-
1
-
-
84928209346
-
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
-
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405-24.
-
(2015)
Genet Med.
, vol.17
, pp. 405-424
-
-
Richards, S.1
Aziz, N.2
Bale, S.3
Bick, D.4
Das, S.5
Gastier-Foster, J.6
-
2
-
-
79960763462
-
dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions
-
Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat. 2011;32:894-9.
-
(2011)
Hum Mutat
, vol.32
, pp. 894-899
-
-
Liu, X.1
Jian, X.2
Boerwinkle, E.3
-
3
-
-
84973338712
-
The Ensembl Variant Effect Predictor
-
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17:122.
-
(2016)
Genome Biol.
, vol.17
, pp. 122
-
-
McLaren, W.1
Gil, L.2
Hunt, S.E.3
Riat, H.S.4
Ritchie, G.R.5
Thormann, A.6
-
4
-
-
84989958164
-
Performance of ACMG-AMP variant-interpretation guidelines among nine laboratories in the Clinical Sequencing Exploratory Research Consortium
-
Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, et al. Performance of ACMG-AMP variant-interpretation guidelines among nine laboratories in the Clinical Sequencing Exploratory Research Consortium. Am J Hum Genet. 2016;99:247.
-
(2016)
Am J Hum Genet.
, vol.99
, pp. 247
-
-
Amendola, L.M.1
Jarvik, G.P.2
Leo, M.C.3
McLaughlin, H.M.4
Akkari, Y.5
Amaral, M.D.6
-
5
-
-
84976904305
-
ClinVar: public archive of interpretations of clinically relevant variants
-
Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016;44:D862-8.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D862-D868
-
-
Landrum, M.J.1
Lee, J.M.2
Benson, M.3
Brown, G.4
Chao, C.5
Chitipiralla, S.6
-
6
-
-
84968902315
-
Evaluation of ACMG-guideline-based variant classification of cancer susceptibility and non-cancer-associated genes in families affected by breast cancer
-
Maxwell KN, Hart SN, Vijai J, Schrader KA, Slavin TP, Thomas T, et al. Evaluation of ACMG-guideline-based variant classification of cancer susceptibility and non-cancer-associated genes in families affected by breast cancer. Am J Hum Genet. 2016;98:801-17.
-
(2016)
Am J Hum Genet.
, vol.98
, pp. 801-817
-
-
Maxwell, K.N.1
Hart, S.N.2
Vijai, J.3
Schrader, K.A.4
Slavin, T.P.5
Thomas, T.6
-
7
-
-
84958105945
-
Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care
-
Sawyer SL, Hartley T, Dyment DA, Beaulieu CL, Schwartzentruber J, Smith A, et al. Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Clin Genet. 2016;89:275-84.
-
(2016)
Clin Genet.
, vol.89
, pp. 275-284
-
-
Sawyer, S.L.1
Hartley, T.2
Dyment, D.A.3
Beaulieu, C.L.4
Schwartzentruber, J.5
Smith, A.6
-
8
-
-
85011898493
-
EFHC1 variants in juvenile myoclonic epilepsy: reanalysis according to NHGRI and ACMG guidelines for assigning disease causality
-
Bailey JN, Patterson C, de Nijs L, Duron RM, Nguyen VH, Tanaka M, et al. EFHC1 variants in juvenile myoclonic epilepsy: reanalysis according to NHGRI and ACMG guidelines for assigning disease causality. Genet Med. 2017;19:144-56.
-
(2017)
Genet Med.
, vol.19
, pp. 144-156
-
-
Bailey, J.N.1
Patterson, C.2
Nijs, L.3
Duron, R.M.4
Nguyen, V.H.5
Tanaka, M.6
-
9
-
-
84957942283
-
dbNSFP v3.0: A One-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs
-
Liu X, Wu C, Li C, Boerwinkle E. dbNSFP v3.0: A One-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs. Hum Mutat. 2016;37:235-41.
-
(2016)
Hum Mutat
, vol.37
, pp. 235-241
-
-
Liu, X.1
Wu, C.2
Li, C.3
Boerwinkle, E.4
-
10
-
-
79952764520
-
Performance of mutation pathogenicity prediction methods on missense variants
-
Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011;32:358-68.
-
(2011)
Hum Mutat.
, vol.32
, pp. 358-368
-
-
Thusberg, J.1
Olatubosun, A.2
Vihinen, M.3
-
11
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-9.
-
(2010)
Nat Methods.
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
-
12
-
-
0043122919
-
SIFT: Predicting amino acid changes that affect protein function
-
Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812-4.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3812-3814
-
-
Ng, P.C.1
Henikoff, S.2
-
13
-
-
77955151784
-
MutationTaster evaluates disease-causing potential of sequence alterations
-
Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575-6.
