Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data

PLoS Genetics

Volumn 9, Issue 12, 2013, Pages

  Moore, Carrie B ^a,b   Wallace, John R ^b   Wolfe, Daniel J ^b   Frase, Alex T ^b   Pendergrass, Sarah A ^b   Weiss, Kenneth M ^c   Ritchie, Marylyn D ^b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; BIOINFORMATICS; BIOLOGICAL TRAIT; COLLAPSING METHOD; CONTROLLED STUDY; CORRELATIONAL STUDY; DNA SEQUENCE; EXON; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; INTRON; KNOWLEDGE BASE; NATURAL SELECTION; POPULATION GENETICS; REGULATORY SEQUENCE; SEQUENCE ANALYSIS; STRATIFIED SAMPLE;

BASE SEQUENCE; DATABASES, GENETIC; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME PROJECT; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 84892707535     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003959     Document Type: Article

References (55)

1. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753 doi:[];[]nature08494 [pii];10.1038/nature08494 [doi].
2. Nelson MR, Wegmann D, Ehm MG, Kessner D, Jean PS, et al. (2012) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People. Science 337: 100-104 doi:10.1126/science.1217876.
3. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, et al. (2012) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes. Science 337: 64-69 doi:10.1126/science.1219240.
4. Messer PW, (2009) Measuring the Rates of Spontaneous Mutation From Deep and Large-Scale Polymorphism Data. Genetics 182: 1219-1232 doi:10.1534/genetics.109.105692.
5. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI, (2008) Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms. The American Journal of Human Genetics 82: 100-112 doi:10.1016/j.ajhg.2007.09.006.
6. Casals F, Bertranpetit J, (2012) Human Genetic Variation, Shared and Private. Science 337: 39-40 doi:10.1126/science.1224528.
7. Li B, Leal SM, (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83: 311-321 doi:[];[]S0002-9297(08)00408-4 [pii];10.1016/j.ajhg.2008.06.024 [doi].
8. Madsen BE, Browning SR, (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoSGenet 5: e1000384 doi:[]10.1371/journal.pgen.1000384 [doi].
9. Hoffmann TJ, Marini NJ, Witte JS, (2010) Comprehensive approach to analyzing rare genetic variants. PLoSOne 5: e13584 doi:[]10.1371/journal.pone.0013584 [doi].
10. Yandell M, Huff C, Hu H, Singleton M, Moore B, et al. (2011) A probabilistic disease-gene finder for personal genomes. Genome Res 21: 1529-1542 doi:[];[]gr.123158.111 [pii];10.1101/gr.123158.111 [doi].
11. Consortium T 1000 GP (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56 doi:10.1038/nature11632.
12. Roberson EDO, Pevsner J, (2009) Visualization of Shared Genomic Regions and Meiotic Recombination in High-Density SNP Data. PLoS ONE 4: e6711 doi:10.1371/journal.pone.0006711.
13. Abecasis GR, Cherny SS, Cookson WO, Cardon LR, (2001) GRR: graphical representation of relationship errors. Bioinformatics 17: 742-743.
14. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al. (2010) The UCSC Genome Browser database: update 2011. Nucl Acids Res 39 (Database issue):: D876-82 Available: http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963. Accessed 31 July 2012.
15. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26: 2069-2070 doi:10.1093/bioinformatics/btq330.
16. Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081 doi:10.1038/nprot.2009.86.
17. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249 doi:10.1038/nmeth0410-248.
18. Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, et al. (2013) Identifying Recent Adaptations in Large-Scale Genomic Data. Cell 152: 703-713 doi:10.1016/j.cell.2013.01.035.
19. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L, (2008) Natural selection has driven population differentiation in modern humans. Nature Genetics 40: 340 doi:10.1038/ng.78.
20. Li B, Leal SM, (2009) Discovery of rare variants via sequencing: implications for the design of complex trait association studies. PLoS Genet 5: e1000481 doi:10.1371/journal.pgen.1000481.
21. Rosenfeld JA, Mason CE, Smith TM, (2012) Limitations of the human reference genome for personalized genomics. PLoS ONE 7: e40294 doi:10.1371/journal.pone.0040294.
22. Li R, Li Y, Zheng H, Luo R, Zhu H, et al. (2010) Building the sequence map of the human pan-genome. Nature Biotechnology 28: 57-63 doi:10.1038/nbt.1596.
23. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, et al. (2010) Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature Methods 7: 365-371 doi:10.1038/nmeth.1451.
24. Pemberton TJ, Wang C, Li JZ, Rosenberg NA, (2010) Inference of Unexpected Genetic Relatedness among Individuals in HapMap Phase III. Am J Hum Genet 87: 457-464 doi:10.1016/j.ajhg.2010.08.014.
25. Nembot-Simo AJ, McNeney JG and B (2012) CrypticIBDcheck: Identifying cryptic relatedness in genetic association studies. Available: http://cran.r-project.org/web/packages/CrypticIBDcheck/index.html. Accessed 20 June 2013.
26. Hodgkinson A, Eyre-Walker A, (2011) Variation in the mutation rate across mammalian genomes. Nature Reviews Genetics 12: 756-766 doi:10.1038/nrg3098.
27. Ellegren H, Smith NG, Webster MT, (2003) Mutation rate variation in the mammalian genome. Current Opinion in Genetics & Development 13: 562-568 doi:10.1016/j.gde.2003.10.008.
28. Beleza S, Santos AM, McEvoy B, Alves I, Martinho C, et al. (2013) The Timing of Pigmentation Lightening in Europeans. Mol Biol Evol 30: 24-35 doi:10.1093/molbev/mss207.
29. Jablonski NG, Chaplin G, (2012) Human skin pigmentation, migration and disease susceptibility. Phil Trans R Soc B 367: 785-792 doi:10.1098/rstb.2011.0308.
30. Lamason RL, Mohideen M-APK, Mest JR, Wong AC, Norton HL, et al. (2005) SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. Science 310: 1782-1786 doi:10.1126/science.1116238.
31. ENCODE Project Consortium (2012) Dunham I, Kundaje A, Aldred SF, Collins PJ, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74 doi:10.1038/nature11247.
32. Wray NR, Purcell SM, Visscher PM, (2011) Synthetic Associations Created by Rare Variants Do Not Explain Most GWAS Results. PLoS Biol 9: e1000579 doi:10.1371/journal.pbio.1000579.
33. Liu Q, Nicolae DL, Chen LS, (2013) Marbled Inflation From Population Structure in Gene-Based Association Studies With Rare Variants. Genetic Epidemiology 37: 286-292 doi:10.1002/gepi.21714.
34. He H, Zhang X, Ding L, Baye TM, Kurowski BG, et al. (2011) Effect of population stratification analysis on false-positive rates for common and rare variants. BMC Proc 5 Suppl 9: S116 doi:10.1186/1753-6561-5-S9-S116.
35. Price AL, Zaitlen NA, Reich D, Patterson N, (2010) New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics 11: 459-463 doi:10.1038/nrg2813.
36. Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD, (2013) Using BioBin to Explore Rare Variant Population Stratification. Pacific Symposium on Biocomputing.
37. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 39: D38-D51 doi:10.1093/nar/gkq1172.
38. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M, (2011) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 40: D109-D114 doi:10.1093/nar/gkr988.
39. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, et al. (2010) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research 39: D691-D697 doi:10.1093/nar/gkq1018.
40. Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, et al. (2011) The UniProt-GO Annotation database in 2011. Nucleic Acids Research 40: D565-D570 doi:10.1093/nar/gkr1048.
41. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Research 40: D290-D301 doi:10.1093/nar/gkr1065.
42. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GSS, et al. (2010) NetPath: a public resource of curated signal transduction pathways. Genome Biol 11: R3 doi:10.1186/gb-2010-11-1-r3.
43. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40: D857-861 doi:10.1093/nar/gkr930.
44. Stark C, Breitkreutz B-J, Chatr-Aryamontri A, Boucher L, Oughtred R, et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39: D698-704 doi:10.1093/nar/gkq1116.
45. McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB, Klein TE, (2011) From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med 5: 795-806 doi:10.2217/bmm.11.94.
46. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, et al. (2007) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research 36: D107-D113 doi:10.1093/nar/gkm967.
47. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. Available: http://www.R-project.org.
48. Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer New York. Available: http://had.co.nz/ggplot2/book.
49. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073 doi:[];[]nature09534 [pii];10.1038/nature09534 [doi].
50. Browning SR, Thompson EA, (2012) Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies. Genetics 190: 1521-1531 doi:10.1534/genetics.111.136937.
51. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575 doi:[];[]S0002-9297(07)61352-4 [pii];10.1086/519795 [doi].
52. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, et al. (2005) Simultaneous inference of selection and population growth from patterns of variation in the human genome. PNAS 102: 7882-7887 doi:10.1073/pnas.0502300102.
53. Voight BF, Kudaravalli S, Wen X, Pritchard JK, (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4: e72 doi:10.1371/journal.pbio.0040072.
54. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19: 826-837 doi:10.1101/gr.087577.108.
55. López Herráez D, Bauchet M, Tang K, Theunert C, Pugach I, et al. (2009) Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs. PLoS ONE 4: e7888 doi:10.1371/journal.pone.0007888.