Matreyek_2018.yml

title: PTEN VAMP-seq
abstract: >-
  Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the 
  only option. Experimentally characterizing millions of possible missense variants in thousands of clinically 
  important genes requires generalizable, scalable assays. We describe variant abundance by massively parallel 
  sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular 
  abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single-amino-acid variants of PTEN and 
  TPMT, proteins in which functional variants are clinically actionable. We identify 1,138 PTEN and 777 TPMT variants 
  that result in low protein abundance, and may be pathogenic or alter drug metabolism, respectively. We observe 
  selection for low-abundance PTEN variants in cancer, and show that p.Pro38Ser, which accounts for ~10% of PTEN 
  missense variants in melanoma, functions via a dominant-negative mechanism. Finally, we demonstrate that VAMP-seq is 
  applicable to other genes, highlighting its generalizability.
document:
  title: >-
    Multiplex assessment of protein variant abundance by massively parallel 
    sequencing
  system:
    Nature Genetics
  date: "2018-05-21"
  ref: https://doi.org/10.1038/s41588-018-0122-z
datasets:
  - system: MaveDB
    accession: urn:mavedb:00000013-a
    ref: https://mavedb.org/#/experiments/urn:mavedb:00000013-a
    description: processed scores, including scores for each replicate experiment
  - system: BioProject
    accession: PRJNA428380
    ref: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA428380
    description: raw sequencing data
variantLibrary:
  scope:
    type: coding
  targetSequences:
    - sequence: "ATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGA\
        TTCGACTTAGACTTGACCTATATTTATCCAAACATTATTGCTATGGGATTTCCTGCAGAA\
        AGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAAGGTTTTTGGATTCAAAG\
        CATAAAAACCATTACAAGATATACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAA\
        TTTAATTGCAGAGTTGCACAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTT\
        ATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCA\
        GCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTA\
        CATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACC\
        AGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTATTATAGCTAC\
        CTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTT\
        GAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTA\
        AAGGTGAAGATATATTCCTCCAATTCAGGACCCACACGACGGGAAGACAAGTTCATGTAC\
        TTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCAAAGTAGAGTTCTTCCACAAA\
        CAGAACAAGATGCTAAAAAAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATA\
        CCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATC\
        GATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTA\
        ACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCAACCGATACTTTTCTCCAAAT\
        TTTAAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAAATCCAGAGGCTAGC\
        AGTTCAACTTCTGTAACACCAGATGTTAGTGACAATGAACCTGATCATTATAGATATTCT\
        GACACCACTGACTCTGATCCAGAGAATGAACCTTTTGATGAAGATCAGCATACACAAATT\
        ACAAAAGTCTGA"
      sequenceAlphabet: DNA
  generationMethod:
    type: in-vitro construct library
    system: oligo-directed mutagenic PCR
    integration: extra-local construct insertion
    description: Integration using Tet-on landing pad system
  deliveryMethod:
    type: chemical or heat shock transformation
phenotypicAssay:
  dimensionality:
    type: single-dimensional data
  replication:
    type: biological and technical
    description: 8 biological replicate experiments were performed from three
      different transfections (4, 3, and 1 experimental replicate for these
      transfections). Technical replicates were performed as part of QC, but
      the technical replicates were collapsed and analyzed as one experiment
      after passing.
  method:
    type: flow cytometry assay
    description: VAMP-seq
  relevance:
    - system: https://www.omim.org/
      code: "601728"
      label: PHOSPHATASE AND TENSIN HOMOLOG; PTEN
    - system: https://www.omim.org/
      code: "158350"
      label: COWDEN SYNDROME 1; CWS1
    - system: https://mondo.monarchinitiative.org/
      code: MONDO:0017623
      label: PTEN hamartoma tumor syndrome
    - system: https://mondo.monarchinitiative.org/
      code: MONDO:0017623
      label: Cowden syndrome 1
  modelSystem:
    type: immortalized human cells
    description: HEK 293T TetBxb1BFP
    codings:
      - system: https://www.ebi.ac.uk/ols/ontologies/clo
        code: CLO:0037372
        label: HEK293T cell
      - system: https://www.ncbi.nlm.nih.gov/taxonomy
        code: NCBI:txid9606
        label: Homo sapiens
  profilingStrategy: barcode sequencing
  sequencingReadType: single-segment (short read)