-
1
-
-
80051968181
-
Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data. Nature reviews
-
Cooper, G. M. & Shendure, J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature reviews. Genetics 12, 628-640, doi: 10.1038/nrg3046 (2011).
-
(2011)
Genetics
, vol.12
, pp. 628-640
-
-
Cooper, G.M.1
Shendure, J.2
-
2
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073, doi: 10.1038/nature09534 (2010).
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
3
-
-
84891837451
-
The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine
-
Stenson, P. D. et al. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human genetics 133, 1-9, doi: 10.1007/s00439-013-1358-4 (2014).
-
(2014)
Human Genetics
, vol.133
, pp. 1-9
-
-
Stenson, P.D.1
-
4
-
-
33750353461
-
Predicting the effects of amino acid substitutions on protein function
-
Ng, P. C. & Henikoff, S. Predicting the effects of amino acid substitutions on protein function. Annual review of genomics and human genetics 7, 61-80, doi: 10.1146/annurev.genom.7.080505.115630 (2006).
-
(2006)
Annual Review of Genomics and Human Genetics
, vol.7
, pp. 61-80
-
-
Ng, P.C.1
Henikoff, S.2
-
5
-
-
80054746492
-
Exome sequencing as a tool for Mendelian disease gene discovery. Nature reviews
-
Bamshad, M. J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nature reviews. Genetics 12, 745-755, doi: 10.1038/nrg3031 (2011).
-
(2011)
Genetics
, vol.12
, pp. 745-755
-
-
Bamshad, M.J.1
-
6
-
-
85027917625
-
Complex traits: Sequencing for disease architecture. Nature reviews
-
Muers, M. Complex traits: Sequencing for disease architecture. Nature reviews. Genetics 14, 518, doi: 10.1038/nrg3533 (2013).
-
(2013)
Genetics
, vol.14
, pp. 518
-
-
Muers, M.1
-
7
-
-
0035026704
-
Predicting deleterious amino acid substitutions
-
Ng, P. C. & Henikoff, S. Predicting deleterious amino acid substitutions. Genome research 11, 863-874, doi: 10.1101/gr.176601 (2001).
-
(2001)
Genome Research
, vol.11
, pp. 863-874
-
-
Ng, P.C.1
Henikoff, S.2
-
8
-
-
22244437614
-
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
-
Stone, E. A. & Sidow, A. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome research 15, 978-986, doi: 10.1101/gr.3804205 (2005).
-
(2005)
Genome Research
, vol.15
, pp. 978-986
-
-
Stone, E.A.1
Sidow, A.2
-
9
-
-
34547840189
-
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP)
-
Ye, Z. Q. et al. Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). Bioinformatics 23, 1444-1450, doi: 10.1093/bioinformatics/btm119 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1444-1450
-
-
Ye, Z.Q.1
-
10
-
-
70350671733
-
Automated inference of molecular mechanisms of disease from amino acid substitutions
-
Li, B. et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25, 2744-2750, doi: 10.1093/bioinformatics/btp528 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2744-2750
-
-
Li, B.1
-
11
-
-
67749137351
-
Functional annotations improve the predictive score of human disease-related mutations in proteins
-
Calabrese, R., Capriotti, E., Fariselli, P., Martelli, P. L. & Casadio, R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Human mutation 30, 1237-1244, doi: 10.1002/humu.21047 (2009).
-
(2009)
Human Mutation
, vol.30
, pp. 1237-1244
-
-
Calabrese, R.1
Capriotti, E.2
Fariselli, P.3
Martelli, P.L.4
Casadio, R.5
-
12
-
-
84897456458
-
MutationTaster2: Mutation prediction for the deep-sequencing age
-
Schwarz, J. M., Cooper, D. N., Schuelke, M. & Seelow, D. MutationTaster2: mutation prediction for the deep-sequencing age. Nature methods 11, 361-362, doi: 10.1038/nmeth.2890 (2014).
