SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
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METHODOLOGY ARTICLE
Open Access
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing Vivekananda Sarangi1, Alexandre Jourdon2, Taejeong Bae1, Arijit Panda1, Flora Vaccarino2,3 and Alexej Abyzov1*
*Correspondence: [email protected] 1 Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA Full list of author information is available at the end of the article
Abstract Background: The study of mosaic mutation is important since it has been linked to cancer and various disorders. Single cell sequencing has become a powerful tool to study the genome of individual cells for the detection of mosaic mutations. The amount of DNA in a single cell needs to be amplified before sequencing and multiple displacement amplification (MDA) is widely used owing to its low error rate and long fragment length of amplified DNA.However, the phi29 polymerase used in MDA is sensitive to template fragmentation and presence of sites with DNA damage that can lead to biases such as allelic imbalance, uneven coverage and over representation of C to T mutations. It is therefore important to select cells with uniform amplification to decrease false positives and increase sensitivity for mosaic mutation detection. Results: We propose a method, Scellector (single cell selector), which uses haplotype information to detect amplification quality in shallow coverage sequencing data. We tested Scellector on single human neuronal cells, obtained in vitro and amplified by MDA. Qualities were estimated from shallow sequencing with coverage as low as 0.3× per cell and then confirmed using 30× deep coverage sequencing. The high concordance between shallow and high coverage data validated the method. Conclusion: Scellector can potentially be used to rank amplifications obtained from single cell platforms relying on a MDA-like amplification step, such as Chromium Single Cell profiling solution. Keywords: MDA, Single cell, Whole genome amplification
Background Somatic mutations acquired in each cell during and after embryogenesis are passed to the descendant cells such that, within the same individual, different populations of somatic cells have slightly different DNA, resulting in genomic mosaicism. The accumulation of somatic mutations increases with age [1–3],and is also affected by environmental factors like tobacco smoking and alcohol consumption [4]. Somatic mutations can not only cause cancer but also diverse neurological diseases, including cortical malformations, epilepsy, intellectual disability, and neurodegeneration [5, 6]. Some somatic mutations might give the cells proliferative advantage, and ultimately cause cancer, or © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Common
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