-
1
-
-
80054746492
-
Exome sequencing as a tool for Mendelian disease gene discovery
-
Bamshad, M. J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745-755 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 745-755
-
-
Bamshad, M.J.1
-
2
-
-
84938965200
-
The genetic basis of Mendelian phenotypes: Discoveries, challenges, and opportunities
-
Chong, J. X. et al. The genetic basis of Mendelian phenotypes: discoveries, challenges, and opportunities. Am. J. Hum. Genet. 97, 199-215 (2015).
-
(2015)
Am. J. Hum. Genet.
, vol.97
, pp. 199-215
-
-
Chong, J.X.1
-
3
-
-
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 (2015).
-
(2015)
Nature
, vol.526
, pp. 68-74
-
-
-
4
-
-
84982253941
-
Analysis of protein-coding genetic variation in 60, 706 humans
-
Lek, M. et al. Analysis of protein-coding genetic variation in 60, 706 humans. Nature 536, 285-291 (2016).
-
(2016)
Nature
, vol.536
, pp. 285-291
-
-
Lek, M.1
-
5
-
-
80051968181
-
Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data
-
Cooper, G. M. & Shendure, J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12, 628-640 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 628-640
-
-
Cooper, G.M.1
Shendure, J.2
-
6
-
-
84905714943
-
Using VAAST to identify disease-associated variants in next-generation sequencing data
-
Kennedy, B. et al. Using VAAST to identify disease-associated variants in next-generation sequencing data. Curr. Protoc. Hum. Genet. 81, 6. 14. 1-6. 14. 25 (2014).
-
(2014)
Curr. Protoc. Hum. Genet.
, vol.81
, pp. 6141-61425
-
-
Kennedy, B.1
-
7
-
-
77953121307
-
Powerful SNP-set analysis for case-control genome-wide association studies
-
Wu, M. C. et al. Powerful SNP-set analysis for case-control genome-wide association studies. Am. J. Hum. Genet. 86, 929-942 (2010).
-
(2010)
Am. J. Hum. Genet.
, vol.86
, pp. 929-942
-
-
Wu, M.C.1
-
8
-
-
77953121877
-
Pooled association tests for rare variants in exon-resequencing studies
-
Price, A. L. et al. Pooled association tests for rare variants in exon-resequencing studies. Am. J. Hum. Genet. 86, 832-838 (2010).
-
(2010)
Am. J. Hum. Genet.
, vol.86
, pp. 832-838
-
-
Price, A.L.1
-
9
-
-
78449245227
-
A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions
-
Liu, D. J. & Leal, S. M. A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet. 6, e1001156 (2010).
-
(2010)
PLoS Genet
, vol.6
, pp. e1001156
-
-
Liu, D.J.1
Leal, S.M.2
-
10
-
-
50949095168
-
Methods for detecting associations with rare variants for common diseases: Application to analysis of sequence data
-
Li, B. & Leal, S. M. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am. J. Hum. Genet. 83, 311-321 (2008).
-
(2008)
Am. J. Hum. Genet.
, vol.83
, pp. 311-321
-
-
Li, B.1
Leal, S.M.2
-
11
-
-
84904006087
-
Rare-variant association analysis: Study designs and statistical tests
-
Lee, S., Abecasis, G. R., Boehnke, M. & Lin, X. Rare-variant association analysis: study designs and statistical tests. Am. J. Hum. Genet. 95, 5-23 (2014).
-
(2014)
Am. J. Hum. Genet.
, vol.95
, pp. 5-23
-
-
Lee, S.1
Abecasis, G.R.2
Boehnke, M.3
Lin, X.4
-
12
-
-
84881104150
-
Clinical analysis of genome next-generation sequencing data using the Omicia platform
-
Coonrod, E. M., Margraf, R. L., Russell, A., Voelkerding, K. V. & Reese, M. G. Clinical analysis of genome next-generation sequencing data using the Omicia platform. Expert Rev. Mol. Diagn. 13, 529-540 (2013).
-
(2013)
Expert Rev. Mol. Diagn.
, vol.13
, pp. 529-540
-
-
Coonrod, E.M.1
Margraf, R.L.2
Russell, A.3
Voelkerding, K.V.4
Reese, M.G.5
-
13
-
-
85018588544
-
PathOS: A decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories
-
Doig, K. D. et al. PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories. Genome Med. 9, 38 (2017).
-
(2017)
Genome Med.
, vol.9
, pp. 38
-
-
Doig, K.D.1
-
14
-
-
84927151856
-
Bam. Iobio: A web-based, real-time, sequence alignment file inspector
-
Miller, C. A., Qiao, Y., DiSera, T., D'Astous, B. & Marth, G. T. bam. iobio: a web-based, real-time, sequence alignment file inspector. Nat. Methods 11, 1189 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 1189
-
-
Miller, C.A.1
Qiao, Y.2
Disera, T.3
D'astous, B.4
Marth, G.T.5
-
15
-
-
84927914983
-
VariantDB: A flexible annotation and filtering portal for next generation sequencing data
-
Vandeweyer, G., Van Laer, L., Loeys, B., Van den Bulcke, T. & Kooy, R. F. VariantDB: a flexible annotation and filtering portal for next generation sequencing data. Genome Med. 6, 74 (2014).
-
(2014)
Genome Med.
, vol.6
, pp. 74
-
-
Vandeweyer, G.1
Van Laer, L.2
Loeys, B.3
Van Den Bulcke, T.4
Kooy, R.F.5
-
16
-
-
84946081339
-
OMIM. Org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
-
Amberger, J. S., Bocchini, C. A., Schiettecatte, F., Scott, A. F. & Hamosh, A. OMIM. org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43, D789-D798 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D789-D798
-
-
Amberger, J.S.1
Bocchini, C.A.2
Schiettecatte, F.3
Scott, A.F.4
Hamosh, A.5
-
17
-
-
84976904305
-
ClinVar: Public archive of interpretations of clinically relevant variants
-
Landrum, M. J. et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 44, D862-D868 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D862-D868
-
-
Landrum, M.J.1
-
18
-
-
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. Nat. Genet. 43, 491-498 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 491-498
-
-
Depristo, M.A.1
-
19
-
-
79954672317
-
Genome structural variation discovery and genotyping
-
Alkan, C., Coe, B. P. & Eichler, E. E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363-376 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 363-376
-
-
Alkan, C.1
Coe, B.P.2
Eichler, E.E.3
-
20
-
-
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. Curr. Protoc. Bioinformatics 43, 11. 10. 1-11. 10. 33 (2013).
-
(2013)
Curr. Protoc. Bioinformatics
, vol.43
, pp. 11101-111033
-
-
Van Der Auwera, G.A.1
-
21
-
-
84897387657
-
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
-
Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246-251 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 246-251
-
-
Zook, J.M.1
-
22
-
-
79960405019
-
The variant call format and VCFtools
-
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
-
23
-
-
84973338712
-
The Ensembl variant effect predictor
-
McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 122
-
-
McLaren, W.1
-
24
-
-
80051547469
-
A probabilistic disease-gene finder for personal genomes
-
Yandell, M. et al. A probabilistic disease-gene finder for personal genomes. Genome Res. 21, 1529-1542 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 1529-1542
-
-
Yandell, M.1
-
25
-
-
84862506964
-
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; Iso-2; iso-3
-
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80-92 (2012).
-
(2012)
Fly
, vol.6
, pp. 80-92
-
-
Cingolani, P.1
-
26
-
-
22044443709
-
The Sequence Ontology: A tool for the unification of genome annotations
-
Eilbeck, K. et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44 (2005).
-
(2005)
Genome Biol.
, vol.6
, pp. R44
-
-
Eilbeck, K.1
-
27
-
-
84938078941
-
Improving the Sequence Ontology terminology for genomic variant annotation
-
Cunningham, F., Moore, B., Ruiz-Schultz, N., Ritchie, G. R. & Eilbeck, K. Improving the Sequence Ontology terminology for genomic variant annotation. J. Biomed. Semantics 6, 32 (2015).
-
(2015)
J. Biomed. Semantics
, vol.6
, pp. 32
-
-
Cunningham, F.1
Moore, B.2
Ruiz-Schultz, N.3
Ritchie, G.R.4
Eilbeck, K.5
-
28
-
-
0035173378
-
DbSNP: The NCBI database of genetic variation
-
Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
-
29
-
-
85016096622
-
Ensembl 2017
-
Aken, B. L. et al. Ensembl 2017. Nucleic Acids Res. 45, D635-D642 (2017).
