Discovery of Rare Variants via Sequencing: Implications for the Design of Complex Trait Association Studies
Open accessAbstract
There is strong evidence that rare variants are involved in complex disease etiology. The first step in implicating rare variants in disease etiology is their identification through sequencing in both randomly ascertained samples (e.g., the 1,000 Genomes Project) and samples ascertained according to disease status. We investigated to what extent rare variants will be observed across the genome and in candidate genes in randomly ascertained samples, the magnitude of variant enrichment in diseased individuals, and biases that can occur due to how variants are discovered. Although sequencing cases can enrich for casual variants, when a gene or genes are not involved in disease etiology, limiting variant discovery to cases can lead to association studies with dramatically inflated false positive rates.
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
Cites
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?
Comparing allele frequencies in a group of individuals with historical or publicly available control sets in rare variant studies is highly problematic because of stratification and sampling variation effects.
“The practice of identifying and quantifying allele frequencies in a group of individuals and comparing them with historical or publicly available ‘control’ sets in studies involving rare variants is highly problematic due to the potential for stratification and sampling variation effects.96”
From Statistical analysis strategies for association studies involving rare variants (2010) · cites this paper as [96]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
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 · see citing works
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 · see citing works
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 · see citing works
Li, B., & Leal, S. M. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.06.024 · Cited by 1,527 · see citing works
Self-citationAre 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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
The Fine-Scale Structure of Recombination Rate Variation in the Human Genome
McVean, G., Myers, S. R., Hunt, S. E., Deloukas, P., Bentley, D., & Donnelly, P. (2004) · Science · doi:10.1126/science.1092500 · Cited by 968 · see citing works
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× · see citing works
“Genome wide association studies using indirect mapping have been successful in localizing genes which are associated with complex diseases when common variants are the underlying cause of disease etiology [1,2].”
BackgroundRare independent mutations in renal salt handling genes contribute to blood pressure variation
Ji, W., Foo, J. N., O'Roak, B. J., Zhao, H., Larson, M. G., Simon, D. B., Newton-Cheh, C., State, M. W., Levy, D., & Lifton, R. P. (2008) · Nature Genetics · doi:10.1038/ng.118 · Cited by 812 · see citing works
The allelic architecture of human disease genes: common disease-common variant... or not?
Pritchard, J. K. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.20.2417 · Cited by 711 · see citing works
Siva, N. (2008) · Nature Biotechnology · doi:10.1038/nbt0308-256b · Cited by 629 · see citing works
Romeo, S., Pennacchio, L. A., Fu, Y., Boerwinkle, E., Tybjaerg-Hansen, A., Hobbs, H. H., & Cohen, J. C. (2007) · Nature Genetics · doi:10.1038/ng1984 · Cited by 511 · see citing works
Cohen, J. C., Pertsemlidis, A., Fahmi, S., Esmail, S., Vega, G. L., Grundy, S. M., & Hobbs, H. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508483103 · Cited by 373 · see citing works
Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms
Gorlov, I. P., Gorlova, O. Y., Sunyaev, S. R., Spitz, M. R., & Amos, C. I. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.09.006 · Cited by 338 · see citing works
Service, R. F. (2006) · Science · doi:10.1126/science.311.5767.1544 · Cited by 269 · see citing works
Inherited breast and ovarian cancer. What are the risks? What are the choices?
King, M. (1993) · JAMA · doi:10.1001/jama.269.15.1975 · Cited by 237 · see citing works
Medical Sequencing at the Extremes of Human Body Mass
Ahituv, N., Kavaslar, N., Schackwitz, W., Ustaszewska, A., Martin, J., Hébert, S., Doelle, H., Ersoy, B. A., Kryukov, G. V., Schmidt, S., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/513471 · Cited by 221 · see citing works
Inherited breast and ovarian cancer
Szabo, C., & King, M. (1995) · Human Molecular Genetics · doi:10.1093/hmg/4.suppl_1.1811 · Cited by 202 · see citing works
Mathematical properties of the r2 measure of linkage disequilibrium.
VanLiere, J. M., & Rosenberg, N. (2008) · Theoretical Population Biology · doi:10.1016/j.tpb.2008.05.006 · Cited by 190 · see citing works
Brunham, L. R., Singaraja, R. R., & Hayden, M. R. (2006) · Annual Review of Nutrition · doi:10.1146/annurev.nutr.26.061505.111214 · Cited by 142 · see citing works
Keen‐Kim, D., Mathews, C. A., Reus, V. I., Lowe, T. L., Herrera, L. D., Budman, C. L., Gross‐Tsur, V., Pulver, A. E., BRUUN, R. D., Erenberg, G., et al. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl408 · Cited by 89 · see citing works
Azzopardi, D., Dallosso, A. R., Eliason, K., Hendrickson, B. C., Jones, N., Rawstorne, E., Colley, J. P., Moskvina, V., FRYE, C. A., Sampson, J. R., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-5733 · Cited by 85 · see citing works
Cystic Fibrosis in Jews: Frequency and Mutation Distribution
Kerem, B., Chiba‐Falek, O., & Kerem, E. (1997) · Genetic Testing · doi:10.1089/gte.1997.1.35 · Cited by 73 · see citing works
Novel rare mutations and promoter haplotypes in ABCA1 contribute to low‐HDL‐C levels
Slatter, T., Jones, G. T., Williams, M., van Rij, A., & McCormick, S. P. A. (2008) · Clinical Genetics · doi:10.1111/j.1399-0004.2007.00940.x · Cited by 42 · see citing works
Flagged first, then by citations
1 of the 27 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test
Wu, M. C., Lee, S., Cai, T., Li, Y., Boehnke, M., & Lin, X. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.05.029 · Cited by 2,317 · see citing works
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayır, A., Bakkaloğlu, A., Özen, S., Sanjad, S. A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910672106 · Cited by 1,327 · see citing works
Park, J.-H., Wacholder, S., Gail, M. H., Peters, U., Jacobs, K. B., Chanock, S. J., & Chatterjee, N. (2010) · Nature Genetics · doi:10.1038/ng.610 · Cited by 678 · see citing works
Consanguinity, human evolution, and complex diseases
Bittles, A. H., & Black, M. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906079106 · Cited by 620 · see citing works
Statistical power and significance testing in large-scale genetic studies
Sham, P. C., & Purcell, S. M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3706 · Cited by 573 · see citing works
Progress and promise of genome-wide association studies for human complex trait genetics
Stranger, B. E., Stahl, E. A., & Raj, T. (2011) · Genetics · doi:10.1534/genetics.110.120907 · Cited by 567 · see citing works
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 · see citing works
Rare Variant Association Analysis Methods for Complex Traits
Asimit, J. L., & Zeggini, E. (2010) · Annual Review of Genetics · doi:10.1146/annurev-genet-102209-163421 · Cited by 267 · see citing works
Sebat, J., Levy, D. L., & McCarthy, S. E. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.10.004 · Cited by 260 · see citing works
Wei, Z., Wang, W., Hu, P., Lyon, G. J., & Hakonarson, H. H. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr599 · Cited by 249 · see citing works
A genome-wide association study on African-ancestry populations for asthma
Mathias, R. A., Grant, A. V., Rafaels, N. M., Hand, T. A., Gao, L., Vergara, C., Tsai, Y. J., Yang, M., Campbell, M., Foster, C., et al. (2009) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2009.08.031 · Cited by 190 · see citing works
The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits
Lohmueller, K. E. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004379 · Cited by 152 · see citing works
Wang, K., Dickson, S. P., Stolle, C. A., Krantz, I. D., Goldstein, D. B., & Hakonarson, H. H. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.003 · Cited by 151 · see citing works
Recent advances in the molecular genetics of epilepsy
Hildebrand, M. S., Dahl, H. M., Damiano, J. A., Smith, R. J. H., Scheffer, I. E., & Berkovic, S. F. (2013) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2012-101448 · Cited by 148 · see citing works
Liu, L., Sabo, A., Neale, B. M., Nagaswamy, U., Stevens, C., Lim, E., Bodea, C. A., Muzny, D., Reid, J. G., Banks, E., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003443 · Cited by 135 · see citing works
Mackay, T. F. C., & Huang, W. (2017) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.289 · Cited by 134 · see citing works
Extending Rare-Variant Testing Strategies: Analysis of Noncoding Sequence and Imputed Genotypes
Zawistowski, M., Gopalakrishnan, S., Ding, J., Li, Y., Grimm, S. A., & Zöllner, S. K. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.10.012 · Cited by 124 · see citing works
de Magalhães, J. P., Finch, C. E., & Janssens, G. E. (2009) · Ageing Research Reviews · doi:10.1016/j.arr.2009.10.006 · Cited by 116 · see citing works
Ladouceur, M., Dastani, Z., Aulchenko, Y. S., Greenwood, C. M. T., & Richards, J. B. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002496 · Cited by 107 · see citing works
Exome Sequencing of Familial Bipolar Disorder
Goes, F. S., Pirooznia, M., Parla, J. S., Kramer, M., Ghiban, E., Mavruk, S., Chen, Y.-C., Monson, E. T., Willour, V. L., Karchin, R., et al. (2016) · JAMA Psychiatry · doi:10.1001/jamapsychiatry.2016.0251 · Cited by 107 · see citing works
Genetic Approaches to Functional Gastrointestinal Disorders
Saito, Y. A., Mitra, N., & Mayer, E. A. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.02.037 · Cited by 104 · see citing works
Genetic studies of IgA nephropathy: past, present, and future
Kiryluk, K., Julian, B. A., Wyatt, R. J., Scolari, F., Zhang, H., Novák, J., & Gharavi, A. G. (2010) · Pediatric Nephrology · doi:10.1007/s00467-010-1500-7 · Cited by 93 · see citing works
Chatterjee, R., Ramos, E., Hoffman, M., VanWinkle, J., Martin, D. R., Davis, T. K., Hoshi, M., Hmiel, S. P., Beck, A., Hruska, K. A., et al. (2012) · Human Genetics · doi:10.1007/s00439-012-1181-3 · Cited by 92 · see citing works
Mowry, B. J., & Gratten, J. (2012) · Molecular Psychiatry · doi:10.1038/mp.2012.34 · Cited by 81 · see citing works
Landy, D. C., Brinich, M. A., Colten, M. E., Horn, E. J., Terry, S. F., & Sharp, R. R. (2011) · Genetics in Medicine · doi:10.1038/gim.0b013e3182310ba0 · Cited by 77 · see citing works
Urbany, C., Stich, B., Schmidt, L., Simon, L., Berding, H., Junghans, H., Niehoff, K.-H., Braun, A., Tacke, E., Hofferbert, H.-R., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-7 · Cited by 77 · see citing works
Human studies on genetics of the age at natural menopause: a systematic review
Voorhuis, M., Onland‐Moret, N. C., van der Schouw, Y. T., Fauser, B. C. J. M., & Broekmans, F. J. (2010) · Human Reproduction Update · doi:10.1093/humupd/dmp055 · Cited by 74 · see citing works
Impact of QTL properties on the accuracy of multi-breed genomic prediction
Wientjes, Y. C. J., Calus, M. P. L., Goddard, M. E., & Hayes, B. J. (2015) · Genetics Selection Evolution · doi:10.1186/s12711-015-0124-6 · Cited by 72 · see citing works
A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families
Li, B., Chen, W., Zhan, X., Busonero, F., Sanna, S., Sidore, C., Cucca, F., Kang, H. M., & Abecasis, G. R. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002944 · Cited by 71 · see citing works
Self-citationMoens, L., Rijk, P. D., Reumers, J., Bossche, M. J. A. V. D., Glassee, W., Zutter, S. D., Lenaerts, A., Nordin, A., Nilsson, L., Castello, I. M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023450 · Cited by 68 · see citing works
Identification of rare alleles and their carriers using compressed se(que)nsing
Shental, N., Amir, A., & Zuk, O. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq675 · Cited by 68 · see citing works
Using Populus as a lignocellulosic feedstock for bioethanol
Porth, I. M., & El-Kassaby, Y. A. (2015) · Biotechnology Journal · doi:10.1002/biot.201400194 · Cited by 63 · see citing works
Liu, D. J., & Leal, S. M. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.10.025 · Cited by 58 · see citing works
Self-citationMutations in the NRG1 gene are associated with Hirschsprung disease
Tang, C. S.-M., Ngan, E., Tang, W.-K., So, M., Cheng, G., Miao, X., Leon, T. Y. Y., Leung, B. M.-C., Hui, K. J. W. S., Lui, V. C. H., et al. (2011) · Human Genetics · doi:10.1007/s00439-011-1035-4 · Cited by 58 · see citing works
Transmission ratio distortion: review of concept and implications for genetic association studies
Huang, L. O., Labbe, A., & Infante‐Rivard, C. (2012) · Human Genetics · doi:10.1007/s00439-012-1257-0 · Cited by 58 · see citing works
A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis
Yu, H., Artomov, M., Brähler, S., Stander, M. C., Shamsan, G. A., Sampson, M. G., White, J. M., Kretzler, M., Miner, J. H., Jain, S. R., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci82592 · Cited by 57 · see citing works
Li, Q. S., Cheng, P. Y., Favis, R., Wickenden, A., Romano, G. J., & Wang, H. (2015) · Clinical Journal of Pain · doi:10.1097/ajp.0000000000000205 · Cited by 54 · see citing works
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 53 · see citing works
Efficient study design for next generation sequencing
Sampson, J. N., Jacobs, K. B., Yeager, M., Chanock, S. J., & Chatterjee, N. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20575 · Cited by 48 · see citing works
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 · see citing works
Genome-wide association studies in asthma
Wjst, M., Sargurupremraj, M., & Arnold, M. (2012) · Current Opinion in Allergy and Clinical Immunology · doi:10.1097/aci.0b013e32835c1674 · Cited by 42 · see citing works
Genetics of Parkinson disease and essential tremor
Wider, C. W., Ross, O. A., & Wszołek, Z. K. (2010) · Current Opinion in Neurology · doi:10.1097/wco.0b013e32833b1f4c · Cited by 40 · see citing works
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 39 · see citing works
Self-citationInvestigation of SHANK3 in schizophrenia
Cortabitarte, A. D. S., Degenhardt, F., Strohmaier, J., Lang, M., Weiß, B., Roeth, R., Giegling, I., Heilmann‐Heimbach, S., Hofmann, A., Rujescu, D., et al. (2017) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32528 · Cited by 39 · see citing works
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 · see citing works
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 37 · see citing works
Self-citationOptimum 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 36 · see citing works
Moore, C., Wallace, J. R., Wolfe, D., Frase, A., Pendergrass, S. A., Weiss, K. M., & Ritchie, M. D. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003959 · Cited by 31 · see citing works
Key issues in essential tremor genetics research: Where are we now and how can we move forward?
Testa, C. M. (2013) · Tremor and Other Hyperkinetic Movements · doi:10.5334/tohm.160 · Cited by 31 · see citing works
Is gastroschisis truly a sporadic defect? Familial cases of gastroschisis in Utah, 1997 to 2008
Feldkamp, M. L., Carey, J. C., Pimentel, R., Krikov, S. V., & Botto, L. D. (2011) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.22844 · Cited by 29 · see citing works
Lencz, T., Yu, J., Khan, R. R., Flaherty, E. K., Carmi, S., Lam, M., Ben‐Avraham, D., Barzilai, N., Bressman, S., Darvasi, A., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.03.004 · Cited by 29 · see citing works
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 28 · see citing works
Zhi, D., & Chen, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031358 · Cited by 27 · see citing works
Köttgen, A., Yang, Q., Shimmin, L. C., Tin, A., Schaeffer, C., Coresh, J., Liu, X., Rampoldi, L., Hwang, S., Boerwinkle, E., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038311 · Cited by 27 · see citing works
Song, K., Nelson, M. R., Aponte, J., Manas, E. S., Bacanu, S., Yuan, X., Kong, X., Cardon, L. R., Mooser, V., Whittaker, J. C., et al. (2011) · The Pharmacogenomics Journal · doi:10.1038/tpj.2011.20 · Cited by 26 · see citing works
Genes associated with multiple sclerosis: 15 and counting
Habek, M., Brinar, V. V., & Borovečki, F. (2010) · Expert Review of Molecular Diagnostics · doi:10.1586/erm.10.77 · Cited by 26 · see citing works
Genetic Association Studies: An Information Content Perspective
Wu, C., Li, S., & Cui, Y. (2012) · Current Genomics · doi:10.2174/138920212803251382 · Cited by 25 · see citing works
Pathogenic EFHC 1 mutations are tolerated in healthy individuals dependent on reported ancestry
Subaran, R. L., Conte, J. M., Stewart, W. C. L., & Greenberg, D. A. (2014) · Epilepsia · doi:10.1111/epi.12864 · Cited by 23 · see citing works
AlChawa, T., Ludwig, K. U., Fier, H. L., Pötzsch, B., Reich, R. H., Schmidt, G., Braumann, B., Daratsianos, N., Böhmer, A. C., Schuencke, H., et al. (2014) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.23244 · Cited by 22 · see citing works
Next-generation sequencing approaches for genetic mapping of complex diseases
Casals, F., Idaghdour, Y., Hussin, J., & Awadalla, P. (2012) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2011.12.017 · Cited by 22 · see citing works
Kang, G., Lin, D., Hakonarson, H. H., & Chen, J. (2012) · Human Heredity · doi:10.1159/000337300 · Cited by 19 · see citing works
On optimal pooling designs to identify rare variants through massive resequencing
Lee, J. S., Choi, M., Yan, X., Lifton, R. P., & Zhao, H. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20561 · Cited by 18 · see citing works
GWAS to Sequencing: Divergence in Study Design and Analysis
King, C., & Nicolae, D. L. (2014) · Genes · doi:10.3390/genes5020460 · Cited by 17 · see citing works
Sampling strategies for rare variant tests in case–control studies
Zöllner, S. K. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.58 · Cited by 17 · see citing works
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 · see citing works
Self-citationResequencing of VAX1 in patients with nonsyndromic cleft lip with or without cleft palate
Nasser, E., Mangold, E., Tradowsky, D. C., Fier, H. L., Becker, J., Boehmer, A. C., Herberz, R., Fricker, N., Barth, S., Wahle, P., et al. (2012) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.23078 · Cited by 16 · see citing works
Investigation of the role of TCF4 rare sequence variants in schizophrenia
Basmanav, F. B., Forstner, A. J., Fier, H. L., Herms, S., Meier, S., Degenhardt, F., Hoffmann, P., Barth, S., Fricker, N., Strohmaier, J., et al. (2015) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32318 · Cited by 16 · see citing works
Unraveling the biological mechanisms in Alzheimer's disease — Lessons from genomics
