-
1
-
-
46149121706
-
Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms
-
Anderson, C. A., Pettersson, F. H., Barrett, J. C., Zhuang, J. J., Ragoussis, J., Cardon, L. R., et al. (2008). Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms. Am. J. Hum. Genet. 83, 112–119. doi: 10.1016/j.ajhg.2008.06.008
-
(2008)
Am. J. Hum. Genet.
, vol.83
, pp. 112-119
-
-
Anderson, C.A.1
Pettersson, F.H.2
Barrett, J.C.3
Zhuang, J.J.4
Ragoussis, J.5
Cardon, L.R.6
-
2
-
-
84954234248
-
Genotype imputation with millions of reference samples
-
Browning, B. R., and Browning, S. R. (2016). Genotype imputation with millions of reference samples. Am. J. Hum. Genet. 7, 116–126. doi: 10.1016/j.ajhg.2015.11.020
-
(2016)
Am. J. Hum. Genet.
, vol.7
, pp. 116-126
-
-
Browning, B.R.1
Browning, S.R.2
-
3
-
-
15944414175
-
The human genome diversity project: Past, present and future
-
Cavalli-Sforza, L. L. (2005). The human genome diversity project: past, present and future. Nat. Rev. Genet. 6, 333–340. doi: 10.1038/nrg1596
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 333-340
-
-
Cavalli-Sforza, L.L.1
-
4
-
-
84930213392
-
Second-generation PLINK: Rising to the challenge of larger and richer datasets
-
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., and Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4:7. doi: 10.1186/s13742-015-0047-8
-
(2015)
GigaScience
, vol.4
, pp. 7
-
-
Chang, C.C.1
Chow, C.C.2
Tellier, L.C.3
Vattikuti, S.4
Purcell, S.M.5
Lee, J.J.6
-
5
-
-
84892473992
-
Genome-wide association study of ancestry-specific TB risk in the south african coloured population
-
Chimusa, E. R., Zaitlen, N., Daya, M., Möller, M., van Helden, P. D., Mulder, N. J., et al. (2014). Genome-wide association study of ancestry-specific TB risk in the south african coloured population. Hum. Mol. Genet. 1, 796–809. doi: 10.1093/hmg/ddt462
-
(2014)
Hum. Mol. Genet.
, vol.1
, pp. 796-809
-
-
Chimusa, E.R.1
Zaitlen, N.2
Daya, M.3
Möller, M.4
Van Helden, P.D.5
Mulder, N.J.6
-
6
-
-
84984598118
-
Next-generation genotype imputation service and methods
-
Das, S., Forer, L., Schönherr, S., Sidore, C., Locke, A. E., Kwong, A., et al. (2016). Next-generation genotype imputation service and methods. Nat. Genet. 48, 1284–1287. doi: 10.1038/ng.3656
-
(2016)
Nat. Genet.
, vol.48
, pp. 1284-1287
-
-
Das, S.1
Forer, L.2
Schönherr, S.3
Sidore, C.4
Locke, A.E.5
Kwong, A.6
-
7
-
-
84893396201
-
A panel of ancestry informative markers for the complex five-way admixed south african coloured population
-
Daya, M., Merwe, L., van der Galal, U., Möller, M., Salie, M., Chimusa, E. R., et al. (2013). A panel of ancestry informative markers for the complex five-way admixed south african coloured population. PLoS One 8:e82224. doi: 10.1371/journal.pone.0082224
-
(2013)
PLoS One
, vol.8
-
-
Daya, M.1
Merwe, L.2
Van Der Galal, U.3
Möller, M.4
Salie, M.5
Chimusa, E.R.6
-
8
-
-
77955296064
-
Genome-wide analysis of the structure of the south african coloured population in the western cape
-
de Wit, E., Delport, W., Rugamika, C. E., Meintjes, A., Möller, M., van Helden, P. D., et al. (2010). Genome-wide analysis of the structure of the south african coloured population in the western cape. Hum. Genet. 128, 145–153. doi: 10.1007/s00439-010-0836-1
-
(2010)
Hum. Genet.
, vol.128
, pp. 145-153
-
-
De Wit, E.1
Delport, W.2
Rugamika, C.E.3
Meintjes, A.4
Möller, M.5
Van Helden, P.D.6
-
9
-
-
84928813777
-
Genotype harmonizer: Automatic strand alignment and format conversion for genotype data integration
-
Deelen, P., Bonder, M. J., van der Velde, K. J., Westra, H.-J., Winder, E., Hendriksen, D., et al. (2014). Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Res. Notes 7:901. doi: 10.1186/1756-0500-7-901
-
(2014)
BMC Res. Notes
, vol.7
, pp. 901
-
-
Deelen, P.1
Bonder, M.J.2
Van Der Velde, K.J.3
Westra, H.-J.4
Winder, E.5
Hendriksen, D.6
-
10
-
-
84856478855
-
A linear complexity phasing method for thousands of genomes
-
Delaneau, O., Marchini, J., and Zagury, J.-F. (2012). A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179–181. doi: 10.1038/nmeth.1785
-
(2012)
Nat. Methods
, vol.9
, pp. 179-181
-
-
Delaneau, O.1
Marchini, J.2
Zagury, J.-F.3
-
11
-
-
73449104771
-
High-throughput methods for SNP genotyping
-
Ding, C., and Jin, S. (2009). High-throughput methods for SNP genotyping. Methods Mol. Biol. 578, 245–254. doi: 10.1007/978-1-60327-411-1_16
-
(2009)
Methods Mol. Biol.
, vol.578
, pp. 245-254
-
-
Ding, C.1
Jin, S.2
-
12
-
-
84899540087
-
Efficient haplotype matching and storage using the positional burrows-wheeler transform (PBWT)
-
Durbin, R. (2014). Efficient haplotype matching and storage using the positional burrows-wheeler transform (PBWT). Bioinformatics 1, 1266–1272. doi: 10.1093/bioinformatics/btu014
-
(2014)
Bioinformatics
, vol.1
, pp. 1266-1272
-
-
Durbin, R.1
-
13
-
-
84923186799
-
The african genome variation project shapes medical genetics in Africa
-
Gurdasani, D., Carstensen, T., Tekola-Ayele, F., Pagani, L., Tachmazidou, I., Hatzikotoulas, K., et al. (2015). The african genome variation project shapes medical genetics in africa. Nature 517, 327–332. doi: 10.1038/nature13997
-
(2015)
Nature
, vol.517
, pp. 327-332
-
-
Gurdasani, D.1
Carstensen, T.2
Tekola-Ayele, F.3
Pagani, L.4
Tachmazidou, I.5
Hatzikotoulas, K.6
-
14
-
-
84870616969
-
Assessment of genotype imputation performance using 1000 genomes in african American studies
-
Hancock, D. B., Levy, J. L., Gaddis, N. C., Bierut, L. J., Saccone, N. L., Page, G. P., et al. (2012). Assessment of genotype imputation performance using 1000 genomes in african american studies. PLoS One 7:e50610. doi: 10.1371/journal.pone.0050610
-
(2012)
PLoS One
, vol.7
-
-
Hancock, D.B.1
Levy, J.L.2
Gaddis, N.C.3
Bierut, L.J.4
Saccone, N.L.5
Page, G.P.6
-
15
-
-
67651222400
-
Flexible and accurate genotype imputation method for the next generation of genome-wide association studies
-
Howie, B. N., Donnelly, P., and Marchini, J. A. (2009). flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5:e1000529. doi: 10.1371/journal.pgen.1000529
-
(2009)
PLoS Genet
, vol.5
-
-
Howie, B.N.1
Donnelly, P.2
Marchini, J.A.3
-
16
-
-
62649089065
-
Genotype-imputation accuracy across worldwide human populations
-
Huang, L., Li, Y., Singleton, A. B., Hardy, J. A., Abecasis, G., Rosenberg, N. A., et al. (2009). Genotype-imputation accuracy across worldwide human populations. Am. J. Hum. Genet. 84, 235–250. doi: 10.1016/j.ajhg.2009.01.013
-
(2009)
Am. J. Hum. Genet.
, vol.84
, pp. 235-250
-
-
Huang, L.1
Li, Y.2
Singleton, A.B.3
Hardy, J.A.4
Abecasis, G.5
Rosenberg, N.A.6
-
17
-
-
77956331627
-
Integrating common and rare genetic variation in diverse human populations
-
International HapMap 3 Consortium, Altshuler, D. M., Gibbs, R. A., Peltonen, L., Altshuler, D. M., Gibbs, R. A., et al. (2010). Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58. doi: 10.1038/nature09298
-
(2010)
Nature
, vol.467
, pp. 52-58
-
-
Altshuler, D.M.1
Gibbs, R.A.2
Peltonen, L.3
Altshuler, D.M.4
Gibbs, R.A.5
-
18
-
-
84952882965
-
A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data
-
Kim, Y. J., Lee, J., Kim, B.-J., T2D-Genes Consortium, and Park, T. (2015). A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data. BMC Genomics 16:1109. doi: 10.1186/s12864-015-2192-y
-
(2015)
BMC Genomics
, vol.16
, pp. 1109
-
-
Kim, Y.J.1
Lee, J.2
Kim, B.-J.3
Park, T.4
-
19
-
-
78649508578
-
Mach: Using sequence and genotype data to estimate haplotypes and unobserved genotypes
-
Li, Y., Willer, C. J., Ding, J., Scheet, P., and Abecasis, G. R. (2010). MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol. 34, 816–834. doi: 10.1002/gepi.20533
-
(2010)
Genet. Epidemiol.
