---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21987'
abstract:
- lang: eng
  text: 'We introduce JODIE, a genetic joint modeling approach that estimates how
    DNA loci influence human traits by partitioning genetic effects into four components:
    direct effects (from a child’s alleles), indirect maternal and paternal effects
    (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental
    transmission of alleles), while uniquely accounting for assortative mating. We
    analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian
    Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood
    educational test scores. We find direct effects to be the largest contributor
    to trait variation, but combined, indirect parental and PofO effects are similarly
    substantial. We support our results by within-family genome-wide association testing
    and identify 276 independently associated DNA regions with a complex interplay
    between direct, indirect, and PofO effects. By joint modeling, we show that direct,
    indirect, and PofO effects collectively shape human phenotypic variation across
    loci genome-wide.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson
  group at ISTA for their comments, which improved this manuscript. This work was
  funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding
  from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father,
  and Child Cohort Study is supported by the Norwegian Ministry of Health and Care
  Services and the Ministry of Education and Research. We are grateful to all the
  participating families in Norway who take part in this on-going cohort study. We
  thank the Norwegian Institute of Public Health (NIPH) for generating high-quality
  genomic data. The research is part of the HARVEST collaboration, supported by the
  Research Council of Norway (#229624). We also thank the NORMENT Center for providing
  genotype data, funded by the Research Council of Norway (#223273), South East Norway
  Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration
  with deCODE Genetics. We further thank the Center for Diabetes Research, the University
  of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED,
  Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council
  of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western
  Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for
  Sensitive Data) facilities, owned by the University of Oslo, operated and developed
  by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no).
  E.Y. is supported by the European Union (grant numbers 101045526 and 101073237)
  and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe
  would like to acknowledge the participants and investigators of the Generation Scotland
  Cohort study. Generation Scotland received core support from the Chief Scientist
  Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish
  Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples
  was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research
  Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK
  and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and
  Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank
  and acknowledge the participants and investigators of the Estonian Biobank (EstBB)
  study. The research was conducted using the Estonian Center of Genomics/Roadmap
  II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses
  were performed on resources provided by Sigma2 - the National Infrastructure for
  High-Performance Computing and Data Storage in Norway. Estonian Data analysis was
  carried out in the High-Performance Computing Center cloud provided by University
  of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained
  from the other analyses was conducted at IST Austria and is supported by the Scientific
  Service Units (SSU) of IST Austria through resources provided by Scientific Computing
  (SciComp)."
article_number: '101277'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ilse
  full_name: Krätschmer, Ilse
  id: 30d4014e-7753-11eb-b44b-db6d61112e73
  last_name: Krätschmer
  orcid: 0000-0002-5636-9259
- first_name: Laura
  full_name: Hegemann, Laura
  last_name: Hegemann
- first_name: Robin J.
  full_name: Hofmeister, Robin J.
  last_name: Hofmeister
- first_name: Elizabeth C.
  full_name: Corfield, Elizabeth C.
  last_name: Corfield
- first_name: Mahdi
  full_name: Mahmoudi, Mahdi
  last_name: Mahmoudi
- first_name: Olivier
  full_name: Delaneau, Olivier
  last_name: Delaneau
- first_name: Ole A.
  full_name: Andreassen, Ole A.
  last_name: Andreassen
- first_name: Archie
  full_name: Campbell, Archie
  last_name: Campbell
- first_name: Caroline
  full_name: Hayward, Caroline
  last_name: Hayward
- first_name: Riccardo E.
  full_name: Marioni, Riccardo E.
  last_name: Marioni
- first_name: Eivind
  full_name: Ystrom, Eivind
  last_name: Ystrom
- first_name: Alexandra
  full_name: Havdahl, Alexandra
  last_name: Havdahl
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
citation:
  ama: Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect,
    and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>.
    2026;6(7). doi:<a href="https://doi.org/10.1016/j.xgen.2026.101277">10.1016/j.xgen.2026.101277</a>
  apa: Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi,
    M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin
    genetic effects in the human population. <i>Cell Genomics</i>. Elsevier. <a href="https://doi.org/10.1016/j.xgen.2026.101277">https://doi.org/10.1016/j.xgen.2026.101277</a>
  chicago: Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield,
    Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct,
    Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell
    Genomics</i>. Elsevier, 2026. <a href="https://doi.org/10.1016/j.xgen.2026.101277">https://doi.org/10.1016/j.xgen.2026.101277</a>.
  ieee: I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin
    genetic effects in the human population,” <i>Cell Genomics</i>, vol. 6, no. 7.
