Evidence map›Paper›PMID 37609320›Full record

ArticlebioRxiv : the preprint server for biology2023

Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.

Ester Kalef-Ezra, Zeliha Gozde Turan, Diego Perez-Rodriguez, Ida Bomann, Sairam Behera, Caoimhe Morley, Sonja W Scholz, Zane Jaunmuktane, Jonas Demeulemeester, Fritz J Sedlazeck and 1 more

Open access · greenAbstract 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, 2 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 4 institutions in 3 countries.

Ester Kalef-EzraDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0000-0002-1297-3315
Zeliha Gozde TuranDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0000-0001-8312-7725
Diego Perez-RodriguezDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0000-0003-4903-3914
Ida BomannDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0009-0004-3628-8023
Sairam BeheraHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA.ORCID 0000-0002-9047-0203
Caoimhe MorleyDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0000-0001-6258-9250
Sonja W ScholzNeurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.ORCID 0000-0002-6623-0429
Zane JaunmuktaneDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0000-0001-7738-8881
Jonas DemeulemeesterAligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815.ORCID 0000-0002-2660-2478
Fritz J SedlazeckAligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815.ORCID 0000-0001-6040-2691
Christos ProukakisDepartment of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.ORCID 0000-0001-6423-6539
National Hospital for Neurology and Neurosurgery · GBBaylor College of Medicine · USJohns Hopkins University · USThe Francis Crick Institute · GB

Funding

Genetic characterization of atypical parkinsonismZIANS003154 · NINDS · NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE · PI SCHOLZ, SONJA · 2016 to 2025
$15.4M
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
Identification of somatic/ mosaic SV and transposon activity and their crosstalk to DNA epigenetic ModificationsUG3NS132105 · NINDS · BAYLOR COLLEGE OF MEDICINE · PI SEDLAZECK, FRITZ J, WU, TAO · 2023 to 2024
$580k
Intramural NIH HHS ZIA NS003154NHGRI NIH HHS U01 HG011758NINDS NIH HHS UG3 NS132105
6 · The paper itself

Abstract

The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. We compared PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrated different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we performed CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We found that 38% of brain cells have at least one Mb-scale CNV, with some supported by bulk sequencing or single-cells from other brain regions. Our study highlights the importance of selecting whole genome amplification method and reference genome for CNV calling, while supporting the existence of somatic CNVs in healthy and diseased human brain.

Identifiers

PMID37609320
PMCPMC10441336
OpenAlexW4385667615

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.