Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error

Genome Research

Volumn 20, Issue 1, 2010, Pages 101-109

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

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

Author keywords

[No Author keywords available]

Indexed keywords

ANGPLT 4 PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; CHI SQUARE TEST; COMPUTER SIMULATION; DNA SEQUENCE; GROWTH; MAXIMUM LIKELIHOOD METHOD; MUTATION RATE; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; PROBABILITY; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMATIC ERROR;

AFRICAN AMERICANS; AFRICAN CONTINENTAL ANCESTRY GROUP; ANGIOPOIETINS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 74949095858     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.097543.109     Document Type: Article

References (29)

1. Achaz G. 2008. Testing for neutrality in samples with sequencing errors. Genetics 179: 1409-1424.
2. Clark AG, Whittam TS. 1992. Sequencing errors and molecular evolutionary analysis. Mol Biol Evol 9: 744-752.
3. Fu YX. 1994. 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.
4. Fu YX. 1995. Statistical properties of segregating sites. Theor Popul Biol 48: 172-197.
5. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.
6. 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.
7. Hudson RR. 2001. Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
8. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
9. Jiang R, Tavaré S, Marjoram P. 2009. Population genetic inference from resequencing data. Genetics 181: 187-197.
10. Johnson PLF, Slatkin M. 2006. Inference of population genetic parameters in metagenomics: A clean look at messy data. Genome Res 16: 1320-1327.
11. Johnson PLF, Slatkin M. 2008. Accounting for bias from sequencing error in population genetic estimates. Mol Biol Evol 25: 199-206.
12. Knudsen B, Miyamoto MM. 2007. Incorporating experimental design and error into coalescent/mutation models of population history. Genetics 176: 2335-2342.
13. Knudsen B, Miyamoto M. 2009. Accurate and fast methods to estimate the population mutation rate from error prone sequences. BMC Bioinformatics 10: 247. doi: 10.1186/1471-2105-10-247.
14. Liu X, Maxwell TJ, Boerwinkle E, Fu Y-X. 2009. Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences. Mol Biol Evol 26: 1479-1490.
15. Lynch M. 2008. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Mol Biol Evol 25: 2409-2419.
16. Lynch M. 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301.
17. Nielsen R. 2000. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
18. Polanski A, Kimmel M. 2003. New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics 165: 427-436.
19. Polanski A, Bobrowski A, Kimmel M. 2003. A note on distributions of times to coalescence, under time-dependent population size. Theor Popul Biol 63: 33-40.
20. Press WH, Teukolsky SA, Vetterling WT, Flannery BP. 2007: Numerical recipes: The art of scientific computing, 3rd ed. Cambridge University Press.
21. Rambaut A, Ho SYW, Drummond AJ, Shapiro B. 2009. Accommodating the effect of ancient dna damage on inferences of demographic histories. Mol Biol Evol 26: 245-248.
22. Romeo S, Pennacchio LA, Fu Y, Boerwinkle E, Tybjaerg-Hansen A, Hobbs HH, Cohen JC. 2007. Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet 39: 513-516.
23. Romeo S, Yin W, Kozlitina J, Pennacchio LA, Boerwinkle E, Hobbs HH, Cohen JC. 2009. Rare loss-of-function mutations in angptl family members contribute to plasma triglyceride levels in humans. J Clin Invest 119: 70-79.
24. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
25. Tajima F. 1983. Evolutionary relationship of DNA-sequences in finite populations. Genetics 105: 437-460.
26. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
27. Watterson GA. 1975. Number of segregating sites in genetic models without recombination. Theor Popul Biol 7: 256-276.
28. Whitaker RJ, Banfield JF. 2006. Population genomics in natural microbial communities. Trends Ecol Evol 21: 508-516.
29. Zwick ME. 2005. A genome sequencing center in every lab. Eur J Hum Genet 13: 1167-1168.