-
(2010)
Nat Methods.
, vol.7
, pp. 575-576
-
-
Schwarz, J.M.1
Rodelsperger, C.2
Schuelke, M.3
Seelow, D.4
-
14
-
-
84895858942
-
A general framework for estimating the relative pathogenicity of human genetic variants
-
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310-5.
-
(2014)
Nat Genet.
, vol.46
, pp. 310-315
-
-
Kircher, M.1
Witten, D.M.2
Jain, P.3
O'Roak, B.J.4
Cooper, G.M.5
Shendure, J.6
-
15
-
-
84867301515
-
Predicting the functional effect of amino acid substitutions and indels
-
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012;7:e46688.
-
(2012)
PLoS One.
, vol.7
-
-
Choi, Y.1
Sims, G.E.2
Murphy, S.3
Miller, J.R.4
Chan, A.P.5
-
16
-
-
70350671733
-
Automated inference of molecular mechanisms of disease from amino acid substitutions
-
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics. 2009;25:2744-50.
-
(2009)
Bioinformatics.
, vol.25
, pp. 2744-2750
-
-
Li, B.1
Krishnan, V.G.2
Mort, M.E.3
Xin, F.4
Kamati, K.K.5
Cooper, D.N.6
-
17
-
-
79953715693
-
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score
-
Gonzalez-Perez A, Lopez-Bigas N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score. Condel Am J Hum Genet. 2011;88:440-9.
-
(2011)
Condel. Am J Hum Genet.
, vol.88
, pp. 440-449
-
-
Gonzalez-Perez, A.1
Lopez-Bigas, N.2
-
18
-
-
84874741731
-
Identifying Mendelian disease genes with the variant effect scoring tool
-
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics. 2013;14 Suppl 3:S3.
-
(2013)
BMC Genomics.
, vol.14
, pp. S3
-
-
Carter, H.1
Douville, C.2
Stenson, P.D.3
Cooper, D.N.4
Karchin, R.5
-
19
-
-
84991615407
-
REVEL: an ensemble method for predicting the pathogenicity of rare missense variants
-
Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am J Hum Genet. 2016;99:877-85.
-
(2016)
Am J Hum Genet.
, vol.99
, pp. 877-885
-
-
Ioannidis, N.M.1
Rothstein, J.H.2
Pejaver, V.3
Middha, S.4
McDonnell, S.K.5
Baheti, S.6
-
20
-
-
84926430386
-
Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies
-
Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015;24:2125-37.
-
(2015)
Hum Mol Genet.
, vol.24
, pp. 2125-2137
-
-
Dong, C.1
Wei, P.2
Jian, X.3
Gibbs, R.4
Boerwinkle, E.5
Wang, K.6
-
21
-
-
84992389439
-
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity
-
Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, et al. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nat Genet. 2016;48:1581-6.
-
(2016)
Nat Genet.
, vol.48
, pp. 1581-1586
-
-
Jagadeesh, K.A.1
Wenger, A.M.2
Berger, M.J.3
Guturu, H.4
Stenson, P.D.5
Cooper, D.N.6
-
22
-
-
84956688641
-
A spectral approach integrating functional genomic annotations for coding and noncoding variants
-
Ionita-Laza I, McCallum K, Xu B, Buxbaum JD. A spectral approach integrating functional genomic annotations for coding and noncoding variants. Nat Genet. 2016;48:214-20.
-
(2016)
Nat Genet.
, vol.48
, pp. 214-220
-
-
Ionita-Laza, I.1
McCallum, K.2
Xu, B.3
Buxbaum, J.D.4
-
23
-
-
84913588353
-
A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
-
Katsonis P, Lichtarge O. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. Genome Res. 2014;24:2050-8.
-
(2014)
Genome Res.
, vol.24
, pp. 2050-2058
-
-
Katsonis, P.1
Lichtarge, O.2
-
24
-
-
78651237647
-
Identifying a high fraction of the human genome to be under selective constraint using GERP++
-
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010;6:e1001025.
-
(2010)
PLoS Comput Biol.
, vol.6
-
-
Davydov, E.V.1
Goode, D.L.2
Sirota, M.3
Cooper, G.M.4
Sidow, A.5
Batzoglou, S.6
-
25
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
Cooper GM, Stone EA, Asimenos G, Comparative Sequencing Program NISC, Green ED, Batzoglou S, et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-13.
-
(2005)
Genome Res.
, vol.15
, pp. 901-913
-
-
Cooper, G.M.1
Stone, E.A.2
Asimenos, G.3
Comparative Sequencing Program, N.I.S.C.4
Green, E.D.5
Batzoglou, S.6
-
26
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034-50.
