Evidence map›Paper›PMID 37163057›Full record

ArticlebioRxiv : the preprint server for biology2023

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk.

S Behera, J R Belyeu, X Chen, L F Paulin, N Q H Nguyen, E Newman, M Mahmoud, V K Menon, Q Qi, P Joshi and 16 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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

26 authors.

S BeheraHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
J R BelyeuIllumina Inc., San Diego, CA, USA.
X ChenIllumina Inc., San Diego, CA, USA.
L F PaulinHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
N Q H NguyenSchool of Public Health, University of Texas Health Science Center at Houston, TX, USA.
E NewmanIllumina Inc., San Diego, CA, USA.
M MahmoudHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
V K MenonHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Q QiDepartment of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
P JoshiMedpace Reference Laboratories, Cincinnati, OH, USA.
S MarcovinaUniversity of Texas Southwestern Medical Center, Dallas, TX, USA.
M RossiIllumina Inc., San Diego, CA, USA.
E RollerIllumina Inc., San Diego, CA, USA.
J HanIllumina Inc., San Diego, CA, USA.
V OnuchicIllumina Inc., San Diego, CA, USA.
C L AveryDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
C M BallantyneDepartment of Medicine, Baylor College of Medicine, Houston, TX, USA.
C J RodriguezDepartment of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
R C KaplanDepartment of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
D M MuznyHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
G A MetcalfHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
R GibbsHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
B YuSchool of Public Health, University of Texas Health Science Center at Houston, TX, USA.
E BoerwinkleHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
M A EberleIllumina Inc., San Diego, CA, USA.
F J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.

Funding

Genomic Architecture of Common Disease in Diverse Populations: WGS of Ongoing Hemorrhagic Stroke Study SupplementUM1HG008898 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2016 to 2020
$77.0M
Frequency of variants of unknown significance by ancestry groups in the All of Us Research Program cohortU01HG011758 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI RICHARD A GIBBS, JAMES R. LUPSKI · 2021 to 2026
$13.8M
HISPANIC COMMUNITY HEALTH STUDY-268065233N01HC065233 · HC · COORDINATING CENTER · PI CHAMBLESS, LLOYD E · 2006 to 2006
–
NHGRI NIH HHS HHSN268201300003CNHGRI NIH HHS U01 HG011758NHGRI NIH HHS UM1 HG008898NHLBI NIH HHS HHSN268201300001CNHLBI NIH HHS HHSN268201300003INHLBI NIH HHS HHSN268201300004CNHLBI NIH HHS HHSN268201300005CNHLBI NIH HHS HHSN268201700001CNHLBI NIH HHS HHSN268201700001INHLBI NIH HHS HHSN268201700002CNHLBI NIH HHS HHSN268201700002INHLBI NIH HHS HHSN268201700003CNHLBI NIH HHS HHSN268201700003INHLBI NIH HHS HHSN268201700004CNHLBI NIH HHS HHSN268201700004INHLBI NIH HHS HHSN268201700005CNHLBI NIH HHS HHSN268201700005INHLBI NIH HHS N01 HC065233NHLBI NIH HHS N01 HC065234NHLBI NIH HHS N01 HC065235NHLBI NIH HHS N01 HC065236NHLBI NIH HHS N01 HC065237
6 · The paper itself

Abstract

The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase ~50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.

Indexed as

cardiovascular diseasecopy number variationIlluminaLPANext Generation sequencing

Identifiers

PMID37163057
PMCPMC10168217

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.