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D635-D642
-
-
Aken, B.L.1
-
30
-
-
84876527890
-
DbVar and DGVa: Public archives for genomic structural variation
-
Lappalainen, I. et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 41, D936-D941 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D936-D941
-
-
Lappalainen, I.1
-
31
-
-
62549098614
-
Quantitative measures for the management and comparison of annotated genomes
-
Eilbeck, K., Moore, B., Holt, C. & Yandell, M. Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10, 67 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 67
-
-
Eilbeck, K.1
Moore, B.2
Holt, C.3
Yandell, M.4
-
32
-
-
77957278356
-
Between a chicken and a grape: Estimating the number of human genes
-
Pertea, M. & Salzberg, S. L. Between a chicken and a grape: estimating the number of human genes. Genome Biol. 11, 206 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. 206
-
-
Pertea, M.1
Salzberg, S.L.2
-
33
-
-
84911444179
-
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
-
Ezkurdia, I. et al. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Hum. Mol. Genet. 23, 5866-5878 (2014).
-
(2014)
Hum. Mol. Genet.
, vol.23
, pp. 5866-5878
-
-
Ezkurdia, I.1
-
34
-
-
84863116742
-
A systematic survey of loss-of-function variants in human protein-coding genes
-
MacArthur, D. G. et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828 (2012).
-
(2012)
Science
, vol.335
, pp. 823-828
-
-
Macarthur, D.G.1
-
35
-
-
85017562274
-
Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity
-
Saleheen, D. et al. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Nature 544, 235-239 (2017).
-
(2017)
Nature
, vol.544
, pp. 235-239
-
-
Saleheen, D.1
-
36
-
-
84880335431
-
Gly16Gly in MECP2 Exon 1, causes a cryptic splice event in a Rett syndrome patient
-
Sheikh, T. I., Mittal, K., Willis, M. J. & Vincent, J. B. A synonymous change, p. Gly16Gly in MECP2 Exon 1, causes a cryptic splice event in a Rett syndrome patient. Orphanet J. Rare Dis. 8, 108 (2013).
-
(2013)
Orphanet J. Rare Dis.
, vol.8
, pp. 108
-
-
Sheikh, T.I.1
Mittal, K.2
Willis, M.J.3
Vincent, J.B.4
-
37
-
-
33845899137
-
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
-
Nackley, A. G. et al. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314, 1930-1933 (2006).
-
(2006)
Science
, vol.314
, pp. 1930-1933
-
-
Nackley, A.G.1
-
38
-
-
33846504706
-
A 'silent' polymorphism in the MDR1 gene changes substrate specificity
-
Kimchi-Sarfaty, C. et al. A 'silent' polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525-528 (2007).
-
(2007)
Science
, vol.315
, pp. 525-528
-
-
Kimchi-Sarfaty, C.1
-
39
-
-
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. Nat. Genet. 46, 310-315 (2014).
-
(2014)
Nat Genet.
, vol.46
, pp. 310-315
-
-
Kircher, M.1
-
40
-
-
84924039302
-
A method for calculating probabilities of fitness consequences for point mutations across the human genome
-
Gulko, B., Hubisz, M. J., Gronau, I. & Siepel, A. A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat. Genet. 47, 276-283 (2015).
-
(2015)
Nat Genet.
, vol.47
, pp. 276-283
-
-
Gulko, B.1
Hubisz, M.J.2
Gronau, I.3
Siepel, A.4
-
41
-
-
0035026704
-
Predicting deleterious amino acid substitutions
-
Ng, P. C. & Henikoff, S. Predicting deleterious amino acid substitutions. Genome Res. 11, 863-874 (2001).
-
(2001)
Genome Res.
, vol.11
, pp. 863-874
-
-
Ng, P.C.1
Henikoff, S.2
-
42
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249 (2010).
-
(2010)
Nat Methods
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
-
43
-
-
0036380553
-
Sequence variation at the human ABO locus
-
Yip, S. P. Sequence variation at the human ABO locus. Ann. Hum. Genet. 66, 1-27 (2002).
-
(2002)
Ann. Hum. Genet.
, vol.66
, pp. 1-27
-
-
Yip, S.P.1
-
44
-
-
84943755428
-
Homozygous loss-of-function variants in European cosmopolitan and isolate populations
-
Kaiser, V. B. et al. Homozygous loss-of-function variants in European cosmopolitan and isolate populations. Hum. Mol. Genet. 24, 5464-5474 (2015).
-
(2015)
Hum. Mol. Genet.
, vol.24
, pp. 5464-5474
-
-
Kaiser, V.B.1
-
45
-
-
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 (2010).
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
46
-
-
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 (2012).
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
47
-
-
84943182461
-
An integrated map of structural variation in 2, 504 human genomes
-
Sudmant, P. H. et al. An integrated map of structural variation in 2, 504 human genomes. Nature 526, 75-81 (2015).
-
(2015)
Nature
, vol.526
, pp. 75-81
-
-
Sudmant, P.H.1
-
48
-
-
84863556835
-
Evolution and functional impact of rare coding variation from deep sequencing of human exomes
-
Tennessen, J. A. et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69 (2012).
-
(2012)
Science
, vol.337
, pp. 64-69
-
-
Tennessen, J.A.1
-
49
-
-
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 Res. 38, e164 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e164
-
-
Wang, K.1
Li, M.2
Hakonarson, H.3
-
50
-
-
84867241644
-
Population genetic inference from personal genome data: Impact of ancestry and admixture on human genomic variation
-
Kidd, J. M. et al. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am. J. Hum. Genet. 91, 660-671 (2012).
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 660-671
-
-
Kidd, J.M.1
-
51
-
-
0028062781
-
Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model
-
Gabriel, S. E., Brigman, K. N., Koller, B. H., Boucher, R. C. & Stutts, M. J. Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model. Science 266, 107-109 (1994).
-
(1994)
Science
, vol.266
, pp. 107-109
-
-
Gabriel, S.E.1
Brigman, K.N.2
Koller, B.H.3
Boucher, R.C.4
Stutts, M.J.5
-
52
-
-
80053050662
-
Population genetics of malaria resistance in humans
-
Hedrick, P. W. Population genetics of malaria resistance in humans. Heredity 107, 283-304 (2011).
-
(2011)
Heredity
, vol.107
, pp. 283-304
-
-
Hedrick, P.W.1
-
53
-
-
85029478862
-
Identification of misclassified ClinVar variants using disease population prevalence
-
Shah, N. et al. Identification of misclassified ClinVar variants using disease population prevalence. Preprint at bioRxiv http://dx. doi. org/10. 1101/075416 (2016).
-
(2016)
Preprint at BioRxiv
-
-
Shah, N.1
-
54
-
-
84992437341
-
Publicly available data provide evidence against NR1H3 R415Q Causing multiple sclerosis
-
Minikel, E. V. & MacArthur, D. G. Publicly available data provide evidence against NR1H3 R415Q Causing multiple sclerosis. Neuron 92, 336-338 (2016).
-
(2016)
Neuron
, vol.92
, pp. 336-338
-
-
Minikel, E.V.1
Macarthur, D.G.2
-
55
-
-
84884592445
-
Genic intolerance to functional variation and the interpretation of personal genomes
-
Petrovski, S., Wang, Q., Heinzen, E. L., Allen, A. S. & Goldstein, D. B. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 9, e1003709 (2013).
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003709
-
-
Petrovski, S.1
Wang, Q.2
Heinzen, E.L.3
Allen, A.S.4
Goldstein, D.B.5
-
56
-
-
84922394049
-
A framework for the interpretation of de novo mutation in human disease
-
Samocha, K. E. et al. A framework for the interpretation of de novo mutation in human disease. Nat. Genet. 46, 944-950 (2014).
-
(2014)
Nat Genet.
, vol.46
, pp. 944-950
-
-
Samocha, K.E.1
-
57
-
-
84946548774
-
FLAGS, frequently mutated genes in public exomes
-
Shyr, C. et al. FLAGS, frequently mutated genes in public exomes. BMC Med. Genomics 7, 64 (2014).
-
(2014)
BMC Med. Genomics
, vol.7
, pp. 64
-
-
Shyr, C.1
-
58
-
-
84863116641
-
Truncations of titin causing dilated cardiomyopathy
-
Herman, D. S. et al. Truncations of titin causing dilated cardiomyopathy. N. Engl. J. Med. 366, 619-628 (2012).
-
(2012)
N. Engl. J. Med.
, vol.366
, pp. 619-628
-
-
Herman, D.S.1
-
59
-
-
84900524773
-
Genetic basis of limb-girdle muscular dystrophies: The 2014 update
-
Nigro, V. & Savarese, M. Genetic basis of limb-girdle muscular dystrophies: the 2014 update. Acta Myol. 33, 1-12 (2014).
-
(2014)
Acta Myol.
, vol.33
, pp. 1-12
-
-
Nigro, V.1
Savarese, M.2
-
60
-
-
0036723943
-
Tibial muscular dystrophy is a titinopathy caused by mutations in TTN, the gene encoding the giant skeletal-muscle protein titin
-
Hackman, P. et al. Tibial muscular dystrophy is a titinopathy caused by mutations in TTN, the gene encoding the giant skeletal-muscle protein titin. Am. J. Hum. Genet. 71, 492-500 (2002).
-
(2002)
Am. J. Hum. Genet.
, vol.71
, pp. 492-500
-
-
Hackman, P.1
-
62
-
-
79952682059
-
Keratin gene mutations in disorders of human skin and its appendages
-
Chamcheu, J. C. et al. Keratin gene mutations in disorders of human skin and its appendages. Arch. Biochem. Biophys. 508, 123-137 (2011).
-
(2011)
Arch. Biochem. Biophys.
, vol.508
, pp. 123-137
-
-
Chamcheu, J.C.1
-
63
-
-
61449168010
-
A groupwise association test for rare mutations using a weighted sum statistic
-
Madsen, B. E. & Browning, S. R. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 5, e1000384 (2009).
-
(2009)
PLoS Genet
, vol.5
, pp. e1000384
-
-
Madsen, B.E.1
Browning, S.R.2
-
64
-
-
84924907990
-
Rare variant association studies: Considerations, challenges and opportunities
-
Auer, P. L. & Lettre, G. Rare variant association studies: considerations, challenges and opportunities. Genome Med. 7, 16 (2015).
-
(2015)
Genome Med.
, vol.7
, pp. 16
-
-
Auer, P.L.1
Lettre, G.2
-
65
-
-
84864942403
-
Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies
-
Lee, S. et al. Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am. J. Hum. Genet. 91, 224-237 (2012).
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 224-237
-
-
Lee, S.1
-
66
-
-
84881609951
-
VAAST 2. 0: Improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix
-
Hu, H. et al. VAAST 2. 0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genet. Epidemiol. 37, 622-634 (2013).
-
(2013)
Genet. Epidemiol.
, vol.37
, pp. 622-634
-
-
Hu, H.1
-
67
-
-
84904025285
-
A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data
-
Hu, H. et al. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat. Biotechnol. 32, 663-669 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 663-669
-
-
Hu, H.1
-
68
-
-
78650031174
-
Huntington's disease: From molecular pathogenesis to clinical treatment
-
Ross, C. A. & Tabrizi, S. J. Huntington's disease: from molecular pathogenesis to clinical treatment. Lancet Neurol. 10, 83-98 (2011).
-
(2011)
Lancet Neurol.
, vol.10
, pp. 83-98
-
-
Ross, C.A.1
Tabrizi, S.J.2
-
69
-
-
84880800567
-
GEMINI: Integrative exploration of genetic variation and genome annotations
-
Paila, U., Chapman, B. A., Kirchner, R. & Quinlan, A. R. GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput. Biol. 9, e1003153 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003153
-
-
Paila, U.1
Chapman, B.A.2
Kirchner, R.3
Quinlan, A.R.4
-
70
-
-
84899859455
-
Variant association tools for quality control and analysis of large-scale sequence and genotyping array data
-
Wang, G. T., Peng, B. & Leal, S. M. Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. Am. J. Hum. Genet. 94, 770-783 (2014).
-
(2014)
Am. J. Hum. Genet.
, vol.94
, pp. 770-783
-
-
Wang, G.T.1
Peng, B.2
Leal, S.M.3
-
71
-
-
85015982066
-
The human phenotype ontology in 2017
-
Köhler, S. et al. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 45, D865-D876 (2017).
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D865-D876
-
-
Köhler, S.1
-
72
-
-
84880508099
-
PhenoTips: Patient phenotyping software for clinical and research use
-
Girdea, M. et al. PhenoTips: patient phenotyping software for clinical and research use. Hum. Mutat. 34, 1057-1065 (2013).
-
(2013)
Hum. Mutat.
, vol.34
, pp. 1057-1065
-
-
Girdea, M.1
-
73
-
-
84875514203
-
PhenoDB: A new web-based tool for the collection, storage, and analysis of phenotypic features
-
Hamosh, A. et al. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum. Mutat. 34, 566-571 (2013).
-
(2013)
Hum. Mutat.
, vol.34
, pp. 566-571
-
-
Hamosh, A.1
-
74
-
-
84939151435
-
Phenotype-driven strategies for exome prioritization of human Mendelian disease genes
-
Smedley, D. & Robinson, P. N. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med. 7, 81 (2015).
-
(2015)
Genome Med.
, vol.7
, pp. 81
-
-
Smedley, D.1
Robinson, P.N.2
-
75
-
-
84947907035
-
Next-generation diagnostics and disease-gene discovery with the Exomiser
-
Smedley, D. et al. Next-generation diagnostics and disease-gene discovery with the Exomiser. Nat. Protoc. 10, 2004-2015 (2015).
-
(2015)
Nat. Protoc.
