Cited by 1,113Genetic Associations and EpidemiologyGenomics and Rare DiseasesGenetic Mapping and Diversity in Plants and Animals

The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.

A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic

Open access

Madsen, Bo Eskerod, Browning, Sharon R.·2009·PLoS Genetics

DOI 10.1371/journal.pgen.1000384PMC PMC2633048

Open this paper in CoChat — free account Open PDF

Abstract

Resequencing is an emerging tool for identification of rare disease-associated mutations. Rare mutations are difficult to tag with SNP genotyping, as genotyping studies are designed to detect common variants. However, studies have shown that genetic heterogeneity is a probable scenario for common diseases, in which multiple rare mutations together explain a large proportion of the genetic basis for the disease. Thus, we propose a weighted-sum method to jointly analyse a group of mutations in order to test for groupwise association with disease status. For example, such a group of mutations may result from resequencing a gene. We compare the proposed weighted-sum method to alternative methods and show that it is powerful for identifying disease-associated genes, both on simulated and Encode data. Using the weighted-sum method, a resequencing study can identify a disease-associated gene with an overall population attributable risk (PAR) of 2%, even when each individual mutation has much lower PAR, using 1,000 to 7,000 affected and unaffected individuals, depending on the underlying genetic model. This study thus demonstrates that resequencing studies can identify important genetic associations, provided that specialised analysis methods, such as the weighted-sum method, are used.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1371/journal.pgen.1000384

Cites

43 of 43 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Individual Comparisons by Ranking Methods
Wilcoxon, F. (1945) · Biometrics Bulletin · doi:10.2307/3001968 · Cited by 15,354
Statistical Methods for Research Workers
Fisher, R. A. (1945) · American Journal of Clinical Pathology · doi:10.1093/ajcp/15.11.552b · Cited by 10,883
EVOLUTION IN MENDELIAN POPULATIONS
Wright, S. (1931) · Genetics · doi:10.1093/genetics/16.2.97 · Cited by 9,237
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Empirical threshold values for quantitative trait mapping.
Churchill, G. A., & Doerge, R. W. (1994) · Genetics · doi:10.1093/genetics/138.3.963 · Cited by 4,935
A new multipoint method for genome-wide association studies by imputation of genotypes
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609
The UCSC Table Browser data retrieval tool
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh103 · Cited by 2,314
Genetic Data Analysis II.
Weir, B. S. (1997) · Biometrics · doi:10.2307/2533134 · Cited by 2,263
Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia
Walsh, T., McClellan, J. M., McCarthy, S. E., Addington, A. M., Pierce, S. B., Cooper, G. M., Nord, A. S., Kusenda, M., Malhotra, D., Bhandari, A., et al. (2008) · Science · doi:10.1126/science.1155174 · Cited by 1,800
The Diploid Genome Sequence of an Individual Human
Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778

