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      Biochemical and molecular predictors for prognosis in nonketotic hyperglycinemia

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          Abstract

          Objective

          Nonketotic hyperglycinemia is a neurometabolic disorder characterized by intellectual disability, seizures, and spasticity. Patients with attenuated nonketotic hyperglycinemia make variable developmental progress. Predictive factors have not been systematically assessed.

          Methods

          We reviewed 124 patients stratified by developmental outcome for biochemical and molecular predictive factors. Missense mutations were expressed to quantify residual activity using a new assay.

          Results

          Patients with severe nonketotic hyperglycinemia required multiple anticonvulsants, whereas patients with developmental quotient (DQ) > 30 did not require anticonvulsants. Brain malformations occurred mainly in patients with severe nonketotic hyperglycinemia (71%) but rarely in patients with attenuated nonketotic hyperglycinemia (7.5%). Neonatal presentation did not correlate with outcome, but age at onset ≥ 4 months was associated with attenuated nonketotic hyperglycinemia. Cerebrospinal fluid (CSF) glycine levels and CSF:plasma glycine ratio correlated inversely with DQ; CSF glycine > 230 μM indicated severe outcome and CSF:plasma glycine ratio ≤ 0.08 predicted attenuated outcome. The glycine index correlated strongly with outcome. Molecular analysis identified 99% of mutant alleles, including 96 novel mutations. Mutations near the active cleft of the P‐protein maintained stable protein levels. Presence of 1 mutation with residual activity was necessary but not sufficient for attenuated outcome; 2 such mutations conferred best outcome. Divergent outcomes for the same genotype indicate a contribution of other genetic or nongenetic factors.

          Interpretation

          Accurate prediction of outcome is possible in most patients. A combination of 4 factors available neonatally predicted 78% of severe and 49% of attenuated patients, and a score based on mutation severity predicted outcome with 70% sensitivity and 97% specificity. Ann Neurol 2015;78:606–618

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          Most cited references32

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          Improved splice site detection in Genie.

          We present an improved splice site predictor for the genefinding program Genie. Genie is based on a generalized Hidden Markov Model (GHMM) that describes the grammar of a legal parse of a multi-exon gene in a DNA sequence. In Genie, probabilities are estimated for gene features by using dynamic programming to combine information from multiple content and signal sensors, including sensors that integrate matches to homologous sequences from a database. One of the hardest problems in genefinding is to determine the complete gene structure correctly. The splice site sensors are the key signal sensors that address this problem. We replaced the existing splice site sensors in Genie with two novel neural networks based on dinucleotide frequencies. Using these novel sensors, Genie shows significant improvements in the sensitivity and specificity of gene structure identification. Experimental results in tests using a standard set of annotated genes showed that Genie identified 86% of coding nucleotides correctly with a specificity of 85%, versus 80% and 84% in the older system. In further splice site experiments, we also looked at correlations between splice site scores and intron and exon lengths, as well as at the effect of distance to the nearest splice site on false positive rates.
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            ESyPred3D: Prediction of proteins 3D structures.

            Homology or comparative modeling is currently the most accurate method to predict the three-dimensional structure of proteins. It generally consists in four steps: (1) databanks searching to identify the structural homolog, (2) target-template alignment, (3) model building and optimization, and (4) model evaluation. The target-template alignment step is generally accepted as the most critical step in homology modeling. We present here ESyPred3D, a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three-dimensional structure is build using the modeling package MODELLER. ESyPred3D was tested on 13 targets in the CASP4 experiment (Critical Assessment of Techniques for Proteins Structural Prediction). Our alignment strategy obtains better results compared to PSI-BLAST alignments and ESyPred3D alignments are among the most accurate compared to those of participants having used the same template. ESyPred3D is available through its web site at http://www.fundp.ac.be/urbm/bioinfo/esypred/ christophe.lambert@fundp.ac.be; http://www.fundp.ac.be/~lambertc
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              Variant non ketotic hyperglycinemia is caused by mutations in LIAS, BOLA3 and the novel gene GLRX5.

