Mendel: the Swiss army knife of genetic analysis programs
Open accessAbstract
Summary: Mendel is one of the few statistical genetics packages that provide a full spectrum of gene mapping methods, ranging from parametric linkage in large pedigrees to genome-wide association with rare variants. Our latest additions to Mendel anticipate and respond to the needs of the genetics community. Compared with earlier versions, Mendel is faster and easier to use and has a wider range of applications. Supported platforms include Linux, MacOS and Windows. Availability: Free from www.genetics.ucla.edu/software/mendel Contact: klange@ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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?
Because of high endogamy and consanguinity, not all related individuals could be removed without markedly reducing sample size; association testing was performed with Mendel Ped-GWAS to account for relatedness.
“Also, with the high endogamy and consanguinity in the cohort, we could not remove all related individuals from the analysis without markedly reducing our sample size. To address this, we performed association testing with the Mendel software package (v.14.3) using the Ped-GWAS option30 designed for use with a mixture of related and unrelated individuals.”
From Whole-genome sequencing suggests a chemokine gene cluster that modifies age at onset in familial Alzheimer's disease (2015) · cites this paper as [30]
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
The Future of Genetic Studies of Complex Human Diseases
Risch, N., & Merikangas, K. (1996) · Science · doi:10.1126/science.273.5281.1516 · Cited by 5,355 · see citing works
Exact Matrix Completion via Convex Optimization
Candès, E. J., & Recht, B. (2009) · Foundations of Computational Mathematics · doi:10.1007/s10208-009-9045-5 · Cited by 5,102 · see citing works
A General Model for the Genetic Analysis of Pedigree Data
Elston, R. C., & Stewart, J. (1971) · Human Heredity · doi:10.1159/000152448 · Cited by 1,583 · see citing works
Construction of multilocus genetic linkage maps in humans.
Lander, E. S., & Green, P. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.8.2363 · Cited by 1,440 · see citing works
Genome-wide association analysis by lasso penalized logistic regression
Wu, T. T., Chen, Y. F., Hastie, T., Sobel, E., & Lange, K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp041 · Cited by 785 · see citing works
Self-citationCoordinate descent algorithms for lasso penalized regressionPreprint
Wu, T. T., & Lange, K. L. (2008) · Cited by 740 · see citing works
Self-citationPrograms for pedigree analysis: Mendel, Fisher, and dGene
Lange, K. L., Weeks, D. E., Boehnke, M., MacCluer, J. W., & MacCluer, J. W. (1988) · Genetic Epidemiology · doi:10.1002/gepi.1370050611 · Cited by 616 · see citing works
Self-citationCoordinate descent algorithms for lasso penalized regression
Wu, T. T., & Lange, K. (2008) · The Annals of Applied Statistics · doi:10.1214/07-aoas147 · Cited by 563 · see citing works
Self-citationNumerical Analysis for Statisticians
Lange, K. L. (2010) · Statisctics and computing/Statistics and computing · doi:10.1007/978-1-4419-5945-4 · Cited by 517 · see citing works
Self-citationDetection and Integration of Genotyping Errors in Statistical Genetics
Sobel, E. M., Papp, J. C., & Lange, K. L. (2002) · The American Journal of Human Genetics · doi:10.1086/338920 · Cited by 351 · see citing works
Self-citationFamily-based designs for genome-wide association studies
Ott, J., Kamatani, Y., & Lathrop, M. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2989 · Cited by 268 · see citing works
Faster Multipoint Linkage Analysis Using Fourier Transforms
Kruglyak, L., & LANDER, E. S. (1998) · Journal of Computational Biology · doi:10.1089/cmb.1998.5.1 · Cited by 213 · see citing works
Lange, K. L. (2004) · Springer texts in statistics · doi:10.1007/978-1-4757-4182-7 · Cited by 143 · see citing works
Self-citationAssociation screening of common and rare genetic variants by penalized regression
Zhou, H., Sehl, M. E., Sinsheimer, J. S., & Lange, K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq448 · Cited by 137 · see citing works
Self-citationWöhrle, D., Salat, U., Hameister, H., Vogel, W., & Steinbach, P. J. (2001) · The American Journal of Human Genetics · doi:10.1086/322739 · Cited by 123 · see citing works
Sinsheimer, J. S., Blangero, J., & Lange, K. L. (2000) · The American Journal of Human Genetics · doi:10.1086/302826 · Cited by 62 · see citing works
Self-citationGenotype imputation via matrix completionPreprint
Chi, E. C., Zhou, H., Chen, G. K., Vecchyo, D. O., & Lange, K. L. (2012) · Genome Research · doi:10.1101/gr.145821.112 · Cited by 61 · see citing works
Self-citationLinkage analysis without defined pedigrees
Day-Williams, A., Blangero, J., Dyer, T. D., Lange, K. L., & Sobel, E. M. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20584 · Cited by 43 · see citing works
Self-citationPENALIZED REGRESSION FOR GENOME-WIDE ASSOCIATION SCREENING OF SEQUENCE DATA
Zhou, H., Alexander, D., Sehl, M. E., Sinsheimer, J. S., Sobel, E. M., & LANGE, K. (2010) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814335058_0012 · Cited by 25 · see citing works
Self-citationSinsheimer, J. S., McKenzie, C. A., Keavney, B. D., & LANGE, K. (2001) · Annals of Human Genetics · doi:10.1046/j.1469-1809.2001.6550483.x · Cited by 17 · see citing works
Self-citationPenalized estimation of haplotype frequencies
Ayers, K. L., & Lange, K. L. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn236 · Cited by 16 · see citing works
Self-citationSinsheimer, J. S., McKenzie, C. A., Keavney, B. D., et al. (2001) · PubMed · doi:10.1017/s0003480001008843 · Cited by 15 · see citing works
Self-citationRitchie, M. D., & Bush, W. S. (2010) · Advances in genetics · doi:10.1016/b978-0-12-380862-2.00001-1 · Cited by 14 · see citing works
Estimating ethnic admixture from pedigree data.
