References

[CKM+07]

Cano, P., Klitz, W., Mack, S. J., Maiers, M., Marsh, S. G. E., Noreen, H., Reed, E. F., Senitzer, D., Setterholm, M., Smith, A., and Fernández-Viña, M. Common and well-documented HLA alleles: report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics. Human Immunology, 68(5):392–417, 2007. doi:10.1016/j.humimm.2007.01.014.

[CHT+99]

Chen, J. J., Hollenbach, J. A., Trachtenberg, E. A., Just, J. J., Carrington, M., Ronningen, K. S., Begovich, A. B., King, M.-C., McWeeney, S. K., Mack, S. J., Erlich, H. A., and Thomson, G. Hardy-Weinberg testing for HLA class II (DRB1, DQA1, DQB1, and DPB1) loci in 26 human ethnic groups. Tissue Antigens, 54(6):533–542, 1999. doi:10.1034/j.1399-0039.1999.540601.x.

[Cra46]

Cramér, H. Mathematical Methods of Statistics. Princeton University Press, Princeton, NJ, 1946. ISBN 978-0-691-00547-8.

[DLR77]

Dempster, A. P., Laird, N. M., and Rubin, D. B. Maximum Likelihood from Incomplete Data Via the EM Algorithm. Journal of the Royal Statistical Society: Series B (Methodological), 39(1):1–38, 1977. doi:10.1111/j.2517-6161.1977.tb01600.x.

[Ewe72]

Ewens, W. J. The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3(1):87–112, 1972. doi:10.1016/0040-5809(72)90035-4.

[EL10]

Excoffier, L. and Lischer, H. E. L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3):564–567, 2010. doi:10.1111/j.1755-0998.2010.02847.x.

[ES95]

Excoffier, L. and Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution, 12(5):921–927, 1995. doi:10.1093/oxfordjournals.molbev.a040269.

[GT92]

Guo, S. W. and Thompson, E. A. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48(2):361–372, 1992. doi:10.2307/2532296.

[Hed87]

Hedrick, P. W. Gametic disequilibrium measures: proceed with caution. Genetics, 117(2):331–341, 1987. doi:10.1093/genetics/117.2.331.

[LNM+03]

Lancaster, A., Nelson, M. P., Meyer, D., Single, R. M., and Thomson, G. PyPop: a software framework for population genomics: analyzing large-scale multi-locus genotype data. Pacific Symposium on Biocomputing, pages 514–525, 2003. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891851/ (accessed on 2024-01-04)

[LNS+07]

Lancaster, A. K., Nelson, M. P., Single, R. M., Meyer, D., and Thomson, G. Software framework for the Biostatistics Core of the International Histocompatibility Working Group. In Hansen, J. A., editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I, pages 510–517. IHWG Press, Seattle, WA, 2007.

[LSS+07]

Lancaster, A. K., Single, R. M., Solberg, O. D., Nelson, M. P., and Thomson, G. PyPop update – a software pipeline for large-scale multilocus population genomics. Tissue Antigens, 69(s1):192–197, 2007. doi:10.1111/j.1399-0039.2006.00769.x.

[MSMM+07]

Mack, S. J., Sanchez-Mazas, A., Meyer, D., Single, R. M., Tsai, Y., and Erlich, H. A. Methods used in the generation and preparation of data for analysis in the 13th International Histocompatibility Workshop. In Hansen, J. A., editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I, pages 564–579. IHWG Press, Seattle, WA, 2007.

[MSM+07]

Meyer, D., Single, R. M., Mack, S. J., Lancaster, A. K., Nelson, M. P., Erlich, H. A., Fernández-Viña, M., and Thomson, G. Single locus polymorphism of classical HLA genes. In Hansen, J. A., editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I, pages 653–704. IHWG Press, Seattle, WA, 2007.

[SKE+99]

Salamon, H., Klitz, W., Easteal, S., Gao, X., Erlich, H. A., Fernandez-Viña, M., Trachtenberg, E. A., McWeeney, S. K., Nelson, M. P., and Thomson, G. Evolution of HLA class II molecules: Allelic and amino acid site variability across populations. Genetics, 152(1):393–400, 1999. doi:10.1093/genetics/152.1.393.

[SKRE00]

Schneider, S., Kueffer, J.-M., Roessli, D., and Excoffier, L. Arlequin: A software for population genetics data analysis. Ver 2.000. 2000. URL: http://cmpg.unibe.ch/software/arlequin/ (accessed on 2024-01-06)

[SMM+07]

Single, R. M., Meyer, D., Mack, S. J., Lancaster, A. K., Nelson, M. P., Erlich, H. A., Fernández-Viña, M., and Thomson, G. Haplotype frequencies and linkage disequilibrium among classical HLA genes. In Hansen, J. A., editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I, pages 705–746. IHWG Press, Seattle, WA, 2007.

[SMT07]

Single, R. M., Meyer, D., and Thomson, G. Statistical methods for analysis of population genetic data. In Hansen, J. A., editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I, pages 518–522. IHWG Press, Seattle, WA, 2007.

[Sla94]

Slatkin, M. An exact test for neutrality based on the Ewens sampling distribution. Genetics Research, 64(1):71–74, 1994. doi:10.1017/S0016672300032560.

[Sla96]

Slatkin, M. A correction to the exact test based on the Ewens sampling distribution. Genetics Research, 68(3):259–260, 1996. doi:10.1017/S0016672300034236.

[SML+08]

Solberg, O. D., Mack, S. J., Lancaster, A. K., Single, R. M., Tsai, Y., Sanchez-Mazas, A., and Thomson, G. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies. Human Immunology, 69(7):443–464, 2008. doi:10.1016/j.humimm.2008.05.001.

[TS14]

Thomson, G. and Single, R. M. Conditional asymmetric linkage disequilibrium (ALD): extending the bi-allelic r² measure. Genetics, 198(1):321–331, 2014. doi:10.1534/genetics.114.165266.

[Wat78]

Watterson, G. A. The homozygosity test of neutrality. Genetics, 88(2):405–417, 1978. doi:10.1093/genetics/88.2.405.