Citation: Marcos Morey, Ana Fernández-Marmiesse, Jose Angel Cocho, María L. Couce. Influence of technology in genetic epidemiology[J]. AIMS Genetics, 2015, 2(3): 219-229. doi: 10.3934/genet.2015.3.219
[1] | Morton NE (1997) Genetic epidemiology. Ann Hum Genet 61: 1-13. |
[2] | Morton NE (1994) Fundamentals of genetic epidemiology. Genet Epidemiol 11: 389-390. |
[3] | Morton NE (1982) Outline of genetic epidemiology. S. Karger AG (Switzerland), 252. |
[4] | Cohen BH (1980) Chronic obstructive pulmonary disease: A challenge in genetic epidemiology. Am J Epidemiol 112: 274-288. |
[5] | Morey M, Fernández-Marmiesse A, Castiñeiras D, et al. (2013) A glimpse into past, present, and future DNA sequencing. Mol Genet Metab 110: 3-24. |
[6] | Matullo G, Gaetano CD, Guarrera S (2013) Next generation sequencing and rare genetic variants: From human population studies to medical genetics. Environ Mol Mutagen 54: 518-532. |
[7] | IJzerman RG, Stehouwer CDA, Boomsma DI (2000) Evidence for genetic factors explaining the birth Weight–Blood pressure relation: Analysis in twins. Hypertension 36: 1008-1012. |
[8] | Ostern R, Fagerheim T, Hjellnes H, et al. (2014) Segregation analysis in families with charcot-marie-tooth disease allows reclassification of putative disease causing mutations. BMC Med Genet 15: 12. |
[9] | Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res 10: 1435-1444. |
[10] | Guo SW (2001) Does higher concordance in monozygotic twins than in dizygotic twins suggest a genetic component?. Hum Hered 51: 121-132. |
[11] | King RC, Mulligan P, Stansfield W (2013) A dictionary of genetics. Oxford University Press, 641. |
[12] | Wong AHC, Gottesman II, Petronis A (2005) Phenotypic differences in genetically identical organisms: The epigenetic perspective. Hum Mol Genet 14: R11-18. |
[13] | Chaganti RSK, Miller DR, Meyers PA, et al. (1979) Cytogenetic evidence of the intrauterine origin of acute leukemia in monozygotic twins. N Engl J Med 300: 1032-1034. |
[14] | Bell JT, Saffery R (2012) The value of twins in epigenetic epidemiology. Int J Epidemiol 41: 140-150. |
[15] | Elston RC (1981) Segregation analysis. In: Harris H and Hirschhorn K, eds. Springer US, 63-120. |
[16] | Jarvik GP (1998) Complex segregation analyses: Uses and limitations. Am J Hum Genet 63: 942-946. |
[17] | Terwilliger JD, Goring HH (2000) Gene mapping in the 20th and 21st centuries: Statistical methods, data analysis, and experimental design. Hum Biol 72: 63-132. |
[18] | Bateson W, Waunders ER, Punnett RC (1909) Experimental studies in the physiology of heredity. Zeitschrift für Induktive Abstammungs- Und Vererbungslehre 2: 17-19. |
[19] | Stevens WL (1939) Tables of the recombination fraction estimated from the product ratio. J Genet 39: 171-180. |
[20] | Tan YD, Fu YX (2007) A new strategy for estimating recombination fractions between dominant markers from an F2 population. Genetics 175: 923-931. |
[21] | Botstein D, White RL, Skolnick M, et al. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331. |
[22] | Stocker AJ, Rusuwa BB, Blacket MJ, et al. (2012) Physical and linkage maps for drosophila serrata, a model species for studies of clinal adaptation and sexual selection. G3 (Bethesda) 2: 287-297. doi: 10.1534/g3.111.001354 |
[23] | Bailey-Wilson JE (2005) Parametric versus nonparametric and two-point versus multipoint: Controversies in gene mapping. In: Anonymous Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, Ltd. |
[24] | Hirschhorn JN, Lohmueller K, Byrne E, et al. (2002) A comprehensive review of genetic association studies. Genet Med 4: 45-61. |
[25] | Cordell HJ, Clayton DG (2005) Genetic association studies. Lancet 366: 1121-1131. |
[26] | McCarthy MI, Abecasis GR, Cardon LR, et al. (2008) Genome-wide association studies for complex traits: Consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369. |
