© 2019, Genomnis

The UMD PREDICTOR system

Single Nucleotide Substitutions (SNP) represent the majority of human genetics variations with about 80,000 variants per human exome and more than 3,000,000 ​ variations per human genome. SNPs also account for most human disease-causing mutations with approximately 56% of missense and nonsense mutations. If classifying nonsense mutations as disease-causing is trivial, the classification of missense or synonymous mutations is challenging.

The UMD-Predictor system is an innovative bioinformatics solution to predict the pathogenicity of any SNP from any human transcript. It relies on an original combinatorial approach that consistently outperformed other predictors as illustrated in the figure adapted from Salgado et al. 2016.

The UMD-Predictor algorithm combines the following features:

  • Blosum62 conservation matrix (global conservation)

  • Yu’s biochemical substitution matrix (based on 48 physicochemical properties of amino acids)

  • Protein key residues (both for structure or activity)

  • Predicted impact on splicing signals (splice sites and auxiliary sequences)

  •  Variation frequency at the human population level

  • Conservation score in 100 species with Grantham’s substitution matrix (protein specific conservation)

Each parameter has a different weight corresponding to its biological consequence. Thus the alteration of a wild type donor or acceptor splice site has a major weight, while the creation of a cryptic splice site is limited.

 

The accuracy of UMD-Predictor has been assessed with four reference datasets (early 2016 datasets): Varibench [Sasidharan Nair and Vihinen, 2013] with dbSNP [Sherry et al., 2001] (19,335 pathogenic, 7,897 nonpathogenic); Uniprot [UniProt Consortium, 2014] (20,821 pathogenic, 36,825 non- pathogenic); Clinvar [Landrum et al., 2014] (10,669 pathogenic, 1,817 nonpathogenic), and PredictSNP [Bendl et al., 2014] (24,082 pathogenic, 19,800 nonpathogenic). 

The UMD-Predictor database contains all potential SNP from human transcripts. It is thus the fastest system (x16 on average) and produces the shortest list of candidate pathogenic variations (36% of other systems on average) leading to a strong benefit for downstream validation.

The UMD-Predictor system is accessible for regular users through a software as a service  license. It can be integrated in any bioinformatics pipeline through web services. Bioinformatics companies willing to include UMD-Predictor into their systems have various options to do it and should contact us.

Citations (since 2016)

2016

  1. Arnaud, P., Hanna, N., Aubart, M., Leheup, B., Dupuis-Girod, S., Naudion, S., ... & Bal, L. (2016). Homozygous and compound heterozygous mutations in the FBN1 gene: unexpected findings in molecular diagnosis of Marfan syndrome. Journal of Medical Genetics, jmedgenet-2016. [PubMed]

  2. Barbier, M., Gross, M. S., Aubart, M., Hanna, N., Kessler, K., Guo, D. C., ... & Abifadel, M. (2014). MFAP5 loss-of-function mutations underscore the involvement of matrix alteration in the pathogenesis of familial thoracic aortic aneurysms and dissections. The American Journal of Human Genetics, 95(6), 736-743. [PubMed]

  3. Béroud, C., Letovsky, S. I., Braastad, C. D., Caputo, S. M., Beaudoux, O., Bignon, Y. J., ... & Coulet, F. (2016). BRCA Share: A Collection of Clinical BRCA Gene Variants. Human Mutation, 37(12), 1318-1328.[PubMed]

  4. Bernard, V., Bouilly, J., Beau, I., Broutin, I., Chanson, P., Young, J., & Binart, N. (2016). Germline prolactin receptor mutation is not a major cause of sporadic prolactinoma in humans. Neuroendocrinology, 103(6), 738-745. [PubMed]

  5. Boppudi, S., Bögershausen, N., Hove, H. B., Percin, E. F., Aslan, D., Dvorsky, R., ... & Toft, P. B. (2016). Specific mosaic KRAS mutations affecting codon 146 cause oculoectodermal syndrome and encephalocraniocutaneous lipomatosis. Clinical genetics. [PubMed]

