References:
Alsalem, A. B., Halees, A. S., Anazi, S., Alshamekh, S., & Alkuraya, F. S. (2013). Autozygome sequencing expands the horizon of human knockout research and provides novel insights into human phenotypic variation.PLoS Genetics , 9 (12), e1004030. doi: 10.1371/journal.pgen.1004030
Auton, A., Abecasis, G. R., Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., … Abecasis, G. R. (2015). A global reference for human genetic variation. Nature , 526 (7571), 68–74. doi: 10.1038/nature15393
Bittles, A. H., & Black, M. L. (2010). Consanguinity, human evolution, and complex diseases. Proceedings of the National Academy of Sciences , 107 (suppl 1), 1779–1786. doi: 10.1073/pnas.0906079106
Cavalli-Sforza, L. L., & Bodmer, W. F. (1999). The Genetics of Human Populations . Courier Corporation.
Ceballos, F. C., Hazelhurst, S., & Ramsay, M. (2018). Assessing runs of Homozygosity: A comparison of SNP Array and whole genome sequence low coverage data. BMC Genomics , 19 (1), 106. doi: 10.1186/s12864-018-4489-0
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018). Runs of homozygosity: Windows into population history and trait architecture. In Nature Reviews Genetics . doi: 10.1038/nrg.2017.109
Chahrour, M. H., Yu, T. W., Lim, E. T., Ataman, B., Coulter, M. E., Hill, R. S., … Walsh, C. A. (2012). Whole-exome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism. PLoS Genetics , 8 (4), e1002635. doi: 10.1371/journal.pgen.1002635
Gibson, J., Morton, N. E., & Collins, A. (2006). Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics , 15 (5), 789–795. doi: 10.1093/hmg/ddi493
Gusev, A., Lowe, J. K., Stoffel, M., Daly, M. J., Altshuler, D., Breslow, J. L., … Pe’er, I. (2009). Whole population, genome-wide mapping of hidden relatedness. Genome Research , 19 (2), 318–326. doi: 10.1101/gr.081398.108
Howrigan, D. P., Simonson, M. A., & Keller, M. C. (2011). Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms. BMC Genomics , 12 . doi: 10.1186/1471-2164-12-460
Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., … MacArthur, D. G. (2020). The mutational constraint spectrum quantified from variation in 141,456 humans.Nature , 581 (7809), 434–443. doi: 10.1038/s41586-020-2308-7
Keller, M. C., Visscher, P. M., & Goddard, M. E. (2011). Quantification of Inbreeding Due to Distant Ancestors and Its Detection Using Dense Single Nucleotide Polymorphism Data. Genetics , 189 (1), 237–249. doi: 10.1534/genetics.111.130922
Leutenegger, A.-L., Prum, B., Génin, E., Verny, C., Lemainque, A., Clerget-Darpoux, F., & Thompson, E. A. (2003). Estimation of the Inbreeding Coefficient through Use of Genomic Data. American Journal of Human Genetics , 73 (3), 516–523.
Li, H. (2014). Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics ,30 (20), 2843–2851. doi: 10.1093/bioinformatics/btu356
Magi, A., Tattini, L., Palombo, F., Benelli, M., Gialluisi, A., Giusti, B., … Pippucci, T. (2014). H3M2: Detection of runs of homozygosity from whole-exome sequencing data. Bioinformatics (Oxford, England) , 30 (20), 2852–2859. doi: 10.1093/bioinformatics/btu401
Marioni, J. C., Thorne, N. P., & Tavaré, S. (2006). BioHMM: A heterogeneous hidden Markov model for segmenting array CGH data.Bioinformatics , 22 (9), 1144–1146. doi: 10.1093/bioinformatics/btl089
Narasimhan, V., Danecek, P., Scally, A., Xue, Y., Tyler-Smith, C., & Durbin, R. (2016). BCFtools/RoH: A hidden Markov model approach for detecting autozygosity from next-generation sequencing data.Bioinformatics , 32 (11), 1749–1751. doi: 10.1093/bioinformatics/btw044
Pemberton, T. J., Absher, D., Feldman, M. W., Myers, R. M., Rosenberg, N. A., & Li, J. Z. (2012). Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics ,91 (2), 275–292. doi: 10.1016/j.ajhg.2012.06.014
Pippucci, T., Parmeggiani, A., Palombo, F., Maresca, A., Angius, A., Crisponi, L., … Carelli, V. (2013). A novel null homozygous mutation confirms CACNA2D2 as a gene mutated in epileptic encephalopathy. PLoS ONE , 8 (12). doi: 10.1371/journal.pone.0082154
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R. R., Bender, D., … Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses.American Journal of Human Genetics , 81 (3), 559–575. doi: 10.1086/519795
Rosenberg, N. A., Pemberton, T. J., Li, J. Z., & Belmont, J. W. (2013). Runs of homozygosity and parental relatedness. Genetics in Medicine , 15 (9), 753–754. doi: 10.1038/gim.2013.108
Samuels, D. C., Wang, J., Ye, F., He, J., Levinson, R. T., Sheng, Q., … Guo, Y. (2016). Heterozygosity ratio, a robust global genomic measure of autozygosity and its association with height and disease risk. Genetics , 204 (3), 893–904. doi: 10.1534/genetics.116.189936
Szpiech, Z. A., Xu, J., Pemberton, T. J., Peng, W., Zöllner, S., Rosenberg, N. A., & Li, J. Z. (2013). Long Runs of Homozygosity Are Enriched for Deleterious Variation. American Journal of Human Genetics , 93 (1), 90–102. doi: 10.1016/j.ajhg.2013.05.003
Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., … DePristo, M. A. (2013). From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline. Current Protocols in Bioinformatics ,43 , 11.10.1-33. doi: 10.1002/0471250953.bi1110s43
Vigeland, M. D., Gjøtterud, K. S., & Selmer, K. K. (2016). FILTUS: A desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector.Bioinformatics , 32 (10), 1592–1594. doi: 10.1093/bioinformatics/btw046
Walsh, T., Shahin, H., Elkan-Miller, T., Lee, M. K., Thornton, A. M., Roeb, W., … Kanaan, M. (2010). Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. American Journal of Human Genetics , 87 (1), 90–94. doi: 10.1016/j.ajhg.2010.05.010
Wang, J., Raskin, L., Samuels, D. C., Shyr, Y., & Guo, Y. (2015). Genome measures used for quality control are dependent on gene function and ancestry. Bioinformatics (Oxford, England) , 31 (3), 318–323. doi: 10.1093/bioinformatics/btu668