[27] | St George-Hyslop PH, Haines JL, Farrer LA, et al. (1990) Genetic linkage studies suggest that alzheimer's disease is not a single homogeneous disorder. Nature 347: 194-197. |
[28] | Klein RJ, Zeiss C, Chew EY, et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308: 385-389. |
[29] | Welter D, MacArthur J, Morales J, et al. (2013) The NHGRI GWAS catalog, a curated resource of SNP-trait associations. Nucleic Acids Res 42: D1001-1006. |
[30] | Kooperberg C, LeBlanc M, Obenchain V (2010) Risk prediction using genome-wide association studies. Genet Epidemiol 34: 643-652. |
[31] | Gusev A, Bhatia G, Zaitlen N, et al. (2013) Quantifying missing heritability at known GWAS loci. PLoS Genet 9: e1003993. |
[32] | Stranger BE, Stahl EA, Raj T (2011) Progress and promise of genome-wide association studies for human complex trait genetics. Genetics 187: 367-383. |
[33] | Visscher P, Brown M, McCarthy M, et al. (2012) Five years of GWAS discovery. Am J Hum Genet 90: 7-24. |
[34] | Gibson G (2012) Rare and common variants: Twenty arguments. Nat Rev Genet 13: 135-145. |
[35] | Slatkin M (2008) Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9: 477-485. |
[36] | Cooper GM, Shendure J (2011) Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data. Nat Rev Genet 12: 628-640. |
[37] | Manolio TA, Collins FS, Cox NJ, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753. |
[38] | Frazer KA, Murray SS, Schork NJ, et al. (2009) Human genetic variation and its contribution to complex traits. Nat Rev Genet 10: 241-251. |
[39] | Johnson DS, Mortazavi A, Myers RM, et al. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502. |
[40] | Shen P, Wang W, Krishnakumar S, et al. (2011) High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A 108: 6549-6554. |
[41] | Service RF (2006) The race for the $1000 genome. Science 311: 1544-1546. |
[42] | Wetterstrand KA, DNA Sequencing Costs: Data from the NHGRI Large-Scale Genome Sequencing Program. 2015. Available from: www.genome.gov/sequencingcosts |
[43] | Broadwith P (2012) Sequencing in the fast lane. Chem World 9: 54-58. |
[44] | Feldman AL, Dogan A, Smith DI, et al. (2010) Massively parallel mate pair DNA library sequencing for translocation discovery: Recurrent t(6;7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas. ASH Annual Meeting Abstracts 116: 633. |
[45] | Green R, Malaspinas A, Krause J, et al. (2008) A complete neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134: 416-426. |
[46] | Durbin RM, Altshuler DL, Durbin RM, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. |
[47] | Peters BA, Kermani BG, Sparks AB, et al. (2012) Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487: 190-195. |
[48] | Butler J, MacCallum I, Kleber M, et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res 18: 810-820. |
[49] | Furlotte NA, Heckerman D, Lippert C (2014) Quantifying the uncertainty in heritability. J Hum Genet 59: 269-275. |
[50] | Majewski J, Schwartzentruber J, Lalonde E, et al. (2011) What can exome sequencing do for you?. J Med Genet 48: 580-589. |
[51] | Wooderchak-Donahue W, O’Fallon B, Furtado L, et al. (2012) A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel- clinical diagnostics perspective. BMC Medical Genomics 5: 1-10. |
[52] | Kalender Atak Z, De Keersmaecker K, Gianfelici V, et al. (2012) High accuracy mutation detection in leukemia on a selected panel of cancer genes. PLoS One 7: e38463. |
[53] | Ni T, Wu H, Song S, et al. (2009) Selective gene amplification for high-throughput sequencing. Recent Pat DNA Gene Seq 3: 29-38. |
[54] | Gaugler T, Klei L, Sanders SJ, et al. (2014) Most genetic risk for autism resides with common variation. Nat Genet 46: 881-885. |
[55] | Muona M, Berkovic SF, Dibbens LM, et al. (2015) A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy. Nat Genet 47: 39-46. |
