Evidence map›Paper›PMID 30147985›Full record

ArticleMicrosystems & nanoengineering2017

Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA.

Samuel C Kim, Gayatri Premasekharan, Iain C Clark, Hawi B Gemeda, Pamela L Paris, Adam R Abate

Abstract read
In one paragraph

Article in Microsystems & nanoengineering, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Uncovering microbial inter-domain interactions in complex communities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019
    Article
  7. Droplet microfluidics for high-sensitivity and high-throughput detection and screening of disease biomarkers.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology · 2018
    Review
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

6 authors.

Samuel C Kim *Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco (UCSF), California Institute for Quantitative Biosciences (QB3) San Francisco, California 94158, USA.
Gayatri Premasekharan *Department of Urology, Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, California 94158, USA.
Iain C ClarkDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco (UCSF), California Institute for Quantitative Biosciences (QB3) San Francisco, California 94158, USA.
Hawi B GemedaDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco (UCSF), California Institute for Quantitative Biosciences (QB3) San Francisco, California 94158, USA.
Pamela L ParisDepartment of Urology, Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, California 94158, USA.
Adam R AbateDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco (UCSF), California Institute for Quantitative Biosciences (QB3) San Francisco, California 94158, USA.

Funding

Gigapixel digital PCR in Giant Unilamellar VesiclesR01EB019453 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ABATE, ADAM R., CHIU, CHARLES YEN · 2014 to 2022
$3.9M
Microfluidic immunoprofiling for biomarker discovery in rheumatoid arthritisDP2AR068129 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ABATE, ADAM R. · 2014 to 2014
$2.4M
SINGLE-CELL TRANSCRIPTOMIC ANALYSIS OF HIV-INFECTED CD4 T CELLS IN BLOOD AND LYMPHOID TISSUE USING PCR-ACTIVATED CELL SORTINGU01AI129206 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ABATE, ADAM R., BORITZ, ELI A · 2017 to 2020
$1.6M
Accurate, long-read sequencing with droplet-microfluidic barcodingR21HG007233 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ABATE, ADAM R., HERNANDEZ, RYAN D. · 2013 to 2014
$433k
NHGRI NIH HHS R21 HG007233NIAID NIH HHS U01 AI129206NIAMS NIH HHS DP2 AR068129NIBIB NIH HHS R01 EB019453
6 · The paper itself

Abstract

Uniform amplification of low input DNA is important for applications across biology, including single-cell genomics, forensic science, and microbial and viral sequencing. However, the requisite biochemical amplification methods are prone to bias, skewing sequence proportions and obscuring signals relating to copy number. Digital droplet multiple displacement amplification enables uniform amplification, but requires expert knowledge of microfluidics to generate monodisperse emulsions. In addition, existing microfluidic methods are tedious and labor intensive for preparing many samples. Here, we introduce rapid emulsification multiple displacement amplification, a method to generate monodisperse droplets with a hand-held syringe and hierarchical droplet splitter. While conventional microfluidic devices require >10 minutes to emulsify a sample, our system takes tens of seconds and yields data of equivalent quality. We demonstrate the approach by using it to accurately measure copy number variation in single cancer cells.

Indexed as

amplification biascopy number variationddMDAdroplet microfluidicsmultiple displacement amplification

Identifiers

PMID30147985
PMCPMC6108428

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.