Sinsheimer, J., Plaisier, C., Huertas-Vázquez, A., Aguilar-Salinas, C., Tusié-Luna, T., Pajukanta, P., & Lange, K. (2008) · American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.12.014 · Cited by 11 · see citing works
Self-citationLange, K. L., & Sinsheimer, J. S. (2004) · Human Heredity · doi:10.1159/000083031 · Cited by 10 · see citing works
Self-citationA heterozygote–homozygote test of Hardy–Weinberg equilibrium
Zhou, J. J., Lange, K. L., Papp, J. C., & Sinsheimer, J. S. (2009) · European Journal of Human Genetics · doi:10.1038/ejhg.2009.57 · Cited by 10 · see citing works
Self-citationQuantitative Trait Loci Association Mapping by Imputation of Strain Origins in Multifounder Crosses
Zhou, J. J., Ghazalpour, A., Sobel, E. M., Sinsheimer, J. S., & Lange, K. L. (2011) · Genetics · doi:10.1534/genetics.111.135095 · Cited by 9 · see citing works
Self-citationModeling maternal‐offspring gene‐gene interactions: the extended‐MFG test
Childs, E. J., Palmer, C. G. S., Lange, K. L., & Sinsheimer, J. S. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20508 · Cited by 9 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
O'Connell, J., Gurdasani, D., Delaneau, O., Pirastu, N., Ulivi, S., Cocca, M., Traglia, M., Huang, J., Huffman, J. E., Rudan, I., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004234 · Cited by 593 · see citing works
Genetic linkage analysis in the age of whole-genome sequencing
Ott, J., Wang, J., & Leal, S. M. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3908 · Cited by 286 · see citing works
Collaborators, T. U., Leongamornlert, D. A., Saunders, E. J., Dadaev, T., Tymrakiewicz, M., Goh, C. L., Jugurnauth-Little, S., Kozarewa, I., Fenwick, K., Assiotis, I., et al. (2014) · British Journal of Cancer · doi:10.1038/bjc.2014.30 · Cited by 157 · see citing works
“This was implemented in the pedigree analysis software MENDEL (Lange et al, 2013).”
MethodMicrohaplotypes provide increased power from short‐read DNA sequences for relationship inference
Baetscher, D. S., Clemento, A. J., Ng, T. C., Anderson, E. C., & Garza, J. C. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12737 · Cited by 152 · see citing works
“Simulations in CKMRSIM were then performed assuming physical linkage using the package’s ability to call the software MENDEL (Lange et al., 2013).”
MethodHeritability of Chronic Obstructive Pulmonary Disease and Related Phenotypes in Smokers
Zhou, J. J., Cho, M. H., Castaldi, P. J., Hersh, C. P., Silverman, E. K., & Laird, N. M. (2013) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201302-0263oc · Cited by 138 · see citing works
Xicola, R. M., Li, S., Rodriguez, N. J., Reinecke, P., Karam, R., Speare, V., Black, M. H., LaDuca, H., & Llor, X. (2019) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2019-105991 · Cited by 129 · see citing works
Eu‐ahsunthornwattana, J., Miller, E. N., Fakiola, M., Jerônimo, S. M. B., Blackwell, J. M., & Cordell, H. J. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004445 · Cited by 121 · see citing works
“the package Mendel [35], through making use of Mendel’s ability to include household effects.”
InfluentialNovel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways
Duffy, D. L., Zhu, G., Li, X., Sanna, M., Iles, M. M., Jacobs, L. C., Evans, D. M., Yazar, S., Beesley, J., Law, M. H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06649-5 · Cited by 114 · see citing works
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos
Ko, A., Cantor, R. M., Weissglas‐Volkov, D., Nikkola, E., Reddy, P. M. V. L., Sinsheimer, J. S., Paşaniuc, B., Brown, R., Alvarez, M., Rodríguez, A., et al. (2014) · Nature Communications · doi:10.1038/ncomms4983 · Cited by 102 · see citing works
Self-citationRisk of Pancreatic Cancer Among Individuals With Pathogenic Variants in the <i>ATM</i> Gene
Hsu, F.-C., Roberts, N. J., Childs, E., Porter, N., Rabe, K. G., Borgida, A., Ukaegbu, C., Goggins, M. G., Hruban, R. H., Zogopoulos, G., et al. (2021) · JAMA Oncology · doi:10.1001/jamaoncol.2021.3701 · Cited by 91 · see citing works
Koch, I. J., Clark, M. M., Thompson, M. J., Deere, K. A., Wang, J., Duarte, L., Gnanadesikan, G. E., McCoy, E. L., Rubbi, L., Stahler, D. R., et al. (2015) · Molecular Ecology · doi:10.1111/mec.13480 · Cited by 86 · see citing works
“To limit the analysis to relevant members and thus reduce computation time, the pedigree was reduced to include only wolves with methylation values, along with their relatives using the statistical genetics software Mendel’s pedigree trimming option (Lange & Sinsheimer 2004; Lange et al. 2013).”
MethodSelf-citationAPOE , MAPT , and COMT and Parkinson’s Disease Susceptibility and Cognitive Symptom Progression
Paul, K. C., Rausch, R., Creek, M. M., Sinsheimer, J. S., Bronstein, J. M., Bordelon, Y. M., & Ritz, B. R. (2016) · Journal of Parkinson s Disease · doi:10.3233/jpd-150762 · Cited by 81 · see citing works
“, Cary, NC) and Mendel [25] for all analysis.”
MethodInfluentialSelf-citationLalli, M. A., Bettcher, B. M., Arcila, M. L., Garcia, G., Guzman, C., Madrigal, L., Ramirez, L., Acosta-Uribe, J., Baena, A., Wojta, K. J., et al. (2015) · Molecular Psychiatry · doi:10.1038/mp.2015.131 · Cited by 73 · see citing works
Bermejo, J. L., Boekstegers, F., Silos, R. G., Marcelain, K., Pablo Báez, B., Ponce, C. B., Müller, B., Catterina Ferreccio, R., Koshiol, J. E., Fischer, C., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006756 · Cited by 69 · see citing works
Self-citationGerman, C., Sinsheimer, J. S., Klimentidis, Y. C., Zhou, H., & Zhou, J. J. (2019) · Genetic Epidemiology · doi:10.1002/gepi.22276 · Cited by 59 · see citing works
Self-citationWielaender, F., Sarviaho, R., James, F., Hytönen, M. K., Cortez, M. A., Kluger, G. J., Koskinen, L. L. E., Arumilli, M., Kornberg, M., Bathen‐Nöthen, A., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614478114 · Cited by 58 · see citing works
“A case-control association test was performed by PLINK (50) and by Mendel software’s Ped-GWAS (51).”
MethodWeiss, R. B., Vieland, V. J., Dunn, D. M., Kaminoh, Y., Flanigan, K. M., & for the United Dystrophinopathy Project (2018) · Annals of Neurology · doi:10.1002/ana.25283 · Cited by 53 · see citing works
An Extended Twin-Pedigree Study of Neuroticism in the Netherlands Twin Register
Boomsma, D. I., Helmer, Q., Nieuwboer, H. A., Hottenga, J., de Moor, M. H. M., van den Berg, S. M., Davies, G. E., Vink, J. M., Schouten, M. J., Dolan, C. V., et al. (2017) · Behavior Genetics · doi:10.1007/s10519-017-9872-0 · Cited by 51 · see citing works
“Genetic analyses, aiming at estimating total and narrow-sense heritability and the effects of sharing a household, were carried out in Mendel (Lange et al. 2013).”
InfluentialPrevalence and Penetrance of BRCA1 and BRCA2 Germline Mutations in Colombian Breast Cancer Patients
Torres, D., Bermejo, J. L., Rashid, M. U., Briceño, I., Gil, F., López, Á. P. B., Ariza, V. M., & Hamann, U. (2017) · Scientific Reports · doi:10.1038/s41598-017-05056-y · Cited by 47 · see citing works
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 44 · see citing works
Self-citationHomeobox B13 G84E Mutation and Prostate Cancer Risk
Nyberg, T., Govindasami, K., Leslie, G., Dadaev, T., Bancroft, E. K., Raghallaigh, H. N., Brook, M. N., Hussain, N., Keating, D., Lee, A., et al. (2018) · European Urology · doi:10.1016/j.eururo.2018.11.015 · Cited by 41 · see citing works
Nyberg, T., Brook, M. N., Ficorella, L., Lee, A., Dennis, J., Yang, X., Wilcox, N., Dadaev, T., Govindasami, K., Lush, M. J., et al. (2022) · Journal of Clinical Oncology · doi:10.1200/jco.22.01453 · Cited by 35 · see citing works
“3).(54) We adjusted for the nonrandom ascertainment of families by conditioning on data that may have influenced the ascertainment.”
MethodGupta, A., Labus, J. S., Kilpatrick, L. A., Bonyadi, M., Ashe-McNalley, C., Heendeniya, N., Bradesi, S., Chang, L., & Mayer, E. A. (2015) · Brain Structure and Function · doi:10.1007/s00429-015-0996-9 · Cited by 35 · see citing works
“To determine the potential gene predictors of sgACC thickness, a penalized ordinary least squares linear regression analysis controlling for TGMV, race and age was performed using Mendel software, version 13 (Lange et al. 2013; Zhou et al. 2010).”
MethodAnastasopoulos, E., Coleman, A. L., Wilson, M. R., Sinsheimer, J. S., Yu, F., Katafigiotis, S., Founti, P., Salonikiou, A., Pappas, T., Koskosas, A., et al. (2014) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.14-13991 · Cited by 34 · see citing works
“0.(17,18) Linkage disequilibrium (LD) and haplotype analysis was also performed using Mendel version 13.”
MethodSelf-citationSul, J. H., Service, S. K., Huang, A., Ramensky, V. E., Hwang, S., Teshiba, T. M., Park, Y., Ori, A. P. S., Zhang, Z., Mullins, N., et al. (2020) · Translational Psychiatry · doi:10.1038/s41398-020-0758-1 · Cited by 33 · see citing works
“Inspection of available trios (n=67) demonstrated low levels of Mendelian inconsistencies across these candidate sites (0.0026±0.00067, Figure S14).”
