PXD069116-1

PXD069116 is an original dataset announced via ProteomeXchange.

Title	Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Description	Most genetic variants in the human genome reside in non-coding regions, where they can perturb regulatory elements, influence gene expression, and contribute to various phenotypes and diseases. However, identifying such functionally relevant genetic variation remains challenging. Here we integrate personal genomics, allele-specific gene regulation, and deep learning predictions to map the impact of non-coding variation in its native allelic and regulatory context. We identify and validate hundreds of cell-type-specific transcription factor binding events disrupted by genetic variants, providing mechanistic insights underlying allele-specific gene regulation. Using this framework, we discover a rare variant that modulates PIK3R5 gene expression by disrupting an OCT2 binding site within a distal enhancer. Our study establishes a generalisable strategy for interpreting non-coding regulatory variation, enabling systematic dissection of variant effects across diverse biological systems and offering an alternative framework to investigate the disease mechanisms.
HostingRepository	PRIDE
AnnounceDate	2026-04-22
AnnouncementXML	Submission_2026-04-22_10:20:05.691.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miguel Hernandez Quiles
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-03 05:20:46	ID requested
⏵ 1	2026-04-22 10:20:06	announced

Dataset with its publication pending

submitter keyword: LC-MSMS,Non-coding variants, Deep learning

Michiel Vermeulen
contact affiliation	Division of Molecular Genetics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
contact email	mi.Vermeulen@nki.nl
lab head
Miguel Hernandez Quiles
contact affiliation	Netherlands Cancer Institute
contact email	m.hernandez@nki.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069116

PRIDE project URI

• PRIDE
  1. PXD069116
     1. Label: PRIDE project
     2. Name: Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning