GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification

Bioinformatics

Volumn 33, Issue 13, 2017, Pages 2059-2062

  Szpiech, Zachary A ^a   Blant, Alexandra ^b   Pemberton, Trevor J ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MANITOBA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DNA SEQUENCE; GENOMICS; HAPLOTYPE; HOMOZYGOTE; HUMAN; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; STATISTICAL MODEL;

COMPUTER SIMULATION; GENOMICS; HAPLOTYPES; HOMOZYGOTE; HUMANS; LIKELIHOOD FUNCTIONS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85021789583     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx102     Document Type: Article

References (39)

1. Broman, K. W., Weber, J. L. (1999) Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain. Am. J. Hum. Genet., 65, 1493-1500.
2. Browning, B. L., Browning, S. R. (2013) Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics, 194, 459-471.
3. Campbell, H., et al. (2007) Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits. Hum. Mol. Genet., 16, 233-241.
4. Christofidou, P., et al. (2015) Runs of homozygosity: Association with coronary artery disease and gene expression in monocytes and macrophages. Am. J. Hum. Genet., 97, 228-237.
5. Curik, I., et al. (2014) Inbreeding and runs of homozygosity: A possible solution to an old problem. Livest. Sci., 166, 26-34.
6. Fareed, M., Afzal, M. (2014) Evidence of inbreeding depression on height, weight, body mass index: A population-based child cohort study. Am. J. Hum. Biol., 26, 784-795.
7. Ghani, M., et al. (2015) Association of long runs of homozygosity with Alzheimer disease among African American individuals. JAMA Neurol., 72, 1313-1323.
8. Gibson, J., et al. (2006) Extended tracts of homozygosity in outbred human populations. Hum. Mol. Genet., 15, 789-795.
9. Gusev, A., et al. (2009) Whole population, genome-wide mapping of hidden relatedness. Genome Res., 19, 318-326.
10. Howrigan, D. P., et al. (2015) Genome-wide autozygosity is associated with lower general cognitive ability. Mol. Psychiatry, 21, 837-843.
11. Joshi, P. K., et al. (2015) Directional dominance on stature and cognition in diverse human populations. Nature, 523, 459-462.
12. Kardos, M., et al. (2015) Measuring individual inbreeding in the age of genomics: Marker-based measures are better than pedigrees. Heredity (Edinb), 115, 63-72.
13. Keller, M. C., et al. (2012) Runs of homozygosity implicate autozygosity as a schizophrenia risk factor. PLoS Genet., 8, e1002656.
14. Lander, E. S., Botstein, D. (1987) Homozygosity mapping: A way to map human recessive traits with the DNA of inbred children. Science, 236, 1567-1570.
15. Lencz, T., et al. (2007) Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc. Natl. Acad. Sci. U. S. A., 104, 19942-19947.
16. Magi, A., et al. (2014) H3M2: Detection of runs of homozygosity from wholeexome sequencing data. Bioinformatics, 30, 2852-2859.
17. McLaughlin, R. L., et al. (2015) Homozygosity mapping in an Irish ALS casecontrol cohort describes local demographic phenomena and points towards potential recessive risk loci. Genomics, 105, 237-241.
18. McQuillan, R., et al. (2012) Evidence of inbreeding depression on human height. PLoS Genet., 8, e1002655.
19. McQuillan, R., et al. (2008) Runs of homozygosity in European populations. Am. J. Hum. Genet., 83, 359-372.
20. Meyer, M., et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222-226.
21. Morariu, V. I., et al. (2009) Automatic online tuning for fast Gaussian summation. In: Koller, D., et al. (eds. ) Advances in Neural Information Processing Systems 21, pp. 1113-1120. Curran Associates, Inc., Red Hook, NY.
22. Nalls, M. A., et al. (2009) Measures of autozygosity in decline: Globalization, urbanization, its implications for medical genetics. PLoS Genet., 5, e1000415.
23. Narasimhan, V., et al. (2016) BCFtools/RoH: A hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics, 32, 1749-1751.
24. Pemberton, T. J., et al. (2012) Genomic patterns of homozygosity in worldwide human populations. Am. J. Hum. Genet., 91, 275-292.
25. Power, R. A., et al. (2014) Genome-wide estimates of inbreeding in unrelated individuals and their association with cognitive ability. Eur. J. Hum. Genet., 22, 386-390.
26. Prado-Martinez, J., et al. (2013) Great ape genetic diversity and population history. Nature, 499, 471-475.
27. Prufer, K., et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505, 43-49.
28. Purcell, S., et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
29. Rudan, I., et al. (2003) Inbreeding and the genetic complexity of human hypertension. Genetics, 163, 1011-1021.
30. Speir, M. L., et al. (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Res., 44, D717-D725.
31. Sud, A., et al. (2015) Genome-wide homozygosity signature and risk of Hodgkin lymphoma. Sci. Rep., 5, 14315.
32. Szpiech, Z. A., et al. (2013) Long runs of homozygosity are enriched for deleterious variation. Am. J. Hum. Genet., 93, 90-102.
33. Vigeland, M. D., et al. (2016) FILTUS: A desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector. Bioinformatics, 32, 1592-1594.
34. Wang, S., et al. (2009) Genome-wide autozygosity mapping in human populations. Genet. Epidemiol., 33, 172-180.
35. Xue, Y., et al. (2015) Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science, 348, 242-245.
36. Yang, H. C., et al. (2012) A genome-wide homozygosity association study identifies runs of homozygosity associated with rheumatoid arthritis in the human major histocompatibility complex. PLoS One, 7, e34840.
37. Yang, T. L., et al. (2010) Runs of homozygosity identify a recessive locus 12q21. 31 for human adult height. J. Clin. Endocrinol. Metab., 95, 3777-3782.
38. Zhang, L., et al. (2013) cgaTOH: Extended approach for identifying tracts of homozygosity. PLoS One, 8, e57772.
39. Zhang, Q., et al. (2015) Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genomics, 16, 542.