Borovečki, F., Klepac, N., Mück‐Šeler, D., Hajnšek, S., Mubrin, Z., & Pivac, N. (2010) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2010.12.019 · Cited by 15 · see citing works
The theory of discovering rare variants via DNA sequencing
Wendl, M. C., & Wilson, R. K. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-485 · Cited by 15 · see citing works
Rare-Variant Kernel Machine Test for Longitudinal Data from Population and Family Samples
Yan, Q., Weeks, D. E., Tiwari, H. K., Yi, N., Zhang, K., Gao, G., Lin, W., Lou, X., Chen, W., & Liu, N. (2015) · Human Heredity · doi:10.1159/000445057 · Cited by 15 · see citing works
Resequencing and follow-up of neurexin 1 (NRXN1) in schizophrenia patients
Mühleisen, T. W., Basmanav, F. B., Forstner, A. J., Mattheisen, M., Priebe, L., Herms, S., Breuer, R., Moebus, S., Nenadić, I., Sauer, H., et al. (2011) · Schizophrenia Research · doi:10.1016/j.schres.2011.01.001 · Cited by 14 · see citing works
Zhao, Z., Wang, W., & Wei, Z. (2013) · The Annals of Applied Statistics · doi:10.1214/13-aoas660 · Cited by 14 · see citing works
Exonic DNA Sequencing of ERBB4 in Bipolar Disorder
Goes, F. S., Rongione, M. A., Chen, Y.-C., Karchin, R., Elhaik, E., Study, T. B. G., & Potash, J. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020242 · Cited by 14 · see citing works
Altmüller, J., Haenisch, B., Kawalia, A., Menzen, M., Nöthen, M. M., Fier, H., & Molderings, G. J. (2017) · Immunogenetics · doi:10.1007/s00251-017-0981-y · Cited by 14 · see citing works
A Two‐Platform Design for Next Generation Genome‐Wide Association Studies
Sampson, J. N., Jacobs, K. B., Wang, Z., Yeager, M., Chanock, S. J., & Chatterjee, N. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21634 · Cited by 13 · see citing works
Gassó, P., Mas, S., Oliveira, C., Bioque, M., Parellada, E., Bernardo, M., Trias, G., Comeche, J., & Lafuente, A. (2010) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2010.06.006 · Cited by 13 · see citing works
Meta-analysis identifies mitochondrial DNA sequence variants associated with walking speed
Manini, T. M., Buford, T. W., Kairalla, J. A., McDermott, M. M., Fragoso, C. A. V., Fielding, R. A., Hsu, F., Johannsen, N. M., Kritchevsky, S. B., Harris, T. B., et al. (2018) · GeroScience · doi:10.1007/s11357-018-0043-x · Cited by 12 · see citing works
Discriminant Analysis of Lung Cancer Using Nonlinear Clustering of Copy Numbers
Kachouie, N. N., Shutaywi, M., & Christiani, D. C. (2020) · Cancer Investigation · doi:10.1080/07357907.2020.1719501 · Cited by 12 · see citing works
Imputation of Rare Variants in Next-Generation Association Studies
Asimit, J. L., & Zeggini, E. (2012) · Human Heredity · doi:10.1159/000345602 · Cited by 12 · see citing works
Insufficient evidence for a role of SERPINF1 in otosclerosis
Valgaeren, H., Sommen, M., Beyens, M., Vandeweyer, G., Schrauwen, I., Schepers, A., Schatteman, I., Topsakal, V., Dhooge, I. J. M., Kunst, H. P. M., et al. (2019) · Molecular Genetics and Genomics · doi:10.1007/s00438-019-01558-8 · Cited by 12 · see citing works
Efficient clustering of identity-by-descent between multiple individuals
Qian, Y., Browning, B. L., & Browning, S. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt734 · Cited by 11 · see citing works
Enriching targeted sequencing experiments for rare disease alleles
Edwards, T. L., Song, Z., & Li, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr324 · Cited by 10 · see citing works
Rare Variants Detection with Kernel Machine Learning Based on Likelihood Ratio Test
Zeng, P., Zhao, Y., Zhang, L., Huang, S., & Chen, F. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093355 · Cited by 10 · see citing works
Gordon, D., Finch, S. J., & Vega, F. M. D. L. (2011) · Human Heredity · doi:10.1159/000325590 · Cited by 9 · see citing works
Wilke, R. A. (2010) · The Pharmacogenomics Journal · doi:10.1038/tpj.2010.86 · Cited by 9 · see citing works
Two-Stage Design of Sequencing Studies for Testing Association with Rare Variants
Yang, F., & Thomas, D. C. (2011) · Human Heredity · doi:10.1159/000328193 · Cited by 9 · see citing works
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 · see citing works
Association Claims in the Sequencing Era
Pulit, S. L., Leusink, M., Menelaou, A., & de Bakker, P. I. W. (2014) · Genes · doi:10.3390/genes5010196 · Cited by 9 · see citing works
Boutry, S., Helaers, R., Lenaerts, T., & Vikkula, M. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad412 · Cited by 8 · see citing works
Alfayyadh, M. M., Maksemous, N., Sutherland, H. G. E., Lea, R. A., & Griffiths, L. R. (2024) · Genes · doi:10.3390/genes15040443 · Cited by 8 · see citing works
Kang, C. J., & Marjoram, P. (2011) · Genetics · doi:10.1534/genetics.111.130898 · Cited by 8 · see citing works
He, L., Pitkäniemi, J. M., Sarin, A., Salomaa, V. V., Sillanpää, M. J., & Ripatti, S. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21871 · Cited by 8 · see citing works
Ordered subset analysis for case‐control studies
Qin, X., Hauser, E. R., & Schmidt, S. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20489 · Cited by 8 · see citing works
Liu, D. J., & Leal, S. M. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts263 · Cited by 8 · see citing works
Self-citationShared genomic segments in high‐risk multigenerational pedigrees with gastroschisis
Feldkamp, M. L., Krikov, S. V., Gardner, J., Madsen, M., Darlington, T. M., Sargent, R., & Camp, N. J. (2019) · Birth Defects Research · doi:10.1002/bdr2.1567 · Cited by 7 · see citing works
Genetic-Based Hypertension Subtype Identification Using Informative SNPs
Ma, Y., Jiang, H., Shah, S. J., Arnett, D. K., Irvin, M. R., & Luo, Y. (2020) · Genes · doi:10.3390/genes11111265 · Cited by 6 · see citing works
Yan, Q., Liu, N., Forno, E., CANINO, G. J., Celedon, J. C., & Chen, W. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008142 · Cited by 6 · see citing works
Two-stage case–control designs for rare genetic variants
Schaid, D. J., & Sinnwell, J. P. (2010) · Human Genetics · doi:10.1007/s00439-010-0811-x · Cited by 5 · see citing works
Zhi, D., Liu, N., & Zhang, K. (2015) · Methods · doi:10.1016/j.ymeth.2015.01.016 · Cited by 5 · see citing works
Labbe, A., Huang, L. O., & Infante‐Rivard, C. (2013) · Springer eBooks · doi:10.1007/978-1-4614-8078-5_12 · Cited by 5 · see citing works
- Authors
- Li, B., & Leal, S. M.
- Affiliations
- Baylor College of Medicine (US)
- Corresponding author
- Leal, Suzanne M.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-05-15
- Volume
- 5
- Issue
- 5
- Pages
- e1000481
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2674213
- OpenAlex
- W2108409892
- Cited by
- 142
- References
- 27
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2021: 1 · 2020: 2 · 2019: 5 · 2018: 2 · 2017: 3 · 2016: 7 · 2015: 14 · 2014: 12 · 2013: 16 · 2012: 23
- FWCI
- 14.93
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- 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)
- Funders
- National Institutes of Health (R01-DC03594, DC03594)
- National Institute on Deafness and Other Communication Disorders (R01-DC03594, R01DC003594)
- 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 › Forensic and Genetic Research
- Keywords
- rare variants, candidate genes, etiology, 1000 Genomes Project, causal variants
- MeSH terms
- Chromosome Mapping, False Positive Reactions, Gene Frequency, Haplotypes, Humans, Genetic Linkage, Models, Genetic, Probability, Genetic Variation, Models, Statistical, Genome, Human, Sequence Analysis, DNA, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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
