Mendel

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The Mendel software program performs likelihood-based statistical analysis to solve a variety of genetic problems. Implementations are included for all common, and several novel, statistical genetic tests. Data sets can consist of qualitative or quantitative traits, pedigree or population samples, limited loci or dense SNPs. Where appropriate, the analysis will use either the Elston-Stewart or Lander-Green-Kruglyak algorithms, whichever is more efficient for each individual pedigree.

Mendel includes options to:

  1. order and map a set of markers along a chromosome;
  2. use parametric linkage methods to localize a gene on a fixed marker map;
  3. use non-parametric linkage (NPL) methods to localize a gene on a fixed marker map;
  4. estimate haplotypes;
  5. identify potential genotyping errors;
  6. test for allelic association by the TDT or the gamete-competition model;
  7. determine kinship coefficients conditional on marker data;
  8. perform genetic risk calculations;
  9. test for paternity or other pedigree relationships;
  10. estimate allele frequencies using either pedigrees or a random sample;1
  11. estimate trait genotype penetrances;
  12. estimate ethnic composition using pedigree data;
  13. identify deviations from Hardy-Weinberg and linkage equilibrium;
  14. simulate genetic data by gene dropping;
  15. localize QTLs, including X-linked QTLs, using variance component analysis;
  16. perform association analysis on quantitative traits;
  17. test for association given linkage; and
  18. trim pedigrees to a core group and all necessary connecting relatives.
  19. dense SNP genotype imputation, including haplotypes.
  20. dense SNP association testing.

Contact and Citation Information

Contact Information:

Kenneth Lange

mendel@genetics.ucla.edu

Citation:

Lange K, Cantor R, Horvath S, Perola M, Sabatti C, Sinsheimer J, Sobel E (2001) Mendel version 4.0: A complete package for the exact genetic analysis of discrete traits in pedigree and population data sets. Amer J Hum Genetics 69(supplement):504.

New Features

New Features in Mendel version 9.0.0

Significant new analysis options have been added to Mendel to enable analysis of high-density, genome-wide SNP data. First, new data file formats are now used by Mendel to efficiently handle the possibly billions of genotypes in these data sets. The new file formats are discussed in Section 0.6 of the documentation. Standard, SNP-major PLINK binary pedigree files, so-called "bed" files, can now be used by Mendel. In addition, we allow for ordered SNP genotypes through the use of a coordinated SNP phase file. Conversions between comma-separated Mendel files and these new binary data files, in either direction, are performed by the new FILE_CONVERSION analysis option, which is discussed in Section 25 of the documentation.

Two major new analysis options require these binary SNP data files as their input, SNP_IMPUTATION and SNP_ASSOCIATION. SNP imputation, as described in Section 23, fills in all missing SNP genotypes based predominantly on linkage disequilibrium (LD) considerations. This option can also impute all SNP haplotypes if requested.

SNP association testing, as discussed in Section 24, tests for association between SNPs and a quantitative trait or a case-control disease status. This option performs both univariate SNP-by-SNP analysis and lasso penalized multivariate analysis. It will test for interactions among the most potent predictors. You can select this set of predictors or let Mendel do it for you. If you request higher-order interactions, please keep in mind that Mendel can be overwhelmed by the sheer number of interactions sought.

Several additions have been made to the TRIM_PEDIGREES analysis option. Input data for this option can now come from binary SNP data files. In this case, the results are repackaged into new binary data files. Four new trimming models have also been introduced, for a total of nine. Each of the new models extracts specified individuals and puts them in new files as unrelateds.

Hardy-Weinberg equilibrium testing can now be performed on pedigrees as part of allele frequency estimation; see the documentation for more details. There is also a new quantitative transformation function, THRESHOLD. In the transformed variable, this new function replaces all values at or above a user-specified threshold with 1.0, and all other values (including missing values) with 0.0. Use the new keyword INDICATOR_THRESHOLD to set the threshold value.

For genotypes not listed in the penetrance file, or under control of penetrance commands in the control file, the default penetrance value is now 1. As always this can be changed using the keyword DEFAULT_PENETRANCE in the control file. Regardless of its default penetrance value, Mendel assigns a penetrance of 1 to each legal genotype of someone missing both a penetrance in the penetrance file and a phenotype at the locus.

Finally, the map file is no longer necessary if all loci listed in the definition file should be included in the analysis, and should be treated as unlinked loci. The sole exception at this time is Location Score analysis, where the map file is still required since the first locus listed in the map file is mapped against all the other model loci.

Any comments, suggestions, and questions regarding Mendel are welcome at mendel@genetics.ucla.edu.

Mendel 2009 Software License Agreement

Please read and specify that you agree or disagree at the bottom of this document.

Name of software being licensed: MENDEL

THIS IS A LEGAL AGREEMENT BETWEEN YOU (EITHER AS AN INDIVIDUAL OR ENTITY) AND KENNETH L. LANGE. BY INSTALLING THIS SOFTWARE, YOU ARE CONSENTING TO BE BOUND BY AND ARE BECOMING A PARTY TO THIS AGREEMENT. IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT, DO NOT INSTALL MENDEL.

THIS LICENSE COVERS ONLY THE YEAR 2009 AND THE FIRST THREE MONTHS OF THE FOLLOWING YEAR. AT THE EXPIRATION OF THIS LICENSE, YOU MUST DESTROY ANY COPIES OF MENDEL OBTAINED UNDER THIS LICENSE. IF YOU WISH TO CONTINUE USING MENDEL, THEN YOU MUST DOWNLOAD A NEW COPY AND AGREE TO A NEW LICENSE.

TERMS OF THE LICENSE:

FEES: You may download Mendel as often as necessary, free of charge.

RESTRICTIONS: You may NOT

(a) copy, redistribute, post, or otherwise enable or permit other individuals to access or use MENDEL except under the terms listed herein;

(b) permit concurrent use of the Software except under the terms listed herein;

(c) modify, translate, reverse engineer, decompile, disassemble, or create derivative works based on MENDEL;

(d) rent, lease, grant a security interest in, or otherwise transfer rights to Mendel; or

(e) remove or put any proprietary notices or labels on MENDEL.

TITLE: Title, ownership rights, and intellectual property rights in MENDEL shall remain with Kenneth Lange. MENDEL is protected by copyright and other intellectual property laws and by international treaties.

DISCLAIMER OF WARRANTY: MENDEL IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND. KENNETH LANGE MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT. THE ENTIRE RISK ARISING OUT OF THE USE OR PERFORMANCE OF MENDEL AND ITS DOCUMENTATION REMAINS WITH LICENSEE. IN NO EVENT SHALL KENNETH LANGE BE LIABLE FOR ANY CONSEQUENTIAL, INCIDENTAL, DIRECT, INDIRECT, SPECIAL, PUNITIVE, OR OTHER DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION OR OTHER PECUNIARY LOSS) ARISING OUT OF THIS AGREEMENT OR THE USE OF OR INABILITY TO USE MENDEL.

INSTALLATION: LICENSEE warrants and represents that a competent System Administrator will install MENDEL, and that the System Administrator will carefully review all documentation, manual pages, and release notes included with MENDEL prior to installation.

USE: LICENSEE agrees to provide KENNETH LANGE with a report of any errors encountered in LICENSEE'S use of MENDEL.

RISK: The entire risk as to the use and performance of MENDEL is assumed by LICENSEE. LICENSEE shall defend, indemnify and hold harmless KENNETH LANGE AND HIS EMPLOYER, THE UNIVERSITY OF CALIFORNIA, for and against any and all claims, demands, damages, losses, and expenses of any kind (including but not limited to attorneys' fees), relating to or arising from any use or disposition by LICENSEE or its transferees of MENDEL.

MAINTENANCE: Neither KENNETH LANGE nor the UNIVERSITY OF CALIFORNIA is obligated to provide maintenance, technical support, interpretation of results, or updates for MENDEL.

TERMINATION: This license will terminate automatically if you fail to comply with the limitations described herein. On termination, you must destroy all copies of the Software and Documentation.

ACKNOWLEDGEMENT: LICENSEE agrees to reference MENDEL in every publication that employs it. See the top of every standard output file generated by MENDEL for the preferred citation to use.