Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

被引：13

作者：

Clark, Wyatt T. ^{[1
]}

Kasak, Laura ^{[2
,3
]}

Bakolitsa, Constantina ^{[2
]}

Hu, Zhiqiang ^{[2
]}

Andreoletti, Gaia ^{[2
]}

Babbi, Giulia ^{[4
]}

Bromberg, Yana ^{[5
]}

Casadio, Rita ^{[4
]}

Dunbrack, Roland ^{[6
]}

Folkman, Lukas ^{[7
]}

Ford, Colby T. ^{[8
]}

Jones, David ^{[9
]}

Katsonis, Panagiotis ^{[10
]}

Kundu, Kunal ^{[11
,20
]}

Lichtarge, Olivier ^{[10
,12
,13
,14
]}

Martelli, Pier L. ^{[3
]}

Mooney, Sean D. ^{[15
]}

Nodzak, Conor ^{[8
]}

Pal, Lipika R. ^{[11
]}

Ivojac, Pred Rag Rad ^{[16
]}

Savojardo, Castrense ^{[4
]}

Shi, Xinghua ^{[8
]}

Zhou, Yaoqi ^{[17
]}

Uppal, Aneeta ^{[8
]}

Xu, Qifang ^{[6
]}

Yin, Yizhou ^{[11
,20
]}

Pejaver, Vikas ^{[16
,18
]}

Wang, Meng ^{[19
]}

Wei, Liping ^{[19
]}

Moult, John ^{[11
,21
]}

Yu, Guoying Karen ^{[1
]}

Brenner, Steven E. ^{[2
]}

LeBowitz, Jonathan H. ^{[1
]}

机构：

[1] BioMarin Pharmaceut, Human Genet, San Rafael, CA USA

[2] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[3] Univ Tartu, Dept Biomed, Inst Biomed & Translat Med, Tartu, Estonia

[4] Univ Bologna, Dept Pharm & Biotechnol, Biocomp Grp, Bologna, Italy

[5] Rutgers State Univ, Dept Biochem & Microbiol, New Brunswick, NJ USA

[6] Fox Chase Canc Ctr, Inst Canc Res, 7701 Burholme Ave, Philadelphia, PA 19111 USA

[7] ETH, Dept Biosyst Sci & Engn, Machine Learning & Computat Biol Lab, Zurich, Switzerland

[8] Univ North Carolina Charlotte, Dept Bioinformat & Genom, Charlotte, NC USA

[9] UCL, Bioinformat Grp, Dept Comp Sci, London, England

[10] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[11] Univ Maryland, Inst Biosci & Biotechnol Res, Rockville, MD USA

[12] Baylor Coll Med, Dept Biochem & Mol Biol, Houston, TX 77030 USA

[13] Baylor Coll Med, Dept Pharmacol, Houston, TX 77030 USA

[14] Baylor Coll Med, Computat & Integrat Biomed Res Ctr, Houston, TX 77030 USA

[15] Buck Inst Res Aging, Novato, CA USA

[16] Indiana Univ, Dept Comp Sci, Bloomington, IN 47405 USA

[17] Indiana Univ Sch Med, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA

[18] Indiana Univ, Dept Informat, Bloomington, IN USA

[19] Peking Univ, Ctr Bioinformat, State Key Lab Prot & Plant Gene Res, Sch Life Sci, Beijing, Peoples R China

[20] Univ Maryland, Computat Biol Bioinformat & Genom, Biol Sci Grad Program, College Pk, MD 20742 USA

[21] Univ Maryland, Dept Cell Biol & Mol Genet, College Pk, MD 20742 USA

来源：

HUMAN MUTATION | 2019年 / 40卷 / 09期

关键词：

CAGI; critical assessment; enzymatic activity; machine learning; Sanfilippo syndrome; variants of unknown significance; alpha-N-acetylglucosaminidase; NAGLU; WEB SERVER; PROTEIN; SEQUENCE; GLUCOSAMINIDASE; PATHOGENICITY; STABILITY; PHENOTYPE; GENOTYPE; IMPACT;

D O I：

10.1002/humu.23875

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The NAGLU challenge of the fourth edition of the Critical Assessment of Genome Interpretation experiment (CAGI4) in 2016, invited participants to predict the impact of variants of unknown significance (VUS) on the enzymatic activity of the lysosomal hydrolase alpha-N-acetylglucosaminidase (NAGLU). Deficiencies in NAGLU activity lead to a rare, monogenic, recessive lysosomal storage disorder, Sanfilippo syndrome type B (MPS type IIIB). This challenge attracted 17 submissions from 10 groups. We observed that top models were able to predict the impact of missense mutations on enzymatic activity with Pearson's correlation coefficients of up to .61. We also observed that top methods were significantly more correlated with each other than they were with observed enzymatic activity values, which we believe speaks to the importance of sequence conservation across the different methods. Improved functional predictions on the VUS will help population-scale analysis of disease epidemiology and rare variant association analysis.

