Discovery of Rare Variants via Sequencing: Implications for the Design of Complex Trait Association Studies

Principal components analysis corrects for stratification in genome-wide association studies

Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P. A., & Hirschhorn, J. N. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2344 · Cited by 2,891

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

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

Are Rare Variants Responsible for Susceptibility to Complex Diseases?

Pritchard, J. K. (2001) · The American Journal of Human Genetics · doi:10.1086/321272 · Cited by 1,197

Population stratification and spurious allelic association

Cardon, L. R., & Palmer, L. J. (2003) · The Lancet · doi:10.1016/s0140-6736(03)12520-2 · Cited by 1,189

Common and rare variants in multifactorial susceptibility to common diseases

Bodmer, W., & Bonilla, C. (2008) · Nature Genetics · doi:10.1038/ng.f.136 · Cited by 1,131

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

The Fine-Scale Structure of Recombination Rate Variation in the Human Genome

McVean, G., Myers, S., Hunt, S. E., Deloukas, P., Bentley, D., & Donnelly, P. (2004) · Science · doi:10.1126/science.1092500 · Cited by 989

A HapMap harvest of insights into the genetics of common disease

Manolio, T. A., Brooks, L. D., & Collins, F. S. (2008) · Journal of Clinical Investigation · doi:10.1172/jci34772 · Cited by 889 · cited 1×

Improved Detection of Rare Genetic Variants for Diseases

Zhang, L., Pei, Y., Li, J., Papasian, C. J., & Deng, H. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013857 · Cited by 5

Gene-Based Burden Testing of Rare Variants in Hemiplegic Migraine: A Computational Approach to Uncover the Genetic Architecture of a Rare Brain Disorder

Alfayyadh, M. M., Maksemous, N., Sutherland, H. G. E., Lea, R. A., & Griffiths, L. R. (2025) · Genes · doi:10.3390/genes16070807 · Cited by 4

Connecting the Human Variome Project to nutrigenomics

Kaput, J., Evelo, C. T., Perozzi, G., van Ommen, B., & Cotton, R. G. H. (2010) · Genes & Nutrition · doi:10.1007/s12263-010-0186-6 · Cited by 4

Likelihood-based complex trait association testing for arbitrary depth sequencing data

Yan, S., Yuan, S., Xu, Z. Q., Zhang, B., Zhang, B., Kang, G., Byrnes, A., & Li, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv307 · Cited by 4

An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data

Huang, G., Wang, S., Wang, X., & You, N. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw409 · Cited by 4

Detection of rare variant effects in association studies: extreme values, iterative regression, and a hybrid approach

Zhang, Z., Sha, Q., Wang, X., & Zhang, S. (2011) · BMC Proceedings · doi:10.1186/1753-6561-5-s9-s112 · Cited by 4

Prioritizing Rare Variants with Conditional Likelihood Ratios

Li, W., Dobbins, S. E., Tomlinson, I. P. M., Houlston, R. S., Pal, D. K., & Strug, L. J. (2015) · Human Heredity · doi:10.1159/000371579 · Cited by 4

Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data

Li, B., Wei, Q., Zhan, X., Zhong, X. Y., Chen, W., Li, C., & Haines, J. L. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005271 · Cited by 4

PreCimp: Pre‐collapsing imputation approach increases imputation accuracy of rare variants in terms of collapsed variables

Kim, Y. J., Lee, J., Kim, B., & Park, T. (2016) · Genetic Epidemiology · doi:10.1002/gepi.22020 · Cited by 3

Identification of Novel Genetic Markers and Improved Treatment Options for Diabetic Kidney Disease

DiStefano, J. K. (2010) · Biomarkers in Medicine · doi:10.2217/bmm.10.83 · Cited by 3

A Method to Prioritize Quantitative Traits and Individuals for Sequencing in Family-Based Studies

Shah, K. P., & Douglas, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062545 · Cited by 3

BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing

Yan, S., & Li, Y. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt719 · Cited by 2

DNA Copy Number Gain in Lung Cancer and NonInvolved Tissue

Kachouie, N. N. (2016) · Journal of Bioanalysis & Biostatistics · doi:10.13188/2641-8681.1000002 · Cited by 2

A parametric Bayesian method to test the association of rare variants

Shen, Y., Cheung, Y. H., Wang, S., & Pe’er, I. (2011) · IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) · doi:10.1109/bibmw.2011.6112366 · Cited by 1

Next-generation sequencing for complex disorders

Casals, F., & Bosch, E. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781107337459.018 · Cited by 1

Estimation and hypothesis testing with additive kernel machines for high-dimensional data

Clark, J. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/qxg4-yg09 · Cited by 1

Generalizing from sequencing studiesPreprint

King, C. R., Rathouz, P. J., & Nicolae, D. L. (2013) · arXiv (Cornell University) · Cited by 1

Research on Rare Variants for Complex Diseases

Ku, C., Magnusson, P. K. E., Chia, K. S., & Yudi Pawitan, Y. (2010) · Wiley eBooks · doi:10.1002/9780470015902.a0022658 · Cited by 1

Improving Significance in Association Studies: a New Perspective for Association Studies Submitted to the Journal of Molecular Neuroscience

Nicolas, G., Charbonnier, C., & de Oliveira, J. R. M. (2015) · Journal of Molecular Neuroscience · doi:10.1007/s12031-015-0557-y · Cited by 1

Prediction and replication from case-control sequencing studies using custom genotyping and additional sequencingPreprint

King, C. R., Rathouz, P. J., & Nicolae, D. L. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1312.7714 · Cited by 2

Biochips: Bright Future in Clinical Dx?

Kohl, M., & Koch, S. (2011) · Journal of Biochips & Tissue Chips · doi:10.4172/2153-0777.s1-e003 · Cited by 1

KS-Burden: Assessing distributional differences of rare variants in dichotomous traitsPreprint

Porsch, R. M., Mak, T. S. H., Tang, C. S.-M., & Sham, P. C. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/368696 · Cited by 1

Nutritional Genomics: Fundamental Role of Diet in Chronic Disease Prevention and Control

Tucker, A. J., Deschambault, B. R., & Bakovic, M. (2011) · Wiley eBooks · doi:10.1002/9780470960844.ch3

Identification of Genetic and Epigenetic Risk Factors for Psoriasis and Psoratic Arthritis

Liu, Y. (2011) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k74x55th

Statistical Methods and Analysis in Next Generation Sequencing.

Zhan, X. (2014) · Deep Blue (University of Michigan)

The Genetics of Common Epilepsy Disorders: Lessons Learned from the Channelopathy Era

Subaran, R. L., & Greenberg, D. A. (2014) · Current Genetic Medicine Reports · doi:10.1007/s40142-014-0040-z

Evaluating rare variants under two-stage design

Li, Q., Pan, D., Yue, W., Gao, Y., & Yu, K. F. (2012) · Journal of Human Genetics · doi:10.1038/jhg.2012.33

MOLECULAR GENETIC ANALYSIS OF SELECTED NEUROLOGICAL INHERITED DISEASES

Saleha, B. S. (2012)

Discovering rare variants from populations to families

Indap, A. R. (2013)

Rastreamento de variantes de significado desconhecido (VUS) no gene RET em indivíduos-controle e em pacientes com carcinoma medular de tireoide

Hatanaka, R. (2016) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.5.2016.tde-24022016-111259

Rare Diseases and Common Diseases: Understanding their Fundamental Differences

Berman, J. J. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-419988-0.00011-0

The statistical analysis of genetic sequencing and rare variant association studies

Urrutia, E. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/e5qv-fa49

Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data

Song, Z. (2012)

Computational methods for the analysis of next generation sequencing data

Wang, W. (2014)

Identification of a genetic contribution to Meniere's disease

Campbell, C. A. (2010) · doi:10.17077/etd.xozz58vv

Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies.

Lo, Y. (2015) · Deep Blue (University of Michigan)

Finding the Missing Heritability: Gene Mapping Strategies for Complex Pedigrees.

Shah, K. P. (2013) · Deep Blue (University of Michigan)

Faculty Opinions recommendation of Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.

Quaggin, S. E., & Ly, J. (2010) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.1403956.879054

Grand Celebration: 10th Anniversary of the Human Genome Project

Rampelotto, P. H., Burn, J., Lupski, J., & Nelson, K. (2016) · MDPI eBooks · doi:10.3390/books978-3-03842-170-2

DNA Technology

Meisenberg, G., & Simmons, W. H. (2012) · Elsevier eBooks · doi:10.1016/b978-0-323-07155-0.00011-3

SNP variant discovery in pedigrees using Bayesian networks

Indap, A. R. (2015) · Figshare · doi:10.6084/m9.figshare.1439805

Genetic and functional studies of osteoarthritis susceptibility at COL11A1 and GDF5

Dodd, A. W. (2013)

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

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 General Framework for Detecting Disease Associations with Rare Variants in Sequencing Studies

Lin, D.-Y., & Tang, Z.-Z. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.07.015 · Cited by 275

Three Ways of Combining Genotyping and Resequencing in Case-Control Association Studies

Longmate, J., Larson, G. P., Krontiris, T. G., & Sommer, S. S. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014318 · Cited by 9

Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies

Lin, J.-R., Zhang, Q., Cai, Y., Morrow, B. E., & Zhang, Z. D. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1007142 · Cited by 7