Genome-wide patterns and properties of de novo mutations in humans

Nature Genetics

Volumn 47, Issue 7, 2015, Pages 822-826

  Francioli, Laurent C ^a   Polak, Paz P ^b   Koren, Amnon ^c   Menelaou, Androniki ^a   Chun, Sung ^b   Renkens, Ivo ^a   Van Duijn, Cornelia M ^d   Swertz, Morris ^e   Wijmenga, Cisca ^e   Van Ommen, Gertjan ^f   Slagboom, P Eline ^f   Boomsma, Dorret I ^g   Ye, Kai ^f,h   Guryev, Victor ^e   Arndt, Peter F ⁱ   Kloosterman, Wigard P ^a   De Bakker, Paul I W ^a   Sunyaev, Shamil R ^b  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d ERASMUS MEDICAL CENTER   (Netherlands)

^e UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^f LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^g VU UNIVERSITY AMSTERDAM   (Netherlands)

^h WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CPG DINUCLEOTIDE; CYTOSINE DEAMINASE; DINUCLEOTIDE; DNA GLYCOSYLTRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; BACKGROUND SELECTION; CHROMATIN STRUCTURE; DE NOVO MUTATION; DNA REPLICATION TIMING; EXCISION REPAIR; GENE CONVERSION; GENE EXPRESSION; GENE MUTATION; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GERMLINE MUTATION; HUMAN; MATERNAL AGE; MUTATION RATE; PATERNAL AGE; POPULATION GENETICS; PRIORITY JOURNAL; PROGENY; SOMATIC MUTATION; SPERMATOGENESIS; SPERMATOGONIUM; ANIMAL; BIOLOGICAL MODEL; FEMALE; GENETICS; HUMAN GENOME; MALE; MOLECULAR EVOLUTION; PAN TROGLODYTES; TWINS;

PAN;

ANIMALS; EVOLUTION, MOLECULAR; FEMALE; GENOME, HUMAN; GERM-LINE MUTATION; HUMANS; MALE; MODELS, GENETIC; MUTATION RATE; PAN TROGLODYTES; PATERNAL AGE;

EID: 84937191220     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3292     Document Type: Article

References (48)

1. Sawyer, S.A. & Hartl, D.L. Population genetics of polymorphism and divergence. Genetics 132, 1161-1176 (1992).
2. Felsenstein, J. & Churchill, G.A. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13, 93-104 (1996).
3. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
4. Cooper, G.M. et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15, 901-913 (2005).
5. Veltman, J.A. & Brunner, H.G. De novo mutations in human genetic disease. Nat. Rev. Genet. 13, 565-575 (2012).
6. Friedberg, E.C., Walker, G.C. & Siede, W. DNA Repair and Mutagenesis (ASM Press, 1995).
7. Kondrashov, A.S. Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases. Hum. Mutat. 21, 12-27 (2003).
8. Lynch, M. Rate, molecular spectrum, and consequences of human mutation. Proc. Natl. Acad. Sci. USA 107, 961-968 (2010).
9. Hodgkinson, A. & Eyre-Walker, A. Variation in the mutation rate across mammalian genomes. Nat. Rev. Genet. 12, 756-766 (2011).
10. Schaibley, V.M. et al. The influence of genomic context on mutation patterns in the human genome inferred from rare variants. Genome Res. 23, 1974-1984 (2013).
11. Michaelson, J.J. et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 151, 1431-1442 (2012).
12. Kong, A. et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488, 471-475 (2012).
13. Genomes of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 46, 818-825 (2014).
14. Jenkins, T.G., Aston, K.I., Pflueger, C., Cairns, B.R. & Carrell, D.T. Age-associated sperm DNA methylation alterations: possible implications in offspring disease susceptibility. PLoS Genet. 10, e1004458 (2014).
15. Koren, A. DNA replication timing: coordinating genome stability with genome regulation on the X chromosome and beyond. Bioessays 36, 997-1004 (2014).
16. Arndt, P.F., Petrov, D.A. & Hwa, T. Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol. Biol. Evol. 20, 1887-1896 (2003).
17. Schmidt, S. et al. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genet. 4, e1000281 (2008).
18. Subramanian, S. & Kumar, S. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13, 838-844 (2003).
19. Polak, P. et al. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nat. Biotechnol. 32, 71-75 (2014).
20. Pleasance, E.D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184-190 (2010).
21. Campbell, C.D. et al. Estimating the human mutation rate using autozygosity in a founder population. Nat. Genet. 44, 1277-1281 (2012).
22. Roberts, S.A. et al. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol. Cell 46, 424-435 (2012).
23. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-993 (2012).
24. Chan, K., Resnick, M.A. & Gordenin, D.A. The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis. DNA Repair (Amst.) 12, 878-889 (2013).
25. Arndt, P.F., Hwa, T. & Petrov, D.A. Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J. Mol. Evol. 60, 748-763 (2005).
26. Hellmann, I., Ebersberger, I., Ptak, S.E., Pääbo, S. & Przeworski, M. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72, 1527-1535 (2003).
27. Begun, D.J. & Aquadro, C.F. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356, 519-520 (1992).
28. Lercher, M.J. & Hurst, L.D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18, 337-340 (2002).
29. Kong, A. et al. A high-resolution recombination map of the human genome. Nat. Genet. 31, 241-247 (2002).
30. Duret, L. & Arndt, P.F. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 4, e1000071 (2008).
31. Kong, A. et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467, 1099-1103 (2010).
32. McVicker, G., Gordon, D., Davis, C. & Green, P. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5, e1000471 (2009).
33. Asthana, S., Roytberg, M., Stamatoyannopoulos, J. & Sunyaev, S. Analysis of sequence conservation at nucleotide resolution. PLOS Comput. Biol. 3, e254 (2007).
34. Gratten, J., Visscher, P.M., Mowry, B.J. & Wray, N.R. Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease. Nat. Genet. 45, 234-238 (2013).
35. DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
36. McKenna, A. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
37. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
38. Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033-1040 (2012).
39. Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
40. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
41. Ryba, T. et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 20, 761-770 (2010).
42. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
43. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011).
44. Paten, B., Herrero, J., Beal, K., Fitzgerald, S. & Birney, E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 18, 1814-1828 (2008).
45. Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48-D55 (2013).
46. R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2014).
47. Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004).
48. Murphy, W.J. et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348-2351 (2001).