-
(2014)
Nature Methods
, vol.11
, pp. 361-362
-
-
Schwarz, J.M.1
Cooper, D.N.2
Schuelke, M.3
Seelow, D.4
-
13
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nature methods 7, 248-249, doi: 10.1038/ nmeth0410-248 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
-
14
-
-
84863875415
-
A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome
-
Bergman, J. E. et al. A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome. Human mutation 33, 1251-1260, doi: 10.1002/humu.22106 (2012).
-
(2012)
Human Mutation
, vol.33
, pp. 1251-1260
-
-
Bergman, J.E.1
-
15
-
-
84901366485
-
ATP1A3 Mutations and Genotype-Phenotype Correlation of Alternating Hemiplegia of Childhood in Chinese Patients
-
Yang, X. et al. ATP1A3 Mutations and Genotype-Phenotype Correlation of Alternating Hemiplegia of Childhood in Chinese Patients. PloS one 9, e97274, doi: 10.1371/journal.pone.0097274 (2014).
-
(2014)
PloS One
, vol.9
-
-
Yang, X.1
-
16
-
-
79851484043
-
Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy
-
Jordan, D. M. et al. Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy. American journal of human genetics 88, 183-192, doi: 10.1016/j.ajhg.2011.01.011 (2011).
-
(2011)
American Journal of Human Genetics
, vol.88
, pp. 183-192
-
-
Jordan, D.M.1
-
17
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65, doi: 10.1038/nature11632 (2012).
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
18
-
-
58149189856
-
McKusick's Online Mendelian Inheritance in Man (OMIM)
-
Amberger, J., Bocchini, C. A., Scott, A. F. & Hamosh, A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic acids research 37, D793-D796, doi: 10.1093/nar/gkn665 (2009).
-
(2009)
Nucleic Acids Research
, vol.37
, pp. D793-D796
-
-
Amberger, J.1
Bocchini, C.A.2
Scott, A.F.3
Hamosh, A.4
-
19
-
-
34047097309
-
A database of locus-specific databases
-
Horaitis, O., Talbot, C. C. Jr., Phommarinh, M., Phillips, K. M. & Cotton, R. G. A database of locus-specific databases. Nature genetics 39, 425, doi: 10.1038/ng0407-425 (2007).
-
(2007)
Nature Genetics
, vol.39
, pp. 425
-
-
Horaitis, O.1
Talbot, C.C.2
Phommarinh, M.3
Phillips, K.M.4
Cotton, R.G.5
-
20
-
-
79953715693
-
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel
-
Gonzalez-Perez, A. & Lopez-Bigas, N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. American journal of human genetics 88, 440-449, doi: 10.1016/j.ajhg.2011.03.004 (2011).
-
(2011)
American Journal of Human Genetics
, vol.88
, pp. 440-449
-
-
Gonzalez-Perez, A.1
Lopez-Bigas, N.2
-
21
-
-
84873486397
-
Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies
-
Li, M. X. et al. Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS genetics 9, e1003143, doi: 10.1371/journal.pgen.1003143 (2013).
-
(2013)
PLoS Genetics
, vol.9
-
-
Li, M.X.1
-
22
-
-
84886247811
-
Assessment of computational methods for predicting the effects of missense mutations in human cancers
-
Gnad, F., Baucom, A., Mukhyala, K., Manning, G. & Zhang, Z. Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC genomics 14 Suppl 3, S7, doi: 10.1186/1471-2164-14-S3-S7 (2013).
-
(2013)
BMC Genomics 14 Suppl
, vol.3
-
-
Gnad, F.1
Baucom, A.2
Mukhyala, K.3
Manning, G.4
Zhang, Z.5
-
23
-
-
33745495950
-
The muscle protein Dok-7 is essential for neuromuscular synaptogenesis
-
Okada, K. et al. The muscle protein Dok-7 is essential for neuromuscular synaptogenesis. Science 312, 1802-1805, doi: 10.1126/ science.1127142 (2006).
-
(2006)
Science
, vol.312
, pp. 1802-1805
-
-
Okada, K.1
-
24
-
-
84865067553
-
The spectrum of mutations that underlie the neuromuscular junction synaptopathy in DOK7 congenital myasthenic syndrome
-
Cossins, J. et al. The spectrum of mutations that underlie the neuromuscular junction synaptopathy in DOK7 congenital myasthenic syndrome. Human molecular genetics 21, 3765-3775, doi: 10.1093/hmg/dds198 (2012).
