An evaluation of statistical approaches to rare variant analysis in genetic association studies

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442

A haplotype map of the human genome

The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858

The Wellcome Trust Case Control Consortium, U.K.

Mossman, K. (2008) · Scientific American · doi:10.1038/scientificamerican0108-42a · Cited by 2,714

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

the NIDDK IBD Genetics Consortium, Barrett, J. C., the Belgian-French IBD Consortium, the Wellcome Trust Case Control Consortium, Hansoul, S., Nicolae, D. L., Cho, J. H., Duerr, R. H., Rioux, J. D., Brant, S. R., et al. (2008) · Nature Genetics · doi:10.1038/ng.175 · Cited by 2,593

Generating samples under a Wright–Fisher neutral model of genetic variation

Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397

Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

(1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040269 · Cited by 1,950

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

Wellcome Trust Case Control Consortium, Zeggini, E., Scott, L. J., Saxena, R., Voight, B. F., Marchini, J. L., Hu, T., de Bakker, P. I., Abecasis, G. R., Almgren, P., et al. (2008) · Nature Genetics · doi:10.1038/ng.120 · Cited by 1,864

Six new loci associated with body mass index highlight a neuronal influence on body weight regulation

the GIANT Consortium (2009) · Nature Genetics · doi:10.1038/ng.287 · Cited by 1,720

Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data

Li, B., & Leal, S. M. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.06.024 · Cited by 1,527

Multiple Rare Alleles Contribute to Low Plasma Levels of HDL Cholesterol

Cohen, J. C., Kiss, R. S., Pertsemlidis, A., Marcel, Y. L., McPherson, R., & Hobbs, H. H. (2004) · Science · doi:10.1126/science.1099870 · Cited by 1,108

Incorporating model uncertainty in detecting rare variants: the Bayesian risk index

Quintana, M. A., Jl, B., Thomas, D. C., & Conti, D. V. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20613 · Cited by 43

The genetic associations of acute anterior uveitis and their overlap with the genetics of ankylosing spondylitis

Robinson, P. C., Leo, P. J., Pointon, J. J., Harris, J., Cremin, K., Bradbury, L. A., Donnelly, P., Barroso, I., Blackwell, J. M., Bramon, E., et al. (2015) · Genes and Immunity · doi:10.1038/gene.2015.49 · Cited by 43

Exome-wide study of ankylosing spondylitis demonstrates additional shared genetic background with inflammatory bowel disease

Robinson, P. C., Leo, P. J., Pointon, J. J., Harris, J., Cremin, K., Bradbury, L. A., Stebbings, S. M., Harrison, A. A., McCloskey, E. V., Eisman, J. A., et al. (2016) · npj Genomic Medicine · doi:10.1038/npjgenmed.2016.8 · Cited by 44

Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa

Huckins, L. M., Hatzikotoulas, K., Southam, L., Thornton, L. M., Steinberg, J., Aguilera-McKay, F., Treasure, J. L., Schmidt, U., Gunasinghe, C., Romero, A., et al. (2017) · Molecular Psychiatry · doi:10.1038/mp.2017.88 · Cited by 44

Whole-exome sequencing reveals a role of HTRA1 and EGFL8 in brain white matter hyperintensities

Malik, R., Beaufort, N., Frerich, S., Gesierich, B. G., Georgakis, M. K., Rannikmäe, K., Ferguson, A., Haffner, C., Traylor, M., Ehrmann, M., et al. (2021) · Brain · doi:10.1093/brain/awab253 · Cited by 45

Mutational Analysis of Known ALS Genes in an Italian Population-Based Cohort

Grassano, M., Calvo, A., Moglia, C., Brunetti, M., Barberis, M., Sbaiz, L., Canosa, A., Manera, U., Vasta, R., Corrado, L., et al. (2020) · Neurology · doi:10.1212/wnl.0000000000011209 · Cited by 40

The impact of a fine-scale population stratification on rare variant association test results

Persyn, E., Redon, R., Bellanger, L., & Christian Dina, C. (2018) · PLoS ONE · doi:10.1371/journal.pone.0207677 · Cited by 39

Multi-trait analysis of rare-variant association summary statistics using MTAR

Luo, L., Shen, J., Zhang, H., Chhibber, A., Mehrotra, D. V., & Tang, Z.-Z. (2020) · Nature Communications · doi:10.1038/s41467-020-16591-0 · Cited by 40

Genetic association of cyclic AMP signaling genes with bipolar disorder

McDonald, M.-L., MacMullen, C., Liu, D., Leal, S. M., & Davis, R. (2012) · Translational Psychiatry · doi:10.1038/tp.2012.92 · Cited by 41

The effect of phenotypic outliers and non-normality on rare-variant association testing

Auer, P. L., Reiner, A. P., & Leal, S. M. (2016) · European Journal of Human Genetics · doi:10.1038/ejhg.2015.270 · Cited by 40

Study Designs for Identification of Rare Disease Variants in Complex Diseases: The Utility of Family-Based Designs

Ionita‐Laza, I., & Ottman, R. (2011) · Genetics · doi:10.1534/genetics.111.131813 · Cited by 37

Reconsidering Association Testing Methods Using Single-Variant Test Statistics as Alternatives to Pooling Tests for Sequence Data with Rare Variants

Kinnamon, D. D., Hershberger, R. E., & Martin, E. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030238 · Cited by 36

Optimum designs for next-generation sequencing to discover rare variants for common complex disease

Shi, G., & Rao, D. C. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20597 · Cited by 37

Introduction to Genetics and Genomics in Asthma: Genetics of Asthma

Mathias, R. A. (2013) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-8603-9_9 · Cited by 36

Incorporating Gene-Environment Interaction in Testing for Association with Rare Genetic Variants

Chen, H., Meigs, J. B., & Dupuis, J. (2014) · Human Heredity · doi:10.1159/000363347 · Cited by 36

Assessing the Impact of Population Stratification on Association Studies of Rare Variation

Jiang, Y., Epstein, M. P., & Conneely, K. N. (2013) · Human Heredity · doi:10.1159/000353270 · Cited by 39

Exome chip analyses in adult attention deficit hyperactivity disorder

Zayats, T., Jacobsen, K. K., Kleppe, R., Jacob, C., Kittel‐Schneider, S., Marta Ribasés, A., Ramos‐Quiroga, J. A., Vanesa Richarte, B., Casas, M., Mota, N. R., et al. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.196 · Cited by 36

Calibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories

Lali, R., Chong, M., Omidi, A., Mohammadi‐Shemirani, P., Le, A., Cui, E., & Paré, G. (2021) · Nature Communications · doi:10.1038/s41467-021-26114-0 · Cited by 38

Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4

Grosche, S., Marenholz, I., Esparza-Gordillo, J., Arnau‐Soler, A., Pairo‐Castineira, E., Rüschendorf, F., Ahluwalia, T. S., Almqvist, C., Arnold, A., Baurecht, H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26783-x · Cited by 36

Statistical analysis of genetic interactions

Yi, N. (2010) · Genetics Research · doi:10.1017/s0016672310000595 · Cited by 36

Estimating Genetic Effects and Quantifying Missing Heritability Explained by Identified Rare-Variant Associations

Liu, D. J., & Leal, S. M. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.08.008 · Cited by 34

Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis

UKRAG, Bowes, J., Lawrence, R., Eyre, S., Panoutsopoulou, K., Orozco, G., Elliott, K. S., Ke, X., Morris, A. P., Thomson, W., et al. (2010) · Human Genetics · doi:10.1007/s00439-010-0889-1 · Cited by 34

Powerful extreme phenotype sampling designs and score tests for genetic association studies

Bjørnland, T., Bye, A., Ryeng, E., Wisløff, U., & Langaas, M. (2018) · Statistics in Medicine · doi:10.1002/sim.7914 · Cited by 34

Identification of rare variants in Alzheimer’s disease

Lord, J., Lu, A. J., & Cruchaga, C. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00369 · Cited by 36

An allelic-series rare-variant association test for candidate-gene discovery

McCaw, Z. R., O’Dushlaine, C. T., Somineni, H., Bereket, M. D., Klein, C., Karaletsos, T., Casale, F. P., Koller, D., & Soare, T. W. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.07.001 · Cited by 33

Brief Report: High‐Throughput Sequencing of IL23R Reveals a Low‐Frequency, Nonsynonymous Single‐Nucleotide Polymorphism That Is Associated With Ankylosing Spondylitis in a Han Chinese Population

Davidson, S. I., Jiang, L., Cortés, A., Wu, X., Glazov, E. A., Zheng, Y., Danoy, P., Liu, Y., Thomas, G. P., Brown, M. A., et al. (2013) · Arthritis & Rheumatism · doi:10.1002/art.37976 · Cited by 32

Mendelian genes for Parkinson's disease contribute to the sporadic forms of the disease†

Spataro, N., Calafell, F., Cervera‐Carles, L., Casals, F., Pagonabarraga, J., Pascual‐Sedano, B., Campolongo, A., Kulisevsky, J., Lleó, A., Navarro, A., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu616 · Cited by 32

Novel Genetic Loci Associated With Retinal Microvascular Diameter

Jensen, R. A., Sim, X., Smith, A. V., Li, X., Jakobsdóttir, J., Cheng, C., Brody, J. A., Cotch, M. F., McKnight, B., Klein, R., et al. (2015) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.115.001142 · Cited by 33

Haplotype‐Based Methods for Detecting Uncommon Causal Variants With Common SNPs

Lin, W., Yi, N., Zhi, D., Zhang, K., Gao, G., Tiwari, H. K., & Liu, N. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21650 · Cited by 30

Power of Family‐Based Association Designs to Detect Rare Variants in Large Pedigrees Using Imputed Genotypes

Saad, M., & Wijsman, E. M. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21776 · Cited by 31

Region-Based Association Analysis of Human Quantitative Traits in Related Individuals

Belonogova, N. M., Svishcheva, G. R., van Duijn, C. M., Aulchenko, Y. S., & Axenovich, T. I. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065395 · Cited by 30

Generalized Functional Linear Models for Gene‐Based Case‐Control Association Studies

Fan, R., Wang, Y., Mills, J. L., Carter, T. C., Lobach, I. V., Wilson, A. F., Wilson, J., Weeks, D. E., & Xiong, M. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21840 · Cited by 30

Incorporating Functional Information in Tests of Excess De Novo Mutational Load

Jiang, Y., Han, Y., Petrovski, S., Owzar, K., Goldstein, D. B., & Allen, A. S. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.06.013 · Cited by 30

Genome‐Wide Association Analysis of Imputed Rare Variants: Application to Seven Common Complex Diseases

Mägi, R., Asimit, J. L., Day-Williams, A., Zeggini, E., & Morris, A. P. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21675 · Cited by 30

Rare Variant Association Testing by Adaptive Combination of P-values

Lin, W., Lou, X., Gao, G., & Liu, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085728 · Cited by 30

A kernel machine method for detecting effects of interaction between multidimensional variable sets: An imaging genetics application

Ge, T., Nichols, T. E., Ghosh, D., Mormino, E. C., Smoller, J. W., & Sabuncu, M. R. (2015) · NeuroImage · doi:10.1016/j.neuroimage.2015.01.029 · Cited by 31

Confounded by sequencing depth in association studies of rare alleles

Garner, C. P. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20574 · Cited by 31

Meta-Analysis of Sequencing Studies With Heterogeneous Genetic Associations

Tang, Z.-Z., & Lin, D.-Y. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21798 · Cited by 30

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

Marttinen, P., Pirinen, M., Sarin, A., Gillberg, J., Kettunen, J., Surakka, I. L., Kangas, A. J., Soininen, P., O’Reilly, P. F., Kaakinen, M., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu140 · Cited by 28

Strategies for Imputing and Analyzing Rare Variants in Association Studies

Hoffmann, T. J., & Witte, J. S. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.07.006 · Cited by 30

Blindly Using Wald's Test Can Miss Rare Disease‐Causal Variants in Case‐Control Association Studies

Xing, G., Lin, C., Wooding, S., & Xing, C. (2012) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2011.00700.x · Cited by 29

On Efficient and Accurate Calculation of Significance P ‐Values for Sequence Kernel Association Testing of Variant Set

Wu, B., Guan, W., & Pankow, J. S. (2016) · Annals of Human Genetics · doi:10.1111/ahg.12144 · Cited by 28

Evaluating methods for the analysis of rare variants in sequence data

Luedtke, A. R., Powers, S., Petersen, A. J., Sitarik, A. R., Bekmetjev, A., & Tintle, N. (2011) · BMC Proceedings · doi:10.1186/1753-6561-5-s9-s119 · Cited by 28

A Robust Model-free Approach for Rare Variants Association Studies Incorporating Gene-Gene and Gene-Environmental Interactions

Fan, R., & Lo, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083057 · Cited by 27

Statistical Guidance for Experimental Design and Data Analysis of Mutation Detection in Rare Monogenic Mendelian Diseases by Exome Sequencing

Zhi, D., & Chen, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031358 · Cited by 29

A simple and accurate method to determine genomewide significance for association tests in sequencing studies

Lin, D. Y. (2019) · Genetic Epidemiology · doi:10.1002/gepi.22183 · Cited by 27

A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data

Zhao, L., He, Z., Zhang, D., Wang, G. T., Renton, A. E., Vardarajan, B. N., Nothnagel, M., Goate, A., Mayeux, R. P., & Leal, S. M. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.09.006 · Cited by 27

Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency

Bestetti, I., Barbieri, C., Sironi, A., Specchia, V., Yatsenko, S. A., Donno, M. D. D., Caslini, C., Gentilini, D., Crippa, M., Larizza, L., et al. (2021) · Human Reproduction · doi:10.1093/humrep/deab192 · Cited by 26

Integration of bioinformatics and imaging informatics for identifying rare PSEN1 variants in Alzheimer’s disease

ADNI, Nho, K. T., Horgusluoglu, E., Kim, S., Risacher, S. L., Kim, D., Foroud, T., Aisen, P. S. S., Petersen, R. C., Jack, C. R., et al. (2016) · BMC Medical Genomics · doi:10.1186/s12920-016-0190-9 · Cited by 26

Haplotype Kernel Association Test as a Powerful Method to Identify Chromosomal Regions Harboring Uncommon Causal Variants

Lin, W., Yi, N., Lou, X., Zhi, D., Zhang, K., Gao, G., Tiwari, H. K., & Liu, N. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21740 · Cited by 27

Region-Based Association Test for Familial Data under Functional Linear Models

Svishcheva, G. R., Belonogova, N. M., & Axenovich, T. I. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128999 · Cited by 25

Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models

Fan, R., Wang, Y., Boehnke, M., Chen, W., Li, Y., Ren, H., Lobach, I. V., & Xiong, M. (2015) · Genetics · doi:10.1534/genetics.115.178343 · Cited by 24

Assessing the Impact of Differential Genotyping Errors on Rare Variant Tests of Association

Mayer-Jochimsen, M., Fast, S., & Tintle, N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056626 · Cited by 24

Boosting the Power of the Sequence Kernel Association Test by Properly Estimating Its Null Distribution

Wang, K. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.05.011 · Cited by 24

Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia

Chen, J., Lee, G., Fanous, A. H., Zhao, Z., Jia, P., O’Neill, F. A., Walsh, D., Kendler, K. S., & Chen, X. (2011) · Schizophrenia Research · doi:10.1016/j.schres.2011.06.023 · Cited by 25

Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations

Wu, L., Schaid, D. J., Sicotte, H., Wieben, E. D., Li, H., & Petersen, G. M. (2014) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2014-102697 · Cited by 25

Prioritizing Disease-Linked Variants, Genes, and Pathways with an Interactive Whole-Genome Analysis Pipeline

Lee, I., Lee, K., Hsing, M., Choe, Y., Park, J., Kim, S. H., Bohn, J. M., Neu, M. B., Hwang, K., Green, R. C., et al. (2014) · Human Mutation · doi:10.1002/humu.22520 · Cited by 23

FFBSKAT: Fast Family-Based Sequence Kernel Association Test

Svishcheva, G. R., Belonogova, N. M., & Axenovich, T. I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099407 · Cited by 23

Adrenergic Alpha-1 Pathway Is Associated with Hypertension among Nigerians in a Pathway-focused Analysis

Reder, N. P., Tayo, B. O., Salako, B. O., Ogunniyi, A. O., Adeyemo, A., Rotimi, C. N., & Cooper, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037145 · Cited by 23

Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)

Zhu, C., Li, X., & Yu, J. (2011) · G3 Genes Genomes Genetics · doi:10.1534/g3.111.000364 · Cited by 24

A Fast and Noise‐Resilient Approach to Detect Rare‐Variant Associations With Deep Sequencing Data for Complex Disorders

Cheung, Y. H., Wang, G., Leal, S. M., & Wang, S. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21662 · Cited by 23

Pathway‐Based Approaches for Sequencing‐Based Genome‐Wide Association Studies

Wu, G., & Zhi, D. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21728 · Cited by 24

Testing for Rare Variant Associations in the Presence of Missing Data

Auer, P. L., Wang, G. T., & Leal, S. M. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21736 · Cited by 22

Population‐based and family‐based designs to analyze rare variants in complex diseases

Kazma, R., & Bailey, J. N. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20648 · Cited by 22

A weighted burden test using logistic regression for integrated analysis of sequence variants, copy number variants and polygenic risk score

Curtis, D. (2018) · European Journal of Human Genetics · doi:10.1038/s41431-018-0272-6 · Cited by 25

Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests

Zawistowski, M., Reppell, M., Wegmann, D., Jean, P. L. S., Ehm, M. G., Nelson, M. R., Novembre, J., & Zöllner, S. K. (2014) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.297 · Cited by 24

Genetic association studies in cardiovascular diseases: Do we have enough power?

Auer, P. L., & Stitziel, N. O. (2017) · Trends in Cardiovascular Medicine · doi:10.1016/j.tcm.2017.03.005 · Cited by 21

Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1

Mackelprang, R. D., Bamshad, M. J., Chong, J. X., Hou, X., Buckingham, K. J., Shively, K. M., de Bruyn, G., Mugo, N., Mullins, J. I., McElrath, M. J., et al. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006703 · Cited by 21

Methods for Collapsing Multiple Rare Variants in Whole‐Genome Sequence Data

Sung, Y. J., Korthauer, K. D., Swartz, M. D., & Engelman, C. D. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21820 · Cited by 21

A Statistical Approach for Rare-Variant Association Testing in Affected Sibships

Epstein, M. P., Duncan, R., Ware, E. B., Jhun, M. A., Bielak, L. F., Zhao, W., Smith, J. A., Peyser, P. A., Kardia, S. L. R., & Satten, G. A. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.01.020 · Cited by 20

Imaging genetics — towards discovery neuroscience

Ge, T., Schumann, G., & Feng, J. (2013) · Quantitative Biology · doi:10.1007/s40484-013-0023-1 · Cited by 21

A variance component based multi-marker association test using family and unrelated data

Wang, X., Morris, N. J., Zhu, X., & Elston, R. C. (2013) · BMC Genetics · doi:10.1186/1471-2156-14-17 · Cited by 20

Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study

Lin, W. (2016) · Scientific Reports · doi:10.1038/srep21824 · Cited by 20

Genomic determinants of long-term cardiometabolic complications in childhood acute lymphoblastic leukemia survivors

England, J., Drouin, S., Beaulieu, P., St-Onge, P., Krajinović, M., Laverdière, C., Levy, E. H., Marcil, V., & Sinnett, D. (2017) · BMC Cancer · doi:10.1186/s12885-017-3722-6 · Cited by 20

EPHA2 sequence variants are associated with susceptibility to Kaposi’s sarcoma-associated herpesvirus infection and Kaposi’s sarcoma prevalence in HIV-infected patients

Blumenthal, M. J., Schutz, C., Meintjes, G., Mohamed, Z., Mendelson, M., Ambler, J. M., Whitby, D., Mackelprang, R. D., Carse, S., Katz, A. A., et al. (2018) · Cancer Epidemiology · doi:10.1016/j.canep.2018.08.005 · Cited by 20

A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Wu, P., Wang, K., Zhou, J., Chen, D., Jiang, A., Jiang, Y., Zhu, L., Qiu, X., Li, X., & Tang, G. (2021) · Communications Biology · doi:10.1038/s42003-021-02416-3 · Cited by 20

The Next Generation of Complex Lung Genetic Studies

Yang, I. V., & Schwartz, D. A. (2012) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201207-1178pp · Cited by 19

A Geometric Framework for Evaluating Rare Variant Tests of Association

Liu, K., Fast, S., Zawistowski, M., & Tintle, N. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21722 · Cited by 19

Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits

Moutsianas, L., & Morris, A. P. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu012 · Cited by 20

Progress in methods for rare variant association

Santorico, S. A., & Hendricks, A. E. (2016) · BMC Genetics · doi:10.1186/s12863-015-0316-7 · Cited by 22

Effect of population stratification analysis on false-positive rates for common and rare variants

He, H., Zhang, X., Ding, L., Baye, T. M., Kurowski, B. G., & Martin, L. J. (2011) · BMC Proceedings · doi:10.1186/1753-6561-5-s9-s116 · Cited by 19

Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT)

Urrutia, E., Lee, S., Maity, A., Zhao, N., Shen, J., Li, Y., & Wu, M. C. (2015) · Statistics and Its Interface · doi:10.4310/sii.2015.v8.n4.a8 · Cited by 19

Improving power for rare‐variant tests by integrating external controls

Lee, S., Kim, S., & Fuchsberger, C. (2017) · Genetic Epidemiology · doi:10.1002/gepi.22057 · Cited by 21

Digging into the extremes: a useful approach for the analysis of rare variants with continuous traits?

Lamina, C. (2011) · BMC Proceedings · doi:10.1186/1753-6561-5-s9-s105 · Cited by 19

Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies

Derkach, A., Zhang, H., & Chatterjee, N. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx770 · Cited by 21

Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors

Pankratz, N., Wei, P., Brody, J. A., Chen, M., de Vries, P. S., Huffman, J. E., Nalehua, M. R., Auer, P. L., Boerwinkle, E., Cushman, M., et al. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac100 · Cited by 18

Methods for Association Analysis and Meta‐Analysis of Rare Variants in Families

Feng, S., Pistis, G., Zhang, H., Zawistowski, M., Mulas, A., Żołędziewska, M., Holmen, O. L., Busonero, F., Sanna, S., Hveem, K., et al. (2015) · Genetic Epidemiology · doi:10.1002/gepi.21892 · Cited by 20

CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies

Lawrence, R., Day-Williams, A., Elliott, K. S., Morris, A. P., & Zeggini, E. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-527 · Cited by 18

Common and rare genetic markers of lipid variation in subjects with type 2 diabetes from the ACCORD clinical trial

Marvel, S. W., Rotroff, D. M., Wagner, M. J., Buse, J. B., Havener, T. M., McLeod, H. L., Motsinger‐Reif, A. A., & The ACCORD/ACCORDion Investigators (2017) · PeerJ · doi:10.7717/peerj.3187 · Cited by 18

Meta-analysis of Complex Diseases at Gene Level with Generalized Functional Linear Models

Fan, R., Wang, Y., Chiu, C., Chen, W., Ren, H., Li, Y., Boehnke, M., Amos, C. I., Moore, J. H., & Xiong, M. (2015) · Genetics · doi:10.1534/genetics.115.180869 · Cited by 17

GWAS to Sequencing: Divergence in Study Design and Analysis

King, C., & Nicolae, D. L. (2014) · Genes · doi:10.3390/genes5020460 · Cited by 17

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

Yang, T., Deng, H., & Niu, T. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-3 · Cited by 17

Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method

Yan, Q., Weeks, D. E., Celedon, J. C., Tiwari, H. K., Li, B., Wang, X., Lin, W., Lou, X., Gao, G., Chen, W., et al. (2015) · Genetics · doi:10.1534/genetics.115.178590 · Cited by 17

Influence of Common and Rare Genetic Variation on Warfarin Dose Among African–Americans and European–Americans Using the Exome Array

Liu, N., Irvin, M. R., Zhi, D., Patki, A., Beasley, T. M., Nickerson, D. A., Hill, C. E., Chen, J., Kimmel, S. E., & Limdi, N. A. (2017) · Pharmacogenomics · doi:10.2217/pgs-2017-0046 · Cited by 17

An evaluation of different meta-analysis approaches in the presence of allelic heterogeneity

Asimit, J. L., Day-Williams, A., Zgaga, L., Rudan, I., Perica, V. B., & Zeggini, E. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.274 · Cited by 19

A Generalized Genetic Random Field Method for the Genetic Association Analysis of Sequencing Data

Li, M., He, Z., Zhang, M., Zhan, X., Wei, C., Elston, R. C., & Lu, Q. L. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21790 · Cited by 16

AN APPLICATION AND EMPIRICAL COMPARISON OF STATISTICAL ANALYSIS METHODS FOR ASSOCIATING RARE VARIANTS TO A COMPLEX PHENOTYPE

Bansal, V., Libiger, O., Torkamani, A., & Schork, N. J. (2010) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814335058_0009 · Cited by 16

Post-Selection Estimation and Testing Following Aggregate Association Tests

Heller, R., Meir, A., & Chatterjee, N. (2019) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/rssb.12318 · Cited by 18

Assessing the Impact of Non-Differential Genotyping Errors on Rare Variant Tests of Association

Powers, S., Gopalakrishnan, S., & Tintle, N. (2011) · Human Heredity · doi:10.1159/000332222 · Cited by 16

Common and Rare Variant Association Study for Plasma Lipids and Coronary Artery Disease

Tada, H., Kawashiri, M., Konno, T., Yamagishi, M., & Hayashi, K. (2015) · Journal of Atherosclerosis and Thrombosis · doi:10.5551/jat.31393 · Cited by 15

Statistical analysis strategies for association studies involving rare variants

Bansal, V., Libiger, O., Torkamani, A., & Schork, N. J. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2867 · Cited by 455

Identifying Rare Variants Associated with Complex Traits via Sequencing

Li, B., Liu, D. J., & Leal, S. M. (2013) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg0126s78 · Cited by 41

Rare-variant collapsing analyses for complex traits: guidelines and applications

Povysil, G., Petrovski, S., Hostyk, J. A., Aggarwal, V. S., Allen, A. S., & Goldstein, D. B. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0177-4 · Cited by 211

Rare-Variant Genome-Wide Association Studies: A New Frontier in Genetic Analysis of Complex Traits

Wagner, M. J. (2013) · Pharmacogenomics · doi:10.2217/pgs.13.36 · Cited by 42

Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits

Moutsianas, L., & Morris, A. P. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu012 · Cited by 20