引用

页码：1519 / 1529

页数：11

共 36 条

[1] A method and server for predicting damaging missense mutations [J].

Adzhubei, Ivan A. ;

Schmidt, Steffen ;

Peshkin, Leonid ;

Ramensky, Vasily E. ;

Gerasimova, Anna ;

Bork, Peer ;

Kondrashov, Alexey S. ;

Sunyaev, Shamil R. .

NATURE METHODS, 2010, 7 (04) :248-249

[2] Sanfilippo syndrome: Overall review [J].

Andrade, Fernando ;

Aldamiz-Echevarria, Luis ;

Llarena, Marta ;

Luz Couce, Maria .

PEDIATRICS INTERNATIONAL, 2015, 57 (03) :331-338

[3] Clearance of Heparan Sulfate and Attenuation of CNS Pathology by Intracerebroventricular BMN 250 in Sanfilippo Type B Mice [J].

Aoyagi-Scharber, Mika ;

Crippen-Harmon, Danielle ;

Lawrence, Roger ;

Vincelette, Jon ;

Yogalingam, Gouri ;

Prill, Heather ;

Yip, Bryan K. ;

Baridon, Brian ;

Vitelli, Catherine ;

Lee, Amanda ;

Gorostiza, Olivia ;

Adintori, Evan G. ;

Minto, Wesley C. ;

Van Vleet, Jeremy L. ;

Yates, Bridget ;

Rigney, Sara ;

Christianson, Terri M. ;

Tiger, Pascale M. N. ;

Lo, Melanie J. ;

Holtzinger, John ;

Fitzpatrick, Paul A. ;

LeBowitz, Jonathan H. ;

Bullens, Sherry ;

Crawford, Brett E. ;

Bunting, Stuart .

MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT, 2017, 6 :43-53

[4] Structural characterization of the α-N-acetylglucosaminidase, a key enzyme in the pathogenesis of Sanfilippo syndrome B [J].

Birrane, Gabriel ;

Dassier, Anne-Laure ;

Romashko, Alla ;

Lundberg, Dianna ;

Holmes, Kevin ;

Cottle, Thomas ;

Norton, Angela W. ;

Zhang, Bohong ;

Concino, Michael F. ;

Meiyappan, Muthuraman .

JOURNAL OF STRUCTURAL BIOLOGY, 2019, 205 (03) :65-71

[5] SNAP: predict effect of non-synonymous polymorphisms on function [J].

Bromberg, Yana ;

Rost, Burkhard .

NUCLEIC ACIDS RESEARCH, 2007, 35 (11) :3823-3835

[6] WS-SNPs& GO: a web server for predicting the deleterious effect of human protein variants using functional annotation [J].

Capriotti, Emidio ;

Calabrese, Remo ;

Fariselli, Piero ;

Martelli, Pier Luigi ;

Altman, Russ B. ;

Casadio, Rita .

BMC GENOMICS, 2013, 14

[7] Functional assays for BRCA1 and BRCA2 [J].

Carvalho, Marcelo A. ;

Couch, Fergus J. ;

Monteiro, Alvaro N. A. .

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 2007, 39 (02) :298-310

[8] PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels [J].

Choi, Yongwook ;

Chan, Agnes P. .

BIOINFORMATICS, 2015, 31 (16) :2745-2747

[9] Utilizing ExAC to assess the hidden contribution of variants of unknown significance to Sanfilippo Type B incidence [J].

Clark, Wyatt T. ;

Yu, G. Karen ;

Aoyagi-Scharber, Mika ;

LeBowitz, Jonathan H. .

PLOS ONE, 2018, 13 (07)

[10] Glycosaminoglycan Storage Disorders: A Review [J].

Coutinho, Maria Francisca ;

Lacerda, Lucia ;

Alves, Sandra .

BIOCHEMISTRY RESEARCH INTERNATIONAL, 2012, 2012

← 1 2 3 4 →