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GAMBLR.data

The GAMBLR.data package, which is installed and loaded as part of GAMBLR.open, comes with many different bundled objects with various uses. These can be divided in the following categories:

Somatic variants

  • sample_data A list of data frames containing the metadata, simple somatic, copy number, and structural variants collected together from the supplemental tables of large sequencing studies of B-cell lymphomas.

Important

The data stored in sample_data is not meant to be accessed directly. You should use one of the various get_ functions in GAMBLR.open to retrieve the data for your use case.

Curated gene lists

  • gene_blacklist A tibble with gene symbols (Hugo) that fall within blacklisted regions of the genome. The genes in this data object represent common sequencing artifacts and are discarded during the data analysis.
# Look at 15 randomly sampled genes in the blacklist
slice_sample(gene_blacklist,n=15)
Gene
KRTAP20-2
PABPC1
GYPB
MUC22
MUC17
IGKV1D-8
RPL10
MUC6
KRTAP10-8
KRTAP1-5
NFATC4
KRTAP4-5
OR2L9P
PCDHB13
HSP90AB1
  • lymphoma_genes A data frame with a manually curated set of genes commonly mutated in lymphomas. For each pathology, there is a column that indicates whether (TRUE) or not (FALSE) each gene is in either the Tier 1 or Tier 2 list for that pathology. For more granularity, you can also use the corresponding PATHOLOGY_Tier column e.g. DLBCL_Tier.
# Look at the first 15 DLBCL genes in Tier 1
dplyr::filter(lymphoma_genes,DLBCL_Tier == 1) %>% 
    slice_head(n=15)
Gene MCL_Tier MCL FL_Tier FL DLBCL_Tier DLBCL BL_Tier BL ensembl_gene_id hgnc_symbol LymphGen Reddy Chapuy
ACTB NA FALSE 1 TRUE 1 TRUE NA FALSE ENSG00000075624 ACTB TRUE TRUE TRUE
ACTG1 NA FALSE 2 TRUE 1 TRUE NA FALSE ENSG00000267807 ACTG1 TRUE FALSE FALSE
ARID1A NA FALSE 1 TRUE 1 TRUE 1 TRUE ENSG00000117713 ARID1A TRUE TRUE FALSE
ATM 1 TRUE NA FALSE 1 TRUE NA FALSE ENSG00000149311 ATM FALSE TRUE FALSE
B2M 2 TRUE 1 TRUE 1 TRUE 2 TRUE ENSG00000166710 B2M FALSE TRUE TRUE
BCL10 NA FALSE 1 TRUE 1 TRUE NA FALSE ENSG00000142867 BCL10 TRUE TRUE TRUE
BCL2 NA FALSE 1 TRUE 1 TRUE 2 TRUE ENSG00000171791 BCL2 TRUE TRUE TRUE
BCL6 NA FALSE 1 TRUE 1 TRUE 1 TRUE ENSG00000113916 BCL6 TRUE TRUE TRUE
BCL7A NA FALSE 1 TRUE 1 TRUE 1 TRUE ENSG00000110987 BCL7A FALSE TRUE FALSE
BIRC6 NA FALSE NA FALSE 1 TRUE NA FALSE ENSG00000115760 BIRC6 FALSE TRUE FALSE
BRAF NA FALSE NA FALSE 1 TRUE NA FALSE ENSG00000157764 BRAF FALSE TRUE TRUE
BTG1 NA FALSE 2 TRUE 1 TRUE 2 TRUE ENSG00000133639 BTG1 TRUE TRUE TRUE
BTG2 NA FALSE 2 TRUE 1 TRUE NA FALSE ENSG00000159388 BTG2 TRUE TRUE TRUE
BTK NA FALSE 1 TRUE 1 TRUE NA FALSE ENSG00000010671 BTK FALSE TRUE FALSE
CARD11 1 TRUE 1 TRUE 1 TRUE 2 TRUE ENSG00000198286 CARD11 FALSE TRUE TRUE
  • lymphoma_genes_comprehensive An older (and outdated) curated list of genes reported as significantly mutated in the large lymphoma studies. Both Ensembl ID and Hugo Symbol are available as gene identifiers. This data contains annotations for the studies by Chapuy, Reddy, Wright (LymphGen), Lacy, as well as annotations for whether the gene is curated, reported as SMG in other_studies, or a target of aSHM. This is mostly included for backwards compatability and you should use lymphoma_genes instead.

Coordinate-based resources

  • chromosome_arms_grch37: A data frame with the chromosome arm coordinates with respect to the grch37 projection.
  • chromosome_arms_hg38 A data frame with the chromosome arm coordinates with respect to the hg38 projection.
  • grch37_gene_coordinates A data frame of all gene coordinates with respect to grch37. Contains both Ensembl ID and Hugo Symbol as identifiers.
  • grch37_lymphoma_genes_bed A data frame in the bed format for genes commonly associated with B-cell lymphomas. Coordinates are with respect to grch37.
  • grch37_oncogene A data frame with the coordinates of lymphoma oncogenes relative to grch37. Used in mapping of the breakpoint coordinates.
  • grch37_partners A data frame of translocation partners for oncogenes with coordinates relative to grch37.
  • hg38_gene_coordinates A data frame of all gene coordinates with respect to hg38. Contains both Ensembl ID and Hugo Symbol as identifiers.
  • hg38_lymphoma_genes_bed A data frame in the bed format for genes commonly associated with B-cell lymphomas. Coordinates are with respect to hg38.
  • hg38_oncogene A data frame with the coordinates of lymphoma oncogenes relative to the hg38. Used in mapping of the breakpoint coordinates.
  • hg38_partners A data frame of translocation partners for oncogenes with relative coordinates to hg38.
  • grch37_all_gene_coordinates A data frame of protein-coding gene coordinates relative to grch37. Contains both Ensembl ID and Hugo Symbol as identifiers. Mainly here for backwards compatibility with earlier GAMBLR versions.
  • hotspot_regions_grch37 A data frame of mutation hotspot regions relative to grch37.
  • hotspot_regions_hg38 A data frame of mutation hotspot regions relative to hg38.
  • target_regions_grch37 A data frame with coordinates of the regions of the genome targeted by the whole exome sequencing panel Agilent V5 (no UTR) relative to grch37.
  • target_regions_hg38 A data frame with coordinates of the regions of the genome targeted by the whole exome sequencing panel Agilent V5 (no UTR) relative to hg38.

aSHM regions

  • grch37_ashm_regions Aberrant somatic hypermutation (aSHM) regions relative to grch37. This object always by default refers to the most recent version of the aSHM regions.
# Peek at the first 15 rows
grch37_ashm_regions %>%
    slice_head(n=15)
chr_name hg19_start hg19_end gene region regulatory_comment
chr1 6661482 6662702 KLHL21 TSS NA
chr1 23885584 23885835 ID3 TSS NA
chr1 28832551 28836339 RCC1 TSS NA
chr1 31229012 31232011 LAPTM5 TSS NA
chr1 150550814 150552135 MCL1 intron NA
chr2 88904839 88909096 EIF2Ak3 intron NA
chr2 88925456 88927581 EIF2Ak3 TSS NA
chr2 232572640 232574297 PTMA TSS NA
chr2 157669490 157671299 FCRL3 TSS NA
chr1 203274698 203275778 BTG2 intron active_promoter
chr1 206285239 206288105 RHEX TSS NA
chr1 226864857 226873452 ITPKB intron weak_enhancer
chr1 226920563 226927885 ITPKB TSS active_promoter
chr1 226921088 226927982 ITPKB intron-1 enhancer
chr1 245023502 245029083 HNRNPU TSS NA
  • hg38_ashm_regions Aberrant somatic hypermutation (aSHM) regions relative to hg38. This object always by default refers to the most recent version of the aSHM regions.
# Peek at the first 15 rows
hg38_ashm_regions %>%
    slice_head(n=15)
chr_name hg38_start hg38_end gene region regulatory_comment
chr1 6601422 6602642 KLHL21 TSS NA
chr1 23559093 23559344 ID3 TSS NA
chr1 28506039 28509827 RCC1 TSS NA
chr1 30756165 30759164 LAPTM5 TSS NA
chr1 150578338 150579659 MCL1 intron NA
chr2 88605321 88609578 EIF2Ak3 intron NA
chr2 88625938 88628063 EIF2Ak3 TSS NA
chr2 231707930 231709587 PTMA TSS NA
chr2 156812978 156814787 FCRL3 TSS NA
chr1 203305570 203306650 BTG2 intron active_promoter
chr1 206053265 206054139 RHEX TSS NA
chr1 226677156 226685751 ITPKB intron weak_enhancer
chr1 226732862 226740184 ITPKB TSS active_promoter
chr1 226733387 226740281 ITPKB intron-1 enhancer
chr1 244860200 244865781 HNRNPU TSS NA

Other resources

  • colour_codes A data frame with colour codes (HEX) arranged into different categories, groups.
  • dhitsig_genes_with_weights A data frame with double hit signature genes (both as ensembl IDs and Hugo symbols) and importance scores.
  • gambl_metadata A data frame with metadata for a collection of GAMBL samples. This represents a collection of whole genome, exome, targeted, RNA, and PrometION sequencing samples available as a data set known as GAMBL. This object rather serves an FYI purpose as not all samples listed here are published and bundled with GAMBLR.data.
  • hgnc2pfam.df A dataset containing the mapping table between Hugo symbol, UniProt ID, and Pfam ACC. This dataset comes from the g3viz package and was obtained via this URL: https://github.com/morinlab/g3viz/tree/master/data
  • hotspots_annotations Hotspot coordinates used in the feature annotation during matrix assembly of data for cFL classifier.
  • mirage_metrics A data frame providing the data reported in the Supplemental Table of the MIRAGE study by Dreval et al, 2022
  • mutation.table.df A data frame providing the linkage between Variant Classification, Mutation_Class, and Short_Name for the simple somatic mutations.
  • reddy_genes A data frame of the genes reported as significantly mutated by the study of Reddy et al, 2017
  • wright_genes_with_weights Wright genes with weight values from the study by Scott et al, 2014.