Extracting complementary insights from molecular phenotypes for prioritization of disease-associated mutations

Current Opinion in Systems Biology - Tập 11 - Trang 107-116 - 2018
Shayne D. Wierbowski1,2, Robert Fragoza2,3, Siqi Liang1,2, Haiyuan Yu1,2
1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
2Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
3Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA

Tài liệu tham khảo

Snyder, 2010, Personal genome sequencing: current approaches and challenges, Genes Dev, 24, 423, 10.1101/gad.1864110 The 1000 Genomes Project Consortium, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature, 491, 56, 10.1038/nature11632 Fu, 2013, Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, Nature, 493, 216, 10.1038/nature11690 Stenson, 2009, The human gene mutation database: 2008 update, Genome Med, 1, 13, 10.1186/gm13 Hindorff, 2009, Potential etiologic and functional implications of genome-wide association loci for human diseases and traits, Proc Natl Acad Sci Unit States Am, 106, 9362, 10.1073/pnas.0903103106 Ng, 2003, SIFT: predicting amino acid changes that affect protein function, Nucleic Acids Res, 31, 3812, 10.1093/nar/gkg509 Choi, 2012 Adzhubei, 2013, Predicting functional effect of human missense mutations using PolyPhen-2, Curr Protoc Hum Genet, 10.1002/0471142905.hg0720s76 Adzhubei, 2010, A method and server for predicting damaging missense mutations, Nat Methods, 7, 248, 10.1038/nmeth0410-248 Kircher, 2014, A general framework for estimating the relative pathogenicity of human genetic variants, Nat Genet, 46, 310, 10.1038/ng.2892 Seifi, 2018, Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms, PLoS One, 13, e0195971, 10.1371/journal.pone.0195971 Choi, 2012, Predicting the functional effect of amino acid substitutions and indels, PLoS One, 7, e46688, 10.1371/journal.pone.0046688 Choi, 2015, PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels, Bioinformatics, 31, 2745, 10.1093/bioinformatics/btv195 Ritchie, 2014, Functional annotation of noncoding sequence variants, Nat Methods, 11, 294, 10.1038/nmeth.2832 Huang, 2017, Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data, Nat Genet, 49, 618, 10.1038/ng.3810 Rosenberg, 2018, A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas, Nat Commun, 9, 2371, 10.1038/s41467-018-04622-w Graf, 2018, Identification of rare sequence variation underlying heritable pulmonary arterial hypertension, Nat Commun, 9, 1416, 10.1038/s41467-018-03672-4 Bhattacharya, 2018, Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia, Genome Res, 28, 423, 10.1101/gr.223693.117 Tubeleviciute-Aydin, 2018, Rare human Caspase-6-R65W and Caspase-6-G66R variants identify a novel regulatory region of Caspase-6 activity, Sci Rep, 8, 4428, 10.1038/s41598-018-22283-z Bhatnager, 2018, Comprehensive in-silico prediction of damage associated SNPs in Human Prolidase gene, Sci Rep, 8, 9430, 10.1038/s41598-018-27789-0 Cunningham, 2017, Coupling between protein stability and catalytic activity determines pathogenicity of G6PD variants, Cell Rep, 18, 2592, 10.1016/j.celrep.2017.02.048 Iossifov, 2014, The contribution of de novo coding mutations to autism spectrum disorder, Nature, 515, 216, 10.1038/nature13908 Geisheker, 2017, Hotspots of missense mutation identify neurodevelopmental disorder genes and functional domains, Nat Neurosci, 20, 1043, 10.1038/nn.4589 Li, 2016, Variants in TRIM22 that affect NOD2 signaling are associated with very-early-onset inflammatory bowel disease, Gastroenterology, 150, 1196, 10.1053/j.gastro.2016.01.031 Miosge, 2015, Comparison of predicted and actual consequences of missense mutations, Proc Nat Acad Sci U S A, 112, E5189, 10.1073/pnas.1511585112 Wang, 2018, Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database, Nat Commun, 9, 441, 10.1038/s41467-017-02806-4 Ernst, 2018, Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics, BMC Med Genom, 11, 35, 10.1186/s12920-018-0353-y Cooper, 2011, Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data, Nat Rev Genet, 12, 628, 10.1038/nrg3046 Henn, 2015, Estimating mutation load in human genomes, Nat Rev Genet, 16, 333, 10.1038/nrg3931 Ng, 2006, Predicting the effects of amino acid substitutions on protein function, Annu Rev Genom Hum Genet, 7, 61, 10.1146/annurev.genom.7.080505.115630 Tennessen, 2012, Evolution and functional impact of rare coding variation from deep sequencing of human exomes, Science, 337, 64, 10.1126/science.1219240 Care, 2007, Deleterious SNP prediction: be mindful of your training data!, Bioinformatics, 23, 664, 10.1093/bioinformatics/btl649 Thomas, 