Flagged first, then by citations

Show all 43 references

Sorted by citations

Items 101–200 of 1,000

Pooled Association Tests for Rare Genetic Variants: A Review and Some New Results
Derkach, A., Lawless, J. F., & Sun, L. (2014) · Statistical Science · doi:10.1214/13-sts456 · Cited by 78
Functional Linear Models for Association Analysis of Quantitative Traits
Fan, R., Wang, Y., Mills, J. L., Wilson, A. F., Wilson, J., & Xiong, M. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21757 · Cited by 76
DUOX2 variants associate with preclinical disturbances in microbiota-immune homeostasis and increased inflammatory bowel disease risk
Grasberger, H., Magis, A. T., Sheng, E., Conomos, M. P., Zhang, M., Garzotto, L. S., Hou, G., Bishu, S., Nagao‐Kitamoto, H., Zaatari, M. E., et al. (2021) · Journal of Clinical Investigation · doi:10.1172/jci141676 · Cited by 78
Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression
Tzeng, J., Zhang, D., Pongpanich, M., Smith, C., McCarthy, M. I., Sale, M. M., Worrall, B. B., Hsu, F., Thomas, D. C., & Sullivan, P. F. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.07.007 · Cited by 82
Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data
Wang, G. T., Peng, B., & Leal, S. M. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.04.004 · Cited by 80
From SNPs to Genes: Disease Association at the Gene Level
Lehne, B. C., Lewis, C. M., & Schlitt, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020133 · Cited by 84
Test for Rare Variants by Environment Interactions in Sequencing Association Studies
Lin, X., Lee, S., Wu, M. C., Wang, C., Chen, H., Li, Z., & Lin, X. (2015) · Biometrics · doi:10.1111/biom.12368 · Cited by 71
Rare-Variant Extensions of the Transmission Disequilibrium Test: Application to Autism Exome Sequence Data
He, Z., O’Roak, B. J., Smith, J. D., Wang, G., Hooker, S. E., Santos‐Cortez, R. L. P., Li, B., Kan, M., Krumm, N., Nickerson, D. A., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.11.021 · Cited by 75
Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis
Goldfeder, R. L., Wall, D. P., Khoury, M. J., Ioannidis, J. P. A., & Ashley, E. A. (2017) · American Journal of Epidemiology · doi:10.1093/aje/kww224 · Cited by 75
Bayesian analysis of rare variants in genetic association studies
Yi, N., & Zhi, D. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20554 · Cited by 74
Dissecting complex traits using the Drosophila Synthetic Population Resource
Long, A. D., Macdonald, S. J., & King, E. G. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.009 · Cited by 73
Detecting Association of Rare and Common Variants by Testing an Optimally Weighted Combination of Variants
Sha, Q., Wang, X., Wang, X., & Zhang, S. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21649 · Cited by 72
Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect
Thornton, K., Foran, A. J., & Long, A. D. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003258 · Cited by 65
Pathway analysis of complex diseases for GWAS, extending to consider rare variants, multi-omics and interactions
Kao, P. Y. P., Leung, K. H., Chan, L., Yip, S. P., & Yap, M. K. H. (2016) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2016.11.030 · Cited by 73
Whole genome sequence analysis of blood lipid levels in >66,000 individuals
Selvaraj, M. S., Li, X., Li, Z., Pampana, A., Zhang, D. Y., Park, J., Aslibekyan, S. W., Bis, J. C., Brody, J. A., Cade, B. E., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33510-7 · Cited by 69
The contribution of rare and common variants in 30 genes to risk nicotine dependence
Yang, J., Wang, S., Yang, Z., Hodgkinson, C. A., Iarikova, P., Ma, J. Z., Payne, T. J., Goldman, D. A., & Li, M. D. (2014) · Molecular Psychiatry · doi:10.1038/mp.2014.156 · Cited by 66
Sequence Kernel Association Test for Survival Traits
Chen, H., Lumley, T., Brody, J. A., Heard‐Costa, N. L., Fox, C. S., Cupples, L. A., & Dupuis, J. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21791 · Cited by 64
Targeted Resequencing and Systematic In Vivo Functional Testing Identifies Rare Variants in MEIS1 as Significant Contributors to Restless Legs Syndrome
Schulte, E. C., Kousi, M., Tan, P. L., Tilch, E., Knauf, F., Lichtner, P., Trenkwalder, C., Högl, B., Frauscher, B., Berger, K., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.06.005 · Cited by 66
Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics
Hu, Y., Berndt, S. I., Gustafsson, S., Ganna, A., Berndt, S. I., Gustafsson, S., Mägi, R., Ganna, A., Wheeler, E., Feitosa, M. F., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.011 · Cited by 65
Multiancestry Study of Gene–Lifestyle Interactions for Cardiovascular Traits in 610 475 Individuals From 124 Cohorts
Rao, D. C., Sung, Y. J., Winkler, T. W., Schwander, K., Borecki, I. B., Cupples, L. A., Gauderman, W. J., Rice, K. M., Munroe, P. B., & Psaty, B. M. (2017) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.116.001649 · Cited by 61
Mitochondrial DNA Sequence Variation and Risk of Pancreatic Cancer
Lam, E. T., Bracci, P. M., Holly, E. A., Chu, C., Poon, A., Wan, E., Thomas-White, K. J., Kwok, P., Pawlikowska, L., & Tranah, G. J. (2011) · Cancer Research · doi:10.1158/0008-5472.can-11-1682 · Cited by 65
Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project
