Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences

Molecular Biology and Evolution

Volumn 26, Issue 7, 2009, Pages 1479-1490

  Liu, Xiaoming ^a   Maxwell, Taylor J ^a   Boerwinkle, Eric ^a   Fu, Yun Xin ^a  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Coalescent theory; Generalized least squares; Mutation rate; Sequencing error; SNP frequency spectrum

Indexed keywords

ANALYTICAL ERROR; ARTICLE; DNA SEQUENCE; GENE SEQUENCE; MUTATION RATE; POPULATION GENETICS; REGRESSION ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

BASE SEQUENCE; COMPUTER SIMULATION; HUMANS; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 67349156737     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp059     Document Type: Article

References (23)

1. Achaz G. 2008. Testing for neutrality in samples with sequencing errors. Genetics. 179:1409-1424.
2. Achaz G, Palmer S, Kearney M, Maldarelli F, Mellors JW, Coffin JM, Wakeley J. 2004. A robust measure of HIV-1 population turnover within chronically infected individuals. Mol. Biol. Evol. 21:1902-1912.
3. Clark AG, Whittam TS. 1992. Sequencing errors and molecular evolutionary analysis. Mol. Biol. Evol. 9:744-752.
4. Crawford DC, Akey DT, Nickerson DA. 2005. The patterns of natural variation in human genes. Annu. Rev. Genomics. Hum. Genet. 6:287-312.
5. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic. Acids. Res. 32:1792-1797.
6. Fu YX. 1994a. A phylogenetic estimator of effective populationsize or mutation-rate. Genetics. 136:685-692.
7. Fu YX. 1994b. Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics. 138:1375-1386.
8. Fu YX. 1995. Statistical properties of segregating sites. Theor. Popul. Biol. 48:172-197.
9. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics. 133:693-709.
10. Hellmann I, Mang Y, Gu Z, Li P, de la Vega FM, Clark AG, Nielsen R. 2008. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome. Res. 18:1020-1029.
11. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18: 337-338.
12. Jiang R, Tavaré S, Marjoram P. 2009. Population genetic inference from resequencing data. Genetics. 181:187-197.
13. Johnson PLF, Slatkin M. 2006. Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome. Res. 16:1320-1327.
14. Johnson PLF, Slatkin M. 2008. Accounting for bias from sequencing error in population genetic estimates. Mol. Biol. Evol. 25:199-206.
15. Knudsen B, Miyamoto MM. 2007. Incorporating experimental design and error into coalescent/mutation models of population history. Genetics. 176:2335-2342.
16. Lynch M. 2008. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from highcoverage genome-sequencing projects. Mol. Biol. Evol. 25: 2409-2419.
17. Mackay T, Richards S, Gibbs R. 2008. Proposal to sequence a Drosophila genetic reference panel: a community resource for the study of genotypic and phenotypic variation [white paper]. FlyBase. org. Available from http://flybase.org/static pages/news/wpapers.html. Last accessed on April 14, 2009.
18. Rosenbaum P, Robertson J, Zamudio K. 2007. Unexpectedly low genetic divergences among populations of the threatened bog turtle (Glyptemys muhlenbergii). Conserv. Genet. 8:331-342.
19. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
20. Tajima F. 1983. Evolutionary relationship of DNA-sequences in finite populations. Genetics. 105:437-460.
21. Watterson GA. 1975. Number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7:256-276.
22. Zhao Z, Jin L, Fu YX et al. 2000. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. U.S.A. 97:11354-11358.
23. Zwick ME. 2005. A genome sequencing center in every lab. Eur. J. Hum. Genet. 13:1167-1168.