Physiogenomic analysis of the Puerto Rican population

Pharmacogenomics

Volumn 10, Issue 4, 2009, Pages 565-577

  Ruaño, Gualberto ^a   Duconge, Jorge ^b   Windemuth, Andreas ^a   Cadilla, Carmen L ^b   Kocherla, Mohan ^a   Villagra, David ^a   Renta, Jessica ^b   Holford, Theodore ^c   Santiago Borrero, Pedro J ^b  

^a Genomas Inc   (United States)

^b UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Admixture; Ancestry; Personalized medicine; Physiogenomics; Population genetics; Puerto Rico; SNP

Indexed keywords

GENOMIC DNA;

ARTICLE; BIRTH RATE; CAUCASIAN; GENE FREQUENCY; GENETIC DISTANCE; GENETIC MARKER; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HAPLOTYPE MAP; HETEROZYGOSITY; HUMAN; INDIAN; NEGRO; NEWBORN; PHARMACOGENETICS; PHYSIOGENOMICS; POPULATION DIFFERENTIATION; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; PUERTO RICO; RACEMIC MIXTURE; SINGLE NUCLEOTIDE POLYMORPHISM;

CLUSTER ANALYSIS; CROSS-SECTIONAL STUDIES; DNA; GENE FREQUENCY; GENETIC SCREENING; HETEROZYGOTE; HISPANIC AMERICANS; MARKOV CHAINS; MONTE CARLO METHOD; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE; PUERTO RICO; RETROSPECTIVE STUDIES;

EID: 66849126349     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.09.5     Document Type: Article

References (54)