              Patients with nonketotic hyperglycinemia and deficient glycine cleavage enzyme activity, but without mutations in AMT, GLDC or GCSH, the genes encoding its constituent proteins, constitute a clinical group which we call 'variant nonketotic hyperglycinemia'. We hypothesize that in some patients the aetiology involves genetic mutations that result in a deficiency of the cofactor lipoate, and sequenced genes involved in lipoate synthesis and iron-sulphur cluster biogenesis. Of 11 individuals identified with variant nonketotic hyperglycinemia, we were able to determine the genetic aetiology in eight patients and delineate the clinical and biochemical phenotypes. Mutations were identified in the genes for lipoate synthase (LIAS), BolA type 3 (BOLA3), and a novel gene glutaredoxin 5 (GLRX5). Patients with GLRX5-associated variant nonketotic hyperglycinemia had normal development with childhood-onset spastic paraplegia, spinal lesion, and optic atrophy. Clinical features of BOLA3-associated variant nonketotic hyperglycinemia include severe neurodegeneration after a period of normal development. Additional features include leukodystrophy, cardiomyopathy and optic atrophy. Patients with lipoate synthase-deficient variant nonketotic hyperglycinemia varied in severity from mild static encephalopathy to Leigh disease and cortical involvement. All patients had high serum and borderline elevated cerebrospinal fluid glycine and cerebrospinal fluid:plasma glycine ratio, and deficient glycine cleavage enzyme activity. They had low pyruvate dehydrogenase enzyme activity but most did not have lactic acidosis. Patients were deficient in lipoylation of mitochondrial proteins. There were minimal and inconsistent changes in cellular iron handling, and respiratory chain activity was unaffected. Identified mutations were phylogenetically conserved, and transfection with native genes corrected the biochemical deficiency proving pathogenicity. Treatments of cells with lipoate and with mitochondrially-targeted lipoate were unsuccessful at correcting the deficiency. The recognition of variant nonketotic hyperglycinemia is important for physicians evaluating patients with abnormalities in glycine as this will affect the genetic causation and genetic counselling, and provide prognostic information on the expected phenotypic course.
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                Author and article information

                Journal
                Ann Neurol
                Ann. Neurol
                10.1002/(ISSN)1531-8249
                ANA
                Annals of Neurology
                John Wiley and Sons Inc. (Hoboken )
                0364-5134
                1531-8249
                10 August 2015
                October 2015
                : 78
                : 4 ( doiID: 10.1002/ana.v78.4 )
                : 606-618
                Affiliations
                [ 1 ] Department of PediatricsUniversity of Colorado Aurora CO
                [ 2 ] Center for Human GeneticsUniversity of Leuven LeuvenBelgium
                [ 3 ] Department of Pediatric and Adolescent MedicineUniversity Medical Center Mainz MainzGermany
                [ 4 ] Department of PediatricsUniversity of British Columbia Vancouver British ColumbiaCanada
                [ 5 ]Present address: Department of PediatricsMedical College of Wisconsin Milwaukee WI
                Author notes
                [*] [* ]Address correspondence to Dr Van Hove, Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Mailstop 8400, Education 2 South, L28‐4122, 13121 E 17th Avenue, Aurora, CO 80045. E‐mail: Johan.Vanhove@ 123456childrenscolorado.org
                Article
                ANA24485
                10.1002/ana.24485
                4767401
                26179960
                8af0ad0c-75a8-4188-9257-995b0a29ada1
                © 2015 The Authors Annals of Neurology published by Wiley Periodicals, Inc. on behalf of American Neurological Association

                This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 13 April 2015
                : 14 July 2015
                : 14 July 2015
                Page count
                Pages: 13
                Funding
                Funded by: NKH Crusaders Fund
                Funded by: Hope for NKH Fund
                Funded by: CU Nonketotic Hyperglycinemia Fund
                Funded by: Joseph's Goal Fund
                Funded by: Brodyn's Friends Fund
                Funded by: Smiles for Miles NKH Research Fund
                Funded by: Lucy's BEElievers Fund
                Funded by: Madi's Mission to Find a Cure for NKH Fund
                Funded by: Les Petits Bourdons
                Funded by: Children's Clinical Research Organization at Children's Hospital Colorado
                Funded by: Rocky Mountain Neurological Disorders Core Center
                Award ID: NIH/NS048154
                Funded by: University of Colorado DNA Sequencing and Analysis Core
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                ana24485
                October 2015
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.9.4 mode:remove_FC converted:09.09.2016

                Neurology
                Neurology

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