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We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/) to get the transcripts, then assembling these using VDJ Puzzle: https://www.biorxiv.org/content/early/2017/08/26/181156

The output will be a list of about 100k base pairs per patient per cell sequenced. I will then have clinical information ... how can I compute the number of patients needed to establish a statistically significant association between SNPs and clinical outcomes / disease state?

Furthermore how many cells would we need to sequence per patient?

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  • $\begingroup$ I don't know about the number of cells per patient, but there is a vast literature on power calculation for association studies. Power depends on several parameters. This tool developed by Goncalo Abecasis' group might be of help in exploring power while changing several parameters: csg.sph.umich.edu/abecasis/gas_power_calculator/index.html $\endgroup$ – Fabio Marroni Jun 21 at 12:31

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