Evidence map›Paper›PMID 33372593›Full record

ArticleBMC genomics2020

Red panda: a novel method for detecting variants in single-cell RNA sequencing.

Adam Cornish, Shrabasti Roychoudhury, Krishna Sarma, Suravi Pramanik, Kishor Bhakat, Andrew Dudley, Nitish K Mishra, Chittibabu Guda

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2020. 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

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

8 authors.

Adam CornishDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Shrabasti RoychoudhuryDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Krishna SarmaDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Suravi PramanikDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Kishor BhakatDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Andrew DudleyDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Nitish K MishraDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Chittibabu GudaDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA. babu.guda@unmc.edu.ORCID http://orcid.org/0000-0002-5393-9316

Funding

UNMC Structural Biology CoreP20GM103427 · NIGMS · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI Heather Colleen Jensen-Smith · 2012 to 2026
$59.2M
UNMC/EPPLEY CANCER CENTER SUPPORT GRANTP30CA036727 · NCI · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI Apar Kishor Ganti · 1985 to 2026
$55.0M
Therapeutics Core (Page 286)P30MH062261 · NIMH · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI GENDELMAN, HOWARD E · 2000 to 2021
$37.7M
The Aging Pituitary/Gonadal AxisP01AG029531 · NIA · WICHITA STATE UNIVERSITY · PI GEORGE R BOUSFIELD · 2009 to 2026
$25.9M
UNMC Histology/Imaging and Creighton University Imaging Core FacilityP30GM110768 · NIGMS · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI SMITH, SHELLEY D · 2014 to 2018
$5.1M
Cell biological mechanisms that regulate development of cartilage architectureR01AR070242 · NIAMS · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI DUDLEY, ANDREW T · 2016 to 2020
$1.7M
Cancer Therapeutic Resistance: Implication of AcAPE1 Mediated DNA Repair and T-Cell Based ImmunotherapyK00CA223064 · NCI · DANA-FARBER CANCER INST · PI ROYCHOUDHURY, SHRABASTI · 2019 to 2022
$392k
Cancer Therapeutic Resistance: Implication of AcAPE1 Mediated DNA Repair and T-Cell Based ImmunotherapyF99CA223064 · NCI · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI ROYCHOUDHURY, SHRABASTI · 2017 to 2018
$61k
NCI NIH HHS F99 CA223064NCI NIH HHS K00 CA223064NCI NIH HHS P30 CA036727NCI NIH HHS P30CA036727NIAMS NIH HHS R01 AR070242NIA NIH HHS 2P01AG029531NIA NIH HHS P01 AG029531NIGMS NIH HHS 1P30GM110768NIGMS NIH HHS P20GM103427NIGMS NIH HHS P30 GM110768NIMH NIH HHS P30 MH062261
6 · The paper itself

Abstract

backgroundSingle-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50 bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others.

resultsIn this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools-FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus-ranged from 5.8-41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%.

conclusionsWe show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently existing software. However, methods for identification of genomic variants using scRNA-seq data can be still improved.

Indexed as

FibroblastsPolymorphism, Single NucleotideAnimalsExome SequencingHigh-Throughput Nucleotide SequencingMiceSequence Analysis, RNASingle-Cell AnalysisSoftwareHeterozygous variant callingHuman articular chondrocytesRed pandaSingle cell sequencingVariant calling using scRNAseq

Identifiers

PMID33372593
PMCPMC7771073

What OpenQuestion holds

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LicenceCC BY
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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.