    Elsevier, 2026.
  ista: Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau
    O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson
    MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in
    the human population. Cell Genomics. 6(7), 101277.
  mla: Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin
    Genetic Effects in the Human Population.” <i>Cell Genomics</i>, vol. 6, no. 7,
    101277, Elsevier, 2026, doi:<a href="https://doi.org/10.1016/j.xgen.2026.101277">10.1016/j.xgen.2026.101277</a>.
  short: I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi,
    O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom,
    A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "Information on how to access the MoBaPsychGen post-imputation
  QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian
  Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this
  project. For access to be granted to the Estonian Biobank genotypic and corresponding
  phenotypic data, a preliminary application must be presented to the oversight committee,
  who must first approve the project. Ethics permission must then be obtained from
  the Estonian Committee on Bioethics and Human Research. Finally, a full project
  must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation
  Scotland data is available with appropriate permission from the Generation Scotland
  Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe
  code for JODIE developed in this work is open source and is publicly available on
  zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype
  Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729)
  are available by application to a Data Access Committee (DAC) of the Wellcome Trust
  Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org."
date_created: 2026-06-10T07:39:08Z
date_published: 2026-07-08T00:00:00Z
date_updated: 2026-07-28T07:27:01Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.xgen.2026.101277
external_id:
  pmid:
  - '40909755'
file:
- access_level: open_access
  checksum: f896b510480d2d4e4a7fd46c2e2761f4
  content_type: application/pdf
  creator: dernst
  date_created: 2026-07-28T07:24:50Z
  date_updated: 2026-07-28T07:24:50Z
  file_id: '22597'
  file_name: 2026_CellGenomics_Kraetschmer.pdf
  file_size: 3679297
  relation: main_file
  success: 1
file_date_updated: 2026-07-28T07:24:50Z
has_accepted_license: '1'
intvolume: '         6'
issue: '7'
keyword:
- direct genetic effects
- DGE
- indirect genetic effects
- IGE
- parent-of-origin effects
- phenotypic variation
- assortative mating
- within-family GWAS
- MoBa
- EstBB
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
  grant_number: PCEGP3_181181
  name: Improving estimation and prediction of common complex disease risk
publication: Cell Genomics
publication_identifier:
  eissn:
  - 2666-979X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Separating direct, indirect, and parent-of-origin genetic effects in the human
  population
tmp:
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  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2026'
...
---
_id: '5553'
abstract:
- lang: eng
  text: "Genotypic, phenotypic and demographic data for 2128 wild snapdragons and
    1127 open-pollinated progeny from a natural hybrid zone, collected as part of
    Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent
    to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers
    by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been
    removed from this dataset.\r\n\r\nOther data were retreived from an online database
    of this population at www.antspec.org."
article_processing_charge: No
author:
- first_name: David
  full_name: Field, David
  id: 419049E2-F248-11E8-B48F-1D18A9856A87
  last_name: Field
  orcid: 0000-0002-4014-8478
- first_name: Thomas
  full_name: Ellis, Thomas
  id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
  last_name: Ellis
  orcid: 0000-0002-8511-0254
citation:
  ama: Field D, Ellis T. Inference of mating patterns among wild snapdragons in a
    natural hybrid zone in 2012. 2016. doi:<a href="https://doi.org/10.15479/AT:ISTA:37">10.15479/AT:ISTA:37</a>
  apa: Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild
    snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology
    Austria. <a href="https://doi.org/10.15479/AT:ISTA:37">https://doi.org/10.15479/AT:ISTA:37</a>
  chicago: Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild
    Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology
    Austria, 2016. <a href="https://doi.org/10.15479/AT:ISTA:37">https://doi.org/10.15479/AT:ISTA:37</a>.
  ieee: D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons
    in a natural hybrid zone in 2012.” Institute of Science and Technology Austria,
    2016.
  ista: Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons
    in a natural hybrid zone in 2012, Institute of Science and Technology Austria,
    <a href="https://doi.org/10.15479/AT:ISTA:37">10.15479/AT:ISTA:37</a>.
  mla: Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild
    Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology
    Austria, 2016, doi:<a href="https://doi.org/10.15479/AT:ISTA:37">10.15479/AT:ISTA:37</a>.
  short: D. Field, T. Ellis, (2016).
contributor:
- contributor_type: project_manager
  first_name: Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
datarep_id: '37'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2026-04-09T10:52:06Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:37
file:
- access_level: open_access
  checksum: 4ae751b1fa4897fa216241f975a57313
  content_type: application/zip
  creator: system
  date_created: 2018-12-12T13:03:02Z
  date_updated: 2020-07-14T12:47:01Z
  file_id: '5620'
  file_name: IST-2016-37-v1+1_paternity_archive.zip
  file_size: 132808
  relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- paternity assignment
- pedigree
- matting patterns
- assortative mating
- Antirrhinum majus
- frequency-dependent selection
- plant-pollinator interaction
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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status: public
title: Inference of mating patterns among wild snapdragons in a natural hybrid zone
  in 2012
tmp:
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  legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
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  short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...