Evidence map›Paper›PMID 35145108›Full record

ArticleNature communications2022

A mammalian methylation array for profiling methylation levels at conserved sequences.

Adriana Arneson, Amin Haghani, Michael J Thompson, Matteo Pellegrini, Soo Bin Kwon, Ha Vu, Emily Maciejewski, Mingjia Yao, Caesar Z Li, Ake T Lu and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
143citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

143 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Review
  6. Population-scale detection of methylation outliers from long-read genome sequencing.medRxiv : the preprint server for health sciences · 2026
    Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Review
  16. Article
  17. Emerging opportunities for DNA methylation biomarkers in cattle improvement.The Journal of reproduction and development · 2026
    Review
  18. Review
  19. Article
  20. Article

83 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

Adriana Arneson *Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.
Amin Haghani *Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Michael J ThompsonMolecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-2914-1080
Matteo PellegriniMolecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Soo Bin KwonBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-8670-0993
Ha VuBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.
Emily MaciejewskiDepartment of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Mingjia YaoDept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Caesar Z LiDept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-3907-7983
Ake T LuDept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Marco MorselliMolecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0003-3351-5791
Liudmilla RubbiMolecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Bret BarnesIllumina, Inc, 5200 Illumina Way, San Diego, CA, 92122, USA.
Kasper D HansenDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Wanding ZhouCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, USA.
Charles E BreezeAltius Institute for Biomedical Sciences, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-5294-915X
Jason ErnstBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA. jason.ernst@ucla.edu.ORCID http://orcid.org/0000-0003-4026-7853
Steve HorvathDept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA. shorvath@mednet.ucla.edu.ORCID http://orcid.org/0000-0002-4110-3589

Funding

Deciphering the Relationship between Substance Use and Psychiatric Disorders from Whole Genome Sequencing DataDP1DA044371 · NIDA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ERNST, JASON · 2017 to 2021
$2.3M
NIDA NIH HHS DP1 DA044371
6 · The paper itself

Abstract

Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.

Indexed as

Conserved SequenceDNA MethylationAnimalsBiomarkersCpG IslandsEpigenesis, GeneticHumansMammalsMiceMutationProtein Processing, Post-TranslationalRatsTranscriptomeBiomarkers

Identifiers

PMID35145108
PMCPMC8831611

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.