get St. Jude SNVs

Source: R/get_stjude_snvs.R

This function downloads and reads in the "validated SNVs" from the paper "Recurrent Somatic Structural Variations Contribute to Tumorigenesis in Pediatric Osteosarcoma." Cell Reports, April 10, 2014. The paper describes 20 WGS samples and 14 validation osteosarcoma samples analyzed at St Jude.

get_stjude_snvs()

Value

a tibble of results

References

Chen, Xiang, Armita Bahrami, Alberto Pappo, John Easton, James Dalton, Erin Hedlund, David Ellison, et al. 2014. “Recurrent Somatic Structural Variations Contribute to Tumorigenesis in Pediatric Osteosarcoma.” Cell Reports, April 10, 2014. https://doi.org/10.1016/j.celrep.2014.03.003. Specifically, the data are derived from https://www.cell.com/cms/10.1016/j.celrep.2014.03.003/attachment/281e4b0f-814f-45a0-ae9c-c6fdb812cb8b/mmc4.xlsx

Examples

snvs = get_stjude_snvs()
head(snvs)
#> # A tibble: 6 x 8
#>   sample gene  variant chromosome    pos class reference_allele non_reference_a…
#>   <chr>  <chr> <chr>   <chr>       <dbl> <chr> <chr>            <chr>           
#> 1 SJOS0… CAMT… CAMTA1… 1          7.72e6 MISS… A                G               
#> 2 SJOS0… UBXN… UBXN10… 1          2.05e7 UTR_3 C                G               
#> 3 SJOS0… SESN2 SESN2_… 1          2.86e7 UTR_3 A                C               
#> 4 SJOS0… GRIK3 GRIK3_… 1          3.73e7 SILE… G                T               
#> 5 SJOS0… PPAP… PPAP2B… 1          5.70e7 MISS… C                A               
#> 6 SJOS0… DAB1  DAB1_E… 1          5.83e7 UTR_5 T                C               
colnames(snvs)
#> [1] "sample"               "gene"                 "variant"             
#> [4] "chromosome"           "pos"                  "class"               
#> [7] "reference_allele"     "non_reference_allele"
head(sort(table(snvs$gene), decreasing=TRUE),20)
#> 
#>  NCAPD2    TP53 TMEM55B ZDHHC15  ZNF793   MUC16   41337    ATRX   KCMF1  MRPS30 
#>       9       9       7       7       7       6       5       5       5       5 
#>   MYBL1  AHNAK2     EYS  HNRNPC MGC2752    PAX3    PEX5     RB1    ROS1   SCN7A 
#>       5       4       4       4       4       4       4       4       4       4