1. Kalow W: Pharmacogenetics of Drug Metabolism. Elsevier Science Publishing Co., USA (1992).
2. Saltelli A, Chan K, Scott EM: Sensitivity Analysis. John Wiley and Sons, Chichester, UK (2000).
3. Suarez-Kurtz G, Pena SD: Pharmacogenomics in the Americas: the impact of genetic admixture. Curr. Drug Targets 7, 1649-1658 (2006).
4. Jakobsson M, Scholz SW, Scheet P et al.: Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451, 998-1003 (2002).
5. Rosenberg NA, Li LM, Ward R, Pritchard JK: Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 73, 1402-1422 (2003).
6. Lao O, van Duijn K, Kersbergen P, de Knijff P, Kayser M: Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry. Am. J. Hum. Genet. 78, 680-690 (2006).
7. Li JZ, Absher DM, Tang H et al.: Worldwide human relationships inferred from genomewide patterns of variation. Science 319, 1100-1104 (2008).
8. Rajeevan H, Cheung KH, Gadagkar R et al.: ALFRED: an Allele Frequency Database for Microevolutionary Studies. Evolutionary Bioinformatics 31, 270-271 (2005).
9. Marsh S: Pharmacogenetics: global clinical markers. Pharmacogenomics. 9, 371-373 (2008).
10. Tang H, Choudhry S, Mei R et al.: Recent genetic selection in the ancestral admixture of Puerto Ricans. Am. J. Hum. Genet. 81, 626-633 (2007).
11. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L: Natural selection has driven population differentiation in modern humans. Nat. Genet. 40, 340-345 (2008).
12. Voight BF, Kudaravalli S, Wen X, Pritchard JK: A map of recent positive selection in the human genome. PLoS Biol. 4, E72 (2006).
13. Ruaño G, Windemuth A, Holford T: Physiogenomics: integrating system engineering and nanotechnology for personalized medicine. In: The Biomedical Engineering Handbook. Bronzino JD (Ed.). CRC Press, London, UK (2005).
14. Seip RL, Volek JS, Windemuth A et al.: Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Nutr. Metab (Lond.) 5, 4 (2008).
15. Ruaño G, Thompson PD, Windemuth A et al.: Physiogenomic analysis links serum creatine kinase activities during statin therapy to vascular smooth muscle homeostasis. Pharmacogenomics 6, 865-872 (2005).
16. Ruaño G, Bernene J, Windemuth A et al.: Physiogenomic comparison of edema and BMI in patients receiving rosiglitazone or pioglitazone. Clin. Chim. Acta 400(1-2), 48-55 (2009).
17. Windemuth A, Calhoun VD, Pearlson GD, Kocherla M, Jagannathan K, Ruaño G: Physiogenomic analysis of localized FMRI brain activity in schizophrenia. Ann. Biomed. Eng. 36, 877-888 (2008).
18. Liu J, Pearlson G, Windemuth A, Ruaño G, Perrone-Bizzozero NI, Calhoun V: Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. Hum. Brain Mapp. 30(1), 241-255 (2009).
19. de Leon J, Correa JC, Ruaño G, Windemuth A, Arranz MJ, Diaz FJ: Exploring genetic variations that may be associated with the direct effects of some antipsychotics on lipid levels. Schizophr. Res. 98, 40-46 (2008).
20. Ruaño G, Thompson PD, Windemuth A et al.: Physiogenomic association of statin-related myalgia to serotonin receptors. Muscle Nerve 36, 329-335 (2007).
21. Ruaño G, Goethe JW, Caley C et al.: Physiogenomic comparison of weight profiles of olanzapine- and risperidonetreated patients. Mol. Psychiatry 12, 474-482 (2007).
22. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS: BeadArray technology: enabling an accurate, cost-effective approach to high-througbput genotyping. Biotechniques Suppl. 56-58, 60-61 (2002).
23. Fan JB, Oliphant A, Shen R et al.: Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69-78 (2003).
24. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000).
25. Falush D, Stephens M, Pritchard JK: Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol, Ecol. Notes 7. 574-578 (2007).
26. Johnson SC: Hierarchical clustering schemes. Psychometrika 32, 241-254 (1967).
27. Hartigan J: Clustering Algorithms. John Wiley & Sons, Inc., NY, USA (1975).
28. Hair JF Jr, Black WC, Babin BJ, Anderson RE: Multivariate Data Analysis. Prentice Hall, NJ, USA (1998).
29. Maindonald J, Braun J: Data Analysis and Graphics Using R. Cambridge Press, Cambridge, UK (2003).
30. Murtagh F: Multidimensional Clustering Algorithms. Physica-Verlag, Wuerzburg, Germany (1985).
31. The International HapMap Consortium: A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
32. Estrela RC, Ribeiro FS, Carvalho RS et al.: Distribution of ABCB1 polymorphisms among Brazilians: impact of population admixture. Pharmacogenomics 9, 267-276 (2008).
33. Teixeira RL, Miranda AB, Pacheco AG et al.: Genetic profile of the arylamine N-acetyltransferase 2 coding gene among individuals from two different regions of Brazil. Mutat. Res. 624, 31-40 (2007).
34. Bertoni B, Budowle B, Sans M, Barton SA, Chakrabarty R: Admixture in Hispanics: distribution of ancestral population contributions in the Continental United States. Hum. Biol. 75, 1-11 (2003).
35. Martinez-Cruzado JC, Toro-Labrador G, Viera-Vera J et al.: Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am. J. Phys. Anthropol. 128, 131-155 (2005).
36. Bonilla C, Parra EJ, Pfaff CL et al.: Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping. Ann. Hum. Genet 68, 139-153 (2004).
37. Choudhry S, Coyle NE, Tang H et al.: Population stratification confounds genetic association studies among Latinos. Hum. Genet 118, 652-664 (2006).
38. Martinez-Cruzado JC, Toro-Labrador G, Ho-Fung V et al.: Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico. Hum. Biol. 73, 491-511 (2001).
39. Hanis CL, Hewett-Emmett D, Bertin TK, Schull WJ: Origins of US Hispanics. Implications for diabetes. Diabetes Care 14, 618-627 (1991).
40. Hammer MF, Chamberlain VF, Kearney VF et al.: Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases. Forensic Sci. Int. 164, 45-55 (2006).
41. Kayser M, Brauer S, Schadlich H et al.: Y chromosome STR haplotypes and the genetic structure of US populations of African, European, and Hispanic ancestry. Genome Res. 13, 624-634 (2003).
42. Redd AJ, Chamberlain VF, Kearney VF et al.: Genetic structure among 38 populations from the United States based on 11 US core Y chromosome STRs. J. Forensic Sci. 51, 580-585 (2006).
43. Budowle B, Adamowicz M, Aranda XG et al.: Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Sci. Int. 150, 1-15 (2005).
44. Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR: Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city. Hum. Genet. 115, 57-68 (2004).
45. Novembre J, Johnson T, Bryc K et al.: Genes mirror geography within Europe. Nature 456, 98-101 (2008).
46. Parra EJ, Kittles RA, Shriver MD: Implications of correlations between skin color and genetic ancestry for biomedical research. Nat. Genet. 36, S54-S60 (2004).
47. Gonzalez BE, Borrell LN, Choudhry S et al.: Latino populations: a unique opportunity for the study of race, genetics, and social environment in epidemiological research. Am. J. Public Health 95, 2161-2168 (2005).
48. Salari K, Choudhry S, Tang H et al.: Genetic admixture and asthma-related phenotypes in Mexican American and Puerto Rican asthmatics. Genet. Epidemiol. 29, 76-86 (2005).
49. Jennings J: Across an Arctic Bridge. In: The World of the American Indian. Billard J (Ed.). National Geographic Society, Washington, DC, USA (1979).
50. Stewart TD: The People of America. Scribner, New York, NY, USA (1973)
51. Wang S, Lewis CM, Jakobsson M et al.: Genetic variation and population structure in native Americans. PLoS Genet. 3, E185 (2007).
52. Choudhry S, Burchard EG, Borrell LN et al.: Ancestry-environment interactions and asthma risk among Puerto Ricans. Am. J. Respir. Crit. Care Med. 174, 1088-1093 (2006).
53. Mao X, Bigham AW, Mei R et al.: A genomewide admixture mapping panel for Hispanic/Latino populations. Am. J. Hum. Genet. 80, 1171-1178 (2007).
54. Ruaño G: Quo Vadis personalized medicine? Personalized Medicine 1, 1-7 (2004).