2004, Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects, Proc Nat Acad Sci U S A, 101, 15398, 10.1073/pnas.0404380101 Corder, 1993, Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families, Science, 261, 921, 10.1126/science.8346443 Strittmatter, 1993, Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease, Proc Nat Acad Sci U S A, 90, 1977, 10.1073/pnas.90.5.1977 Deary, 2002, Cognitive change and the APOE ɛ4 allele, Nature, 418, 932, 10.1038/418932a Robitaille, 2003, The PPAR-gamma P12A polymorphism modulates the relationship between dietary fat intake and components of the metabolic syndrome: results from the Québec Family Study, Clin Genet, 63, 109, 10.1034/j.1399-0004.2003.00026.x Florez, 2007, Effects of the type 2 diabetes-associated PPARG P12A polymorphism on progression to diabetes and response to troglitazone, J Clin Endocrinol Metab, 92, 1502, 10.1210/jc.2006-2275 Kanda, 2007, A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration, Proc Natl Acad Sci Unit States Am, 104, 16227, 10.1073/pnas.0703933104 Rivera, 2005, Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk, Hum Mol Genet, 14, 3227, 10.1093/hmg/ddi353 Norrgard, 1998, Double mutation (A171T) and (D444H) is a common cause of profound biotinidase deficiency in children ascertained by newborn screening in the United States, Hum Mutat, 11, 10.1002/(SICI)1098-1004(1998)11:5<410::AID-HUMU10>3.0.CO;2-8 Borsatto, 2014, Biotinidase deficiency: clinical and genetic studies of 38 Brazilian patients, BMC Med Genet, 15, 96, 10.1186/s12881-014-0096-3 Klein, 2005, Complement factor H polymorphism in age-related macular degeneration, Science, 308, 385, 10.1126/science.1109557 Edwards, 2005, Complement factor H polymorphism and age-related macular degeneration, Science, 308, 421, 10.1126/science.1110189 Haines, 2005, Complement factor H variant increases the risk of age-related macular degeneration, Science, 308, 419, 10.1126/science.1110359 Jeanne, 2012, COL4A2 mutations impair COL4A1 and COL4A2 secretion and cause hemorrhagic stroke, Am J Hum Genet, 90, 91, 10.1016/j.ajhg.2011.11.022 Chand, 2007, Functional analysis of the human inhibin α subunit variant A257T and its potential role in premature ovarian failure, Hum Reprod, 22, 3241, 10.1093/humrep/dem323 Chand, 2010, Inhibin and premature ovarian failure, Hum Reprod Update, 16, 39, 10.1093/humupd/dmp031 Shelling, 2000, Inhibin: a candidate gene for premature ovarian failure, Hum Reprod, 15, 2644, 10.1093/humrep/15.12.2644 Witt, 1999, A signal peptide cleavage site mutation in the cationic trypsinogen gene is strongly associated with chronic pancreatitis, Gastroenterology, 117, 7, 10.1016/S0016-5085(99)70543-3 Chen, 1999, The A16V signal peptide cleavage site mutation in the cationic trypsinogen gene and chronic pancreatitis, Gastroenterology, 117, 1508, 10.1016/S0016-5085(99)70313-6 Kujovich, 2010, Factor V leiden thrombophilia, Genet Med, 13, 1, 10.1097/GIM.0b013e3181faa0f2 van Mens, 2013, Evolution of factor V leiden, Thromb Haemostasis, 110, 23, 10.1160/TH13-02-0115 Beutler, 2003, The HFE Cys282Tyr mutation as a necessary but not sufficient cause of clinical hereditary hemochromatosis, Blood, 101, 3347, 10.1182/blood-2002-06-1747 McCune, 2006, Iron loading and morbidity among relatives of HFE C282Y homozygotes identified either by population genetic testing or presenting as patients, Gut, 55, 554, 10.1136/gut.2005.070342 Whitlock, 2006, Screening for hereditary hemochromatosis: a systematic review for the u.s. preventive services task force, Ann Intern Med, 145, 209, 10.7326/0003-4819-145-3-200608010-00009 Rossi, 2008, Clinical penetrance of C282Y homozygous HFE hemochromatosis, Expet Rev Hematol, 1, 205, 10.1586/17474086.1.2.205 Cooper, 2013, Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease, Hum Genet, 132, 1077, 10.1007/s00439-013-1331-2 Lek, 2016, Analysis of protein-coding genetic variation in 60,706 humans, Nature, 536, 285, 10.1038/nature19057 Walsh, 2016, Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples, Genet Med, 19, 192, 10.1038/gim.2016.90 Sahni, 2015, Widespread macromolecular interaction perturbations in human genetic disorders, Cell, 161, 647, 10.1016/j.cell.2015.04.013 Wei, 2014, A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations, PLoS Genet, 10, e1004819, 10.1371/journal.pgen.1004819 Zhong, 2009, Edgetic perturbation models of human inherited disorders, Mol Syst Biol, 5, 10.1038/msb.2009.80 Barrera, 2016, Survey of variation in human transcription factors reveals prevalent DNA binding changes, Science, 351, 1450, 10.1126/science.aad2257 Fuxman Bass, 2015, Human gene-centered transcription