-
(2005)
Genome Res.
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
-
27
-
-
77951651879
-
Single-nucleotide evolutionary constraint scores highlight disease-causing mutations
-
Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, et al. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat Methods. 2010;7:250-1.
-
(2010)
Nat Methods.
, vol.7
, pp. 250-251
-
-
Cooper, G.M.1
Goode, D.L.2
Ng, S.B.3
Sidow, A.4
Bamshad, M.J.5
Shendure, J.6
-
28
-
-
66349086264
-
Identifying novel constrained elements by exploiting biased substitution patterns
-
Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics. 2009;25:i54-62.
-
(2009)
Bioinformatics.
, vol.25
, pp. 54-62
-
-
Garber, M.1
Guttman, M.2
Clamp, M.3
Zody, M.C.4
Friedman, N.5
Xie, X.6
-
29
-
-
84875490185
-
Cancer genome landscapes
-
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz Jr LA, Kinzler KW. Cancer genome landscapes. Science. 2013;339:1546-58.
-
(2013)
Science.
, vol.339
, pp. 1546-1558
-
-
Vogelstein, B.1
Papadopoulos, N.2
Velculescu, V.E.3
Zhou, S.4
Diaz, L.A.5
Kinzler, K.W.6
-
30
-
-
84982253941
-
Analysis of protein-coding genetic variation in 60,706 humans
-
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285-91.
-
(2016)
Nature.
, vol.536
, pp. 285-291
-
-
Lek, M.1
Karczewski, K.J.2
Minikel, E.V.3
Samocha, K.E.4
Banks, E.5
Fennell, T.6
-
31
-
-
84928198929
-
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity
-
Grimm DG, Azencott CA, Aicheler F, Gieraths U, MacArthur DG, Samocha KE, et al. The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. Hum Mutat. 2015;36:513-23.
-
(2015)
Hum Mutat.
, vol.36
, pp. 513-523
-
-
Grimm, D.G.1
Azencott, C.A.2
Aicheler, F.3
Gieraths, U.4
MacArthur, D.G.5
Samocha, K.E.6
-
32
-
-
84871578629
-
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models
-
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013;34:57-65.
-
(2013)
Hum Mutat.
, vol.34
, pp. 57-65
-
-
Shihab, H.A.1
Gough, J.2
Cooper, D.N.3
Stenson, P.D.4
Barker, G.L.5
Edwards, K.J.6
-
33
-
-
79957621519
-
Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed
-
Hicks S, Wheeler DA, Plon SE, Kimmel M. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat. 2011;32:661-8.
-
(2011)
Hum Mutat.
, vol.32
, pp. 661-668
-
-
Hicks, S.1
Wheeler, D.A.2
Plon, S.E.3
Kimmel, M.4
-
34
-
-
33644537810
-
Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral
-
Tavtigian SV, Deffenbaugh AM, Yin L, Judkins T, Scholl T, Samollow PB, et al. Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral. J Med Genet. 2006;43:295-305.
-
(2006)
J Med Genet.
, vol.43
, pp. 295-305
-
-
Tavtigian, S.V.1
Deffenbaugh, A.M.2
Yin, L.3
Judkins, T.4
Scholl, T.5
Samollow, P.B.6
-
35
-
-
33745612095
-
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
-
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006;22:1540-2.
-
(2006)
Bioinformatics.
, vol.22
, pp. 1540-1542
-
-
Suzuki, R.1
Shimodaira, H.2
-
36
-
-
84947476425
-
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
-
Galili T. dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics. 2015;31:3718-20.
-
(2015)
Bioinformatics
, vol.31
, pp. 3718-3720
-
-
Galili, T.1
-
37
-
-
84867724867
-
An informatics approach to analyzing the incidentalome
-
Berg JS, Adams M, Nassar N, Bizon C, Lee K, Schmitt CP, et al. An informatics approach to analyzing the incidentalome. Genet Med. 2013;15:36-44.
-
(2013)
Genet Med.
, vol.15
, pp. 36-44
-
-
Berg, J.S.1
Adams, M.2
Nassar, N.3
Bizon, C.4
Lee, K.5
Schmitt, C.P.6
-
38
-
-
45449101500
-
Natural selection on genes that underlie human disease susceptibility
-
Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, et al. Natural selection on genes that underlie human disease susceptibility. Curr Biol. 2008;18:883-9.
-
(2008)
Curr Biol.
, vol.18
, pp. 883-889
-
-
Blekhman, R.1
Man, O.2
Herrmann, L.3
Boyko, A.R.4
Indap, A.5
Kosiol, C.6
|