MethodInfluentialA fast algorithm for detecting gene–gene interactions in genome-wide association studies
Li, J., Zhong, W., Li, R., & Wu, R. (2014) · The Annals of Applied Statistics · doi:10.1214/14-aoas771 · Cited by 30 · see citing works
“Although most of the available interaction detection methods are designed for binary phenotypes, the Mendel software program [Lange et al. (2001, 2013)] and the Screen and Clean (SC) method [Wu et al. (2010)] can identify important 5On average, the total number of main effects and interactions…”
OpenMendel: a cooperative programming project for statistical genetics
Zhou, H., Sinsheimer, J. S., Bates, D. M., Chu, B. B., German, C., Ji, S. S., Keys, K. L., Kim, J., Ko, S., Mosher, G., et al. (2019) · Human Genetics · doi:10.1007/s00439-019-02001-z · Cited by 26 · see citing works
“Readers may be familiar with our existing statistical package MENDEL [46].”
BackgroundSelf-citationVos, J. R., Hsu, L., Brohet, R. M., Mourits, M. J. E., de Vries, J., Malone, K. E., Oosterwijk, J. C., & de Bock, G. H. (2015) · Journal of Clinical Oncology · doi:10.1200/jco.2014.59.0463 · Cited by 29 · see citing works
Factors determining penetrance in familial atypical haemolytic uraemic syndrome
Sansbury, F. H., Cordell, H. J., Bingham, C., Bromilow, G., Nicholls, A., Powell, R. J., Shields, B. M., Smyth, L., Warwicker, P., Strain, L., et al. (2014) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2014-102498 · Cited by 28 · see citing works
Genetics of Coronary Artery Disease in Taiwan: A Cardiometabochip Study by the Taichi Consortium
Assimes, T. L., Lee, I., Juang, J. J., Guo, X., Wang, T., Kim, E. T., Lee, W., Absher, D., Chiu, Y., Hsu, C., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0138014 · Cited by 27 · see citing works
“Penalized logistic regression was employed using the software MENDEL v14 [24] available from http://www.”
MethodMM Algorithms for Variance Components Models
Zhou, H., Hu, L., Zhou, J. J., & Lange, K. L. (2018) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.2018.1529601 · Cited by 30 · see citing works
“…We simulated a quantitative trait y from a genetic model with two variance components and covariance matrix = σ 2a ̂+σ 2e I, where ̂ is a full-rank empirical kinship matrix estimated from the genome-wide measurements of 212 individuals using Option 29 of the Mendel software (Lange et al. 2013).”
MethodSelf-citationHill, S. Y., Sharma, V., & Jones, B. L. (2016) · Psychiatry Research Neuroimaging · doi:10.1016/j.pscychresns.2016.05.009 · Cited by 26 · see citing works
Black, M. H., Wu, J., Takayanagi, M., Wang, N., Taylor, K. D., Haritunians, T., Trigo, E., Lawrence, J. M., Watanabe, R. M., Buchanan, T. A., et al. (2015) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2014-3246 · Cited by 25 · see citing works
Fine-mapping QTLs in advanced intercross lines and other outbred populations
Gonzales, N. M., & Palmer, A. A. (2014) · Mammalian Genome · doi:10.1007/s00335-014-9523-1 · Cited by 23 · see citing works
“Mendel is a multi-purpose genetics program that can be used for mixed model QTL mapping with marker or pedigree-based estimates of relatedness (Lange et al. 2013).”
Heritability of interpack aggression in a wild pedigreed population of North American grey wolves
vonHoldt, B. M., DeCandia, A. L., Heppenheimer, E., Janowitz‐Koch, I., Shi, R., Zhou, H., German, C. A., Brzeski, K. E., Cassidy, K. A., Stahler, D. R., et al. (2020) · Molecular Ecology · doi:10.1111/mec.15349 · Cited by 22 · see citing works
Self-citationZhou, J. J., Cho, M. H., Lange, C., Lutz, S. M., Silverman, E. K., & Laird, N. M. (2015) · Human Heredity · doi:10.1159/000381641 · Cited by 22 · see citing works
Adjusting for Familial Relatedness in the Analysis of GWAS Data
Thomson, R. J., & McWhirter, R. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6613-4_10 · Cited by 21 · see citing works
GENLIB: an R package for the analysis of genealogical data
Gauvin, H., Lefebvre, J.-F., Moreau, C., Lavoie, È.-M., Labuda, D., Vézina, H., & Roy‐Gagnon, M. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0581-5 · Cited by 21 · see citing works
“Other software implementing gene-dropping simulations (such as Mendel [40]), were conceived with a focus on whole pedigrees as opposed to reconstructed ascending genealogies from large founder populations, resulting in different functionalities and usage compared to GENLIB such as, for example, the…”
MethodGrarup, N., Moltke, I., Andersen, M. K., Bjerregaard, P., Larsen, C. V. L., Dahl‐Petersen, I. K., Jørsboe, E., Tiwari, H. K., Hopkins, S. E., Wiener, H. W., et al. (2018) · Diabetologia · doi:10.1007/s00125-018-4659-2 · Cited by 20 · see citing works
“In CANHRYup ’ ik samples, allele frequencies for the SNPs of interest were estimated using the Mendel program v16 (https://www.genetics.ucla.edu/software/mendel) [33, 34].”
Fedko, I. O., Hottenga, J., Helmer, Q., Mbarek, H., Huider, F., Amin, N., Beulens, J. W. J., Bremmer, M. A., Elders, P. J. M., Galesloot, T. E., et al. (2020) · Psychological Medicine · doi:10.1017/s0033291720000100 · Cited by 20 · see citing works
“Finally, we estimated a genetic correlation between MDD as assessed by LIDAS and clinical MDD as assessed by CIDI, as estimated in the Mendel software package for pedigree analyses (Lange et al., 2013).”
