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We developed Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which simultaneously measures the effects of thousands of missense variants on protein intracellular abundance, and applied it to study PTEN and TPMT, two clinically actionable genes. This repository houses the analysis scripts used for this study.
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This repository houses the files needed to recreate the anaylses required for the VAMP-seq manuscript. The "VAMP-seq_analysis.Rmd" R Markdown file is intended to be run with R Studio. To run this script, place these four files in the same directory:

  1. "PTEN_variant_data.tsv"
  2. "TPMT_variant_data.tsv"
  3. "PTEN_positional_data.tsv"
  4. "TPMT_positional_data.tsv"

Furthermore, please create a directory titled "Output", which will house image files of the plots included in the manuscript. Notably, once run, this R Markdown will also create a series of ".pml" files in the "Output" directory. These ".pml" files can be loaded into PyMOL to start interactive sessions with the VAMP-seq abundance scores overlaid on the PTEN and TPMT crystal structures.

TPMT/PTEN Protein Variant Abundance Scores Academic License Agreement

The University of Washington hereby allows User and Institution to search, download, copy or use TPMT/PTEN Variant Abundance Scores (TPMT/PTEN variant abundance scores) on the following conditions:

  1. The scores are being made available here for non-profit, non-commercial uses only. If User wishes to use TPMT/PTEN variant abundance scores, derivatives of TPMT/PTEN variant abundance scores, or the data on which they are based, for any commercial or for-profit purpose, please contact the corresponding authors. Low-cost or no-cost licenses will be extended for commercial or for-profit uses, contingent on the engagement of the licensing entity in best practices specified by ClinGen for TPMT/PTEN variant data sharing.

  2. The University of Washington owns the intellectual property for TPMT/PTEN variant abundance scores. In any reposting of the scores or their derivatives, User agrees to retain the copyright, trademark, or other notices pertaining to TPMT/PTEN variant abundance scores as provided by UW associated with the TPMT/PTEN variant abundance scores. Use of the copyright in any printed excerpts shall include the following notice (or the equivalent thereof): 'TPMT/PTEN variant abundance scores are the copyright of the University of Washington.'

  3. Any risk associated with using TPMT/PTEN variant abundance scores by User is with User and Institution. TPMT/PTEN variant abundance scores are experimental in nature and is made available as a research courtesy 'AS IS,' without obligation by the University of Washington to provide accompanying services or support. The TPMT/PTEN variant abundance scores are for informational purposes only, and is not intended to be a substitute for professional medical advice, diagnosis, or treatment. UW and the developer expressly disclaim any and all warranties regarding the TPMT/PTEN abundance scores, whether expressed or implied, including but not limited to warranties pertaining to non-infringement, merchantability or fitness for a particular purpose.

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