A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST)

Morgenthaler, Stephan, Thilly, William G.·2007·Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
DOI 10.1016/j.mrfmmm.2006.09.003

Cited by (508)

Items 301–400 of 508

  1. Genetic-Based Hypertension Subtype Identification Using Informative SNPs
    Yuanjing Ma, Hongmei Jiang, Sanjiv Jayendra Shah, Donna K. Arnett, Marguerite R. Irvin, Yuan Luo · 2020 · Genes
  2. Unified views on variant impact across many diseases
    Sushant Kumar, Mark Gerstein · 2023 · Trends in Genetics
  3. A subregion‐based burden test for simultaneous identification of susceptibility loci and subregions within
    Bin Zhu, Lisa J. Mirabello, Nilanjan Chatterjee · 2018 · Genetic Epidemiology
  4. Semen quality is affected by HLA class I alleles together with sexually transmitted diseases
    Patrícia Marques, Joana Gonçalves, Catarina Monteiro, Bruno Cavadas, Liina Nagirnaja, Nuno Barros, Alberto Barros, Filipa Carvalho, Alexandra Manuel Lopes, Susana Seixas · 2019 · Andrology
  5. Does Accounting for Gene-Environment Interactions Help Uncover Association between Rare Variants and Complex Diseases?
    Rémi Kazma, Niall J. Cardin, John S. Witte · 2012 · Human Heredity
  6. Generalization of Rare Variant Association Tests for Longitudinal Family Studies
    Li‐Chu Chien, Fang‐Chi Hsu, Donald W. Bowden, Yen‐Feng Chiu · 2016 · Genetic Epidemiology
  7. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
    Jun Wang, Li Zhao, Xia Wang, Yong Chen, Mingchu Xu, Zachry T. Soens, Zhongqi Ge, Peter Ronghan Wang, Fei Wang, Rui Chen · 2018 · Genome biology
  8. A Novel Test for Testing the Optimally Weighted Combination of Rare and Common Variants Based on Data of Parents and Affected Children
    Qiuying Sha, Shuanglin Zhang · 2013 · Genetic Epidemiology
  9. Use of principal components to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates
    Rémi Kazma, Thomas J. Hoffmann, John S. Witte · 2011 · BMC Proceedings
  10. Statistical inference of genetic pathway analysis in high dimensions
    Yang Liu, Wei Sun, Alex P. Reiner, Charles L Kooperberg, Qianchuan He · 2019 · Biometrika
  11. Deep resequencing identifies candidate functional genes in leprosy GWAS loci
    Vinicius M. Fava, Monica Dallmann-Sauer, Marianna Orlova, Wilian Correa-Macedo, Nguyen Van Thuc, Vu Hong Thai, Alexandre Alcaïs, Laurent Abel, Aurélie Cobat, Erwin Schurr · 2021 · PLoS neglected tropical diseases
  12. Rare genetic variants underlie outlying levels of DNA methylation and gene-expression
    V. Kartik Chundru, Riccardo Emilio Marioni, James G. D. Prendergast, Tian Lin, Allan J. Beveridge, Nicholas G. Martin, Grant W. Montgomery, David Arthur Hume, Ian J. Deary, Peter M. Visscher et al. · 2023 · Human Molecular Genetics
  13. Strategies in Aggregation Tests for Rare Variants
    Farid Rajabli, Brian W. Kunkle · 2023 · Current Protocols
  14. Trans-Ethnic Fine-Mapping of Rare Causal Variants
    Xu Wang, Yik‐Ying Teo · 2015 · Springer eBooks
  15. Family-Based Association Test Using Both Common and Rare Variants and Accounting for Directions of Effects for Sequencing Data
    Ren-Hua Chung, Wei‐Yun Tsai, Eden R. Martin · 2014 · PLoS ONE
  16. A powerful association test of multiple genetic variants using a random-effects model
    K. F. Cheng, J.Y. Lee, Wei Zheng, Chun Li · 2013 · Statistics in Medicine
  17. Cohen’s h for detection of disease association with rare genetic variants
    Shu‐Hui Wen, Jih‐I Yeh · 2014 · BMC Genomics
  18. Simultaneous Analysis of Common and Rare Variants in Complex Traits: Application to SNPs (SCARVAsnp)
    Guanjie Chen, Ao Yuan, Yanxun Zhou, Amy R. Bentley, Jie Zhou, Weiping Chen, Daniel Shriner, Adebowale Adeyemo, Charles N. Rotimi · 2012 · Bioinformatics and Biology Insights
  19. An Optimum Projection and Noise Reduction Approach for Detecting Rare and Common Variants Associated with Complex Diseases
    Asuman Turkmen, Shili Lin · 2012 · Human Heredity
  20. A fast collapsed data method for estimating haplotype frequencies from pooled genotype data with applications to the study of rare variants
    Anthony Y. C. Kuk, Xiang Li, Jinfeng Xu · 2012 · Statistics in Medicine
  21. Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow
    M. J. Rivas, Sara Domínguez-García, Antonio Carvajal‐Rodríguez · 2015 · Current Genomics
  22. Adaptive-weight burden test for associations between quantitative traits and genotype data with complex correlations
    Xiaowei Wu, Ting Guan, Dajiang J. Liu, Luis G. León Novelo, Dipankar Bandyopadhyay · 2018 · The Annals of Applied Statistics
  23. Integrating germline and somatic genetics to identify genes associated with lung cancer
    Jack W. Pattee, Xiaowei Zhan, Guanghua Xiao, Wei Pan · 2019 · Genetic Epidemiology
  24. A Bayesian hierarchically structured prior for rare‐variant association testing
    Yi Archer Yang, Saonli Basu, Lin Zhang · 2021 · Genetic Epidemiology
  25. Robust genetic model-based SNP-set association test using CauchyGM
    Yeonil Kim, Yueh‐Yun Chi, Judong Shen, Fei Zou · 2022 · Bioinformatics
  26. Genomic approaches to explore susceptibility and pathogenesis of alcohol use disorder and alcohol-associated liver disease
    Trina M. Norden‐Krichmar, Daniel Miller Rotroff, Tae-Hwi Linus Schwantes-An, Ramon A. Bataller, David A Goldman, Laura E. Nagy, Suthat Liangpunsakul · 2023 · Hepatology
  27. Group association test using a hidden Markov model
    Yichen Cheng, James Y. Dai, Charles L Kooperberg · 2016 · Biostatistics
  28. Fast permutation tests and related methods, for association between rare variants and binary outcomes
    Arjun Sondhi, Kenneth M. Rice · 2017 · Annals of Human Genetics
  29. A general statistic to test an optimally weighted combination of common and/or rare variants
    Jianjun Zhang, Baolin Wu, Qiuying Sha, Shuanglin Zhang, Xuexia Wang · 2019 · Genetic Epidemiology
  30. VikNGS: a C++ variant integration kit for next generation sequencing association analysis
    Zeynep Baskurt, Scott Mastromatteo, Jiafen Gong, Richard F. Wintle, Stephen W. Scherer, Lisa J. Strug · 2019 · Bioinformatics
  31. Extension of SKAT to multi-category phenotypes through a geometrical interpretation
    Ozvan Bocher, Gaëlle Marenne, Elisabeth Tournier‐Lasserve, Emmanuelle Génin, Hervé Perdry · 2021 · European Journal of Human Genetics
  32. Insights into blood lipids from rare variant discovery
    Ellen M. Schmidt, Cristen J. Willer · 2015 · Current Opinion in Genetics & Development
  33. Detection of associations with rare and common SNPs for quantitative traits: a nonparametric Bayes-based approach
    Lili Ding, Tesfaye Mersha Baye, Hua He, Xue Zhang, Brad G. Kurowski, Lisa Joy Martin · 2011 · BMC Proceedings
  34. Comparison of collapsing methods for the statistical analysis of rare variants
    Carmen Dering, Andreas Ziegler, Inke Regina König, Claudia Hemmelmann · 2011 · BMC Proceedings
  35. Improved Detection of Rare Genetic Variants for Diseases
    Lei Zhang, Yu‐Fang Pei, Jian Li, Christopher J. Papasian, Hong‐Wen Deng · 2010 · PLoS ONE
  36. Utilizing mutual information for detecting rare and common variants associated with a categorical trait
    Leiming Sun, Chan Wang, Yue‐Qing Hu · 2016 · PeerJ
  37. Rare-variant association studies: When are aggregation tests more powerful than single-variant tests?
    Debraj Bose, Christian Fuchsberger, Michael Boehnke · 2025 · The American Journal of Human Genetics
  38. Gene-Based Burden Testing of Rare Variants in Hemiplegic Migraine: A Computational Approach to Uncover the Genetic Architecture of a Rare Brain Disorder
    Mohammed M. Alfayyadh, Neven Maksemous, Heidi G. E. Sutherland, Rod A. Lea, Lyn Robyn Griffiths · 2025 · Genes
  39. Multifactorial Inheritance and Complex Diseases
    Christine W. Duarte, Laura Kelly Vaughan, T. Mark Beasley, Hemant K. Tiwari · 2014 · Elsevier eBooks
  40. Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis
    Ryo Morikawa, Yuichiro Watanabe, Hirofumi Igeta, Reza K. Arta, Masashi Ikeda, Satoshi Okazaki, Satoshi Hoya, Takeo Saito, Ikuo Otsuka, Jun Egawa et al. · 2022 · Psychiatry Research
  41. Digenic Inheritance Mode in Congenital Hypothyroidism Due to Thyroid Dysgenesis: HYPOTYGEN Translational Cohort Study
    Athanasia Stoupa, Dulanjalee Kariyawasam, Fabienne Jabot‐Hanin, Adrien Nguyen Quoc, Sylvain Hanein, Tioka Rabeony, Caroline Elie, Sandra Colas, Caroline Thalassinos, Isabelle Petit et al. · 2025 · The Journal of Clinical Endocrinology & Metabolism
  42. A Novel Genome-Information Content-Based Statistic for Genome-Wide Association Analysis Designed for Next-Generation Sequencing Data
    Li Luo, Yun Zhu, Momiao Xiong · 2012 · Journal of Computational Biology
  43. Improved power by collapsing rare and common variants based on a data-adaptive forward selection strategy
    Yilin Dai, Ling Guo, Jianping Dong, Renfang Jiang · 2011 · BMC Proceedings
  44. Weighted Score Tests Implementing Model-Averaging Schemes in Detection of Rare Variants in Case-Control Studies
    Brandon J. Coombes, Saonli Basu, Sharmistha Guha, Nicholas J. Schork · 2015 · PLoS ONE
  45. RARE
    Satvik Dasariraju, Ryan J. Urbanowicz · 2021 · Genetic and Evolutionary Computation Conference Companion (GECCO Companion)
  46. Mutations Causing Complex Disease May under Certain Circumstances Be Protective in an Epidemiological Sense
    Sabine Siegert, Andreas Wolf, D.N. Cooper, Michael Krawczak, Michael Nothnagel · 2015 · PLoS ONE
  47. Rare Variant Association Testing for Next-Generation Sequencing Data via Hierarchical Clustering
    Ioanna Tachmazidou, Andrew P. Morris, Eleftheria Zeggini · 2012 · Human Heredity
  48. Detection of rare variant effects in association studies: extreme values, iterative regression, and a hybrid approach
    Zhaogong Zhang, Qiuying Sha, Xinli Wang, Shuanglin Zhang · 2011 · BMC Proceedings
  49. Some Surprising Twists on the Road to Discovering the Contribution of Rare Variants to Complex Diseases
    Duncan C. Thomas · 2012 · Human Heredity
  50. Literature Reviews on Methods for Rare Variant Association Studies
    F Shurong, Z Shuanglin · 2016 · Human Genetics & Embryology
  51. Incorporation of protein binding effects into likelihood ratio test for exome sequencing data
    Dongni Zhang, Hongzhu Cui, Dmitry Korkin, Zheyang Wu · 2016 · BMC Proceedings
  52. RAPIDSNPs: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses
    Bajuna R. Salehe, Chris Ian Jones, Giuseppe Di Fatta, Liam James McGuffin · 2017 · PLoS ONE
  53. Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies
    Sumaiya Nazeen, Xinyuan Wang, Dina Zielinski, Isabel Lam, Erinc Hallacli, Ping Xu, Elizabeth Ethier, Ronya Strom, Camila A. Zanella, Vanitha Nithianandam et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  54. Scalable and accurate rare variant meta-analysis with Meta-SAIGE
    Eunjae Park, K. Nam, Seokho Jeong, Karl Keat, Dokyoon Kim, V. Bansal, Wei Zhou, Seunggeun Lee · 2025 · Nature Genetics
  55. Leveraging functional annotations to map rare variants associated with Alzheimer disease with gruyere
    Anjali Das, Chirag M. Lakhani, Chloé Terwagne, Jui-Shan T Lin, Tatsuhiko Naito, Towfique Raj, David A. Knowles · 2025 · The American Journal of Human Genetics
  56. Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation
    John P. Ferguson, William Wheeler, Yi‐Ping Fu, Ludmila Prokunina‐Olsson, Hongyu Zhao, Joshua Neil Sampson · 2012 · European Journal of Human Genetics
  57. Detecting association of rare and common variants by adaptive combination of P-values
    Ya-Jing Zhou, Yong Wang · 2015 · Genetics Research
  58. A clustering approach to identify rare variants associated with hypertension
    Rui Sun, Qiao Deng, Inchi Hu, Benny Chung-Ying Zee, Maggie Haitian Wang · 2016 · BMC Proceedings
  59. Detecting disease association with rare variants in case-parents studies
    Yumei Li, Yang Xiang · 2017 · Journal of Human Genetics
  60. Modern probabilistic and statistical approaches to search for nucleotide sequence options associated with integrated diseases
    Anastasiia Igorevna Rytova, Eleonora Khlebus, А. Е. Шевцов, Vladimir Aleksandrovich Kutsenko, Н. В. Щербакова, Anastasia A. Zharikova, Alexandra I. Ershova, Anna V. Kiseleva, Sergey Anatol'evich Boytsov, Elena Borisovna Yarovaya et al. · 2017 · Russian Journal of Genetics
  61. Comparing healthcare utilization patterns via global differences in the endorsement of current procedural terminology codes
    Xu Shi, Hristina I. Pashova, Patrick J. Heagerty · 2017 · The Annals of Applied Statistics
  62. Identifying rare variants for quantitative traits in extreme samples of population via Kullback-Leibler distance
    Yang Xiang, Xinrong Xiang, Yumei Li · 2020 · BMC Genetics
  63. Germline and somatic mutations in the pathology of pineal cyst: A whole‐exome sequencing study of 93 individuals
    Yuanqing Yan, Rebecca Martinez, Maria N Rasheed, Joshua Cahal, Zhen Xu, Yan‐Ning Rui, Krista J. Qualmann, John P. Hagan, Dong Kim · 2021 · Molecular Genetics & Genomic Medicine
  64. Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data
    Simon Boutry, Raphaël Helaers, Tom Lenaerts, Miikka Vikkula · 2023 · PLoS Computational Biology
  65. A modified association test for rare and common variants based on affected sib-pair design
    Yixing Guo, Ying Zhou · 2019 · Journal of Theoretical Biology
  66. A novel association test for rare variants based on algebraic statistics
    Jingbo Meng, W. J. Zhu, Canhui Li, Kyongson Jon · 2020 · Journal of Theoretical Biology
  67. Testing for Modes of Inheritance Involving Compound Heterozygotes
    Silviu‐Alin Bacanu · 2013 · Genetic Epidemiology
  68. Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs
    Rui Jiang, Jiaxin Wu · 2011 · IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
  69. A novel statistical method for rare-variant association studies in general pedigrees
    Huanhuan Zhu, Zhenchuan Wang, Xuexia Wang, Qiuying Sha · 2016 · BMC Proceedings
  70. Using Genetic Burden Scores for Gene-by-Methylation Interaction Analysis on Metabolic Syndrome in African Americans
    Jacquelyn Y. Taylor, Erin Bakshis Ware, Michelle L. Wright, Jennifer A. Smith, Sharon L. R. Kardia · 2019 · Biological Research For Nursing
  71. Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling
    Peter Pak‐Hang Cheung, Biaobin Jiang, Gregory T. Booth, Tin Hang Chong, Ilona Christy Unarta, Yuqing Wang, Gianmarco Domenico Suarez, Jiguang Wang, John T. Lis, Xuhui Huang · 2020 · Journal of Molecular Biology
  72. Genetics in Asthma and COPD
    Victor E. Ortega, Eugene R. Bleecker · 2015 · Elsevier eBooks
  73. Tests for detection of rare variants and gene-environment interaction in cohort and twin family studies
    Brandon J. Coombes · 2016 · University of Minnesota Digital Conservancy (University of Minnesota)
  74. Weighted multiple testing procedures in genome-wide association studies
    Ludivine Obry, Cyril Dalmasso · 2023 · PeerJ
  75. Detecting Rare Variants for Psychiatric Disorders Using Next Generation Sequencing: A Methods Primer
    André Altmann, Carina Quast, Peter C Weber · 2012 · Current Psychiatry Reports
  76. Poisson Approximation–Based Score Test for Detecting Association of Rare Variants
    Hongyan Fang, Hong Zhang, Yaning Yang · 2016 · Annals of Human Genetics
  77. Efficient unified rare variant association test by modeling the population genetic distribution in case‐control studies
    Huilin Li, Jinbo Chen · 2016 · Genetic Epidemiology
  78. A gene based combination test using GWAS summary data
    Jianjun Zhang, Xiaoyu Liang, Samantha Gonzales, Jianguo Liu, Xiaoyi Gao, Xuexia Wang · 2023 · BMC Bioinformatics
  79. Learning the kernel for rare variant genetic association test
    Isak Falk, Millie Zhao, Juba Nait Saada, Qi Jin Guo · 2023 · Frontiers in Genetics
  80. Fast Signal Region Detection With Application to Whole Genome Association Studies
    Wei Zhang, Fan Wang, Fang Yao · 2025 · Journal of the American Statistical Association
  81. Rare variants analysis by risk-based variable-threshold method
    Hongyan Fang, Bo Hou, Qi Wang, Yaning Yang · 2013 · Computational Biology and Chemistry
  82. A weighted accumulation test for associating rare genetic variation with quantitative phenotypes
    Chuanhua Xing, Glen A. Satten, Andrew S. Allen · 2011 · BMC Proceedings
  83. Rare variant collapsing in conjunction with mean log p-value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data
    Yauheniya Cherkas, Nandini Raghavan, Stephan Francke, Frank DeFalco, Marsha Wilcox · 2011 · BMC Proceedings
  84. Detecting disease association signals with multiple genetic variants and covariates
    K. F. Cheng, JY Lee · 2015 · Statistical Methods in Medical Research
  85. Extraction of Sequence Conservation Features for the Prioritization of Candidate Single Amino Acid Polymorphisms
    Jiaxin Wu, Mingxin Gan, Wangshu Zhang, Rui Jiang · 2011 · International Journal of Information Engineering and Electronic Business
  86. Assembly and constraint technology for large arrays of capillaries
    Craig R. Forest, Bryan Woodruff, Darragh Buckley, William G. Thilly, Ian W. Hunter · 2008 · Precision Engineering
  87. Longitudinal data analysis for rare variants detection with penalized quadratic inference function
    Hongyan Cao, Zhi Li, Haitao Yang, Yuehua Cui, Yanbo Zhang · 2017 · Scientific Reports
  88. DNA Copy Number Gain in Lung Cancer and NonInvolved Tissue
    Nezamoddin N. Kachouie · 2016 · Journal of Bioanalysis & Biostatistics
  89. Association analysis of multiple traits by an approach of combining $$P$$ P values
    Lili Chen, Yong Wang, Yajing Zhou · 2018 · Journal of Genetics
  90. A permutation method for detecting trend correlations in rare variant association studies
    Lifeng Liu, Pengfei Wang, Jingbo Meng, Lili Chen, W. J. Zhu, Weijun Ma · 2019 · Genetics Research
  91. Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets
    Xiaoyu Cai, Lo‐Bin Chang, Jordan Potter, Chi Wook Song · 2020 · BMC Medical Genomics
  92. SNP-set Tests for Sequencing and Genome-Wide Association Studies
    Ian Barnett · 2014 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
  93. Selection and explosive growth may hamper the performance of rare variant association tests
    Lawrence H. Uricchio, John S. Witte, Ryan D. Hernandez · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
  94. An Optimally Weighted Combination Method to Detect Novel Disease Associated Genes Using Publicly Available GWAS Summary Data
    Jianjun Zhang, Samantha Gonzales, Jianguo Liu, Xiaoyi Gao, Xuexia Wang · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  95. StocSum: stochastic summary statistics for whole genome sequencing studies
    Nannan Wang, Bing Yu, Goo Jun, Qibin Qi, Ramón Durazo-Arvizú, Sara Lindström, Alanna C. Morrison, Robert C. Kaplan, Eric Boerwinkle, Han Chen · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  96. Multi-omics Integration Identifies Genes Influencing Traits Associated with Cardiovascular Risks: The Long Life Family Study
    Sandeep Acharya, Shu Liao, Wooseok J. Jung, Yu Sung Kang, Vaha Akbary Moghaddam, Mary Furlan Feitosa, Mary K. Wojczynski, Shiow J. Lin, Jason A. Anema, Karen Schwander et al. · 2024 · medRxiv
  97. Functional gene embeddings improve rare variant polygenic risk scores
    Shubhankar Londhe, Jonas Lindner, Zhifen Chen, Eva Holtkamp, Florian R. Hölzlwimmer, Francesco Paolo Casale, Felix Brechtmann, Julien Gagneur · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  98. A two-stage testing strategy for detecting genes×environment interactions in association studies
    Jiabin Zhou, Shitao Li, Ying Zhou, Xiaona Sheng · 2021 · G3 Genes Genomes Genetics
  99. DYNATE: Localizing rare‐variant association regions via multiple testing embedded in an aggregation tree
    Xuechan Li, John A. Pura, Andrew S. Allen, Kouros Owzar, Jianfeng Lu, Matthew B. Harms, Jichun Xie · 2023 · Genetic Epidemiology
  100. Multiple-testing corrections in case-control studies using identity-by-descent segments
    Seth D Temple, Nicola H. Chapman, Seung Hoan Choi, Anita L. DeStefano, Timothy A. Thornton, Ellen M. Wijsman, Elizabeth Blue · 2026 · The American Journal of Human Genetics