MethodBoekstegers, F., Scherer, D., Ponce, C. B., Marcelain, K., Gárate‐Calderón, V., Waldenberger, M., Morales, E., Armando Rojas, R., Munoz, C., Retamales, J., et al. (2023) · International Journal of Cancer · doi:10.1002/ijc.34607 · Cited by 19 · see citing works
“The MENDEL software was used to conduct survival analyses, as it allowed the integration of the GBC incidence rates from Chile as the baseline hazard.(11,12) To assess model overfitting and overoptimistic predictions through internal validation, all”
MethodKlimentidis, Y. C., Lemas, D. J., Wiener, H. W., O’Brien, D. M., Havel, P. J., Stanhope, K. L., Hopkins, S. E., Tiwari, H. K., & Boyer, B. B. (2013) · Journal of Diabetes · doi:10.1111/1753-0407.12093 · Cited by 19 · see citing works
Sensitized mutagenesis screen in Factor V Leiden mice identifies thrombosis suppressor loci
Westrick, R. J., Tomberg, K., Siebert, A. E., Zhu, G., Winn, M. E., Dobies, S. L., Manning, S. L., Brake, M. A., Cleuren, A. C. A., Hobbs, L. M., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1705762114 · Cited by 18 · see citing works
Major Depressive Disorder and Lifestyle: Correlated Genetic Effects in Extended Twin Pedigrees
Huider, F., Milaneschi, Y., van der Zee, M. D., de Geus, E. J. C., Helmer, Q., Penninx, B. W. J. H., & Boomsma, D. I. (2021) · Genes · doi:10.3390/genes12101509 · Cited by 19 · see citing works
On the use of dense SNP marker data for the identification of distant relative pairs
Sun, M., Jobling, M. A., Taliun, D., Pramstaller, P. P., Egeland, T., & Sheehan, N. A. (2015) · Theoretical Population Biology · doi:10.1016/j.tpb.2015.10.002 · Cited by 18 · see citing works
Phillips, B. C., Rodrigues, N., van Rensburg, A. J., & Perrin, N. (2019) · Evolution · doi:10.1111/evo.13860 · Cited by 17 · see citing works
“…(65° 58′ 12.6′′N, 16° 12′ 43.8′′ E; 416 m asl) only contains XY males with fully differentiated Y chromosomes, whereas the southern population of Tvedöra (55°42′ 0.85′′ N, 13° 25′ 50.91′′ E; 20 m asl) mostly harbors XY°males with proto-sex chromosomes (Rodrigues et al. 2014; Ma et al. 2016).”
BackgroundMethodInfluentialFamily-based approaches: design, imputation, analysis, and beyond
Wijsman, E. M. (2016) · BMC Genetics · doi:10.1186/s12863-015-0318-5 · Cited by 17 · see citing works
“Several different implementations were used by participants, including MONSTER (minimum p value optimized nuisance parameter score test extended to relatives) [61], GEMMA (genome-wide efficient mixedmodel analysis) [62], FARVAT (family-based rare variant association test) VC [63], Mendel [64], and implementations deri…”
MethodInfluentialGenetic Susceptibility in Acute Pancreatitis
Martins, F. O., Gomes, B. C., Rodrigues, A. S., & Rueff, J. (2016) · Pancreas · doi:10.1097/mpa.0000000000000707 · Cited by 17 · see citing works
“2 (UCLA Human Genetics, Los Angeles, Calif ).(25) The Kolmogorov-Smirnov and Shapiro-Wilk tests were used to verify the normality of continuous variables, and the Levene test was used to analyze the homogeneity of variances.”
MethodClark, M. M., Chazara, O., Sobel, E. M., Gjessing, H. K., Magnus, P. M., Moffett, A., & Sinsheimer, J. S. (2016) · Human Heredity · doi:10.1159/000456033 · Cited by 15 · see citing works
Self-citationMulti-Omics Advancements towards Plasmodium vivax Malaria Diagnosis
Aggarwal, S., Peng, W. K., & Srivastava, S. (2021) · Diagnostics · doi:10.3390/diagnostics11122222 · Cited by 16 · see citing works
Franklin, A. D., Schmidt‐Küntzel, A., Terio, K. A., Marker, L. L., & Crosier, A. E. (2015) · Journal of Heredity · doi:10.1093/jhered/esv089 · Cited by 15 · see citing works
“Allele frequencies for the captive North American and wild Namibian cheetah populations were estimated using the software MENDEL (Lange et al. 2013) utilizing known genotypes and complete pedigree information available for all individuals.”
Influentialvan de Weijer, M. P., Pelt, D. H. M., de Vries, L. P., Huider, F., van der Zee, M. D., Helmer, Q., Ligthart, L., Willemsen, G. A. H. M., Boomsma, D. I., de Geus, E. J. C., et al. (2022) · Genes Brain & Behavior · doi:10.1111/gbb.12796 · Cited by 15 · see citing works
Haplotype Estimation and Genotype Imputation
Marchini, J. (2019) · doi:10.1002/9781119487845.ch3 · Cited by 15 · see citing works
An Extended Twin-Pedigree Study of Different Classes of Voluntary Exercise Behavior
van der Zee, M. D., Helmer, Q., Boomsma, D. I., Dolan, C. V., & de Geus, E. J. C. (2020) · Behavior Genetics · doi:10.1007/s10519-019-09990-7 · Cited by 14 · see citing works
Russell, E. M., Carlson, J. C., Krishnan, M., Hawley, N. L., Sun, G., Cheng, H., Naseri, T. K., Reupena, M. S., Viali, S., Tuitele, J., et al. (2022) · BMJ Open Diabetes Research & Care · doi:10.1136/bmjdrc-2021-002275 · Cited by 13 · see citing works
Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes
Wu, W., Hao, H., Liu, Q., Han, X., Wu, Y., Cheng, J., & Lü, D.-J. (2014) · International Journal of Legal Medicine · doi:10.1007/s00414-014-1032-y · Cited by 13 · see citing works
Mega2: validated data-reformatting for linkage and association analyses
Baron, R. V., Kollar, C., Mukhopadhyay, N., & Weeks, D. E. (2014) · Source Code for Biology and Medicine · doi:10.1186/s13029-014-0026-y · Cited by 12 · see citing works
“For example, one might want to use pedstats [1] to check for data validity, PREST [2,3] to check for relationship errors, SOLAR [4,5] to test for linkage, and Mendel [6-8] to test for association in the presence of linkage.”