  6. Damsky, W., & King, B. A. (2016). Idiopathic erythema multiforme: Evidence of underlying Janus kinase–signal transducer and activator of transcription activation and successful treatment with tofacitinib. JAAD Case Reports, 2(6), 502. [PubMed]

  7. Doss, C. G. P., & Ali, S. K. (2016). Chapter Ten-Role of von Willebrand Factor—A1 Domain Variants P1266L, H1268D, C1272R, and C1272F in VWD: A Molecular Modeling and Simulation Analysis Approach. Advances in Protein Chemistry and Structural Biology, 102, 299-330. [PubMed]

  8. Ferrari, I., Bouilly, J., Beau, I., Guizzardi, F., Ferlin, A., Pollazzon, M., ... & Rossetti, R. (2016). Impaired protein stability and nuclear localization of NOBOX variants associated with Premature Ovarian Insufficiency. Human Molecular Genetics, ddw342. [PubMed]

  9. Gaillard, M. C., Puppo, F., Roche, S., Dion, C., Campana, E. S., Mariot, V., ... & Bernard, R. (2016). Segregation between SMCHD1 mutation, D4Z4 hypomethylation and Facio-Scapulo-Humeral Dystrophy: a case report. BMC Medical Genetics, 17(1), 66. [PubMed]

  10. Harris, E., Bladen, C. L., Mayhew, A., James, M., Bettinson, K., Moore, U., ... & Blamire, A. M. (2016). The Clinical Outcome Study for dysferlinopathy An international multicenter study. Neurology Genetics, 2(4), e89. [PubMed]

  11. Jin, S. Q., Yu, M., Zhang, W., Lyu, H., Yuan, Y., & Wang, Z. X. (2016). Dysferlin gene mutation spectrum in a large cohort of chinese patients with dysferlinopathy. Chinese Medical Journal, 129(19), 2287. [PubMed]

  12. Jondeau, G., Ropers, J., Regalado, E., Braverman, A., Evangelista, A., Teixido, G., ... & Morisaki, T. (2016). International Registry of Patients Carrying TGFBR1 or TGFBR2 Mutations: Results of the Montalcino Aortic Consortium. Circulation: Cardiovascular Genetics, CIRCGENETICS-116. [PubMed]

  13. Kraus, C., Hoyer, J., Vasileiou, G., Wunderle, M., Lux, M. P., Fasching, P. A., ... & Reis, A. (2017). Gene panel sequencing in familial breast/ovarian cancer patients identifies multiple novel mutations also in genes others than BRCA1/2. International Journal of Cancer, 140(1), 95-102. [PubMed]

  14. Lerat, J., Jonard, L., Loundon, N., Christin‐Maitre, S., Lacombe, D., Goizet, C., ... & Bonnefont, J. P. (2016). An application of NGS for molecular investigations in Perrault syndrome: study of 14 families and review of the literature. Human Mutation, 37(12), 1354-1362. [PubMed]

  15. Lodder, E. M., De Nittis, P., Koopman, C. D., Wiszniewski, W., de Souza, C. F. M., Lahrouchi, N., ... & Nannenberg, E. A. (2016). GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability. The American Journal of Human Genetics, 99(3), 704-710. [PubMed]

  16. López, C., Bergmann, A. K., Paul, U., Murga Penas, E. M., Nagel, I., Betts, M. J., ... & Jayne, S. (2016). Genes encoding members of the JAK‐STAT pathway or epigenetic regulators are recurrently mutated in T‐cell prolymphocytic leukaemia. British journal of haematology. [PubMed]

  17. Luan, X., Tian, W., & Cao, L. (2016). Limb-girdle congenital myasthenic syndrome in a Chinese family with novel mutations in MUSK gene and literature review. Clinical Neurology and Neurosurgery, 150, 41-45. [PubMed]