, vol.34
, pp. 816-834
-
-
Li, Y.1
Willer, C.J.2
Ding, J.3
Scheet, P.4
Abecasis, G.R.5
-
20
-
-
84904246193
-
Assessing accuracy of genotype imputation in American indians
-
Malhotra, A., Kobes, S., Bogardus, C., Knowler, W. C., Baier, L. J., and Hanson, R. L. (2014). Assessing accuracy of genotype imputation in american indians. PLoS One 9:e102544. doi: 10.1371/journal.pone.0102544
-
(2014)
PLoS One
, vol.9
-
-
Malhotra, A.1
Kobes, S.2
Bogardus, C.3
Knowler, W.C.4
Baier, L.J.5
Hanson, R.L.6
-
21
-
-
77953808087
-
Genotype imputation for genome-wide association studies
-
Marchini, J., and Howie, B. (2010). Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11, 499–511. doi: 10.1038/nrg2796
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 499-511
-
-
Marchini, J.1
Howie, B.2
-
22
-
-
84991369066
-
A continuum of admixture in the western hemisphere revealed by the african diaspora genome
-
Mathias, R. A., Taub, M. A., Gignoux, C. R., Fu, W., Musharoff, S., O’Connor, T. D., et al. (2016). A continuum of admixture in the western hemisphere revealed by the african diaspora genome. Nat. Commun. 11:12522. doi: 10.1038/ncomms12522
-
(2016)
Nat. Commun.
, vol.11
, pp. 12522
-
-
Mathias, R.A.1
Taub, M.A.2
Gignoux, C.R.3
Fu, W.4
Musharoff, S.5
O’Connor, T.D.6
-
23
-
-
84983479616
-
A reference panel of 64,976 haplotypes for genotype imputation
-
McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A. R., Teumer, A., et al. (2016). A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48, 1279–1283. doi: 10.1038/ng.3643
-
(2016)
Nat. Genet.
, vol.48
, pp. 1279-1283
-
-
McCarthy, S.1
Das, S.2
Kretzschmar, W.3
Delaneau, O.4
Wood, A.R.5
Teumer, A.6
-
24
-
-
85000392897
-
Analysis of genome-wide association data
-
McRae, A. F. (2017). Analysis of genome-wide association data. Methods Mol. Biol. 1526, 161–173. doi: 10.1007/978-1-4939-6613-4_9
-
(2017)
Methods Mol. Biol.
, vol.1526
, pp. 161-173
-
-
McRae, A.F.1
-
25
-
-
85014366373
-
Improved imputation accuracy in hispanic/latino populations with larger and more diverse reference panels: Applications in the hispanic community health study/study of latinos (HCHS/SOL)
-
Nelson, S. C., Stilp, A. M., Papanicolaou, G. J., Taylor, K. D., Rotter, J. I., Thornton, T. A., et al. (2016). Improved imputation accuracy in hispanic/latino populations with larger and more diverse reference panels: applications in the hispanic community health study/study of latinos (HCHS/SOL). Hum. Mol. Genet. 1, 3245–3254. doi: 10.1093/hmg/ddw174
-
(2016)
Hum. Mol. Genet.
, vol.1
, pp. 3245-3254
-
-
Nelson, S.C.1
Stilp, A.M.2
Papanicolaou, G.J.3
Taylor, K.D.4
Rotter, J.I.5
Thornton, T.A.6
-
26
-
-
77956277867
-
Analyses and comparison of imputation-based association methods
-
Pei, Y.-F., Zhang, L., Li, J., and Deng, H.-W. (2010). Analyses and comparison of imputation-based association methods. PLoS One 5:e10827. doi: 10.1371/journal.pone.0010827
-
(2010)
PLoS One
, vol.5
-
-
Pei, Y.-F.1
Zhang, L.2
Li, J.3
Deng, H.-W.4
-
27
-
-
34548292504
-
Plink: A tool set for whole-genome association and population-based linkage analyses
-
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575. doi: 10.1086/519795
-
(2007)
Am. J. Hum. Genet.
