Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Zhu, Yuan ^a   Bergland, Alan O ^a   González, Josefa ^a,b   Petrov, Dmitri A ^a  

^a STANFORD UNIVERSITY   (United States)

^b CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DNA DETERMINATION; DROSOPHILA MELANOGASTER; EMPIRICAL RESEARCH; FEMALE; GENE FREQUENCY; GENE MAPPING; GENE SEQUENCE; GENETIC STRAIN; GENETIC VARIABILITY; GENOME ANALYSIS; INSECT GENOME; MALE; NONHUMAN; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY;

ANIMALS; CHROMOSOME MAPPING; DROSOPHILA MELANOGASTER; FEMALE; GENE FREQUENCY; GENOMICS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84864832228     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041901     Document Type: Article

References (39)

1. Erlich Y, Chang Kenneth, Gordon A, Ronen R, Navon O, et al. ((2009)) DNA Sudoku - harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 19:: 1243--1253.
2. Shaw SH, Carrasquillo MM, Kashuk C, Puffenberger EG, Chakravarti A, ((1998)) Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Res 8 (2): 111--23.
3. Van Tassel CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, et al. ((2008)) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5 (3): 247--52.
4. Holt KE, Teo YY, Li H, Nair S, Dougan G, et al. ((2009)) Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. Bioinformatics 25 (16): 2074--2075.
5. Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I, ((2008)) Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB 24:: i32--i40.
6. Out AA, van Minderhout IJ, Geoman JJ, Ariyurek Y, Ossowski S, et al. ((2009)) Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 30 (12): 1703--12.
7. Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, et al. ((2010)) Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res 20 (4): 537--545.
8. Amaral AJ, Ferretti L, Megens H-J, Crooijmans RPMA, Nie H, et al. ((2011)) Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS ONE 6 (4): e14782.
9. Margraf RL, Durtschi JD, Dames S, Pattison DC, Stephens JE, et al. ((2011)) Variant identification in multi-sample pools by Illumina genome analyzer sequencing. Journal of Biomolecular Techniques 22:: 74--84.
10. Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR, et al. ((2010)) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467:: 587--590.
11. Kolaczkowski B, Kern AD, Holloway AK, Begun DJ, ((2011)) Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics 187:: 245--260.
12. Turner TL, Stewart AD, Fields AT, Rice WR, Tarone AM, ((2011)) Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster. PLoS Genet 7 (3): e1001336 doi:10.1371/journal.pgen.1001336.
13. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV, ((2010)) Population re-sequencing revels local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics 42:: 260--263.
14. Cheng C, White BJ, Kamdem C, Mockaitis K, Costantini C, et al. ((2012)) Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach. Genetics 190 (4): 1417--32.
15. Futschik A, Schlötterer C, ((2010)) Massively parallel sequencing of pooled DNA samples - the next generation of molecular markers. Genetics 186:: 207--218.
16. Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, et al. ((2012)) The Drosophila melanogaster Genetic Reference Panel. Nature 482:: 173--178.
17. Huang AM, Rehm EJ, Rubin GM, ((2009)) Quick preparation of genomic DNA from Drosophila. Cold Spring Harb Protoc doi:10.1101/pdb.prot5198.
18. Li H, Durbin R, ((2009)) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25:: 1754--60.
19. DePristo M, Banks E, Poplin R, Garimella K, Maguire J, et al. ((2011)) A framework for variation discovery and genotyping using nextgeneration DNA sequencing data. Nature Genetics 43 (5): 491--498.
20. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. ((2010)) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20 (9): 1297--303 Epub 2010 Jul 19.
21. Li H, Ruan J, Durbin R, ((2008)) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18 (11): 1851--8.
22. R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.
23. Kofler R, Betancourt AJ, Schlötterer C, ((2012)) Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Comples Dynamics of Transposable Element Insertions in Drosophila melanogaster. PLoS Genet 8 (1): e1002487 Doi:10.1371/journal.pgen.1002487.
24. Lynch M, ((2009)) Estimation of allele frequencies from high-coverage gmenome-sequencing projects. Genetics 182:: 295--301.
25. Haubold B, Pfaffelhuber P, Lynch M, ((2010)) mlRho a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Mol Ecol 19:: 277--284.
26. Hellmann I, Mang Y, Gu Z, Li P, de la Vega FM, et al. ((2008)) Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res 18:: 1020--1029.
27. Liu X, Fu Y-X, Maxwell TJ, Boerwinkle E, ((2010)) Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Res 20:: 101--109.
28. Clark AG, Whittam TS, ((1992)) Sequencing errors and molecular evolutionary analysis. Mol Biol Evol 9:: 744--752.
29. Johnson PLF, Slatkin M, ((2008)) Accounting for bias from sequencing error in population genetic estimates. Mol Biol Evol 25:: 199--206.
30. Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, et al. ((2009)) Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res 19:: 1195--1201.
31. Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clarke RM, et al. ((2010)) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:: 92--94.
32. Boitard S, Schlötterer C, Nolte V, Pandey RV, Futschik A, ((2012)) Detecting selective sweeps from pooled next-generation sequencing samples. Mol Biol Evol Doi:10.1093/molbev/mss090.
33. Ingman M, Gyllensten U, ((2009)) SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet 17:: 383--386.
34. Druley TE, Vallania FLM, Wegner DJ, Varley KE, Knowles OL, et al. ((2009)) Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 6:: 263--265.
35. Wen X, Stephens M, ((2010)) Using linear predictors to impute allele frequencies from summary or pooled genotype data. Ann Appl Stat 4 (3): 1158--1182.
36. Wang T, Lin C-Y, Rohan TE, Ye K, ((2010)) Re-sequencing of pooled DNA for detecting disease associations with rare variants. Genetic Epid 34:: 492--501.
37. Bansal V, ((2010)) A statistical method for the detection of variants from next-generation re-sequencing of DNA pools. ISMB 26:: i318--i324.
38. Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, et al. ((2011)) PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals. PLoS ONE 6 (1): e15925 doi:10.1371/journal.pone.0015925.
39. Wang W, Esbensen Y, Kunke D, Suganthan R, Rachek L, et al. ((2011)) Mitochondrial DNA damage level determines neural stem cell differentiation fate. J Neurosci 31 (26):: 9746--9751.