  18. Martins, A. F., Martins, J. M., do Vale, S., Dias, T., Silveira, C., da Silva, I. R., & Carmo-Fonseca, M. (2016). A rare missense variant in RET exon 8 in a Portuguese family with atypical multiple endocrine neoplasia type 2A. HORMONES-INTERNATIONAL JOURNAL OF ENDOCRINOLOGY AND METABOLISM, 15(3), 435-440. [PubMed]

  19. Miltgen, M., Blanchard, A., Mathieu, H., Kreisler, A., Salgado, D., Roubertie, A., ... & Douay, X. (2016). Novel heterozygous mutation in ANO3 responsible for craniocervical dystonia. Movement Disorders, 31(8), 1251-1252. [PubMed]

  20. Natera-de Benito, D., Bestue, M., Vilchez, J. J., Evangelista, T., Töpf, A., Garcia-Ribes, A., ... & Jiménez, E. (2016). Long-term follow-up in patients with congenital myasthenic syndrome due to RAPSN mutations. Neuromuscular Disorders, 26(2), 153-159. [PubMed]

  21. Natera-de Benito, D., Nascimento, A., Abicht, A., Ortez, C., Jou, C., Müller, J. S., ... & Colomer, J. (2016). KLHL40-related nemaline myopathy with a sustained, positive response to treatment with acetylcholinesterase inhibitors. Journal of neurology, 263(3), 517-523. [PubMed]

  22. Oetting, W. S., Brookes, A. J., Béroud, C., & Taschner, P. E. (2016). Clinical Interpretation of Variants from Next‐Generation Sequencing: The 2016 Scientific Meeting of the Human Genome Variation Society. Human Mutation, 37(10), 1110-1113. [PubMed]

  23. Pelzer, N., Blom, D. E., Stam, A. H., Vijfhuizen, L. S., Hageman, A. T. M., van Vliet, J. A., ... & Terwindt, G. M. (2016). Recurrent coma and fever in familial hemiplegic migraine type 2. A prospective 15-year follow-up of a large family with a novel ATP1A2 mutation. Cephalalgia, 0333102416651284. [PubMed]

  24. Pinard, A., Salgado, D., Desvignes, J. P., Rai, G., Hanna, N., Arnaud, P., ... & Boileau, C. (2016). WES/WGS Reporting of Mutations from Cardiovascular “Actionable” Genes in Clinical Practice: A Key Role for UMD Knowledgebases in the Era of Big Databases. Human Mutation, 37(12), 1308-1317. [PubMed]

  25. Pinard, A., Miltgen, M., Blanchard, A., Mathieu, H., Desvignes, J. P., Salgado, D., ... & Grandval, P. (2016). Actionable Genes, Core Databases, and Locus‐Specific Databases. Human Mutation, 37(12), 1299-1307. [PubMed]

  26. Prontera, P., Ottaviani, V., Rogaia, D., Isidori, I., Mencarelli, A., Malerba, N., ... & Merla, G. (2016). A novel MED12 mutation: Evidence for a fourth phenotype. American Journal of Medical Genetics Part A, 170(9), 2377-2382. [PubMed]

  27. Salgado, D., Bellgard, M. I., Desvignes, J. P., & Béroud, C. (2016). How to identify pathogenic mutations among all those variations: Variant annotation and filtration in the genome sequencing era. Human Mutation. [PubMed]

  28. Taïeb, D., Barlier, A., Yang, C., Pertuit, M., Tchoghandjian, A., Rochette, C., ... & Metellus, P. (2016). Somatic gain-of-function HIF2A mutations in sporadic central nervous system hemangioblastomas. Journal of neuro-oncology, 126(3), 473-481. [PubMed]

  29. Thomas, F., Hennebelle, I., Delmas, C., Lochon, I., Dhelens, C., Garnier Tixidre, C., ... & Toulas, C. (2016). Genotyping of a family with a novel deleterious DPYD mutation supports the pretherapeutic screening of DPD deficiency with dihydrouracil/uracil ratio. Clinical Pharmacology & Therapeutics, 99(2), 235-242. [PubMed]

