Evidence map›Paper›PMID 40069819›Full record

ArticleGenome biology2025

Single-cell RNA-seq data have prevalent blood contamination but can be rescued by Originator, a computational tool separating single-cell RNA-seq by genetic and contextual information.

Thatchayut Unjitwattana, Qianhui Huang, Yiwen Yang, Leyang Tao, Youqi Yang, Mengtian Zhou, Yuheng Du, Lana X Garmire

Abstract read
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Thatchayut UnjitwattanaDepartment of Biomedical Engineering, University of Michigan, 2200 , Bonisteel, Ann Arbor, MI, 48109, USA.
Qianhui HuangDepartment of Computation Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI, 48109, USA.
Yiwen YangDepartment of Computation Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI, 48109, USA.
Leyang TaoDepartment of Biomedical Engineering, University of Michigan, 2200 , Bonisteel, Ann Arbor, MI, 48109, USA.
Youqi YangDepartment of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
Mengtian ZhouDepartment of Statistics, University of Michigan, 1085 S University Ave, Ann Arbor, MI, 48109, USA.
Yuheng DuDepartment of Computation Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI, 48109, USA.
Lana X GarmireDepartment of Biomedical Engineering, University of Michigan, 2200 , Bonisteel, Ann Arbor, MI, 48109, USA. lgarmire@umich.edu.

Funding

Proteogenomics of Cancer Training ProgramT32CA140044 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI RAO, ARVIND, SARTOR, MAUREEN AGNES · 2010 to 2024
$3.9M
An Integrative Omics Approach to Identify Biomarkers Related to Preeclampsia and Breast Cancer RisksR01HD084633 · NICHD · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GARMIRE, LANA X · 2016 to 2020
$3.0M
Cancer precision medicine through spatially informative single cell image and transcriptomics data analysisR01LM012373 · NLM · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GARMIRE, LANA X · 2016 to 2024
$2.4M
DR. EPS: Drug Repurposing for Extended Patient SurvivalR01LM012907 · NLM · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GARMIRE, LANA X · 2019 to 2022
$1.0M
NCI NIH HHS T32 CA140044NICHD NIH HHS R01 HD084633NLM NIH HHS R01 LM012373NLM NIH HHS R01 LM012373 and R01 LM012907NLM NIH HHS R01 LM012907
6 · The paper itself

Abstract

Single-cell RNA sequencing (scRNA-seq) data from complex human tissues have prevalent blood cell contamination during the sample preparation process. They may also comprise cells of different genetic makeups. We propose a new computational framework, Originator, which deciphers single cells by genetic origin and separates immune cells of blood contamination from those of expected tissue-resident cells. We demonstrate the accuracy of Originator at separating immune cells from the blood and tissue as well as cells of different genetic origins, using a variety of artificially mixed and real datasets, including pancreatic cancer and placentas as examples.

Indexed as

Computational BiologyRNA-SeqSequence Analysis, RNASingle-Cell AnalysisSoftwareFemaleHumansPancreatic NeoplasmsPlacentaPregnancySingle-Cell Gene Expression AnalysisBlood cellCancerContaminationGenetic originPlacentaScRNA-seqTissue heterogeneity

Identifiers

PMID40069819
PMCPMC11895284

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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.