Using ancestry matching to combine family-based and unrelated samples for genome-wide association studies
Open accessAbstract
We propose a method to analyze family‐based samples together with unrelated cases and controls. The method builds on the idea of matched case–control analysis using conditional logistic regression (CLR). For each trio within the family, a case (the proband) and matched pseudo‐controls are constructed, based upon the transmitted and untransmitted alleles. Unrelated controls, matched by genetic ancestry, supplement the sample of pseudo‐controls; likewise unrelated cases are also paired with genetically matched controls. Within each matched stratum, the case genotype is contrasted with control/pseudo‐control genotypes via CLR, using a method we call matched‐CLR (mCLR). Eigenanalysis of numerous SNP genotypes provides a tool for mapping genetic ancestry. The result of such an analysis can be thought of as a multidimensional map, or eigenmap, in which the relative genetic similarities and differences amongst individuals is encoded in the map. Once constructed, new individuals can be projected onto the ancestry map based on their genotypes. Successful differentiation of individuals of distinct ancestry depends on having a diverse, yet representative sample from which to construct the ancestry map. Once samples are well‐matched, mCLR yields comparable power to competing methods while ensuring excellent control over Type I error. Copyright © 2010 John Wiley & Sons, Ltd.
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?
No evidence was found for unusual ancestral clustering in parents of probands with 16p11.2 or 7q11.23 CNVs.
“We found no evidence for this.”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Crossett et al., 2010
The method to analyze control and family-based data builds on two related ideas: matched case-control analysis using conditional logistic regression and the natural connection between family-based analysis and conditional logistic regression of alleles found in probands and matched pseudo-controls.
“The method to analyze control and family-based data (49) builds on two related ideas: matched case–control analysis using conditional logistic regression (e.g. 52) and the natural connection between family-based analysis and conditional logistic regression of alleles found in probands (the transmitted alleles) and matched pseudo-controls (formed from transmitted and un-transmitted alleles) (49).”
From A genome-wide scan for common alleles affecting risk for autism (2010) · cites this paper as [49]
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
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
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
Finding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336 · see citing works
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280 · see citing works
(1967) · Project Euclid (Cornell University) · Cited by 4,720 · see citing works
Laplacian Eigenmaps and Spectral Techniques for Embedding and Clustering
Belkin, M., & Niyogi, P. (2002) · The MIT Press eBooks · doi:10.7551/mitpress/1120.003.0080 · Cited by 4,534 · see citing works
Maximum Likelihood Estimation of Misspecified Models
White, H. (1982) · Econometrica · doi:10.2307/1912526 · Cited by 4,175 · see citing works
Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013 · see citing works
Maximum Likelihood Estimation of Misspecified Models
White, H. (1983) · Econometrica · doi:10.2307/1912004 · Cited by 3,702 · see citing works
Spielman, R. S., McGinnis, R. E., & Ewens, W. J. (1993) · PubMed · Cited by 3,679 · see citing works
Genetic Dissection of Complex Traits
Lander, E. S., & Schork, N. J. (1994) · Science · doi:10.1126/science.8091226 · Cited by 3,425 · see citing works
Genomic Control for Association Studies
Devlin, B., & Roeder, K. (1999) · Biometrics · doi:10.1111/j.0006-341x.1999.00997.x · Cited by 3,162 · see citing works
Self-citationGenome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
the NIDDK IBD Genetics Consortium, Barrett, J. C., the Belgian-French IBD Consortium, the Wellcome Trust Case Control Consortium, Hansoul, S., Nicolae, D. L., Cho, J. H., Duerr, R. H., Rioux, J. D., Brant, S. R., et al. (2008) · Nature Genetics · doi:10.1038/ng.175 · Cited by 2,593 · see citing works
Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M. W., Cavalli-Sforza, L. L., et al. (2008) · Science · doi:10.1126/science.1153717 · Cited by 1,947 · see citing works
Genes mirror geography within Europe
Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A., King, K. S., Bergmann, S., Nelson, M. R., et al. (2008) · Nature · doi:10.1038/nature07331 · Cited by 1,479 · see citing works
A genome-wide search for human type 1 diabetes susceptibility genes
Davies, J. L., Kawaguchi, Y., Bennett, S. T., Copeman, J. B., Cordell, H. J., Pritchard, L. E., Reed, P. W., Gough, S. C. L., Jenkins, S. C., Palmer, S. M., et al. (1994) · Nature · doi:10.1038/371130a0 · Cited by 1,276 · 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 2× · see citing works
“[2] Manolio TA, Brooks LD, Collins FS.”