factor networks for enhancers and disease variants, Cell, 161, 661, 10.1016/j.cell.2015.03.003 Stefl, 2013, Molecular mechanisms of disease-causing missense mutations, J Mol Biol, 425, 3919, 10.1016/j.jmb.2013.07.014 Schenone, 2013, Target identification and mechanism of action in chemical biology and drug discovery, Nat Chem Biol, 9, 232, 10.1038/nchembio.1199 Pejaver, 2017 Wang, 2012, Three-dimensional reconstruction of protein networks provides insight into human genetic disease, Nat Biotechnol, 30, 159, 10.1038/nbt.2106 Meyer, 2018, Interactome INSIDER: a structural interactome browser for genomic studies, Nat Methods, 15, 107, 10.1038/nmeth.4540 Gulko, 2015, A method for calculating probabilities of fitness consequences for point mutations across the human genome, Nat Genet, 47, 276, 10.1038/ng.3196 The ENCODE Project Consortium, 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 Hopf, 2017, Mutation effects predicted from sequence co-variation, Nat Biotechnol, 35, 128, 10.1038/nbt.3769 Wright, 2003, A polygenic basis for late-onset disease, Trends Genet, 19, 10, 10.1016/S0168-9525(02)00033-1 Chen, 2018, An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders, Nat Genet, 50, 1032, 10.1038/s41588-018-0130-z Sufan, 2004, The role of von Hippel-Lindau tumor suppressor protein and hypoxia in renal clear cell carcinoma, Am J Physiol Ren Physiol, 287, F1, 10.1152/ajprenal.00424.2003 Kaelin, 2007, The von Hippel-lindau tumor suppressor protein, Update, 435, 371 Sahni, 2010, BMPR1a and BMPR1b signaling exert opposing effects on gliosis after spinal cord injury, J Neurosci, 30, 1839, 10.1523/JNEUROSCI.4459-09.2010 Racacho, 2015, Two novel disease-causing variants in BMPR1B are associated with brachydactyly type A1, Eur J Hum Genet, 23, 1640, 10.1038/ejhg.2015.38 Takano, 2012, An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity, Hum Mol Genet, 21, 4497, 10.1093/hmg/dds292 Koczok, 2018, A novel point mutation affecting Asn76 of dystrophin protein leads to dystrophinopathy, Neuromuscul Disord, 28, 129, 10.1016/j.nmd.2017.12.003 Aneichyk, 2018, Dissecting the causal mechanism of X-linked dystonia-parkinsonism by integrating genome and transcriptome assembly, Cell, 172, 10.1016/j.cell.2018.02.011 Hua, 2018, Risk SNP-mediated promoter-enhancer switching drives prostate cancer through lncRNA PCAT19, Cell, 174, 10.1016/j.cell.2018.06.014 Costanzo, 2016, A global genetic interaction network maps a wiring diagram of cellular function, Science, 353, 10.1126/science.aaf1420 Kuzmin, 2018, Systematic analysis of complex genetic interactions, Science, 360, 10.1126/science.aao1729 Horlbeck, 2018, Mapping the genetic landscape of human cells, Cell, 174, 10.1016/j.cell.2018.06.010 Young, 2015, Elucidating molecular phenotypes caused by the SORL1 Alzheimer's disease genetic risk factor using human induced pluripotent stem cells, Cell Stem Cell, 16, 373, 10.1016/j.stem.2015.02.004 Cheng-Hathaway, 2018, The Trem2 R47H variant confers loss-of-function-like phenotypes in Alzheimer's disease, Mol Neurodegener, 13, 29, 10.1186/s13024-018-0262-8 Hauser, 2018, Pharmacogenomics of GPCR drug targets, Cell, 172, 41, 10.1016/j.cell.2017.11.033 Yersal, 2014, Biological subtypes of breast cancer: prognostic and therapeutic implications, World J Clin Oncol, 5, 412, 10.5306/wjco.v5.i3.412 Huang, 2017, Proteogenomic integration reveals therapeutic targets in breast cancer xenografts, Nat Commun, 8, 14864, 10.1038/ncomms14864 Zhang, 2016, Integrated proteogenomic characterization of human high-grade serous ovarian cancer, Cell, 166, 755, 10.1016/j.cell.2016.05.069 Chen, 2017, APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism, Nat Commun, 8, 465, 10.1038/s41467-017-00493-9 Lomberk, 2018, Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes, Nat Commun, 9, 1978, 10.1038/s41467-018-04383-6 Alvarez, 2018, A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors, Nat Genet, 50, 979, 10.1038/s41588-018-0138-4 del-Toro, 2018 Fowler, 2010, High-resolution mapping of protein sequence-function relationships, Nat Methods, 7, 741, 10.1038/nmeth.1492 Fowler, 2014, Deep mutational scanning: a new style of protein science, Nat Methods, 11, 801, 10.1038/nmeth.3027 Starita, 2013, Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis, Proc Natl Acad Sci Unit States Am, 110, E1263, 10.1073/pnas.1303309110 Starita, 2015, Massively parallel functional analysis of BRCA1 RING domain variants, Genetics, 200, 413, 10.1534/genetics.115.175802 Wagih, 2018 Schwarz, 2014, MutationTaster2: mutation prediction for the deep-sequencing age, Nat Methods, 11, 361, 10.1038/nmeth.2890