[56] | Xu B, Ionita-Laza I, Roos JL, et al. (2012) De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat Genet 44: 1365-1369. |
[57] | Cardinale CJ, Kelsen JR, Baldassano RN, et al. (2013) Impact of exome sequencing in inflammatory bowel disease. World J Gastroenterol 19: 6721-6729. |
[58] | Gilissen C, Arts HH, Hoischen A, et al. (2010) Exome sequencing identifies WDR35 variants involved in sensenbrenner syndrome. Am J Hum Genet 87: 418-423. |
[59] | Boycott KM, Vanstone MR, Bulman DE, et al. (2013) Rare-disease genetics in the era of next-generation sequencing: Discovery to translation. Nat Rev Genet 14: 681-691. |
[60] | Roach JC, Glusman G, Smit AF, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636-639. |
[61] | Fernandez-Marmiesse A, Morey M, Pineda M, et al. (2014) Assessment of a targeted resequencing assay as a support tool in the diagnosis of lysosomal storage disorders. Orphanet J Rare Dis 9: 59. |
[62] | Audo I, Bujakowska KM, Leveillard T, et al. (2012) Development and application of a next-generation-sequencing (NGS) approach to detect known and novel gene defects underlying retinal diseases. Orphanet J Rare Dis 7: 8. |
[63] | Mardis ER (2009) New strategies and emerging technologies for massively parallel sequencing: Applications in medical research. Genome Med 1: 40. |
[64] | Wendl MC, Wilson RK (2009) The theory of discovering rare variants via DNA sequencing. BMC Genomics 10: 485. |
[65] | Cooper DN, Krawczak M, Polychronakos C, et al. (2013) Where genotype is not predictive of phenotype: Towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 132: 1077-1130. |
[66] | Venter JC, Adams MD, Myers EW, et al. (2001) The sequence of the human genome. Science 291: 1304-1351. |
[67] | Lander ES, Linton LM, Birren B, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921. |
[68] | Durbin R, Altshuler D, Durbin R, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. |
[69] | Panoutsopoulou K, Tachmazidou I, Zeggini E (2013) In search of low-frequency and rare variants affecting complex traits. Hum Mol Genet 22: R16-21. |
[70] | Li J, Schmieder R, Ward RM, et al. (2012) SEQanswers: An open access community for collaboratively decoding genomes. Bioinformatics 28: 1272-1273. |
[71] | Elgar G, Vavouri T (2008) Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes. Trends Genet 24: 344-352. |
[72] | Eisenberger T, Neuhaus C, Khan AO, et al. (2013) Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: The example of retinal dystrophies. PLoS One 8: e78496. |
[73] | Ward LD, Kellis M (2011) HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res 40: D930-934. |
[74] | Boyle AP, Hong EL, Hariharan M, et al. (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 22: 1790-1797. |
[75] | Kircher M, Witten DM, Jain P, et al. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46: 310-315. |
[76] | Vandeweyer G, Van Laer L, Loeys B, et al. (2014) VariantDB: A flexible annotation and filtering portal for next generation sequencing data. Genome Med 6: 74. |
[77] | Ritchie GRS, Dunham I, Zeggini E, et al. (2014) Functional annotation of noncoding sequence variants. Nat Meth 11: 294-296. |
[78] | Wang K, Li M, Hakonarson H (2010) ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38: e164-. |
[79] | Henry VJ, Bandrowski AE, Pepin A, et al. (2014) OMICtools: An informative directory for multi-omic data analysis. Database (Oxford) bau069. |
[80] | The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74. |
[81] | The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65. |
[82] |
McEwen JE, Boyer JT, Sun KY, et al. (2014) The ethical, legal, and social implications program of the national human genome research institute: Reflections on an ongoing experiment. Annu Rev Genomics Hum Genet 15: 481-505.
|
[83] |