locateVariants Fails to Give the Correct Gene ID

Question

[cisplatin1987]

Hello,

I am using R to find out the corresponding gene that covers the position 10736809, chromosome 1:

> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> library(VariantAnnotation)
> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> rng <- GRanges(seqnames='chr1',ranges=IRanges(10736809,10736809))

However, locateVariants() gives a report like this:

> locateVariants(rng, txdb, AllVariants())
'select()' returned many:1 mapping between keys and columns
GRanges object with 9 ranges and 9 metadata columns:
      seqnames    ranges strand | LOCATION  LOCSTART    LOCEND   QUERYID        TXID         CDSID      GENEID       PRECEDEID
         <Rle> <IRanges>  <Rle> | <factor> <integer> <integer> <integer> <character> <IntegerList> <character> <CharacterList>
  [1]     chr1  10736809      + |   intron     60904     60904         1       10330                      <NA>                
  [2]     chr1  10736809      + |   intron     63204     63204         1       10331                      <NA>                
  [3]     chr1  10736809      + |   intron     59598     59598         1       10332                      <NA>                
  [4]     chr1  10736809      + |   intron     59783     59783         1       10333                      <NA>                
  [5]     chr1  10736809      + |   intron     59598     59598         1      217346                     80781                
  [6]     chr1  10736809      + |   intron     60904     60904         1      217347                     80781                
  [7]     chr1  10736809      + |   intron     63204     63204         1      217348                     80781                
  [8]     chr1  10736809      + |   intron     59783     59783         1      217350                     80781                
  [9]     chr1  10736809      + |   intron    208422    208422         1      217350                     80781                

The Gene ID 80781 refers to a gene in chr21, so totally wrong. The target position actually belongs to the intron of gene CASZ1 (Gene ID 54897). However, txdb seems to have their correct information:

> select(txdb, keys = c("54897", "80781"), columns="TXCHROM", keytype="GENEID")
'select()' returned 1:1 mapping between keys and columns
  GENEID TXCHROM
1   54897    chr1
2   80781   chr21 

What could be wrong? The basic information of my system:

> sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VariantAnnotation_1.38.0                 Rsamtools_2.8.0                          Biostrings_2.60.2                       
 [4] XVector_0.32.0                           SummarizedExperiment_1.22.0              MatrixGenerics_1.4.3                    
 [7] matrixStats_0.61.0                       TxDb.Hsapiens.UCSC.hg38.knownGene_3.13.0 GenomicFeatures_1.44.2                  
[10] AnnotationDbi_1.54.1                     Biobase_2.52.0                           GenomicRanges_1.44.0                    
[13] GenomeInfoDb_1.28.4                      IRanges_2.26.0                           S4Vectors_0.30.2                        
[16] BiocGenerics_0.38.0                     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3             lattice_0.20-45          prettyunits_1.1.1        png_0.1-7                assertthat_0.2.1        
 [6] digest_0.6.29            utf8_1.2.2               BiocFileCache_2.0.0      R6_2.5.1                 RSQLite_2.2.11          
[11] httr_1.4.2               pillar_1.7.0             zlibbioc_1.38.0          rlang_1.0.2              progress_1.2.2          
[16] curl_4.3.2               rstudioapi_0.13          blob_1.2.2               Matrix_1.4-1             BiocParallel_1.26.2     
[21] stringr_1.4.0            RCurl_1.98-1.6           bit_4.0.4                biomaRt_2.48.3           DelayedArray_0.18.0     
[26] compiler_4.1.2           rtracklayer_1.52.1       pkgconfig_2.0.3          tidyselect_1.1.2         KEGGREST_1.32.0         
[31] tibble_3.1.6             GenomeInfoDbData_1.2.6   XML_3.99-0.9             fansi_1.0.3              crayon_1.5.1            
[36] dplyr_1.0.8              dbplyr_2.1.1             GenomicAlignments_1.28.0 bitops_1.0-7             rappdirs_0.3.3          
[41] grid_4.1.2               lifecycle_1.0.1          DBI_1.1.2                magrittr_2.0.2           cli_3.2.0               
[46] stringi_1.7.6            cachem_1.0.6             xml2_1.3.3               ellipsis_0.3.2           filelock_1.0.2          
[51] generics_0.1.2           vctrs_0.3.8              rjson_0.2.21             restfulr_0.0.13          tools_4.1.2             
[56] bit64_4.0.5              BSgenome_1.60.0          glue_1.6.2               purrr_0.3.4              hms_1.1.1               
[61] fastmap_1.1.0            yaml_2.3.5               BiocManager_1.30.16      memoise_2.0.1            BiocIO_1.2.0 

Thank you in advance!

[zx8754]

I am getting the correct gene, using: R version 4.0.2, TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0, VariantAnnotation_1.34.0

      seqnames    ranges strand | LOCATION  LOCSTART    LOCEND   QUERYID        TXID         CDSID      GENEID
         <Rle> <IRanges>  <Rle> | <factor> <integer> <integer> <integer> <character> <IntegerList> <character>
  [1]     chr1  10736809      - |   intron     59598     59598         1       11156                     54897
  [2]     chr1  10736809      - |   intron     59598     59598         1       11159                     54897

I suggest updating your R and Bioconductor packages, and try again.