Evidence map›Paper›PMID 31070582›Full record

ArticleeLife2019

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis.

Satish K Nandakumar, Sean K McFarland, Laura M Mateyka, Caleb A Lareau, Jacob C Ulirsch, Leif S Ludwig, Gaurav Agarwal, Jesse M Engreitz, Bartlomiej Przychodzen, Marie McConkey and 6 more

Abstract read
In one paragraph

Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

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

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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

16 authors.

Satish K Nandakumar *Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.ORCID 0000-0002-7853-426X
Sean K McFarland *Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.
Laura M Mateyka *Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.
Caleb A Lareau *Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.ORCID 0000-0003-4179-4807
Jacob C Ulirsch *Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.
Leif S LudwigDivision of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.
Gaurav AgarwalDivision of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.
Jesse M EngreitzBroad Institute of MIT and Harvard, Cambridge, United States.ORCID 0000-0002-5754-1719
Bartlomiej PrzychodzenDepartment of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, United States.
Marie McConkeyDivision of Hematology, Brigham and Women's Hospital, Boston, United States.
Glenn S CowleyBroad Institute of MIT and Harvard, Cambridge, United States.
John G DoenchBroad Institute of MIT and Harvard, Cambridge, United States.ORCID 0000-0002-3707-9889
Jaroslaw P MaciejewskiDepartment of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, United States.
Benjamin L EbertBroad Institute of MIT and Harvard, Cambridge, United States.
David E RootBroad Institute of MIT and Harvard, Cambridge, United States.
Vijay G SankaranDivision of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.ORCID 0000-0003-0044-443X

Funding

Systematic Genetic Dissection of Human ErythropoiesisR01DK103794 · NIDDK · BOSTON CHILDREN'S HOSPITAL · PI Vijay Ganesh Sankaran · 2014 to 2026
$5.9M
Identifying Genome-wide Association Study-Nominated Regulators of ErythropoiesisR33HL120791 · NHLBI · BOSTON CHILDREN'S HOSPITAL · PI SANKARAN, VIJAY GANESH · 2016 to 2018
$1.7M
NHLBI NIH HHS R33 HL120791NIDDK NIH HHS R01 DK103794NIH HHS R01DK103794NIH HHS R33HL120791
6 · The paper itself

Abstract

Genome-wide association studies (GWAS) have identified thousands of variants associated with human diseases and traits. However, the majority of GWAS-implicated variants are in non-coding regions of the genome and require in depth follow-up to identify target genes and decipher biological mechanisms. Here, rather than focusing on causal variants, we have undertaken a pooled loss-of-function screen in primary hematopoietic cells to interrogate 389 candidate genes contained in 75 loci associated with red blood cell traits. Using this approach, we identify 77 genes at 38 GWAS loci, with most loci harboring 1-2 candidate genes. Importantly, the hit set was strongly enriched for genes validated through orthogonal genetic approaches. Genes identified by this approach are enriched in specific and relevant biological pathways, allowing regulators of human erythropoiesis and modifiers of blood diseases to be defined. More generally, this functional screen provides a paradigm for gene-centric follow up of GWAS for a variety of human diseases and traits.

Indexed as

Genetic Diseases, InbornGenetic Predisposition to DiseaseErythrocytesGenome-Wide Association StudyHematopoiesisHumansPolymorphism, Single NucleotideQuantitative Trait Locierythropoiesisfunctional screengeneticsgenome-wide association studiesgenomicshematopoiesishumanhuman biologyhuman geneticsmedicinemouseshRNA

Identifiers

PMID31070582
PMCPMC6534380

What OpenQuestion holds

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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.