2017

  1. Cerino, M., Gorokhova, S., Laforet, P., Ben Yaou, R., Salort‐Campana, E., Pouget, J., ... & Behin, A. (2017). Genetic Characterization of a French Cohort of GNE‐mutation negative inclusion body myopathy patients with exome sequencing. Muscle & Nerve. [PubMed]

  2. de Almeida, R. M., Tavares, J., Martins, S., Carvalho, T., Enguita, F. J., Brito, D., ... & Lopes, L. R. (2017). Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PloS one, 12(8), e0182946. [PubMed]

  3. Elouej, S., Beleza-Meireles, A., Caswell, R., Colclough, K., Ellard, S., Desvignes, J. P., ... & Des Sandre-Giovannoli, A. (2017). Exome sequencing reveals a de novo POLD1 mutation causing phenotypic variability in mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL). Metabolism, 71, 213-225. [PubMed]

  4. Etienne-Grimaldi, M. C., Boyer, J. C., Beroud, C., Mbatchi, L., van Kuilenburg, A., Bobin-Dubigeon, C., ... & Ferrand, C. (2017). New advances in DPYD genotype and risk of severe toxicity under capecitabine. PloS one, 12(5), e0175998. [PubMed]

  5. Gasparini, A., Tosatto, S. C., Murgia, A., & Leonardi, E. (2017). Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. Scientific reports, 7(1), 6829. [PubMed]

  6. Giorgio, E., Brussino, A., Biamino, E., Belligni, E. F., Bruselles, A., Ciolfi, A., ... & Cavalieri, S. (2017). Exome sequencing in children of women with skewed X-inactivation identifies atypical cases and complex phenotypes. European Journal of Paediatric Neurology, 21(3), 475-484. [PubMed]

  7. Gueneau, L., Fish, R. J., Shamseldin, H. E., Voisin, N., Mau-Them, F. T., Preiksaitiene, E., ... & Ambusaidi, Q. (2017). KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis. The American Journal of Human Genetics. [PubMed]

  8. Guibaud, L., Reversade, B., Chelly, J., & Kucinskas, V. (2017). Please cite this article in press as: Gueneau et al., KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Ar-throgryposis, The American Journal of Human Genetics (2018), https://doi. org/10.1016/j. ajhg. 2017.12. 002. [PubMed]

  9. Guyard, A., Danel, C., Théou-Anton, N., Debray, M. P., Gibault, L., Mordant, P., ... & Cazes, A. (2017). Morphologic and molecular study of lung cancers associated with idiopathic pulmonary fibrosis and other pulmonary fibroses. Respiratory Research, 18(1), 120. [PubMed​]

  10. Hansen, M. F., Johansen, J., Sylvander, A. E., Bjørnevoll, I., Talseth‐Palmer, B. A., Lavik, L. A., ... & Sjursen, W. (2017). Use of multigene‐panel identifies pathogenic variants in several CRC‐predisposing genes in patients previously tested for Lynch Syndrome. Clinical Genetics. [PubMed]

  11. Janin, A., N'Guyen, K., Habib, G., Dauphin, C., Chanavat, V., Bouvagnet, P., ... & Millat, G. (2017). Truncating mutations on myofibrillar myopathies causing genes as prevalent molecular explanations on patients with dilated cardiomyopathy. Clinical Genetics. [PubMed]

  12. Kraus, C., Hoyer, J., Vasileiou, G., Wunderle, M., Lux, M. P., Fasching, P. A., ... & Reis, A. (2017). Gene panel sequencing in familial breast/ovarian cancer patients identifies multiple novel mutations also in genes others than BRCA1/2. International Journal of Cancer, 140(1), 95-102. [PubMed]

  13. Lacoste, C., Fabre, A., Pécheux, C., Lévy, N., Krahn, M., Malzac, P., ... & Bourgeois, P. (2017). Le séquençage d’ADN à haut débit en pratique clinique. Archives de Pédiatrie, 24(4), 373-383. [PubMed]

  14. Maignan, A., Guerin, C., Julliard, V., Paladino, N. C., Kim, E., Roche, P., ... & Clifton-Bligh, R. (2017). Implications of SDHB genetic testing in patients with sporadic pheochromocytoma. Langenbeck's Archives of Surgery, 1-12. [PubMed]

  15. Marquet, S., Bucheton, B., Reymond, C., Argiro, L., EL-Safi, S. H., Kheir, M. M., ... & Dessein, A. J. (2017). Exome sequencing identifies two variants of the alkylglycerol monooxygenase gene (AGMO) as a cause of relapses in visceral leishmaniasis in children, in Sudan. The Journal of Infectious Diseases. [PubMed]

  16. Mohamed, A., Romano, D., Saveanu, A., Roche, C., Albertelli, M., Barbieri, F., ... & Ferone, D. (2017). Anti-proliferative and anti-secretory effects of everolimus on human pancreatic neuroendocrine tumors primary cultures: is there any benefit from combination with somatostatin analogs?. Oncotarget. [PubMed]

  17. Moysés‐Oliveira, M., Giannuzzi, G., Fish, R. J., Rosenfeld, J. A., Petit, F., Soares, M. D. F., ... & Liehr, T. (2017). Inactivation of AMMECR1 is associated with growth, bone, and heart alterations. Human mutation. [PubMed]

  18. Sahrawat, T. R. (2017). Computational Biology Approach for Therapeutic Intervention of Alexander Disease by Post Transcriptional Gene Silencing. International Journal for Computational Biology (IJCB), 6(1), 18-24. [PubMed]

  19. Stäubli, A., Capatina, N., Fuhrer, Y., Munier, F. L., Labs, S., Schorderet, D. F., ... & Wong, T. Y. (2017). Abnormal creatine transport of mutations in monocarboxylate transporter 12 (MCT12) found in patients with age-related cataract can be partially rescued by exogenous chaperone CD147. Human molecular genetics, 26(21), 4203-4214. [PubMed]

  20. Te Riele, A. S., Agullo-Pascual, E., James, C. A., Leo-Macias, A., Cerrone, M., Zhang, M., ... & Amat-Alarcon, N. (2017). Multilevel analyses of SCN5A mutations in arrhythmogenic right ventricular dysplasia/cardiomyopathy suggest non-canonical mechanisms for disease pathogenesis. Cardiovascular research, 113(1), 102-111. [PubMed]

  21. Valenzuela, I., Fernández-Alvarez, P., Munell, F., Sanchez-Montanez, A., Giralt, G., Vendrell, T., & Tizzano, E. F. (2017). Arthrogryposis as neonatal presentation of Loeys-Dietz syndrome due to a novel TGFBR2 mutation. European Journal of Medical Genetics, 60(6), 303-307. [PubMed]

  22. Wan, Y. B. A., Simpson, M. A., Aragon-Martin, J. A., Osborn, D. P., Regalado, E. S., Guo, D., ... & Bharj, J. (2017). A mutation in the LMOD1 actin-binding domain segregating with disease in a large British family with thoracic aortic aneurysms and dissections. bioRxiv, 153452. [PubMed​]

2018

  1. Dhanda, S. K., Grifoni, A., Pham, J., Vaughan, K., Sidney, J., Peters, B., & Sette, A. (2018). Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity. Immunology, 153(1), 118-132. [PubMed]

  2. Shrestha, S., Zhang, C., Jerde, C. R., Nie, Q., Li, H., Offer, S. M., & Diasio, R. B. (2018). Gene‐specific variant classifier (DPYD‐Varifier) to identify deleterious alleles of dihydropyrimidine dehydrogenase. Clinical Pharmacology & Therapeutics. [PubMed]

  3. Takao, M., Yamaguchi, T., Eguchi, H., Tada, Y., Kohda, M., Koizumi, K., ... & Ishida, H. (2018). Characteristics of MUTYH variants in Japanese colorectal polyposis patients. International journal of clinical oncology, 1-7. [PubMed]