MethodChu, B. B., Keys, K. L., German, C., Zhou, H., Zhou, J. J., Sobel, E. M., Sinsheimer, J. S., & Lange, K. L. (2020) · GigaScience · doi:10.1093/gigascience/giaa044 · Cited by 12 · see citing works
“Readers can reproduce our results by accessing the software, documentation, and Jupyter notebooks on our Github page: https://github.com/OpenMendel/MendelIHT.jl”
MethodInfluentialSelf-citationFast Genome‐Wide QTL Association Mapping on Pedigree and Population Data
Zhou, H., Blangero, J., Dyer, T. D., Chan, K. H. K., Lange, K. L., & Sobel, E. M. (2016) · Genetic Epidemiology · doi:10.1002/gepi.21988 · Cited by 12 · see citing works
“4 Other Utilities for Handling Pedigree Data To encourage thorough testing of new statistical methods, such as the current Ped-GWAS score test, we have implemented both genotype and trait simulation in our genetic analysis program MENDEL [Lange et al. 2013].”
BackgroundMethodSelf-citationAlarcon, F., Planté‐Bordeneuve, V., Olsson, M. B., & Nuel, G. (2018) · PLoS ONE · doi:10.1371/journal.pone.0203860 · Cited by 10 · see citing works
“This cut-set version of Elston-Stewart (as well as variants of Lander-Green [17] for multi-point analysis) is implemented in the well-known Mendel software [18] which can efficiently perform likelihood computations in complex pedigrees.”
MethodGood, D. M., Duffy, D. L., Good, M., Guo, C. X., Busfield, F., Shaw, A., & Shaw, J. T. E. (2019) · Twin Research and Human Genetics · doi:10.1017/thg.2019.13 · Cited by 10 · see citing works
“We also used MENDEL 16.0 (Lange et al., 2013) to perform individual SNP and haplotype logistic regression-based association analysis, including birth year and sex as covariates.”
MethodInfluentialFamilial Aspects of Mammographic Density Measures Associated with Breast Cancer Risk
Nguyen, T. L., Li, S., Dowty, J. G., Dite, G. S., Ye, Z., Nguyen‐Dumont, T., Trinh, H. N., Evans, C. F., Tan, M., Sung, J., et al. (2022) · Cancers · doi:10.3390/cancers14061483 · Cited by 9 · see citing works
Recombination analysis of autosomal short tandem repeats in C hinese H an families
Liu, Q., Luo, H., Zhao, H., Huang, X., Cheng, J., & Lü, D.-J. (2013) · Electrophoresis · doi:10.1002/elps.201300417 · Cited by 9 · see citing works
Göbel, T. M. K., Bodner, M., Robino, C., Augustin, C., Huber, G. E., Marra, M., Mutesa, L., Pasino, S., Santovito, A., Zimmermann, B., et al. (2019) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2019.102202 · Cited by 9 · see citing works
“X-STRs [19] were additionally considered for the latter dataset using Mendel [23].”
MethodPotential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis
Liu, Q., Li, X., Wu, W., He, X., Liu, K., Zhao, H., & Lu, D. (2016) · Electrophoresis · doi:10.1002/elps.201600238 · Cited by 9 · see citing works
Nikkola, E., Ko, A., Alvarez, M., Cantor, R. M., Garske, K. M., Kim, E., Gee, S., Rodríguez, A., Muxel, R., Matikainen, N., et al. (2017) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2017.07.024 · Cited by 9 · see citing works
“Combining linkage analysis with whole-exome sequencing has become a common approach to pinpoint candidate chromosomal regions and specific variants for Mendelian diseases [10,11].”
