Exomic variants of an elderly cohort of Brazilians in the ABraOM database

Human Mutation

Volumn 38, Issue 7, 2017, Pages 751-763

  Naslavsky, Michel Satya ^a,b   Yamamoto, Guilherme Lopes ^a   de Almeida, Tatiana Ferreira ^a   Ezquina, Suzana A M ^a   Sunaga, Daniele Yumi ^a   Pho, Nam ^c   Bozoklian, Daniel ^a   Sandberg, Tatiana Orli Milkewitz ^a   Brito, Luciano Abreu ^a   Lazar, Monize ^a   Bernardo, Danilo Vicensotto ^d   Amaro, Edson ^a,b   Duarte, Yeda A O ^a   Lebrão, Maria Lúcia ^a   Passos Bueno, Maria Rita ^a   Zatz, Mayana ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b HOSPITAL ISRAELITA ALBERT EINSTEIN   (Brazil)

^c HARVARD MEDICAL SCHOOL   (United States)

^d FEDERAL UNIVERSITY OF RIO GRANDE   (Brazil)

Author keywords

admixture; aging; pathogenicity interpretation; population genetics; variant database

Indexed keywords

ADULT; AGED; ARTICLE; BIOINFORMATICS; BRAZILIAN; CLINICAL FEATURE; COHORT ANALYSIS; ETHNICITY; EXOME; FEMALE; GENE FREQUENCY; GENETIC DATABASE; GENETIC VARIABILITY; GENOTYPE; HUMAN; LOSS OF FUNCTION MUTATION; MAJOR CLINICAL STUDY; MALE; PATHOGENICITY; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; VERY ELDERLY; WHOLE EXOME SEQUENCING; AGING; ALLELE; BIOLOGY; BRAZIL; ETHNIC GROUP; GENETIC VARIATION; HETEROZYGOTE; INCIDENCE; MIDDLE AGED; MUTATION;

AGED; AGED, 80 AND OVER; AGING; ALLELES; BRAZIL; COHORT STUDIES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; ETHNIC GROUPS; EXOME; FEMALE; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; HETEROZYGOTE; HUMANS; INCIDENCE; MALE; MIDDLE AGED; MUTATION; PHENOTYPE;

EID: 85018319012     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.23220     Document Type: Article

References (58)

