Evidence map›Paper›PMID 37710206›Full record

ArticleBMC genomic data2023

Overestimated prediction using polygenic prediction derived from summary statistics.

David Keetae Park, Mingshen Chen, Seungsoo Kim, Yoonjung Yoonie Joo, Rebekah K Loving, Hyoung Seop Kim, Jiook Cha, Shinjae Yoo, Jong Hun Kim

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomic data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.3field-weighted citation impact, top 29% of its field
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

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Addressing overfitting bias due to sample overlap in polygenic risk scoring.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025
    Article
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

9 authors at 9 institutions in 2 countries.

David Keetae Park *Department of Biomedical Engineering, Columbia University, New York, USA.
Mingshen Chen *Department of Applied Mathematics & Statistics, Stony Brook University, New York, USA.
Seungsoo KimDepartment of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
Yoonjung Yoonie JooSamsung Advanced Institute for Health Sciences & Technology (SAHIST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea.
Rebekah K LovingDepartment of Biology, California Institute of Technology, Pasadena, USA.
Hyoung Seop KimDepartment of Physical Medicine and Rehabilitation, Dementia Center, National Health Insurance Service Ilsan Hospital, Goyang, South Korea.
Jiook ChaDepartment of Psychology, Brain and Cognitive Sciences, AI Institute, Seoul National University, Seoul, South Korea.
Shinjae YooComputational Science Initiative, Brookhaven National Lab. Computer Science and Math, Building 725, Room 2-189, Upton, NY, 11973, USA. sjyoo@bnl.gov.
Jong Hun KimDepartment of Neurology, Dementia Center, National Health Insurance Service Ilsan Hospital, 100 Ilsan-ro Ilsandong-gu, Goyang, Gyeonggi-Do, 10444, South Korea. jh7521@naver.com.
Brookhaven College · USCalifornia Institute of Technology · USColumbia University · USColumbia University Irving Medical Center · USNational Health Insurance Service · KRNational Health Insurance Service Ilsan Hospital · KRSeoul National University · KRStony Brook University · USSungkyunkwan University · KR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundWhen polygenic risk score (PRS) is derived from summary statistics, independence between discovery and test sets cannot be monitored. We compared two types of PRS studies derived from raw genetic data (denoted as rPRS) and the summary statistics for IGAP (sPRS).

resultsTwo variables with the high heritability in UK Biobank, hypertension, and height, are used to derive an exemplary scale effect of PRS. sPRS without APOE is derived from International Genomics of Alzheimer's Project (IGAP), which records ΔAUC and ΔR

conclusionConsidering the high heritability of hypertension and height of UK Biobank and sample size of UK Biobank, sPRS results from AD databases are inflated. Independence between discovery and test sets is a well-known basic requirement for PRS studies. However, a lot of PRS studies cannot follow such requirements because of impossible direct comparisons when using summary statistics. Thus, for sPRS, potential duplications should be carefully considered within the same ethnic group.

Indexed as

Alzheimer DiseaseHypertensionDatabases, FactualEthnicityGenomicsHumansAlzheimer’s diseaseComplex genetic diseaseOverestimation biasPolygenic risk score

Identifiers

PMID37710206
PMCPMC10500750
OpenAlexW4386744456

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.