-
(2012)
Human Molecular Genetics
, vol.21
, pp. 3765-3775
-
-
Cossins, J.1
-
25
-
-
4544336084
-
Integrated evaluation of DNA sequence variants of unknown clinical significance: Application to BRCA1 and BRCA2
-
Goldgar, D. E. et al. Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. American journal of human genetics 75, 535-544, doi: 10.1086/424388 (2004).
-
(2004)
American Journal of Human Genetics
, vol.75
, pp. 535-544
-
-
Goldgar, D.E.1
-
26
-
-
35348834779
-
A systematic genetic assessment of 1, 433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes
-
Easton, D. F. et al. A systematic genetic assessment of 1, 433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. American journal of human genetics 81, 873-883, doi: 10.1086/521032 (2007).
-
(2007)
American Journal of Human Genetics
, vol.81
, pp. 873-883
-
-
Easton, D.F.1
-
27
-
-
84895858942
-
A general framework for estimating the relative pathogenicity of human genetic variants
-
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nature genetics 46, 310-315, doi: 10.1038/ng.2892 (2014).
-
(2014)
Nature Genetics
, vol.46
, pp. 310-315
-
-
Kircher, M.1
-
28
-
-
84871578629
-
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models
-
Shihab, H. A. et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Human mutation 34, 57-65, doi: 10.1002/humu.22225 (2013).
-
(2013)
Human Mutation
, vol.34
, pp. 57-65
-
-
Shihab, H.A.1
-
29
-
-
84928198929
-
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity
-
Grimm, D. G. et al. The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity. Human mutation 36, 513-523, doi: 10.1002/humu.22768 (2015).
-
(2015)
Human Mutation
, vol.36
, pp. 513-523
-
-
Grimm, D.G.1
-
30
-
-
84871614593
-
VariBench: A benchmark database for variations
-
Sasidharan Nair, P. & Vihinen, M. VariBench: a benchmark database for variations. Human mutation 34, 42-49, doi: 10.1002/ humu.22204 (2013).
-
(2013)
Human Mutation
, vol.34
, pp. 42-49
-
-
Sasidharan Nair, P.1
Vihinen, M.2
-
31
-
-
73349110071
-
Exome sequencing identifies the cause of a mendelian disorder
-
Ng, S. B. et al. Exome sequencing identifies the cause of a mendelian disorder. Nature genetics 42, 30-35, doi: 10.1038/ng.499 (2010).
-
(2010)
Nature Genetics
, vol.42
, pp. 30-35
-
-
Ng, S.B.1
-
32
-
-
67651230875
-
Dihydroorotate dehydrogenase polymorphism influences the toxicity of leflunomide treatment in patients with rheumatoid arthritis
-
Grabar, P. B., Rozman, B., Logar, D., Praprotnik, S. & Dolzan, V. Dihydroorotate dehydrogenase polymorphism influences the toxicity of leflunomide treatment in patients with rheumatoid arthritis. Annals of the rheumatic diseases 68, 1367-1368, doi: 10.1136/ ard.2008.099093 (2009).
-
(2009)
Annals of the Rheumatic Diseases
, vol.68
, pp. 1367-1368
-
-
Grabar, P.B.1
Rozman, B.2
Logar, D.3
Praprotnik, S.4
Dolzan, V.5
-
33
-
-
84865684547
-
De novo mutations in ATP1A3 cause alternating hemiplegia of childhood
-
Heinzen, E. L. et al. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. Nature genetics 44, 1030-1034, doi: 10.1038/ng.2358 (2012).
-
(2012)
Nature Genetics
, vol.44
, pp. 1030-1034
-
-
Heinzen, E.L.1
-
34
-
-
84873621432
-
Identification of ATP1A3 mutations by exome sequencing as the cause of alternating hemiplegia of childhood in Japanese patients
-
Ishii, A. et al. Identification of ATP1A3 mutations by exome sequencing as the cause of alternating hemiplegia of childhood in Japanese patients. PloS one 8, e56120, doi: 10.1371/journal.pone.0056120 (2013).
