is Mutated in a Congenital Glycosylation Disorder , 2010, Cell.

[20]  Christian Gilissen,et al.  De novo mutations of SETBP1 cause Schinzel-Giedion syndrome , 2010, Nature Genetics.

[21]  A. Hoischen,et al.  Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy. , 2010, American journal of human genetics.

[22]  K. Claeys,et al.  Muscle glycogenosis due to phosphoglucomutase 1 deficiency. , 2009, The New England journal of medicine.

[23]  Thierry Hennet,et al.  Congenital disorders of glycosylation: an update on defects affecting the biosynthesis of dolichol‐linked oligosaccharides , 2009, Human mutation.

[24]  P. Shannon,et al.  Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.

[25]  J. Hofsteenge,et al.  Deficiency of Dol-P-Man synthase subunit DPM3 bridges the congenital disorders of glycosylation with the dystroglycanopathies. , 2009, American journal of human genetics.

[26]  J. Prestegard,et al.  Solution structure of Alg13: the sugar donor subunit of a yeast N-acetylglucosamine transferase. , 2008, Structure.

[27]  R. Wevers,et al.  Congenital disorder of glycosylation type Ix: Review of clinical spectrum and diagnostic steps , 2008, Journal of Inherited Metabolic Disease.

[28]  M. Zaffanello,et al.  Hypoglycosylation with increased fucosylation and branching of serum transferrin N-glycans in untreated galactosemia. , 2005, Glycobiology.

[29]  W. Tanner,et al.  Solubilization and Characterization of the Initial Enzymes of the Dolichol Pathway from Yeast , 2005 .

[30]  K. von Figura,et al.  Deficiency of GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase causes congenital disorder of glycosylation type Ik. , 2004, American journal of human genetics.

[31]  H. Freeze,et al.  Deficiency of UDP‐GlcNAc:Dolichol Phosphate N‐Acetylglucosamine‐1 Phosphate Transferase (DPAGT1) Causes a Novel Congenital Disorder of Glycosylation Type Ij , 2003, Human mutation.

[32]  K. von Figura,et al.  A New Type of Congenital Disorders of Glycosylation (CDG-Ii) Provides New Insights into the Early Steps of Dolichol-linked Oligosaccharide Biosynthesis* , 2003, Journal of Biological Chemistry.

[33]  F. Hanefeld,et al.  Deficiency of dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl mannosyltransferase causes congenital disorder of glycosylation type Ig. , 2002, The Biochemical journal.

[34]  M. Lehrman,et al.  Conserved sequences in enzymes of the UDP-GlcNAc/MurNAc family are essential in hamster UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase. , 1998, Glycobiology.

[35]  E. Schaftingen,et al.  Phosphomannomutase deficiency is a cause of carbohydrate‐deficient glycoprotein syndrome type I , 1995, FEBS letters.

[36]  P. Orlean,et al.  A 13-amino acid peptide in three yeast glycosyltransferases may be involved in dolichol recognition. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Yigong Shi,et al.  The 1.9 Å crystal structure of Escherichia coli MurG, a membrane‐associated glycosyltransferase involved in peptidoglycan biosynthesis , 2000, Protein science : a publication of the Protein Society.

[38]  H. G. Eijk,et al.  Optimized separation and quantitation of serum and cerebrospinal fluid transferrin subfractions defined by differences in iron saturation or glycan composition. , 1994 .