Evidence map›Paper›PMID 35986254›Full record

ArticleBMC bioinformatics2022

SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances.

Sandra Hui, Rasmus Nielsen

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2022. 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
–field-weighted citation impact
1 · What the graph read from it

What it found

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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

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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. 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

2 authors.

Sandra HuiCenter for Computational Biology, University of California, Berkeley, Berkeley, 94720, USA. sandra_hui@berkeley.edu.ORCID http://orcid.org/0000-0002-3534-6998
Rasmus NielsenCenter for Computational Biology, University of California, Berkeley, Berkeley, 94720, USA.

Funding

Enabling Precision Genomics Using Adaptive VariationR01GM138634 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI NIELSEN, RASMUS · 2020 to 2023
$1.7M
National Institutes of Health (US) R01GM138634-01NIGMS NIH HHS R01 GM138634
6 · The paper itself

Abstract

backgroundSingle cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations. Existing single cell copy number calling methods do not explicitly model the shared evolutionary process of multiple cells, and generally analyze cells independently. Additionally, existing methods for estimating tumor cell phylogenies using copy number profiles are sensitive to profile estimation errors.

resultsWe present SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data. Using simulations, we show that SCONCE2 has higher accuracy in copy number calling and phylogeny estimation than competing methods. We apply SCONCE2 to previously published single cell sequencing data to illustrate the utility of the method.

conclusionsSCONCE2 jointly estimates copy number profiles and a distance metric for inferring tumor phylogenies in single cell whole genome tumor sequencing across multiple cells, enabling deeper understandings of tumor evolution.

Indexed as

DNA Copy Number VariationsNeoplasmsHumansPhylogenyPolymorphism, Single NucleotideCancer genomicsCopy number alterationsSingle cell sequencingTumor evolutionTumor phylogenies

Identifiers

PMID35986254
PMCPMC9392257

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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.