Evidence map›Paper›PMID 38699372›Full record

ArticlemedRxiv : the preprint server for health sciences2024

CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data.

Yujin Kim, Minwoo Jeong, In Gyeong Koh, Chanhee Kim, Hyeji Lee, Jae Hyun Kim, Ronald Yurko, Il Bin Kim, Jeongbin Park, Donna M Werling and 2 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Yujin KimDepartment of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
Minwoo JeongSchool of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea.
In Gyeong KohDepartment of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
Chanhee KimDepartment of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
Hyeji LeeDepartment of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
Jae Hyun KimDepartment of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
Ronald YurkoDepartment of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
Il Bin KimDepartment of Psychiatry, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, 06135, Republic of Korea.
Jeongbin ParkSchool of Biomedical Convergence Engineering, Pusan National University, Busan, 50612, Republic of Korea.
Donna M WerlingLaboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Stephan J SandersInstitute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK.
Joon-Yong AnDepartment of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.

Funding

Alzheimer's Disease Genetics ConsortiumU01AG032984 · NIA · UNIVERSITY OF PENNSYLVANIA · PI SCHELLENBERG, GERARD DAVID · 2009 to 2024
$60.4M
SUPPLEMENT TO RUSH ALZHEIMERS DISEASE CENTER COREP30AG010161 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI LEURGANS, SUE E. · 1991 to 2020
$49.1M
EPIDEMIOLOGY OF NEURAL RESERVE AND NEUROBIOLOGY IN AGINGR01AG017917 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 2001 to 2023
$43.3M
RISK FACTORS, PATHOLOGY, AND CLINICAL EXPRESSIONS OF ADR01AG015819 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1998 to 2024
$21.4M
Multi-omic network-directed proteoform discovery, dissection and functional validation to prioritize novel AD therapeutic targetsU01AG061356 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BENNETT, DAVID ALAN, DE JAGER, PHILIP L · 2018 to 2022
$13.7M
Pathway discovery, validation and compound identification for Alzheimer's disease - SupplementU01AG046152 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BENNETT, DAVID ALAN, DE JAGER, PHILIP L · 2013 to 2017
$13.6M
Genetic Epidemiology of Cognitive Decline in an Aging Population SampleR01AG030146 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI EVANS, DENIS A · 2007 to 2018
$6.2M
4/4 - The Autism Sequencing Consortium: Discovering autism risk genes and how they impact core features of the disorderR01MH129751 · NIMH · UNIVERSITY OF OXFORD · PI Stephan Sanders · 2022 to 2026
$1.4M
4/4 - The Autism Sequencing Consortium: Autism Gene Discovery in >50,000 ExomesU01MH111662 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SANDERS, STEPHAN, STATE, MATTHEW W. · 2017 to 2021
$1.3M
NIA NIH HHS P30 AG010161NIA NIH HHS R01 AG015819NIA NIH HHS R01 AG017917NIA NIH HHS R01 AG030146NIA NIH HHS U01 AG032984NIA NIH HHS U01 AG046152NIA NIH HHS U01 AG061356NIMH NIH HHS R01 MH129751
6 · The paper itself

Abstract

Variants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS) employs both whole-genome sequencing and user-provided functional data to enhance noncoding variant analysis, with a faster and more efficient execution of the CWAS workflow. Here, we used single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type specific enhancers and promoters. Examining autism spectrum disorder whole-genome sequencing data (n = 7,280), CWAS-Plus identified noncoding

Indexed as

genetic associationnoncoding genomerare variantregulatory noncoding variantwhole-genome sequencing

Identifiers

PMID38699372
PMCPMC11065022

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

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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.