BackgroundFull Matching in an Observational Study of Coaching for the SAT
Hansen, B. B. (2004) · Journal of the American Statistical Association · doi:10.1198/016214504000000647 · Cited by 648 · see citing works
A Generalization of the Transmission/Disequilibrium Test for Uncertain-Haplotype Transmission
Clayton, D. G. (1999) · The American Journal of Human Genetics · doi:10.1086/302577 · Cited by 634 · see citing works
Falk, C. T., & Rubinstein, P. G. (1987) · Annals of Human Genetics · doi:10.1111/j.1469-1809.1987.tb00875.x · Cited by 618 · see citing works
A Genealogical Interpretation of Principal Components Analysis
McVean, G. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000686 · Cited by 566 · see citing works
Genomic Control, a New Approach to Genetic-Based Association Studies
Devlin, B., Roeder, K., & Wasserman, L. (2001) · Theoretical Population Biology · doi:10.1006/tpbi.2001.1542 · Cited by 511 · see citing works
Self-citationBalding, D., & Nichols, R. (2005) · Genetica · doi:10.1007/bf01441146 · Cited by 453 · see citing works
Cordell, H. J., & Clayton, D. G. (2002) · The American Journal of Human Genetics · doi:10.1086/338007 · Cited by 411 · see citing works
Learning Eigenfunctions Links Spectral Embedding and Kernel PCA
Bengio, Y., Delalleau, O., Roux, N. L., Paiement, J.-F., Vincent, P., & Ouimet, M. (2004) · Neural Computation · doi:10.1162/0899766041732396 · Cited by 345 · see citing works
Nelson, M. R., Bryc, K., King, K. S., Indap, A., Boyko, A. R., Novembre, J., Briley, L. P., Maruyama, Y., Waterworth, D. M., Waeber, G., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.08.005 · Cited by 293 · see citing works
Genotype relative risks: methods for design and analysis of candidate-gene association studies.
Schaid, D. J., & Sommer, S. S. (1993) · PubMed · Cited by 292 · see citing works
Transmission/Disequilibrium Tests for Extended Marker Haplotypes
Clayton, D. G., & Jones, H. (1999) · The American Journal of Human Genetics · doi:10.1086/302566 · Cited by 279 · see citing works
Comparison of statistics for candidate-gene association studies using cases and parents.
Schaid, D. J., & Sommer, S. S. (1994) · PubMed · Cited by 203 · see citing works
Knapp, M. (1999) · The American Journal of Human Genetics · doi:10.1086/302285 · Cited by 165 · see citing works
Thornton, T. A., & McPeek, M. S. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.01.001 · Cited by 161 · see citing works
Heath, S. C., Gut, I. G., Brennan, P., McKay, J., Bencko, V., Fabiánová, E., Foretová, L., Georges, M., Janout, V., Kabesch, M., et al. (2008) · European Journal of Human Genetics · doi:10.1038/ejhg.2008.210 · Cited by 160 · see citing works
Design and Analysis of Case-Control Studies
Breslow, N. E. (1982) · Annual Review of Public Health · doi:10.1146/annurev.pu.03.050182.000333 · Cited by 160 · see citing works
On Estimating HLA/Disease Association with Application to a Study of Aplastic Anemia
Self, S. G., Longton, G., Kopecky, K. J., & Liang, K. (1991) · Biometrics · doi:10.2307/2532495 · Cited by 160 · see citing works
Genomic Control to the extreme
Devlin, B., Bacanu, S.-A., & Roeder, K. (2004) · Nature Genetics · doi:10.1038/ng1104-1129 · Cited by 157 · see citing works
Self-citationA Simple and Improved Correction for Population Stratification in Case-Control Studies
Epstein, M. P., Allen, A. S., & Satten, G. A. (2007) · The American Journal of Human Genetics · doi:10.1086/516842 · Cited by 143 · see citing works
Zhu, X., Li, S., Cooper, R., & Elston, R. C. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.10.009 · Cited by 129 · see citing works
Luca, D., Ringquist, S., Klei, L., Lee, A. B., Gieger, C., Wichmann, H.-E., Schreiber, S., Krawczak, M., Lu, Y., Styche, A., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.11.003 · Cited by 128 · see citing works
Self-citationCharacterization of multilocus linkage disequilibrium
Rinaldo, A., Bacanu, S., Devlin, B., Sonpar, V. A., Wasserman, L., & Roeder, K. (2005) · Genetic Epidemiology · doi:10.1002/gepi.20056 · Cited by 109 · see citing works
Self-citationLange, C., & Laird, N. M. (2002) · Genetic Epidemiology · doi:10.1002/gepi.209 · Cited by 108 · see citing works
Discovering genetic ancestry using spectral graph theory
Lee, A. B., Luca, D., Klei, L., Devlin, B., & Roeder, K. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20434 · Cited by 108 · cited 14× · see citing works
“Analysis was performed separately for each continent using SpectralGEM.”
BackgroundMethodInfluentialSelf-citationCase-parents design for gene-environment interaction
Schaid, D. J. (1999) · Genetic Epidemiology · doi:10.1002/(sici)1098-2272(1999)16:3 · Cited by 95 · see citing works
Genetic Association Analysis Using Data from Triads and Unrelated Subjects
Epstein, M. P., Veal, C., Trembath, R. C., Barker, J. N. W. N., Li, C., & Satten, G. A. (2005) · The American Journal of Human Genetics · doi:10.1086/429225 · Cited by 70 · see citing works
Nagelkerke, N. J. D., Hoebee, B., Teunis, P. F. M., & Kimman, T. G. (2004) · European Journal of Human Genetics · doi:10.1038/sj.ejhg.5201255 · Cited by 60 · see citing works
Cordell, H. J. (2004) · Genetic Epidemiology · doi:10.1002/gepi.10306 · Cited by 51 · see citing works
Guan, W., Liang, L., Boehnke, M., & Abecasis, G. R. (2009) · Genetic Epidemiology · doi:10.1002/gepi.20403 · Cited by 43 · see citing works
Case‐control association studies with matching and genomic controlling
Lee, W. (2004) · Genetic Epidemiology · doi:10.1002/gepi.20011 · Cited by 27 · see citing works
Genome-wide association database developed in the Japanese Integrated Database Project
Koike, A., Nishida, N., Inoue, I., Tsuji, S., & Tokunaga, K. (2009) · Journal of Human Genetics · doi:10.1038/jhg.2009.68 · Cited by 26 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [39]Huber P The behaviour of maximum likelihood estimates under non-standard conditions. Proceedings of the Fifth Berkeley Symposium in Mathematical Statistics and Probability 1967 1 221 233
Cited by
Sorted by citations
Sanders, S. J., Ercan-Sencicek, A. G., Hus, V., Luo, R., Murtha, M. T., Moreno-De-Luca, D., Chu, S. H., Moreau, M. P., Gupta, A. R., Thomson, S. A., et al. (2011) · Neuron · doi:10.1016/j.neuron.2011.05.002 · Cited by 1,263 · see citing works
Self-citationIdentification of common variants influencing risk of the tauopathy progressive supranuclear palsy
PSP Genetics Study Group, Höglinger, G. U., Melhem, N. M., Dickson, D. W., Sleiman, P. M. A., Wang, L.-S., Klei, L., Rademakers, R., de Silva, R., Litvan, I., et al. (2011) · Nature Genetics · doi:10.1038/ng.859 · Cited by 603 · see citing works
Self-citationA genome-wide scan for common alleles affecting risk for autism
Anney, R., Klei, L., Pinto, D., Regan, R., Conroy, J., Magalhaes, T. R., Correia, C., Abrahams, B. S., Sykes, N., Pagnamenta, A. T., et al. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq307 · Cited by 593 · see citing works
Self-citationIndividual common variants exert weak effects on the risk for autism spectrum disorders
Anney, R., Klei, L., Pinto, D., Almeida, J., Bacchelli, E., Baird, G., Bolshakova, N., Bölte, S., Bolton, P. F., Bourgeron, T., et al. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds301 · Cited by 375 · see citing works
Self-citationChaste, P., Klei, L., Sanders, S. J., Hus, V., Murtha, M. T., Lowe, J. K., Willsey, A. J., Moreno-De-Luca, D., Yu, T. W., Fombonne, E., et al. (2015) · Biological Psychiatry · doi:10.1016/j.biopsych.2014.09.017 · Cited by 144 · see citing works
Self-citationDo common variants play a role in risk for autism? Evidence and theoretical musings
Devlin, B., Melhem, N., & Roeder, K. (2011) · Brain Research · doi:10.1016/j.brainres.2010.11.026 · Cited by 105 · see citing works
Self-citation
- Authors
- Crossett, A., Kent, B. P., Klei, L., Ringquist, S., Trucco, M., Roeder, K., & Devlin, B.
- Affiliations
- Carnegie Mellon University (US)
- University of Pittsburgh (US)
- Children's Hospital of Pittsburgh (US)
- Corresponding author
- Roeder, Kathryn
- Venue
- Statistics in Medicine
- Publisher
- Wiley
- Published
- 2010-09-22
- Volume
- 29
- Issue
- 28
- Pages
- 2932-2945
- ISSN
- 0277-6715 (ISSN-L)
- 1097-0258
- PMC
- PMC4629477
- OpenAlex
- W2134071364
- Cited by
- 15
- References
- 48
- Citations by year
- 2022: 1 · 2021: 2 · 2019: 1 · 2016: 1 · 2015: 1 · 2014: 2 · 2012: 1
- FWCI
- 1.26
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Statistics in Medicine (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Defense
- Autism Speaks (AS7462)
- National Institutes of Health
- Office of Naval Research
- National Institute of Mental Health (R37MH057881, R01MH057881, MH057881)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- family-based association, matched case-control analysis, conditional logistic regression, trio analysis, genome-wide association study, type I error control
- MeSH terms
- Diabetes Mellitus, Type 1, Family, Female, HLA Antigens, Humans, Male, Pedigree, Models, Statistical, Logistic Models, Case-Control Studies, Polymorphism, Single Nucleotide, Racial Groups, Genome-Wide Association Study, Biostatistics
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