Prokopenko, D., Hecker, J., Silverman, E. K., Pagano, M., Nöthen, M. M., Dina, C., Lange, C., & Fier, H. L. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv752 · Cited by 62
Dynamic Scan Procedure for Detecting Rare-Variant Association Regions in Whole-Genome Sequencing Studies
Li, Z., Li, X., Liu, Y., Shen, J., Chen, H., Zhou, H., Morrison, A. C., Boerwinkle, E., & Lin, X. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.03.002 · Cited by 59
Review: High-performance computing to detect epistasis in genome scale data sets
Upton, A., Trelles, O., Cornejo-García, J. A., & Perkins, J. R. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv058 · Cited by 66
The effect of next-generation sequencing technology on complex trait research
Day-Williams, A., & Zeggini, E. (2010) · European Journal of Clinical Investigation · doi:10.1111/j.1365-2362.2010.02437.x · Cited by 63
Detecting rare and common variants for complex traits: sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS)
Feng, T., Elston, R. C., & Zhu, X. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20588 · Cited by 61
A Permutation Procedure to Correct for Confounders in Case-Control Studies, Including Tests of Rare Variation
Epstein, M. P., Duncan, R., Jiang, Y., Conneely, K. N., Allen, A. S., & Satten, G. A. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.06.004 · Cited by 64
Rare Nonsynonymous Variants in Alpha-4 Nicotinic Acetylcholine Receptor Gene Protect Against Nicotine Dependence
Xie, P., Kranzler, H. R., Krauthammer, M. O., Cosgrove, K., Oslin, D. W., Anton, R. F., Farrer, L. A., Picciotto, M. R., Krystal, J. H., Zhao, H., et al. (2011) · Biological Psychiatry · doi:10.1016/j.biopsych.2011.04.017 · Cited by 62
On high-dimensional misspecified mixed model analysis in genome-wide association study
Jiang, J., Li, C., Paul, D., Yang, C., & Zhao, H. (2016) · The Annals of Statistics · doi:10.1214/15-aos1421 · Cited by 63
Resequencing of Nicotinic Acetylcholine Receptor Genes and Association of Common and Rare Variants with the Fagerström Test for Nicotine Dependence
Wessel, J., McDonald, S. M., Hinds, D. A., Stokowski, R. P., Javitz, H. S., Kennemer, M. I., Krasnow, R. E., Dirks, W., Hardin, J., Pitts, S. J., et al. (2010) · Neuropsychopharmacology · doi:10.1038/npp.2010.120 · Cited by 62
Genome-wide searching of rare genetic variants in WTCCC data
Feng, T., & Zhu, X. (2010) · Human Genetics · doi:10.1007/s00439-010-0849-9 · Cited by 60
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies
Li, X., Quick, C., Zhou, H., Gaynor, S. M., Liu, Y., Chen, H., Selvaraj, M. S., Sun, R., Dey, R., Arnett, D. K., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01225-6 · Cited by 51
Phenotypic extremes in rare variant study designs
Peloso, G. M., Rader, D. J., Gabriel, S., Kathiresan, S., Daly, M. J., & Neale, B. M. (2016) · European Journal of Human Genetics · doi:10.1038/ejhg.2015.197 · Cited by 58
Replication Strategies for Rare Variant Complex Trait Association Studies via Next-Generation Sequencing
Liu, D. J., & Leal, S. M. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.10.025 · Cited by 59
ARIEL and AMELIA: Testing for an Accumulation of Rare Variants Using Next-Generation Sequencing Data
Asimit, J. L., Day-Williams, A., Morris, A. P., & Zeggini, E. (2012) · Human Heredity · doi:10.1159/000336982 · Cited by 59
Scan-statistic approach identifies clusters of rare disease variants in LRP2, a gene linked and associated with autism spectrum disorders, in three datasets
Ionita-Laza, I., Makarov, V., & Buxbaum, J. D. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.04.010 · Cited by 57
A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing
Wang, Q., Lu, Q., & Zhao, H. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00149 · Cited by 62
Hierarchical Generalized Linear Models for Multiple Groups of Rare and Common Variants: Jointly Estimating Group and Individual-Variant Effects
Yi, N., Liu, N., Zhi, D., & Li, J. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002382 · Cited by 56
Robust Rare Variant Association Testing for Quantitative Traits in Samples With Related Individuals
Jiang, D., & McPeek, M. S. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21775 · Cited by 57
Pleiotropy Analysis of Quantitative Traits at Gene Level by Multivariate Functional Linear Models
Wang, Y., Liu, A., Mills, J. L., Boehnke, M., Wilson, A. F., Wilson, J., Xiong, M., Wu, C. O., & Fan, R. (2015) · Genetic Epidemiology · doi:10.1002/gepi.21895 · Cited by 56
Next generation analytic tools for large scale genetic epidemiology studies of complex diseases
Mechanic, L. E., Chen, H., Amos, C. I., Chatterjee, N., Cox, N. J., Divi, R. L., Fan, R., Harris, E. L., Jacobs, K. B., Kraft, P. L., et al. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20652 · Cited by 57
Quantitative trait analysis in sequencing studies under trait-dependent sampling
Lin, D.-Y., Zeng, D., & Tang, Z.-Z. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221713110 · Cited by 56
Advances in the Genetics of Hypertension: The Effect of Rare Variants
RUSSO, A. E., Gaetano, C. D., Cugliari, G., & Matullo, G. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19030688 · Cited by 59
Adaptive tests for association analysis of rare variants
