Predicting functional effects of missense variants in voltage-gated sodium and calcium channels

American Association for the Advancement of Science (AAAS) - Tập 12 Số 556 - 2020
Henrike Heyne1,2,3,4, David Báez-Nieto4, Sumaiya Iqbal1,5,3,4, Duncan S. Palmer1,3,4, Andreas Brunklaus6,7, Patrick May8, Katrine M. Johannesen9,10, Stephan Lauxmann11, Johannes R. Lemke12, Rikke S. Møller9,10, Eduardo Pérez‐Palma13,14, Ute I. Scholl15,16, Steffen Syrbe17, Holger Lerche11, Dennis Lal1,13,18,14,3,4, Arthur J. Campbell5,4, Hao-Ran Wang4, Jen Q. Pan4, Mark J. Daly1,2,3,4
1Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 5WR36M Helsinki, Finland.
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
4Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
5Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
6Paediatric Neurosciences Research Group, Royal Hospital for Sick Children, Glasgow G51 4TF, UK.
7School of Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
8Luxembourg Centre for Systems Biomedicine, Belvaux, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg.
9Department of Epilepsy Genetics and Personalized Treatment, Danish Epilepsy Centre, 4293 Dianalund, Denmark.
10Department of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark.
11Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany.
12Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
13Cologne Center for Genomics (CCG), University of Cologne, 50923, Germany.
14Genomic Medicine Institute, Lemer Research Institute Cleveland Clinic, OH G92J47, USA.
15Berlin Institute of Health (BIH), 10178 Berlin, Germany
16Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care and BIH Center for Regenerative Therapies, 10178 Berlin, Germany.
17Division of Pediatric Epileptology, Center for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany.
18Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH G92J47, USA.

Tóm tắt

A machine learning method can predict loss- versus gain-of-function effects of human genetic variants in disease-associated ion channels.

Từ khóa


Tài liệu tham khảo

10.1146/annurev.bi.64.070195.002425

K. J. Karczewski, L. C. Francioli, G. Tiao, B. B. Cummings, J. Alföldi, Q. Wang, R. L. Collins, K. M. Laricchia, A. Ganna, D. P. Birnbaum, L. D. Gauthier, H. Brand, M. Solomonson, N. A. Watts, D. Rhodes, M. Singer-Berk, E. G. Seaby, J. A. Kosmicki, R. K. Walters, K. Tashman, Y. Farjoun, E. Banks, T. Poterba, A. Wang, C. Seed, N. Whiffin, J. X. Chong, K. E. Samocha, E. Pierce-Hoffman, Z. Zappala, A. H. O’Donnell-Luria, E. V. Minikel, B. Weisburd, M. Lek, J. S. Ware, C. Vittal, I. M. Armean, L. Bergelson, K. Cibulskis, K. M. Connolly, M. Covarrubias, S. Donnelly, S. Ferriera, S. Gabriel, J. Gentry, N. Gupta, T. Jeandet, D. Kaplan, C. Llanwarne, R. Munshi, S. Novod, N. Petrillo, D. Roazen, V. Ruano-Rubio, A. Saltzman, M. Schleicher, J. Soto, K. Tibbetts, C. Tolonen, G. Wade, M. E. Talkowski; Genome Aggregation Database Consortium, B. M. Neale, M. J. Daly, D. G. MacArthur, Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv, 531210 (2019).

10.1038/nature13595

10.1038/s41467-018-07524-z

10.1038/s41588-018-0133-9

10.1126/stke.2532004re15

10.1101/gr.073585.107

10.1124/mol.114.097659

10.1126/science.aaw2999

10.1126/science.aau2486

10.1016/j.cell.2019.04.043

10.1007/s13238-017-0372-z

10.1136/jmedgenet-2014-102608

10.1002/ana.25268

10.1016/j.bbamem.2012.11.026

10.3389/fphar.2014.00053

10.1136/jmedgenet-2013-101917

10.1016/j.pneurobio.2015.09.002

10.1038/356441a0

D. Lal, P. May, E. Perez-Palma, K. E. Samocha, J. A. Kosmicki, E. B. Robinson, R. S. Møller, R. Krause, P. Nürnberg, S. Weckhuysen, P. De Jonghe, R. Guerrini, L. M. Niestroj, J. Du, C. Marini; EuroEPINOMICS-RES Consortium, J. S. Ware, M. Kurki, P. Gormley, S. Tang, S. Wu, S. Biskup, A. Poduri, B. A. Neubauer, B. P. C. Koeleman, K. L. Helbig, Y. G. Weber, I. Helbig, A. R. Majithia, A. Palotie, M. J. Daly, Gene family information facilitates variant interpretation and identification of disease-associated genes. bioRxiv, 159780 (2017).

10.1002/humu.22114

I. Adzhubei, D. M. Jordan, S. R. Sunyaev, Predicting functional effect of human missense mutations using PolyPhen-2. Curr. Protoc. Hum. Genet. Chapter 7, Unit7.20 (2013).

10.1038/ng.2892

10.1161/CIRCGENETICS.117.001754

10.1093/bioinformatics/btr365

10.1038/s41598-018-30577-5

10.1136/jmg.31.2.89

10.1038/nature19057

10.1016/j.cell.2019.02.032

10.1161/CIRCGEN.118.002095

10.1016/j.tins.2018.03.011

10.1093/brain/awy326

10.1002/ana.25438

10.1016/S0140-6736(00)03157-3

10.1093/brain/awx054

10.1212/WNL.0000000000001211

10.1177/1756285615607726

10.1093/brain/awm126

10.1093/brain/aws151

10.1126/science.1262110

10.1093/nar/gkw1039

10.1093/nar/gkv1222

10.1038/s41588-018-0143-7

10.1007/s00439-017-1779-6

10.1016/j.ajhg.2018.09.006

10.1038/s41436-019-0531-0

10.1038/gim.2015.30

10.1124/pr.117.014456

10.1038/32675

10.1007/s002490050020

K. E. Samocha, J. A. Kosmicki, K. J. Karczewski, A. H. O'Donnell-Luria, E. Pierce-Hoffman, D. G. MacArthur, B. M. Neale, M. J. Daly, Regional missense constraint improves variant deleteriousness prediction. bioRxiv, 148353 (2017).

10.1093/bioinformatics/16.5.412

10.1002/humu.23943

10.1002/humu.23619

10.1016/j.biopsych.2017.01.009

10.1038/nn.4402

10.1001/jamapsychiatry.2013.268

10.1016/j.ajhg.2019.05.020

10.1016/j.cell.2019.12.036

10.1038/s41593-019-0527-8

10.1113/jphysiol.2010.187484

10.1016/j.ajhg.2019.03.005

10.1038/nrg.2016.86

10.1016/S1474-4422(15)00199-4

10.1080/14737159.2019.1573144

10.1016/j.neuron.2006.10.006

10.1007/s12311-013-0531-6

10.1007/s13311-015-0403-5

10.1136/jnnp-2013-306095

10.1016/S1474-4422(14)70150-4

10.1073/pnas.89.22.10910

10.1074/jbc.M513518200

10.1085/jgp.109.5.589

10.1073/pnas.1411127112

10.1085/jgp.201611586

10.1085/jgp.20028679

10.1093/europace/euu063

10.1161/CIRCGENETICS.113.000138

10.1080/19336950.2015.1075677

10.1007/s00018-011-0832-1

10.1073/pnas.1800077115

10.1212/NXG.0000000000000115

10.1016/j.ajhg.2017.08.004

10.1016/j.neuron.2013.05.036

10.1124/mol.55.1.134

10.18637/jss.v028.i05

H. Wickham ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag New York 2016).

10.18637/jss.v079.c02

10.1214/aos/1013203451

10.1016/S0092-8674(00)81373-2

10.1177/1073858405275554

10.1016/j.ajhg.2016.06.003

10.1038/ejhg.2015.21

10.1016/S0092-8674(00)81381-1

10.1523/JNEUROSCI.20-15-05654.2000

10.1016/j.cell.2004.09.011

10.1038/ng.2695

10.1038/940

10.1093/hmg/ddi336

10.1212/01.wnl.0000342387.65477.46

10.1002/cphy.c140062

10.1212/WNL.53.9.1932

10.1086/320609

10.1073/pnas.1309827110

10.1016/S0140-6736(05)66786-4

10.1016/0092-8674(91)90374-8

10.1016/0896-6273(92)90203-P

10.1113/jphysiol.1994.sp020260

10.1016/0092-8674(95)90359-3

10.1038/376683a0

10.1136/jmedgenet-2014-102813

10.1523/JNEUROSCI.2695-04.2004

10.1136/jmg.2003.012153

10.1038/nature05598

10.1038/gim.2017.26

10.1186/s13059-016-0974-4

10.1038/nprot.2012.085

10.1093/nar/gky092

10.1093/nar/gkh340

10.1126/science.aaf6814

10.1002/bip.360221211

10.1093/nar/gku1028

S. Iqbal, J. B. Jespersen, E. Perez-Palma, P. May, D. Hoksza, H. O. Heyne, S. S. Ahmed, Z. T. Rifat, M. S. Rahman, K. Lage, A. Palotie, J. R. Cottrell, F. F. Wagner, M. J. Daly, A. J. Campbell, D. Lal, Insights into protein structural, physicochemical, and functional consequences of missense variants in 1,330 disease-associated human genes. bioRxiv, 693259 (2019).

10.1126/science.185.4154.862

10.1073/pnas.89.22.10915

10.1093/bioinformatics/btu033

N. Goldman, Z. Yang, A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725–736 (1994).

10.1534/genetics.105.044917

10.1038/s41467-019-10724-w

10.1007/BF01734359

D. Greene, S. Richardson, E. Turro, ontologyX: A suite of R packages for working with ontological data. Bioinformatics 33, 1104–1106 (2017).

10.1007/978-1-4939-7847-2_18

10.1038/srep34233

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American Association for the Advancement of Science (AAAS)

Tập 12 Số 556

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