, vol.81
, pp. 559-575
-
-
Purcell, S.1
Neale, B.2
Todd-Brown, K.3
Thomas, L.4
Ferreira, M.A.R.5
Bender, D.6
-
29
-
-
70350220595
-
Genotyping technologies for genetic research
-
Ragoussis, J. (2009). Genotyping technologies for genetic research. Annu. Rev. Genomics Hum. Genet. 10, 117–133. doi: 10.1146/annurev-genom-082908-150116
-
(2009)
Annu. Rev. Genomics Hum. Genet.
, vol.10
, pp. 117-133
-
-
Ragoussis, J.1
-
30
-
-
84989921938
-
Comparing performance of modern genotype imputation methods in different ethnicities
-
Roshyara, N. R., Horn, K., Kirsten, H., Ahnert, P., and Scholz, M. (2016). Comparing performance of modern genotype imputation methods in different ethnicities. Sci. Rep. 4:34386. doi: 10.1038/srep34386
-
(2016)
Sci. Rep.
, vol.4
, pp. 34386
-
-
Roshyara, N.R.1
Horn, K.2
Kirsten, H.3
Ahnert, P.4
Scholz, M.5
-
31
-
-
85064228235
-
A sex-stratified genome-wide association study of tuberculosis using a multi-ethnic genotyping array
-
Schurz, H., Kinnear, C. J., Gignoux, C. R., Wojcik, G. L., Helden, P. D., van Tromp, G. C., et al. (2018). A sex-stratified genome-wide association study of tuberculosis using a multi-ethnic genotyping array. BIORXIV. 31:405571. doi: 10.1101/405571
-
(2018)
BIORXIV
, vol.31
, pp. 405571
-
-
Schurz, H.1
Kinnear, C.J.2
Gignoux, C.R.3
Wojcik, G.L.4
Helden, P.D.5
Van Tromp, G.C.6
-
32
-
-
84943182461
-
An integrated map of structural variation in 2,504 human genomes
-
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., et al. (2015). An integrated map of structural variation in 2,504 human genomes. Nature 1, 75–81. doi: 10.1038/nature15394
-
(2015)
Nature
, vol.1
, pp. 75-81
-
-
Sudmant, P.H.1
Rausch, T.2
Gardner, E.J.3
Handsaker, R.E.4
Abyzov, A.5
Huddleston, J.6
-
33
-
-
85045133145
-
Genotype imputation performance of three reference panels using african ancestry individuals
-
Vergara, C., Parker, M. M., Franco, L., Cho, M. H., Valencia-Duarte, A. V., Beaty, T. H., et al. (2018). Genotype imputation performance of three reference panels using african ancestry individuals. Hum. Genet. 137, 281–292. doi: 10.1007/s00439-018-1881-4
-
(2018)
Hum. Genet.
, vol.137
, pp. 281-292
-
-
Vergara, C.1
Parker, M.M.2
Franco, L.3
Cho, M.H.4
Valencia-Duarte, A.V.5
Beaty, T.H.6
-
34
-
-
84917732232
-
Imputation and quality control steps for combining multiple genome-wide datasets
-
Verma, S. S., de Andrade, M., Tromp, G., Kuivaniemi, H., Pugh, E., Namjou-Khales, B., et al. (2014). Imputation and quality control steps for combining multiple genome-wide datasets. Front. Genet. 5:370. doi: 10.3389/fgene.2014.00370
-
(2014)
Front. Genet.
, vol.5
, pp. 370
-
-
Verma, S.S.1
De Andrade, M.2
Tromp, G.3
Kuivaniemi, H.4
Pugh, E.5
Namjou-Khales, B.6
-
35
-
-
84922051625
-
Performance of genotype imputation for low frequency and rare variants from the 1000 genomes
-
Zheng, H.-F., Rong, J.-J., Liu, M., Han, F., Zhang, X.-W., Richards, J. B., et al. (2015). Performance of genotype imputation for low frequency and rare variants from the 1000 genomes. PLoS One 10:e0116487. doi: 10.1371/journal.pone.0116487
-
(2015)
PLoS One
, vol.10
-
-
Zheng, H.-F.1
Rong, J.-J.2
Liu, M.3
Han, F.4
Zhang, X.-W.5
Richards, J.B.6
|