Pan, W., & Shen, X. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20586 · Cited by 55
Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variantsPreprint
Uricchio, L. H., Zaitlen, N., Ye, C., Witte, J. S., & Hernandez, R. D. (2016) · Genome Research · doi:10.1101/gr.202440.115 · Cited by 57
An Evolutionary Framework for Association Testing in Resequencing Studies
King, C. R., Rathouz, P. J., & Nicolae, D. L. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001202 · Cited by 54
Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-analysis of Noncoding Variation in Metabochip Data
He, Z., Xu, B., Lee, S., & Ionita‐Laza, I. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.07.011 · Cited by 53
Adjusted Sequence Kernel Association Test for Rare Variants Controlling for Cryptic and Family Relatedness
Oualkacha, K., Dastani, Z., Li, R., Cingolani, P. E., Spector, T. D., Hammond, C. J., Richards, J. B., Ciampi, A., & Greenwood, C. M. T. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21725 · Cited by 58
Quantitative trait locus analysis for next-generation sequencing with the functional linear models
Luo, L., Zhu, Y., & Xiong, M. (2012) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2012-100798 · Cited by 50
An efficient resampling method for calibrating single and gene-based rare variant association analysis in case–control studies
Lee, S., Fuchsberger, C., Kim, S., & Scott, L. J. (2015) · Biostatistics · doi:10.1093/biostatistics/kxv033 · Cited by 53
Discovery of rare variants for complex phenotypes
Kosmicki, J. A., Churchhouse, C. L., Rivas, M. A., & Neale, B. M. (2016) · Human Genetics · doi:10.1007/s00439-016-1679-1 · Cited by 54
A rapid method for combined analysis of common and rare variants at the level of a region, gene, or pathway
Curtis, D. (2012) · Advances and Applications in Bioinformatics and Chemistry · doi:10.2147/aabc.s33049 · Cited by 49
Sequence Kernel Association Test of Multiple Continuous Phenotypes
Wu, B., & Pankow, J. S. (2016) · Genetic Epidemiology · doi:10.1002/gepi.21945 · Cited by 53
Association Tests for Rare Variants
Nicolae, D. L. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022609 · Cited by 50
Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges
Das, S., McClain, C. J., & Rai, S. N. (2020) · Entropy · doi:10.3390/e22040427 · Cited by 53
Transcriptome‐wide association studies: a view from Mendelian randomization
Zhu, H., & Zhou, X. (2020) · Quantitative Biology · doi:10.1007/s40484-020-0207-4 · Cited by 55
A genome-wide scan statistic framework for whole-genome sequence data analysis
He, Z., Xu, B., Buxbaum, J. D., & Ionita‐Laza, I. (2019) · Nature Communications · doi:10.1038/s41467-019-11023-0 · Cited by 50
Deep learning for cancer type classification and driver gene identification
Zeng, Z., Mao, C., Vo, A. H., Li, X., Nugent, J. O., Khan, S. A., Clare, S. E., & Luo, Y. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04400-4 · Cited by 57
Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes
Swan, G. E., Javitz, H. S., Jack, L. M., Wessel, J., Michel, M., Hinds, D. A., Stokowksi, R. P., McClure, J. B., Catz, S. L., Richards, J. A., et al. (2011) · The Pharmacogenomics Journal · doi:10.1038/tpj.2011.19 · Cited by 50
Haplotypes with Copy Number and Single Nucleotide Polymorphisms in CYP2A6 Locus Are Associated with Smoking Quantity in a Japanese Population
Kumasaka, N., Aoki, M., Okada, Y., Takahashi, A., Ozaki, K., Mushiroda, T., Hirota, T., Tamari, M., Tanaka, T., Nakamura, Y., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044507 · Cited by 51
Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms
Ho, W. W. H., Hill, C. B., Doblin, M. S., Shelden, M. C., van de Meene, A., Rupasinghe, T., Bacic, A., & Roessner, U. (2020) · Plant Communications · doi:10.1016/j.xplc.2020.100031 · Cited by 51
Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle
Sahana, G., Cai, Z., Sanchez, M.-P., Bouwman, A. C., & Boichard, D. (2023) · Journal of Dairy Science · doi:10.3168/jds.2022-22694 · Cited by 64
Nonsynonymous Variants in PAX4 and GLP1R Are Associated With Type 2 Diabetes in an East Asian Population
Kwak, S. H., Chae, J., Lee, S., Choi, S., Koo, B. K., Yoon, J. W., Park, J., Cho, B., Moon, M. K., Lim, S. K., et al. (2018) · Diabetes · doi:10.2337/db18-0361 · Cited by 50
Multiple Sclerosis patients carry an increased burden of exceedingly rare genetic variants in the inflammasome regulatory genes
Vidmar, L., Maver, A., Drulovic, J. S., Sepčić, J., Novaković, I. V., Ristič, S., Šega, S., & Peterlin, B. (2019) · Scientific Reports · doi:10.1038/s41598-019-45598-x · Cited by 49
Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites
Bomba, L., Walter, K., Guo, Q. J., Surendran, P., Kundu, K., Nongmaithem, S. S., Karim, M. A., Stewart, I. D., Langenberg, C., Danesh, J., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.04.009 · Cited by 48
Mitochondrial DNA Sequence Variation Associated with Dementia and Cognitive Function in the Elderly
Tranah, G. J., The Health, A. A. B. C. S., Nalls, M. A., Katzman, S. M., Yokoyama, J. S., Lam, E. T., Zhao, Y., Mooney, S. D., Thomas, F., Newman, A. B., et al. (2012) · Journal of Alzheimer s Disease · doi:10.3233/jad-2012-120466 · Cited by 50
Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs
Tang, Z.-Z., & Lin, D.-Y. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.05.001 · Cited by 44
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Lippert, C., Xiang, J., Horta, D., Widmer, C., Kadie, C. M., Heckerman, D. E., & Listgarten, J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu504 · Cited by 47
Finding Disease Variants in Mendelian Disorders By Using Sequence Data: Methods and Applications
Ionita‐Laza, I., Makarov, V., Yoon, S. C., Raby, B. A., Buxbaum, J. D., Nicolae, D. L., & Lin, X. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.003 · Cited by 46
Assessing Methods for Assigning SNPs to Genes in Gene-Based Tests of Association Using Common Variants
Petersen, A. J., Álvarez, C., DeClaire, S., & Tintle, N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062161 · Cited by 43
Sequencing the IL4 locus in African Americans implicates rare noncoding variants in asthma susceptibility
Haller, G., Torgerson, D. G., Ober, C., & Thompson, E. E. (2009) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2009.09.013 · Cited by 46
Genome- and exome-wide association study of serum lipoprotein (a) in the Jackson Heart Study
Li, J., Lange, L. A., Sabourin, J., Duan, Q., Valdar, W. S. J., Willis, M. S., Li, Y., Wilson, J. G., & Lange, E. M. (2015) · Journal of Human Genetics · doi:10.1038/jhg.2015.107 · Cited by 46
Power and sample size calculations for high-throughput sequencing-based experiments
Li, C.-I., Samuels, D. C., Zhao, Y., Shyr, Y., & Guo, Y. P. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx061 · Cited by 46
The promise of explainable deep learning for omics data analysis: Adding new discovery tools to AI
Santorsola, M., & Lescai, F. (2023) · New Biotechnology · doi:10.1016/j.nbt.2023.06.002 · Cited by 45
Next-Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-Dimensional Data
Lange, K. L., Papp, J. C., Sinsheimer, J. S., & Sobel, E. M. (2013) · Annual Review of Statistics and Its Application · doi:10.1146/annurev-statistics-022513-115638 · Cited by 47
An Optimal Weighted Aggregated Association Test for Identification of Rare Variants Involved in Common Diseases
Sul, J. H., Han, B., He, D., & Eskin, E. (2011) · Genetics · doi:10.1534/genetics.110.125070 · Cited by 46
Genome‐Wide Association Studies
Morris, A. P., & Cardon, L. R. (2019) · Wiley eBooks · doi:10.1002/9781119487845.ch21 · Cited by 45
SBERIA: Set‐Based Gene‐Environment Interaction Test for Rare and Common Variants in Complex Diseases
Jiao, S., Hsu, L., Bezieau, S., Brenner, H., Chan, A. T., Chang-Claude, J. C., Marchand, L. L., Lemire, M., Newcomb, P. A., Slattery, M. L., et al. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21735 · Cited by 43
Fine-Scale Patterns of Population Stratification Confound Rare Variant Association Tests
O’Connor, T. D., Kieżun, A., Bamshad, M. J., Rich, S. S., Smith, J. D., Turner, E. H., NHLBIGO Exome Sequencing Project, ESP Population Genetics, S. A. W. G., Leal, S. M., & Akey, J. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065834 · Cited by 47
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
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
Recent advances and challenges of rare variant association analysis in the biobank sequencing era
Chen, W., Coombes, B. J., & Larson, N. B. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1014947 · Cited by 42
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
An Exponential Combination Procedure for Set-Based Association Tests in Sequencing Studies
Chen, L., Hsu, L., Gamazon, E. R., Cox, N. J., & Nicolae, D. L. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.09.017 · Cited by 42
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
MASS: meta-analysis of score statistics for sequencing studies
Tang, Z.-Z., & Lin, D.-Y. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt280 · Cited by 40
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
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
Moore, C., Wallace, J. R., Frase, A., Pendergrass, S. A., & Ritchie, M. D. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-s2-s6 · Cited by 38
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
Adjustment for Population Stratification via Principal Components in Association Analysis of Rare Variants
Zhang, Y., Guan, W., & Pan, W. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21691 · Cited by 38
Epistasis analysis for quantitative traits by functional regression modelPreprint
Zhang, F., Boerwinkle, E., & Xiong, M. (2014) · Genome Research · doi:10.1101/gr.161760.113 · 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
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
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
Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance
Hayeck, T. J., Stong, N., Wolock, C. J., Copeland, B. R., Kamalakaran, S., Goldstein, D. B., & Allen, A. S. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.12.020 · Cited by 35
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
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
PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies
Hall, M. A., Wallace, J. R., Lucas, A., Kim, D., Basile, A. O., Verma, S. S., McCarty, C. A., Brilliant, M. H., Peissig, P. L., Kitchner, T., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00802-2 · Cited by 34

