30.1: Bibliography

[1] G.R. Abe ̧casis, S.S. Cherny, W.O. Cookson, and L.R. Cardon. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genetics, 30(1):97–101, 2002.

[2] H.L. Allen et al. Hundreds of variants clustered in genomic loci and biological pathways a↵ect human height. Nature, 467(7317):832–838, 2010.

[3] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, 57:289–300, 1995.

[4] D. Botstein, R.L. White, M. Skolnick, and R.W. Davis. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32:314–331, 1980.

[5] M.S. Brown and J.L. Goldstein. A receptor-mediated pathway for cholesterol homeostasis. Science, 232(4746):34–47, 1986.

[6] Jonathan C. Cohen, Eric Boerwinkle, Thomas H. Mosley, and Helen H. Hobbs. Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. 354(12):1264–1272.

[7] B. Devlin and K. Roeder. Genomic control for association studies. Biometrics, 55:997–1004, 1999.

[8] R.C. Elston and J. Stewart. A general model for the genetic analysis of pedigree data. Human Heredity,

21:”523–542”, 1971.

[9] Kyle Kai-How Farh, Alexander Marson, Jiang Zhu, Markus Kleinewietfeld, William J. Housley, Saman- tha Beik, Noam Shoresh, Holly Whitton, Russell J. H. Ryan, Alexander A. Shishkin, Meital Hatan, Marlene J. Carrasco-Alfonso, Dita Mayer, C. John Luckey, Nikolaos A. Patsopoulos, Philip L. De Jager, Vijay K. Kuchroo, Charles B. Epstein, Mark J. Daly, David A. Hafler, and Bradley E. Bernstein. Genetic and epigenetic fine mapping of causal autoimmune disease variants.

[10] Sir R.A. Fisher. The correlation between relatives on the supposition of Mendelian inheritance. Trans- actions of the Royal Society of Edinburgh, 52:399–433, 1918.

[11] D.F. Gudbjartsson, K. Jonasson, M.L. Frigge, and A. Kong. Allegro, a new computer program for multipoint linkage analysis. Nature Genetics, 25(1):12–13, 2000.

[12] D.F Gudbjartsson, T. Thorvaldsson, A. Kong, G. Gunnarsson, and A. Ingolfsdottir. Allegro version 2. Nature Genetics, 37(10):1015–1016, 2005.

[13] Joel T. Haas, Harland S. Winter, Elaine Lim, Andrew Kirby, Brendan Blumenstiel, Matthew DeFe- lice, Stacey Gabriel, Chaim Jalas, David Branski, Carrie A. Grueter, Mauro S. Toporovski, Tobias C. Walther, Mark J. Daly, and Robert V. Farese. DGAT1 mutation is linked to a congenital diarrheal disorder. 122(12):4680–4684.

[14] X. Hu, H. Kim, E. Stahl, R. Plenge, M. Daly, and S. Raychaudhuri. Integrating autoimmune risk loci with gene-expression data identifies specific pathogenic immune cell subsets. The American Journal of Human Genetics, 89(4):496–506, 2011.

[15] R.M. Idury and R.C. Elston. A faster and more general hidden markov model algorithm for multipoint likelihood calculations. Human Heredity, 47:197–202, 1997.

[16] A. Ingolfsdottir and D. Gudbjartsson. Genetic linkage analysis algorithms and their implementation. In Corrado Priami, Emanuela Merelli, Pablo Gonzalez, and Andrea Omicini, editors, Transactions on Computational Systems Biology III, volume 3737 of Lecture Notes in Computer Science, pages 123–144. Springer Berlin / Heidelberg, 2005.

[17] L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. Parametric and nonparametric linkage analysis: a unified multipoint approach. American Journal of Human Genetics, 58:1347–1363, 1996.

[18] L. Kruglyak and E.S. Lander. Faster multipoint linkage analysis using fourier transforms. Journal of Computational Biology, 5:1–7, 1998.

[19] P. Kuballa, A. Huett, J.D. Rioux, M.J. Daly, and R.J. Xavier. Impaired autophagy of an intracellular pathogen induced by a crohn’s disease associated atg16l1 variant. PLoS One, 3(10):e3391, 2008.

[20] E.S. Lander and P. Green. Construction of multilocus genetic linkage maps in humans. Proceedings of the National Academy of Sciences, 84(8):2363–2367, 1987.

[21] E.S. Lander, P. Green, J. Abrahamson, A. Barlow, M.J. Daly, S.E. Lincoln, and L. Newburg. Mapmaker: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1(2):174–181, 1987.

[22] Q. Li, J.B. Brown, H. Huang, and P.J. Bickel. Measuring reproducibility of high-throughput experi- ments. Annals of Applied Statistics, 5:1752–1797, 2011.

[23] E.Y. Liu, Q. Zhang, L. McMillan, F.P. de Villena, and W. Wang. Ecient genome ancestry inference in complex pedigrees with inbreeding. Bioinformatics, 26(12):i199–i207, 2010.

[24] D.G. MacArthur, S. Balasubramanian, A. Frankish, N. Huang, J. Morris, K. Walter, L. Jostins, L. Habegger, J.K. Pickrell, S.B. Montgomery, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science, 335(6070):823–828, 2012.

[25] B.P. McEvoy and P.M. Visscher. Genetics of human height. Economics & Human Biology, 7(3):294 – 306, 2009.

[26] N.E. Morton. Sequential tests for the detection of linkage. The American Journal of Human Genetics, 7(3):277–318, 1955.

[27] N. Patterson, A. Price, and D. Reich. Population structure and eigenanalysis. PLoS Genetics, 2:e190, 2006.

[28] A. Piccolboni and D. Gusfield. On the complexity of fundamental computational problems in pedigree analysis. Journal of Computational Biology, 10:763–773, October 2003.

[29] A. Price et al. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38:904–909, 2006.

[30] J. Pritchard, M. Stephens, N. Rosenberg, and P. Donnelly. Association mapping in structured popula- tions. American Journal of Human Genetics, 67:170–181, 2000.

[31] M.A. Rivas, M. Beaudoin, A. Gardet, C. Stevens, Y. Sharma, C.K. Zhang, G. Boucher, S. Ripke, D. Ellinghaus, N. Burtt, et al. Deep resequencing of gwas loci identifies independent rare variants associated with inflammatory bowel disease. Nature genetics, 2011.

[32] Kaitlin E Samocha, Elise B Robinson, Stephan J Sanders, Christine Stevens, Aniko Sabo, Lauren M McGrath, Jack A Kosmicki, Karola Rehnstrm, Swapan Mallick, Andrew Kirby, Dennis P Wall, Daniel G MacArthur, Stacey B Gabriel, Mark DePristo, Shaun M Purcell, Aarno Palotie, Eric Boerwinkle, Joseph D Buxbaum, Edwin H Cook, Richard A Gibbs, Gerard D Schellenberg, James S Sutcliffe, Bernie Devlin, Kathryn Roeder, Benjamin M Neale, and Mark J Daly. A framework for the interpretation of de novo mutation in human disease. 46(9):944–950.

[33] Evan A. Stein, Scott Mellis, George D. Yancopoulos, Neil Stahl, Douglas Logan, William B. Smith, Eleanor Lisbon, Maria Gutierrez, Cheryle Webb, Richard Wu, Yunling Du, Therese Kranz, Evelyn Gasparino, and Gary D. Swergold. E↵ect of a monoclonal antibody to PCSK9 on LDL cholesterol. 366(12):1108–1118.

[34] T. Strachan and A.P. Read. Human Molecular Genetics. Wiley-Liss, New York, 2 edition, 1999.

[35] S. Yang, Y. Xiao, D. Kang, J. Liu, Y. Li, E. A. B. Undheim, J. K. Klint, M. Rong, R. Lai, and G. F. King. Discovery of a selective NaV1.7 inhibitor from centipede venom with analgesic ecacy exceeding morphine in rodent pain models. 110(43):17534–17539.