This small package collects sample information and de novo mutations from published studies of de novo mutations in rare disease.
This also reconciles individuals and variants included in multiple studies, so we don't double count individuals if they are present in multiple studies.
All of the information is obtained from the relevant supplementary data tables associated with each journal publication. Where a study has collected healthy controls (e.g. unaffected siblings), the phenotype of the healthy controls is 'unaffected'.
pip install git+git://github.com/jeremymcrae/dnm_cohorts.git
The data files are included in the package, and can be loaded in python with:
from dnm_cohorts import de_novos, cohort
# to create a table of all individuals in the cohorts
dnm_cohorts --cohorts --output test.txt
# to create a table of all de novo mutations found in those individuals
dnm_cohorts --de-novos --output test.txt
The package contains a dataset of de novos on their original genome build (the default), as well as a dataset lifted to GRCh37 and a dataset lifted to GRCh38.
reference | year | unique individuals | phenotype | assay | deprecated |
---|---|---|---|---|---|
De Ligt et al. N Engl J Med 367:1921-1929 | 2012 | 100 | intellectual disability | exome | no |
Iossifov et al. Neuron 74:285-299 | 2012 | 686 (343 asd, 343 unaffected) | autism spectrum disorder, unaffected siblings | exome | no |
O'Roak et al. Nature 485:246-250 | 2012 | 206 | autism spectrum disorder | exome | no |
Rauch et al. Lancet 380:1674-1682 | 2012 | 51 | intellectual disability | exome | no |
Sanders et al. Nature 485:237-241 | 2012 | 452 (238 asd, 214 unaffected) | autism spectrum disorder, unaffected siblings | exome | no |
Epi4K Consortium. Nature 501:217-221 | 2013 | 264 | epilepsy | exome | no |
EuroEPINOMICS-RES Consortium. AJHG 95:360-370 | 2014 | 92 | epilepsy | exome | no |
Gilissen et al. Nature 511:344-347 | 2014 | 0 | intellectual disability | exome | no, but only extends De ligt et al |
De Rubeis et al. Nature 515:209-215 | 2014 | 1604 (1443 asd, 161 unaffected) | autism spectrum disorder, unaffected siblings | exome | no |
Iossifov et al. Nature 498:216-221 | 2014 | 3095 (1726 asd, 1369 unaffected) | autism spectrum disorder, unaffected siblings | exome | no |
Sanders et al. Neuron 87:1215-1233 | 2015 | 750 (314 asd, 436 unaffected) | autism spectrum disorder, unaffected siblings | exome | no |
Homsy et al. Science 350:1262-1266 | 2015 | 1213 | congenital heart disease | exome | yes, superseded by Jin et al cohort |
Lelieveld et al. Nature Neuroscience 19:1194-1196 | 2016 | 820 | intellectual disability | exome | yes, superseded by Kaplanis et al cohort |
McRae et al. Nature 542:433-438 | 2017 | 4293 | intellectual disability | exome | yes, superseded by Kaplanis et al cohort |
Jónsson et al. Nature 549:519-522 | 2017 | 1458 | unaffected | genome (no chrX in males) | yes |
Jin et al. Nature Genetics 49:1593-1601 | 2017 | 2465 | congenital heart disease | exome | no |
Yuen et al. Nature Neuroscience 20:602-611 | 2017 | 5265 | autism spectrum disorder | genome | no |
An et al. Science 362:eaat6576 | 2018 | 1902 affected, 1902 unaffected | autism spectrum disorder, unaffected siblings | genome | no |
Halldorsson et al. Science | 2019 | 2976 | unaffected, supersedes Jónsson et al | genome | no |
Kaplanis et al. Nature | 2019 | 31058 | intellectual disability, supersedes Lelieveld et al and McRae et al cohorts | exome | no |
Fu et al. Nature Genetics 54:1320-1331 | 2022 | 42607 | autism spectrum disorder | exome (no chrX) | no, but Fu et al and Zhou et al mostly overlap |
Zhou et al. Nature Genetics 54:1305-1319 | 2022 | 42607 | autism spectrum disorder | exome | yes, by Fu et al, because Fu et al include all sample IDs |
We exclude some published cohorts with de novo mutations, for the reasons below:
- Helbig et al in Genetics in Medicine 18:898-905. This study only reported the likely pathogenic de novo mutations.
- Goldman et al. in Nature Genetics 48:935-939. This study includes monozygotic twins, so some de novo mutations are not independent, but does not include sample or family IDs that would permit exclusion of the monozygotic twins.
- Goldmann et al. in Nature Genetics 50:487-492. This study only reported clustered DNMs, so not representative of all coding DNMs.