SCELLECTOR: ranking amplification bias in single cells using shallow sequencing.
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing.
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DOI：
10.1186/s12859-020-03858-y
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发表时间：
2020-11-12
影响因子：
3
通讯作者：
Abyzov A
中科院分区：
文献类型：
--
作者：
Sarangi V;Jourdon A;Bae T;Panda A;Vaccarino F;Abyzov A
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. 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. 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.
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DOI：
10.1126/science.aau3879
发表时间：
2018-11-23
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Martincorena I;Fowler JC;Wabik A;Lawson ARJ;Abascal F;Hall MWJ;Cagan A;Murai K;Mahbubani K;Stratton MR;Fitzgerald RC;Handford PA;Campbell PJ;Saeb-Parsy K;Jones PH
通讯作者：
Jones PH
影响因子：
16
作者：
Sanchez-Luque, Francisco J.;Kempen, Marie-Jeanne H. C.;Faulkner, Geoffrey J.
通讯作者：
Faulkner, Geoffrey J.
影响因子：
64.8
作者：
Wang, Yong;Waters, Jill;Leung, Marco L.;Unruh, Anna;Roh, Whijae;Shi, Xiuqing;Chen, Ken;Scheet, Paul;Vattathil, Selina;Liang, Han;Multani, Asha;Zhang, Hong;Zhao, Rui;Michor, Franziska;Meric-Bernstam, Funda;Navin, Nicholas E.
通讯作者：
Navin, Nicholas E.
影响因子：
8.8
作者：
Cai X;Evrony GD;Lehmann HS;Elhosary PC;Mehta BK;Poduri A;Walsh CA
通讯作者：
Walsh CA
影响因子：
14.9
作者：
Sherman, Maxwell A.;Barton, Alison R.;Park, Peter J.
通讯作者：
Park, Peter J.