, vol.10
, pp. 2004-2015
-
-
Smedley, D.1
-
76
-
-
84921633944
-
Phen-Gen: Combining phenotype and genotype to analyze rare disorders
-
Javed, A., Agrawal, S. & Ng, P. C. Phen-Gen: combining phenotype and genotype to analyze rare disorders. Nat. Methods 11, 935-937 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 935-937
-
-
Javed, A.1
Agrawal, S.2
Ng, P.C.3
-
77
-
-
84887041034
-
EXtasy: Variant prioritization by genomic data fusion
-
Sifrim, A. et al. eXtasy: variant prioritization by genomic data fusion. Nat. Methods 10, 1083-1084 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1083-1084
-
-
Sifrim, A.1
-
78
-
-
84940611109
-
Phenolyzer: Phenotype-based prioritization of candidate genes for human diseases
-
Yang, H., Robinson, P. N. & Wang, K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat. Methods 12, 841-843 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 841-843
-
-
Yang, H.1
Robinson, P.N.2
Wang, K.3
-
79
-
-
84956744263
-
A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics
-
James, R. A. et al. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med. 8, 13 (2016).
-
(2016)
Genome Med
, vol.8
, pp. 13
-
-
James, R.A.1
-
80
-
-
84898743768
-
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families
-
Singleton, M. V. et al. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am. J. Hum. Genet. 94, 599-610 (2014).
-
(2014)
Am. J. Hum. Genet.
, vol.94
, pp. 599-610
-
-
Singleton, M.V.1
-
81
-
-
84892959492
-
Improved exome prioritization of disease genes through cross-species phenotype comparison
-
Robinson, P. N. et al. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 24, 340-348 (2014).
-
(2014)
Genome Res.
, vol.24
, pp. 340-348
-
-
Robinson, P.N.1
-
82
-
-
84965181241
-
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
-
Brownstein, C. A. et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 15, R53 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R53
-
-
Brownstein, C.A.1
-
83
-
-
84977078618
-
Practice guidelines for the evaluation of pathogenicity and the reporting of sequence variants in clinical molecular genetics
-
Wallis, Y. et al. Practice guidelines for the evaluation of pathogenicity and the reporting of sequence variants in clinical molecular genetics. ACGS http://www. acgs. uk. com/media/774853/evaluation-and-reporting-of- sequence-variants-bpgs-june-2013-finalpdf. pdf (2013).
-
(2013)
ACGS
-
-
Wallis, Y.1
-
84
-
-
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. 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. 17, 405-424 (2015).
-
(2015)
Genet. Med.
, vol.17
, pp. 405-424
-
-
Richards, S.1
-
85
-
-
85029504007
-
Consensus statement on adoption of American College of Medical Genetics and Genomics (ACMG) guidelines for sequence variant classification and interpretation
-
Association for Clinical Genetic Science
-
Association for Clinical Genetic Science. Consensus statement on adoption of American College of Medical Genetics and Genomics (ACMG) guidelines for sequence variant classification and interpretation. ACGS http://www. acgs. uk. com/media/1032817/acgs- consensus-state ment-on-adoption-of-acmg- guidelines-1-. pdf (2016).
-
(2016)
ACGS
-
-
-
86
-
-
84961616450
-
HGVS recommendations for the description of sequence variants: 2016 update
-
den Dunnen, J. T. et al. HGVS recommendations for the description of sequence variants: 2016 update. Hum. Mutat. 37, 564-569 (2016).
-
(2016)
Hum. Mutat.
, vol.37
, pp. 564-569
-
-
Den Dunnen, J.T.1
-
87
-
-
84941044607
-
Genenames. Org: The HGNC resources in 2015
-
Gray, K. A., Yates, B., Seal, R. L., Wright, M. W. & Bruford, E. A. Genenames. org: the HGNC resources in 2015. Nucleic Acids Res. 43, D1079-D1085 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D1079-D1085
-
-
Gray, K.A.1
Yates, B.2
Seal, R.L.3
Wright, M.W.4
Bruford, E.A.5
-
88
-
-
84930526399
-
ClinGen-the Clinical Genome Resource
-
Rehm, H. L. et al. ClinGen-the Clinical Genome Resource. N. Engl. J. Med. 372, 2235-2242 (2015).
-
(2015)
N. Engl. J. Med.
, vol.372
, pp. 2235-2242
-
-
Rehm, H.L.1
-
89
-
-
84899476119
-
Guidelines for investigating causality of sequence variants in human disease
-
MacArthur, D. G. et al. Guidelines for investigating causality of sequence variants in human disease. Nature 508, 469-476 (2014).
-
(2014)
Nature
, vol.508
, pp. 469-476
-
-
Macarthur, D.G.1
-
90
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
91
-
-
80555142991
-
What fraction of the human genome is functional
-
Ponting, C. P. & Hardison, R. C. What fraction of the human genome is functional? Genome Res. 21, 1769-1776 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 1769-1776
-
-
Ponting, C.P.1
Hardison, R.C.2
-
92
-
-
74949092081
-
Detection of nonneutral substitution rates on mammalian phylogenies
-
Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R. & Siepel, A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20, 110-121 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 110-121
-
-
Pollard, K.S.1
Hubisz, M.J.2
Rosenbloom, K.R.3
Siepel, A.4
-
93
-
-
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 Comput. Biol. 6, e1001025 (2010).
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1001025
-
-
Davydov, E.V.1
-
94
-
-
85002624508
-
A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease
-
Smedley, D. et al. A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease. Am. J. Hum. Genet. 99, 595-606 (2016).
-
(2016)
Am. J. Hum. Genet.
, vol.99
, pp. 595-606
-
-
Smedley, D.1
-
95
-
-
85015007138
-
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
-
Huang, Y.-F., Gulko, B. & Siepel, A. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat. Genet. 49, 618-624 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 618-624
-
-
Huang, Y.-F.1
Gulko, B.2
Siepel, A.3
-
96
-
-
84903485906
-
Exposing synonymous mutations
-
Hunt, R. C., Simhadri, V. L., Iandoli, M., Sauna, Z. E. & Kimchi-Sarfaty, C. Exposing synonymous mutations. Trends Genet. 30, 308-321 (2014).
-
(2014)
Trends Genet.
, vol.30
, pp. 308-321
-
-
Hunt, R.C.1
Simhadri, V.L.2
Iandoli, M.3
Sauna, Z.E.4
Kimchi-Sarfaty, C.5
-
97
-
-
84929026065
-
Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: A retrospective analysis of diagnostic and clinical findings
-
Willig, L. K. et al. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. Lancet Respir. Med. 3, 377-387 (2015).
-
(2015)
Lancet Respir. Med.
, vol.3
, pp. 377-387
-
-
Willig, L.K.1
-
98
-
-
84925224470
-
TBX6 null variants and a common hypomorphic allele in congenital scoliosis
-
Wu, N. et al. TBX6 null variants and a common hypomorphic allele in congenital scoliosis. N. Engl. J. Med. 372, 341-350 (2015).
-
(2015)
N. Engl. J. Med.
, vol.372
, pp. 341-350
-
-
Wu, N.1
-
99
-
-
84919665541
-
Compound heterozygosity of low-frequency promoter deletions and rare loss-of-function mutations in TXNL4A causes Burn-McKeown syndrome
-
Wieczorek, D. et al. Compound heterozygosity of low-frequency promoter deletions and rare loss-of-function mutations in TXNL4A causes Burn-McKeown syndrome. Am. J. Hum. Genet. 95, 698-707 (2014).
-
(2014)
Am. J. Hum. Genet.
, vol.95
, pp. 698-707
-
-
Wieczorek, D.1
-
100
-
-
84995436852
-
The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies
-
Redin, C. et al. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nat. Genet. 49, 36-45 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 36-45
-
-
Redin, C.1
-
101
-
-
85040456401
-
Long-read whole genome sequencing identifies causal structural variation in a Mendelian disease
-
Merker, J. et al. Long-read whole genome sequencing identifies causal structural variation in a Mendelian disease. Genet. Med. http://dx. doi. org/10. 1038/ gim. 2017. 86 (2017).
-
(2017)
Genet. Med.
-
-
Merker, J.1
-
102
-
-
84964800573
-
Frequency and complexity of de novo structural mutation in autism
-
Brandler, W. M. et al. Frequency and complexity of de novo structural mutation in autism. Am. J. Hum. Genet. 98, 667-679 (2016).
-
(2016)
Am. J. Hum. Genet.
, vol.98
, pp. 667-679
-
-
Brandler, W.M.1
-
103
-
-
84939129835
-
Extending reference assembly models
-
Church, D. M. et al. Extending reference assembly models. Genome Biol. 16, 13 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 13
-
-
Church, D.M.1
-
104
-
-
85003816199
-
Alternate-locus aware variant calling in whole genome sequencing
-
Jäger, M. et al. Alternate-locus aware variant calling in whole genome sequencing. Genome Med. 8, 130 (2016).
-
(2016)
Genome Med.
