The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Genome-wide patterns and properties of de novo mutations in humans
Open accessAbstract
Mutations create variation in the population, fuel evolution and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect. Here we analyze 11,020 de novo mutations from the whole genomes of 250 families. We show that de novo mutations in the offspring of older fathers are not only more numerous but also occur more frequently in early-replicating, genic regions. Functional regions exhibit higher mutation rates due to CpG dinucleotides and show signatures of transcription-coupled repair, whereas mutation clusters with a unique signature point to a new mutational mechanism. Mutation and recombination rates independently associate with nucleotide diversity, and regional variation in human-chimpanzee divergence is only partly explained by heterogeneity in mutation rate. Finally, we provide a genome-wide mutation rate map for medical and population genetics applications. Our results provide new insights and refine long-standing hypotheses about human mutagenesis.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,200
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,456
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2005) · doi:10.1128/9781555816704 · Cited by 5,683
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“This correction was applied for 2,339 1Mb non-overlapping windows across the autosomes after excluding windows where (1) the decode sex-averaged recombination rate is unavailable for more than 10% of the window, (2) the sex-averaged recombination rate across the window is 0 or greater than 3 cM/Mb, (3) the primate loc…”
MethodRate of de novo mutations and the importance of father’s age to disease risk
Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S. A., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., et al. (2012) · Nature · doi:10.1038/nature11396 · Cited by 2,134
Cited by
Characterizing the Major Structural Variant Alleles of the Human Genome
Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.019 · Cited by 492
Parental influence on human germline de novo mutations in 1,548 trios from Iceland
Jónsson, H., Sulem, P., Kehr, B., Kristmundsdottir, S., Zink, F., Hjartarson, E., Hardarson, M. T., Hjorleifsson, K. E., Eggertsson, H. P., Gudjonsson, S. A., et al. (2017) · Nature · doi:10.1038/nature24018 · Cited by 561
Gazal, S., Finucane, H. K., Furlotte, N. A., Loh, P.-R., Palamara, P. F., Liu, X., Schoech, A., Bulik-Sullivan, B., Neale, B. M., Gusev, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3954 · Cited by 525
Eisenberg, M. L., Esteves, S. C., Lamb, D. J., Hotaling, J. M., Giwercman, A., Hwang, K., & Cheng, Y.-S. (2023) · Nature Reviews Disease Primers · doi:10.1038/s41572-023-00459-w · Cited by 536
Inherited and de novo genetic risk for autism impacts shared networks
Ruzzo, E. K., Pérez-Cano, L., Jung, J.-Y., Wang, L.-K., Kashef-Haghighi, D., Hartl, C., Singh, C., Xu, J., Hoekstra, J. N., Leventhal, O., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.015 · Cited by 457
Metadata
- Authors
- Genome of the Netherlands Consortium, Francioli, L. C., Polak, P. P., Koren, A., Menelaou, A., Chun, S., Renkens, I., van Duijn, C. M., Swertz, M., Wijmenga, C., van Ommen, G., Slagboom, P. E., Boomsma, D. I., Ye, K., Guryev, V., Arndt, P. F., Kloosterman, W. P., de Bakker, P. I. W., & Sunyaev, S. R.
- Venue
- Nature Genetics
- Published
- 2015-05-18
- Volume
- 47
- Issue
- 7
- Pages
- 822-826
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W1942248206
- Cited by
- 379
- References
- 48
- FWCI
- 30.02
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Genome-wide patterns and properties of de novo mutations in humans. https://app.cochat.ai/papers/10.1038/ng.3292
- The paper
- Genome of the Netherlands Consortium, Francioli, L. C., Polak, P. P., Koren, A., Menelaou, A., Chun, S., Renkens, I., van Duijn, C. M., Swertz, M., Wijmenga, C., van Ommen, G., Slagboom, P. E., Boomsma, D. I., Ye, K., Guryev, V., Arndt, P. F., Kloosterman, W. P., de Bakker, P. I. W., & Sunyaev, S. R. (2015). Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics. https://doi.org/10.1038/ng.3292
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
