Modeling genome coverage in single-cell sequencing

Bioinformatics

Volumn 30, Issue 22, 2014, Pages 3159-3165

  Daley, Timothy ^a   Smith, Andrew D ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAYES THEOREM; BIOLOGICAL MODEL; DNA SEQUENCE; GENE LIBRARY; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; PROCEDURES; SINGLE CELL ANALYSIS;

BAYES THEOREM; GENE LIBRARY; GENETIC VARIATION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS;

EID: 84911418727     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu540     Document Type: Article

References (40)

1. Barbour, A.D. et al. (1992) Compound poisson approximation for nonnegative random variables via Steins method. Ann. Probab., 20, 1843-1866.
2. Blainey, P.C. (2013) The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev., 37, 407-427.
3. Breiman, L. (1996) Bagging predictors. Mach. Learn., 24, 123-140.
4. DAgostino, R.B. (1970) Transformation to normality of the null distribution of G1. Biometrika, 57, 679-681.
5. Daley, T. and Smith, A.D. (2013) Predicting the molecular complexity of sequencing libraries. Nat. Methods, 10, 325-327.
6. Derrien, T. et al. (2012) Fast computation and applications of genome mappability. PLoS One, 7, e30377.
7. Efron, B. and Thisted, R (1976) Estimating the number of unseen species: how many words did Shakespeare know? Biometrika, 63, 435-447.
8. Enk, J.M. et al. (2014) Ancient whole genome enrichment using baits built from modern DNA. Mol. Biol. Evol., 31, 1292-1294.
9. Evrony, G.D. et al. (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell, 151, 483-496.
10. Geigl, J.B. et al. (2009) Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays. Nucleic Acids Res., 37, e105.
11. Geraedts, J. and De Wert, G. (2009) Preimplantation genetic diagnosis. Clin. Genet., 76, 315-325.
12. Gole, J. et al. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat. Biotechnol., 31, 1126-1132.
13. Good, I. and Toulmin, G. (1956) The number of new species, and the increase in population coverage, when a sample is increased. Biometrika, 43, 45-63.
14. Hiatt, J.B. et al. (2013) Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Res., 23, 843-854.
15. Hosono, S. et al. (2003) Unbiased whole-genome amplification directly from clinical samples. Genome Res., 13, 954-964.
16. Hou, Y. et al. (2013) Genome analyses of single human oocytes. Cell, 155, 1492-1506.
17. Kashtan, N. et al. (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science, 344, 416-420.
18. Kirkness, E.F. et al. (2013) Sequencing of isolated sperm cells for direct haplotyping of a human genome. Genome Res., 23, 826-832.
19. Kivioja, T. et al. (2012) Counting absolute numbers of molecules using unique molecular identifiers. Nature methods, 9, 72-74.
20. Lander, E.S. and Waterman, M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
21. Link, W.A. (2003) Nonidentifiability of population size from capture-recapture data with heterogeneous detection probabilities. Biometrics, 59, 1123-1130.
22. Lu, S. et al. (2012) Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science, 338, 1627-1630.
23. McConnell, M.J. et al. (2013) Mosaic copy number variation in human neurons. Science, 342, 632-637.
24. Narayan, A. et al. (2012) Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing. Cancer Res., 72, 3492-3498.
25. Navin, N. et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472, 90-94.
26. Ni, X. et al. (2013) Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc. Natl Acad. Sci. USA, 110, 21083-21088.
27. Pamp, S.J. et al. (2012) Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Res., 22, 1107-1119.
28. Parkinson, N.J. et al. (2012) Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res., 22, 125-133.
29. Pinard, R. et al. (2006) Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics, 7, 216.
30. Prüfer, K. et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505, 43-49.
31. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
32. Sermon, K. et al. (2004) Preimplantation genetic diagnosis. Lancet, 363, 1633-1641.
33. Shapiro, E. et al. (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet., 14, 618-630.
34. Sims, D. et al. (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet., 15, 121-132.
35. Sun, F., Arnheim, N. and Waterman, M.S. (1995) Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR. Nucleic acids research, 23, 3034-3040.
36. Wang, J. et al. (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell, 150, 402-412.
37. Wang, J.P.Z. and Lindsay, B.G. (2005) A penalized nonparametric maximum likelihood approach to species richness estimation. J. Am. Stat. Assoc., 100, 942-959.
38. Xu, X. et al. (2012) Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell, 148, 886-895.
39. Zhang, K. et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nat. Biotechnol., 24, 680-686.
40. Zong, C. et al. (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338, 1622-1626.