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Related Experiment Video

Updated: Nov 30, 2025

Transcriptome Analysis of Single Cells
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Published on: April 25, 2011

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SCELLECTOR: ranking amplification bias in single cells using shallow sequencing.

Vivekananda Sarangi1, Alexandre Jourdon2, Taejeong Bae1

  • 1Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.

BMC Bioinformatics
|November 13, 2020
PubMed
Summary
This summary is machine-generated.

Scellector identifies high-quality single-cell DNA amplifications using haplotype data. This method improves mosaic mutation detection by selecting uniformly amplified cells, reducing false positives in sequencing.

Keywords:
MDASingle cellWhole genome amplification

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Mosaic mutations are linked to cancer and various disorders.
  • Single-cell sequencing is crucial for detecting mosaic mutations.
  • Multiple displacement amplification (MDA) is widely used for single-cell DNA amplification but can introduce biases.

Purpose of the Study:

  • To develop a method for assessing DNA amplification quality in single cells.
  • To improve the accuracy of mosaic mutation detection by selecting uniformly amplified cells.

Main Methods:

  • Proposed Scellector (single cell selector), a method utilizing haplotype information.
  • Applied Scellector to shallow coverage sequencing data (as low as 0.3× per cell).
  • Validated Scellector's performance using deep coverage sequencing (30×).

Main Results:

  • Scellector accurately estimates amplification quality from shallow sequencing data.
  • High concordance was observed between shallow and deep coverage sequencing results.
  • The method effectively identifies uniform amplifications for reliable mosaic mutation detection.

Conclusions:

  • Scellector can rank amplification quality from single-cell platforms using MDA-like methods.
  • This tool aids in reducing false positives and increasing sensitivity for mosaic mutation detection.
  • Applicable to platforms like Chromium Single Cell profiling solutions.