InfluentialA Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon
Anderson, E. C., Clemento, A. J., Campbell, M. A., Pearse, D. E., Beulke, A. K., Columbus, C. D., Campbell, E., Thompson, N. F., & Garza, J. C. (2025) · Evolutionary Applications · doi:10.1111/eva.70110 · Cited by 8 · see citing works
“The FNRs were estimated in each case using simple Monte Carlo taking account of the physical linkage of the markers by input-ting their genomic positions into “CKMRsim” and using the package's interface to the MENDEL (Lange et al. 2013) software to simulate genotypes of related pairs in the presence of physical linkag…”
Cumulative risks of colorectal cancer in Han Chinese patients with Lynch syndrome in Taiwan
Kamiza, A. B., Wang, W., You, J., Tang, R., Chien, H., Lai, C., Chiu, L.-L., Lo, T.-P., Hung, K., Hsiung, C. A., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-88289-2 · Cited by 8 · see citing works
Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse
Tomberg, K., Westrick, R. J., Kotnik, E. N., Siemieniak, D. R., Zhu, G., Saunders, T. L., Cleuren, A. C. A., & Ginsburg, D. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007658 · Cited by 8 · see citing works
An Effective Method to Identify Heritable Components from Multivariate Phenotypes
Sun, J., Kranzler, H. R., & Bi, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144418 · Cited by 7 · see citing works
Manley, W., Moreau, M., Azaro, M. A., Siecinski, S. K., Davis, G., Buyske, S. G., Vieland, V. J., Bassett, A. S., & Brzustowicz, L. M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0194233 · Cited by 7 · see citing works
Butler, J. M. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-405213-0.00010-5 · Cited by 7 · see citing works
Wang, T., He, P., Ahn, K. W., Wang, X., Ghosh, S., & Laud, P. W. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00120 · Cited by 7 · see citing works
Andersen, M. K., Jørsboe, E., Skotte, L., Hanghøj, K., Sandholt, C. H., Moltke, I., Grarup, N., Kern, T., Mahendran, Y., Søborg, B., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008544 · Cited by 7 · see citing works
“Allele frequencies for rs4936356 were estimated using the MENDEL program [54].”
MethodFrom Matched Certificates to Related Persons
Mourits, R. J., van Dijk, I. K., & Mandemakers, K. (2020) · Historical Life Course Studies · doi:10.51964/hlcs9310 · Cited by 7 · see citing works
Using an Event-History with Risk-Free Model to Study the Genetics of Alcoholism
Yang, H., Chen, I., Tsay, Y., Li, Z.-R. T., Chen, C., Hwu, H., & Chen, C. (2017) · Scientific Reports · doi:10.1038/s41598-017-01791-4 · Cited by 6 · see citing works
Javanrouh, N., Soltanian, A. R., Tapak, L., Azizi, F., Ott, J., & DANESHPOUR, M. S. (2018) · Genetic Epidemiology · doi:10.1002/gepi.22179 · Cited by 6 · see citing works
Li‐Gao, R., Boomsma, D. I., de Geus, E. J. C., Denollet, J., & Kupper, N. H. M. (2020) · Behavior Genetics · doi:10.1007/s10519-020-10023-x · Cited by 6 · see citing works
A Polynesian-specific missense CETP variant alters the lipid profile
Moors, J., Krishnan, M., Sumpter, N., Takei, R., Bixley, M., Cadzow, M. J., Major, T. J., Phipps‐Green, A. J., Topless, R., Merriman, M. E., et al. (2023) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2023.100204 · Cited by 5 · see citing works
Fast genome-wide pedigree quantitative trait loci analysis using MENDEL
Zhou, H., Zhou, J. J., Sobel, E. M., & Lange, K. L. (2014) · BMC Proceedings · doi:10.1186/1753-6561-8-s1-s93 · Cited by 5 · see citing works
Self-citationPeterson, C. B., Service, S. K., Jasinska, A. J., Gao, F., Zelaya, I., Teshiba, T. M., Bearden, C. E., Cantor, R. M., Reus, V. I., Macaya, G., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006046 · Cited by 5 · see citing works
“To identify genes with differential expression in the BP1 vs. non-BP1 individuals accounting for the correlation induced by relatedness, we used a variance components approach, as implemented in Mendel [10].”
InfluentialPuigdevall, P., Piccari, L., Blanco, I., Barberà, J. A., Geiger, D., Bádenas, C., Milà, M., Castelo, R., & Madrigal, I. (2019) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2018-105669 · Cited by 5 · see citing works
Clark, M. M., Blangero, J., Dyer, T. D., Sobel, E. M., & Sinsheimer, J. S. (2015) · Annals of Human Genetics · doi:10.1111/ahg.12137 · Cited by 4 · see citing works
“We implement the QMFG test by modifying the statistical genetics software package Mendel (Lange et al., 2013).”
MethodInfluentialSelf-citationPerera, N., Wijithalal, R., Galhena, G., & Ranawaka, G. R. (2022) · International Journal of Legal Medicine · doi:10.1007/s00414-021-02762-1 · Cited by 4 · see citing works
“The software Mendel v12 [21] based on maximum likelihood estimation (MLE) algorithm was used to carry out a pairwise linkage analyses by calculating the maximum LOD score for all pairs of markers [7].”
MethodIsaacs, A. J., Barysenka, A., ter Bekke, R. M. A., den Enden, A. T. J. M. H.-V., van den Wijngaard, A., Volders, P. G. A., & Stoll, M. (2023) · Heart Rhythm · doi:10.1016/j.hrthm.2023.02.004 · Cited by 4 · see citing works
Iterative hard thresholding for model selection in genome‐wide association studies
Keys, K. L., Chen, G. K., & Lange, K. (2017) · Genetic Epidemiology · doi:10.1002/gepi.22068 · Cited by 4 · see citing works
“Mendel, gpu-lasso, and PLINK 1.9 beta have multicore acceleration capabilities, while SparSNP can be run on compute clusters.”
BackgroundMethodInfluentialSelf-citationGrange, L. J., Bureau, J., Nikolayeva, I., Paul, R. E. L., Steen, K. V., Schwikowski, B., & Sakuntabhai, A. (2015) · BMC Genetics · doi:10.1186/s12863-015-0174-3 · Cited by 3 · see citing works
“Over the past decades, many tools have been developed for epistasis detection using various statistical methods [5,6], including those based on regression [7-11], linkage disequilibrium and haplotypes [12,13], and Bayesian approaches [14,15].”
MethodHidalgo, B., Aslibekyan, S. W., Wiener, H. W., Irvin, M. R., Straka, R. J., Borecki, I. B., Tiwari, H. K., Tsai, M. Y., Hopkins, P. N., Ordovás, J. M., et al. (2015) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0000000000000162 · Cited by 3 · see citing works
Nuel, G., Lefebvre, A., & Bouaziz, O. (2017) · Computational and Mathematical Methods in Medicine · doi:10.1155/2017/9193630 · Cited by 3 · see citing works
“In that sense, it is very similar to the notion of cutset long used to compute likelihoods in complex pedigrees (see Lange et al., 2013, for a recent reference on the MENDEL package).”
BackgroundMethodInfluentialMeta-Analysis for Penalized Regression Methods with Multi-Cohort Genome-Wide Association Studies
Lu, C., O’Connor, G. T., Dupuis, J., & Kolaczyk, E. D. (2016) · Human Heredity · doi:10.1159/000447969 · Cited by 2 · see citing works
The penetrance R package for estimation of age specific risk in family-based studies
Kubista, N., Braun, D., & Parmigiani, G. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf154 · Cited by 2 · see citing works
“For example, the widely used software package MENDEL by Lange et al. (2008) offers an option for penetrance estimation which can account for a full pedigree, but is difficult to use and interpret.”
Statistical Approaches for Detecting Transgenerational Genetic Effects in Humans
Sinsheimer, J. S., & Creek, M. M. (2013) · Springer eBooks · doi:10.1007/978-1-4614-8078-5_11 · Cited by 2 · see citing works
Self-citationBIS-CATTLE: A Web Server for Breed Identification using Microsatellite DNA Markers
Jaiswal, S., Dhanda, S. K., Iquebal, M. A., Arora, V., Shah, T. M., Angadi, U. B., Joshi, C. G., Raghava, G. P. S., Rai, A. K., & Kumar, V. D. (2016) · Current Research in Bioinformatics · doi:10.3844/ajbsp.2016.10.17 · Cited by 2 · see citing works
“Moreover, for breed differentiation, using SNP 50 K data can be done by limited number of software for example Mendel (Lange et al., 2013) which is again not in server mode further compounding the issue of user-friendliness.”
MethodGenome-wide QTL and eQTL analyses using Mendel
Zhou, H., Zhou, J. J., Hu, T., Sobel, E. M., & Lange, K. L. (2016) · BMC Proceedings · doi:10.1186/s12919-016-0037-6 · Cited by 1 · see citing works
“Mendel continues to mature, and geneticists are advised to give it a second look for genetic analysis [1].”
BackgroundMethodSelf-citationA Case of Maternal Half-sisters Sharing Alleles at 18 X-chromosomal Short Tandem Repeat Loci
Lü, D.-J., Liu, Q., Li, X., & Zhao, H. (2016) · Journal of Forensic Science and Medicine · doi:10.4103/2349-5014.184194 · Cited by 1 · see citing works
Efficient Bayesian methods for mixture models with genetic applications
Zuanetti, D. A. (2019) · doi:10.11606/t.104.2019.tde-20082019-083551 · Cited by 1 · see citing works
“We use software Mendel, available at http://www.genetics.ucla.edu/software/mendel, to do the variance component analysis, see Bauman et al. (2005); Lange & Sobel (2006); Lange et al. (1976, 1983, 2013) for details.”
MethodFast Genome-Wide QTL Analysis Using MendelPreprint
Zhou, H., Zhou, J. J., Hu, T., Sobel, E. M., & Lange, K. L. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1407.8259
“give it a second look for genetic analysis (Lange et al., 2013).”
BackgroundMethodInfluentialSelf-citationPeterson, C. B., Service, S., Jasinska, A. J., Gao, F., Zelaya, I., Teshiba, T. M., Bearden, C. E., Reus, V. I., Macaya, G., López‐Jaramillo, C., et al. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/031427
“To identify genes with differential expression in the BP1 vs. non-BP1 individuals accounting for the correlation induced by relatedness, we used a variance components approach, as implemented in Mendel (Lange et al. 2013).”
MethodInfluentialEstimating relationships and relatedness from dense genome-wide data
Sun, M. (2016) · Leicester Research Archive (University of Leicester)
Identification of Thrombosis Modifier Genes Using ENU Mutagenesis in the Mouse.
Tomberg, K. (2016) · Deep Blue (University of Michigan)
- Authors
- Lange, K., Papp, J. C., Sinsheimer, J. S., Sripracha, R., Zhou, H., & Sobel, E. M.
- Affiliations
- North Carolina State University (US)
- Corresponding author
- Lange, Kenneth
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-04-22
- Volume
- 29
- Issue
- 12
- Pages
- 1568-1570
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3673222
- OpenAlex
- W2133379615
- Cited by
- 109
- References
- 28
- Citations by year
- 2025: 2 · 2024: 2 · 2023: 3 · 2022: 6 · 2021: 8 · 2020: 8 · 2019: 9 · 2018: 9 · 2017: 11 · 2016: 16 · 2015: 17 · 2014: 13 · 2013: 5
- FWCI
- 11.27
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (MH059490)
- National Institute of Mental Health (MH-059490, R37MH059490, R01MH059490)
- National Human Genome Research Institute (HG006139, R01HG006139)
- National Institute of General Medical Sciences (R25GM103774, GM-053275, R01GM053275, GM103774)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- gene mapping, parametric linkage analysis, genome-wide association study, rare variants, pedigree
- MeSH terms
- Chromosome Mapping, Data Interpretation, Statistical, Humans, Genetic Linkage, Pedigree, Software, 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
