SPA
Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual's DNA. Accurately modeling ancestry is an important step in identifying genetic variation involved in disease.
SPA was created by Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin
For general questions, comments or suggestions about SPA, please email Eleazar Eskin (eeskin (AT) cs.ucla.edu).
Version 1.10 was released on 2012-10-17, with support of personal genotype file from 23andMe.
23andMe users with genotype file please check here .
2 Dimensional Mapping and 3 Dimensional Mapping
Identifying Loci with Steep Allele Frequency Gradients
News
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v1.1.3 (2013-04-04) version 1.13 was released. Bug fixed for genotype file read.
v1.1.2 (2013-03-24) version 1.12 was released. Bug fixed for minor/major allele swap, and a numerical problem when training model in Mac OS X.
v1.1.1 (2013-03-18) version 1.11 was released. Bug fixed for minor/major allele swap.
v1.1.0 (2012-10-17) version 1.10 was released. SPA can predict ancestry origins for individuals with 23andMe genotype file.
v1.0.0 beta (2012-08-28) version 1.0.0 beta was deployed. Source code was also released in GitHub. A model file for Europe population ancestry inference is released online.
MATLAB version (2012-06-06) MATLAB version was deployed.
v0.9.9 (2012-05-29) Beta 4 version was deloyped. Bug fixed for 3 dimensional mapping and running time is improved.
v0.9.8 (2012-05-24) Beta 3 version was deloyped. Running time is significantly speed up by tuning optimization parameters, bug fixed, and sufficient test is performed.
v0.9.5 (2012-05-21) Beta 2 version was deployed. Binary PED fileset is supported. A bug is fixed and a bitwise strategy is used to significantly reduce memory usage.
v0.9.0 (2012-05-08) Beta version was deployed and user manual is available
v0.1.0 (2012-03-18) Preliminary version was deployed
Selected Press Coverage
Publication
Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin. A model based approach for analysis of spatial structure in genetic data. Nature Genetics, 44, 725–731 (2012). Read more.
Contact
For general questions, comments or suggestions about SPA, please email Eleazar Eskin (eeskin (AT) cs.ucla.edu).
For specific questions or bug report about SPA software, please email Wen-Yun Yang (wenyun (AT) ucla.edu).
Acknowledgements
W.Y. and E.E. are supported by supported by National Science Foundation grants 0513612, 0731455, 0729049, 0916676 and 1065276, and National Institutes of Health grants K25-HL080079, U01-DA024417, P01-HL30568 and PO1-HL28481. J.N. is supported by National Science Foundation grants 0933731 and the Searle Scholars Program. E.H is a faculty fellow of the Edmond J. Safra Program in Tel-Aviv University. E.H was partially supported by the Israeli Science Foundation, grant no. 04514831, and by the IBM open collaborative research.