1. 1000 Genomes Project Consortium, Auton, A, Brooks, L. D., Durbin, R. M., Garrison, E. P., Kang, H. M., … Abecasis, G. R. (2015). A global reference for human genetic variation. Nature, 526(7571), 68–74.
2. Acosta, A., Silva, W., Jr., Carvalho, T., Gomes, M., & Zago, M. (2001). Mutations of the phenylalanine hydroxylase (PAH) gene in Brazilian patients with phenylketonuria. Human Mutation, 17(2), 122–130.
3. Alves-Silva, J., da Silva Santos, M., Guimaraes, P. E., Ferreira, A. C., Bandelt, H. J., Pena, S. D., & Prado, V. F. (2000). The ancestry of Brazilian mtDNA lineages. American Journal of Human Genetics, 67(2), 444–461.
4. Amendola, L. M., Dorschner, M. O., Robertson, P. D., Salama, J. S., Hart, R., Shirts, B. H., … Jarvik, G. P. (2015). Actionable exomic incidental findings in 6503 participants: Challenges of variant classification. Genome Research, 25(3), 305-=315.
5. Busch Tde, A., Duarte, Y. A., Pires Nunes, D., Lebrao, M. L., Satya Naslavsky, M., dos Santos Rodrigues, A., & Amaro, E. Jr. (2015). Factors associated with lower gait speed among the elderly living in a developing country: A cross-sectional population-based study. BMC Geriatrics, 15, 35.
6. Challis, D., Yu, J., Evani, U. S., Jackson, A. R., Paithankar, S., Coarfa, C., & Yu, F. (2012). An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics, 13, 8.
7. Chan, D. K., & Chang, K. W. (2014). GJB2-associated hearing loss: Systematic review of worldwide prevalence, genotype, and auditory phenotype. Laryngoscope, 124(2), E34–E53.
8. Chen, R., Shi, L., Hakenberg, J., Naughton, B., Sklar, P., Zhang, J., … Friend, S. H. (2016). Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotechnology, 34(5), 531–538.
9. Collaboration through competition. (2014). Nature Methods, 11(7), 695.
10. Dewey, F. E., Grove, M. E., Priest, J. R., Waggott, D., Batra, P., Miller, C. L., … Ashley, E. A. (2015). Sequence to medical phenotypes: A framework for interpretation of human whole genome DNA sequence data. PLoS Genetics, 11(10), e1005496.
11. Erikson, G. A., Bodian, D. L., Rueda, M., Molparia, B., Scott, E. R., Scott-Van Zeeland, A. A., … Torkamani, A. (2016). Whole-genome sequencing of a healthy aging cohort. Cell, 165(4), 1002–1011.
12. Everitt, B., & Dunn, G. (2001). Principal components analysis. Applied multivariate data analysis. Second Edition, West Sussex, United Kingdom: John Wiley & Sons, Ltd. https://doi.org/10.1002/9781118887486.ch6
13. Falush, D., Stephens, M., & Pritchard, J. K. (2007). Inference of population structure using multilocus genotype data: Dominant markers and null alleles. Molecular Ecology Notes, 7(4), 574–578.
14. Fernandes, M., Wan, C., Tacutu, R., Barardo, D., Rajput, A., Wang, J., … de Magalhães, J. P. (2016). Systematic analysis of the gerontome reveals links between aging and age-related diseases. Human Molecular Genetics, 25(21): 4804–4818. https://doi.org/10.1093/hmg/ddw307
15. Franco, M. H., Brennan, S. O., Chua, E. K., Kragh-Hansen, U., Callegari-Jacques, S. M., Bezerra, M. Z., & Salzano, F. M. (1999). Albumin genetic variability in South America: Population distribution and molecular studies. American Journal of Human Biology, 11(3), 359–366.
16. Goncalves, V. F., Stenderup, J., Rodrigues-Carvalho, C., Silva, H. P., Goncalves-Dornelas, H., Liryo, A., … Pena, S. D. (2013). Identification of Polynesian mtDNAhaplogroups in remains of Botocudo Amerindians from Brazil. Proceedings of the National Academy of Sciences of The United States Of America, 110(16), 6465–6469.
17. Green, R. C., Berg, J. S., Grody, W. W., Kalia, S. S., Korf, B. R., Martin, C. L., … American College of Medical Genetics and Genomics. (2013). ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genetics in Medicine, 15(7), 565–574.
18. Hakenberg, J., Cheng, W. Y., Thomas, P., Wang, Y. C., Uzilov, A. V., & Chen, R. (2016). Integrating 400 million variants from 80,000 human samples with extensive annotations: Towards a knowledge base to analyze disease cohorts. BMC Bioinformatics, 17, 24.
19. Henn, B. M., Botigue, L. R., Bustamante, C. D., Clark, A. G., & Gravel, S. (2015). Estimating the mutation load in human genomes. Nature Reviews Genetics, 16(6), 333–343.
20. Huckins, L. M., Boraska, V., Franklin, C. S., Floyd, J. A., Southam, L., Gcan, W., … Tachmazidou, I. (2014). Using ancestry-informative markers to identify fine structure across 15 populations of European origin. European Journal of Human Genetics, 22(10), 1190–1200.
21. Huttle, A., Maestre, G. E., Lantigua, R., & Green, N. S. (2015). Sickle cell in Latin America and the United States [corrected]. Pediatric Blood & Cancer, 62(7), 1131–1136.
22. Johnson, L. J., Cotton, J. A., Lichtenstein, C. P., Elgar, G. S., Nichols, R. A., Polly, P. D., & Le Comber, S. C. (2011). Stops making sense: Translational trade-offs and stop codon reassignment. BMC Evolutionary Biology [Electronic Resource], 11, 227.
23. Jombart, T., Devillard, S., & Balloux, F. (2010). Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genetics [Electronic Resource], 11, 94.
24. Karbassi, I., Maston, G. A., Love, A., DiVincenzo, C., Braastad, C. D., Elzinga, C. D., … Higgins, J. J. (2016). A standardized DNA variant scoring system for pathogenicity assessments in Mendelian disorders. Human Mutation, 37(1), 127–134.
25. Kehdy, F. S., Gouveia, M. H., Machado, M., Magalhaes, W. C., Horimoto, A. R., Horta, B. L., … Brazilian EPIGEN Project Consortium. (2015). Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations. Proceedings of the National Academy of Sciences of The United States Of America, 112(28), 8696–8701.
26. Kosoy, R., Nassir, R., Tian, C., White, P. A., Butler, L. M., Silva, G., … Seldin, M. F. (2009). Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Human Mutation, 30(1), 69–78.
27. Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., … Exome Aggregation Consortium. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285–291.
28. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754–1760.
29. Lobo, C. L., Ballas, S. K., Domingos, A. C., Moura, P. G., do Nascimento, E. M., Cardoso, G. P., & de Carvalho, S. M. (2014). Newborn screening program for hemoglobinopathies in Rio de Janeiro, Brazil. Pediatric Blood & Cancer, 61(1), 34–39.
30. MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., … Tyler-Smith, C. (2012). A systematic survey of loss-of-function variants in human protein-coding genes. Science, 335(6070), 823–838.
31. Marth, G. T., Yu, F., Indap, A. R., Garimella, K., Gravel, S., Leong, W. F., … Cartwright, R. A. (2011). The functional spectrum of low-frequency coding variation. Genome Biology, 12(9), R84.
32. McEniry, M. (2013). Early-life conditions and older adult health in low- and middle-income countries: A review. Journal of Developmental Origins of Health and Disease, 4(1), 10–29.
33. Miller, R. M., & Smith, J. D. (1997). Dictionary of Afro-American slavery. Westport, Connecticut: Praeger.
34. Need, A. C., & Goldstein, D. B. (2009). Next generation disparities in human genomics: Concerns and remedies. Trends in Genetics, 25(11), 489–494.
35. Pabayo, R., Chiavegatto Filho, A. D., Lebrao, M. L., & Kawachi, I. (2013). Income inequality and mortality: Results from a longitudinal study of older residents of Sao Paulo, Brazil. American Journal of Public Health, 103(9), e43–49.
36. Palha, T., Gusmao, L., Ribeiro-Rodrigues, E., Guerreiro, J. F., Ribeiro-Dos-Santos, A., & Santos, S. (2012). Disclosing the genetic structure of Brazil through analysis of male lineages with highly discriminating haplotypes. PLoS One, 7(7), e40007.
37. Palloni, A., Pinto-Aguirre, G., & Pelaez, M. (2002). Demographic and health conditions of ageing in Latin America and the Caribbean. International Journal of Epidemiology, 31(4), 762–771.
38. Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38(8), 904–909.
39. Quaio, C. R., Grinberg, H., Vieira, M. L., Paula, A. C., Leal, G. N., Gomy, I., & Kim, C. A. (2012). Report of a large Brazilian family with a very attenuated form of Hunter syndrome (MPS II). JIMD Reports, 4, 125–128.
40. Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., … ACMG Laboratory Quality Assurance Committee. (2015). Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–424.
41. Rodrigues, R., Magalhaes, P. K., Fernandes, M. I., Gabetta, C. S., Ribeiro, A. F., Pedro, K. P., … Maciel, L. M. (2009). Neonatal screening for cystic fibrosis in Sao Paulo State, Brazil: A pilot study. Brazilian Journal of Medical and Biological Research, 42(10), 973–978.
42. Salomon, J. A., Wang, H., Freeman, M. K., Vos, T., Flaxman, A. D., Lopez, A. D., & Murray, C. J. (2012). Healthy life expectancy for 187 countries, 1990-2010: A systematic analysis for the Global Burden Disease Study 2010. Lancet, 380(9859), 2144–2162.
43. Salzano, F. M., & Sans, M. (2014). Interethnic admixture and the evolution of Latin American populations. Genetics and Molecular Biology, 37(1 Suppl), 151–170.
44. Schrodi, S. J., DeBarber, A., He, M., Ye, Z., Peissig, P., Van Wormer, J. J., … Steiner, R. D. (2015). Prevalence estimation for monogenic autosomal recessive diseases using population-based genetic data. Human Genetics, 134(6), 659–669.
45. Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M., & Sirotkin, K. (2001). dbSNP: The NCBI database of genetic variation. Nucleic Acids Research, 29(1), 308–311.
46. Sulem, P., Helgason, H., Oddson, A., Stefansson, H., Gudjonsson, S. A., Zink, F., … Stefansson, K. (2015). Identification of a large set of rare complete human knockouts. Nature Genetics, 47(5), 448–452.
47. Tacutu, R., Craig, T., Budovsky, A., Wuttke, D., Lehmann, G., Taranukha, D., & de Magalhaes, J. P. (2013). Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Research, 41(Database issue), D1027–D1033.
48. Team, R. C. (2016). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
49. Tennessen, J. A., Bigham, A. W., O'Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., … NHLBI Exome Sequencing Project. (2012). Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science, 337(6090), 64–69.
50. United Nations Department of Economic and Social Affairs, Population Division. (2007). World population prospects : The 2006 revision. New York: United Nations.
51. Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., … De Pristo, 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.
52. Vihinen, M. (2012). How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. BMC Genomics [Electronic Resource], 13(Suppl 4), S2.
53. Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38(16), e164.
54. Wickham, H. (2009). Ggplot2: Elegant graphics for data analysis. New York: Springer.
55. Wildeman, M., van Ophuizen, E., den Dunnen, J. T., & Taschner, P. E. (2008). Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Human Mutation, 29(1), 6–13.
56. Xue, Y., Chen, Y., Ayub, Q., Huang, N., Ball, E. V., Mort, M., … the 1000 Genomes Project Consortium. (2012). Deleterious- and disease-allele prevalence in healthy individuals: Insights from current predictions, mutation databases, and population-scale resequencing. American Journal of Human Genetics, 91(6), 1022–1032.
57. Zatz, M., Pavanello, R. C. M., Lazar, M., Yamamoto, G. L., Lourenço, N. C. V., Cerqueira, A., … Vainzof, M. (2014). Milder course in Duchenne patients with nonsense mutations and no muscle dystrophin. Neuromuscular Disorders, 24(11), 986–989.
58. Zheng, X., Levine, D., Shen, J., Gogarten, S. M., Laurie, C., & Weir, B. S. (2012). A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics, 28(24), 3326–3328.