, vol.8
, pp. 130
-
-
Jäger, M.1
-
105
-
-
84992548626
-
Using ClinVar as a resource to support variant interpretation
-
Harrison, S. M. et al. Using ClinVar as a resource to support variant interpretation. Curr. Protoc. Hum. Genet. 89, 8. 16. 1-8. 16. 23 (2016).
-
(2016)
Curr. Protoc. Hum. Genet.
, vol.89
, pp. 8161-81623
-
-
Harrison, S.M.1
-
106
-
-
84994441567
-
The promise and peril of precision medicine: Phenotyping still matters most
-
Ackerman, J. P. et al. The promise and peril of precision medicine: phenotyping still matters most. Mayo Clin. Proc. 91, 1606-1616 (2016).
-
(2016)
Mayo Clin. Proc.
, vol.91
, pp. 1606-1616
-
-
Ackerman, J.P.1
-
107
-
-
77953067567
-
Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Clin
-
Dorfman, R. et al. Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Clin. Genet 77, 464-473 (2010).
-
(2010)
Genet
, vol.77
, pp. 464-473
-
-
Dorfman, R.1
-
108
-
-
84975129608
-
A federated ecosystem for sharing genomic, clinical data
-
Global Alliance For Genomics And Health. GENOMICS.
-
Global Alliance for Genomics and Health. GENOMICS. A federated ecosystem for sharing genomic, clinical data. Science 352, 1278-1280 (2016).
-
(2016)
Science
, vol.352
, pp. 1278-1280
-
-
-
109
-
-
0033987778
-
Human gene mutation database-a biomedical information and research resource
-
Krawczak, M. et al. Human gene mutation database-a biomedical information and research resource. Hum. Mutat. 15, 45-51 (2000).
-
(2000)
Hum. Mutat.
, vol.15
, pp. 45-51
-
-
Krawczak, M.1
-
110
-
-
79956292760
-
The case for locus-specific databases
-
Samuels, M. E. & Rouleau, G. A. The case for locus-specific databases. Nat. Rev. Genet. 12, 378-379 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 378-379
-
-
Samuels, M.E.1
Rouleau, G.A.2
-
111
-
-
84864358886
-
Representation of rare diseases in health information systems: The Orphanet approach to serve a wide range of end users
-
Rath, A. et al. Representation of rare diseases in health information systems: the Orphanet approach to serve a wide range of end users. Hum. Mutat. 33, 803-808 (2012).
-
(2012)
Hum. Mutat.
, vol.33
, pp. 803-808
-
-
Rath, A.1
-
112
-
-
68149165614
-
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
-
Kumar, P., Henikoff, S. & Ng, P. C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4, 1073-1081 (2009).
-
(2009)
Nat. Protoc.
, vol.4
, pp. 1073-1081
-
-
Kumar, P.1
Henikoff, S.2
Ng, P.C.3
-
113
-
-
84878799611
-
Predicting functional effect of human missense mutations using PolyPhen-2
-
Adzhubei, I., Jordan, D. M. & Sunyaev, S. R. Predicting functional effect of human missense mutations using PolyPhen-2. Curr. Protoc. Hum. Genet. 7. 20. 1-7. 20. 41 (2013).
-
(2013)
Curr. Protoc. Hum. Genet.
, vol.7
, pp. 201-72041
-
-
Adzhubei, I.1
Jordan, D.M.2
Sunyaev, S.R.3
-
114
-
-
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. Hum. Mutat. 34, 57-65 (2013).
-
(2013)
Hum. Mutat.
, vol.34
, pp. 57-65
-
-
Shihab, H.A.1
-
115
-
-
84880213068
-
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
-
Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A. & Punta, M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 41, e121 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e121
-
-
Mistry, J.1
Finn, R.D.2
Eddy, S.R.3
Bateman, A.4
Punta, M.5
-
116
-
-
84930619194
-
PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels
-
Choi, Y. & Chan, A. P. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31, 2745-2747 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 2745-2747
-
-
Choi, Y.1
Chan, A.P.2
-
117
-
-
84991615407
-
REVEL: An Ensemble method for predicting the pathogenicity of rare missense variants
-
Ioannidis, N. M. et al. REVEL: an Ensemble method for predicting the pathogenicity of rare missense variants. Am. J. Hum. Genet. 99, 877-885 (2016).
-
(2016)
Am. J. Hum. Genet.
, vol.99
, pp. 877-885
-
-
Ioannidis, N.M.1
-
118
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
-
(2005)
Genome Res.
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
-
119
-
-
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. Nat. Methods 11, 361-362 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 361-362
-
-
Schwarz, J.M.1
Cooper, D.N.2
Schuelke, M.3
Seelow, D.4
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