-
(2013)
PloS One
, vol.8
-
-
Ishii, A.1
-
35
-
-
84961309083
-
The mutation significance cutoff: Gene-level thresholds for variant predictions
-
Itan, Y. et al. The mutation significance cutoff: gene-level thresholds for variant predictions. Nature methods 13, 109-110, doi: 10.1038/nmeth.3739 (2016).
-
(2016)
Nature Methods
, vol.13
, pp. 109-110
-
-
Itan, Y.1
-
36
-
-
84943171338
-
A global reference for human genetic variation
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68-74, doi: 10.1038/ nature15393 (2015).
-
(2015)
Nature
, vol.526
, pp. 68-74
-
-
-
37
-
-
77956534324
-
ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
-
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research 38, e164, doi: 10.1093/nar/gkq603 (2010).
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Wang, K.1
Li, M.2
Hakonarson, H.3
-
38
-
-
78651237647
-
Identifying a high fraction of the human genome to be under selective constraint using GERP+ +
-
Davydov, E. V. et al. Identifying a high fraction of the human genome to be under selective constraint using GERP+ + . PLoS computational biology 6, e1001025, doi: 10.1371/journal.pcbi.1001025 (2010).
-
(2010)
PLoS Computational Biology
, vol.6
-
-
Davydov, E.V.1
-
39
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
Cooper, G. M. et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome research 15, 901-913, doi: 10.1101/gr.3577405 (2005).
-
(2005)
Genome Research
, vol.15
, pp. 901-913
-
-
Cooper, G.M.1
-
41
-
-
79952709519
-
PROC: An open-source package for R and S+ to analyze and compare ROC curves
-
Robin, X. et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC bioinformatics 12, 77, doi: 10.1186/1471-2105-12-77 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 77
-
-
Robin, X.1
-
42
-
-
0043122919
-
SIFT: Predicting amino acid changes that affect protein function
-
Ng, P. C. & Henikoff, S. SIFT: Predicting amino acid changes that affect protein function. Nucleic acids research 31, 3812-3814 (2003).
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3812-3814
-
-
Ng, P.C.1
Henikoff, S.2
-
43
-
-
44949137643
-
Determinants of protein function revealed by combinatorial entropy optimization
-
Reva, B., Antipin, Y. & Sander, C. Determinants of protein function revealed by combinatorial entropy optimization. Genome biology 8, R232, doi: 10.1186/gb-2007-8-11-r232 (2007).
-
(2007)
Genome Biology
, vol.8
-
-
Reva, B.1
Antipin, Y.2
Sander, C.3
-
44
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760, doi: 10.1093/bioinformatics/btp324 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
45
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature genetics 43, 491-498, doi: 10.1038/ng.806 (2011).
-
(2011)
Nature Genetics
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
-
46
-
-
84896009017
-
From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
-
Van der Auwera, G. A. et al. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics 43, 11.10.11-11.10.33, doi: 10.1002/0471250953.bi1110s43 (2013).
-
(2013)
Current Protocols in Bioinformatics
, vol.43
, pp. 111011-111033
-
-
Van Der Auwera, G.A.1
-
47
-
-
0042387707
-
A full-likelihood method for the evaluation of causality of sequence variants from family data
-
Thompson, D., Easton, D. F. & Goldgar, D. E. A full-likelihood method for the evaluation of causality of sequence variants from family data. American journal of human genetics 73, 652-655, doi: 10.1086/378100 (2003).
-
(2003)
American Journal of Human Genetics
, vol.73
, pp. 652-655
-
-
Thompson, D.1
Easton, D.F.2
Goldgar, D.E.3
-
48
-
-
70349303959
-
Bayesian statistical methods for genetic association studies. Nature reviews
-
Stephens, M. & Balding, D. J. Bayesian statistical methods for genetic association studies. Nature reviews. Genetics 10, 681-690, doi: 10.1038/nrg2615 (2009).
-
(2009)
Genetics
, vol.10
, pp. 681-690
-
-
Stephens, M.1
Balding, D.J.2
|