Authors: Madsen, B. E., & Browning, S. R.
Affiliations: Aarhus University (DK)
University of Auckland (NZ)
Corresponding author: Browning, Sharon R.
ORCID: Browning, Sharon R.
Venue: PLoS Genetics
Publisher: Public Library of Science (PLoS)
Published: 2009-02-13
Volume: 5
Issue: 2
Pages: e1000384
ISSN: 1553-7390 (ISSN-L)
1553-7404
DOI: 10.1371/journal.pgen.1000384
PMC: PMC2633048
OpenAlex: W2029387902
Cited by: 1,113
References: 43
Citations by year: 2026: 15 · 2025: 29 · 2024: 23 · 2023: 43 · 2022: 45 · 2021: 46 · 2020: 47 · 2019: 70 · 2018: 68 · 2017: 69 · 2016: 91 · 2015: 87 · 2014: 115 · 2013: 114 · 2012: 96
FWCI: 48.75
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS Genetics (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Funders: University of Auckland
National Institutes of Health
National Institute of General Medical Sciences (R01GM075091)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords: rare mutations, genetic heterogeneity, resequencing, disease-associated genes, population attributable risk, genetic association
MeSH terms: DNA Mutational Analysis, Genetic Testing, Genetics, Population, Humans, Mutation, Genetic Variation, Models, Statistical, Genetic Predisposition to Disease

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks