15  Gene expression model of high-risk multiple myeloma

This document outlines the gene expression model for high-risk multiple myeloma based on the study by Shaughnessy et al. (PMID: 17105813). The study identified 70 genes associated with early disease-related death, with 30% mapping to chromosome 1 (P < .001). These genes were used to calculate risk scores for samples. ## Gene List The following is the list of 70 genes identified in the study, used for risk score calculation.

# Define the vector of 70 genes from Shaughnessy et al.
genes <- c(
  "AD-020", "AHCYL1", "AIM2", "ALDOA", "ASPM", "BIRC5", "C6orf173", "CBX3",
  "CCT2", "CKAP1", "CKS1B", "CPSF3", "CTBS", "DKFZP586L0724", "DKFZp779O175",
  "DSG2", "EIF2C2", "ENO1", "EVI5", "EXOSC4", "FABP5", "FLJ13052", "FLJ20489",
  "FUCA1", "GNG10", "IFI16", "ILF3", "KIAA1754", "KIF14", "LARS2", "LAS1L",
  "LGALS1", "LTBP1", "MCLC", "MGC15606", "MGC4308", "MGC57827", "MPHOSPH1",
  "OPN3", "PAPD1", "PARG1", "PDHA1", "PFN1", "PNPLA4", "PSMD4", "RAD18",
  "RAN", "RFC4", "RFP2", "ROBO1", "RUVBL1", "SELI", "SLCI19A1", "SNX5",
  "STK6", "TAGLN2", "TBRG4", "TCOF1", "TMPO", "TRIM33", "TRIP13", "UBE2I",
  "UBE2R2", "WEE1", "YWHAZ"
)

# Display the gene list as a table
tibble::tibble(Gene = genes) |> 
  knitr::kable(caption = "List of 70 genes associated with high-risk multiple myeloma")

List of 70 genes associated with high-risk multiple myeloma

Gene
AD-020
AHCYL1
AIM2
ALDOA
ASPM
BIRC5
C6orf173
CBX3
CCT2
CKAP1
CKS1B
CPSF3
CTBS
DKFZP586L0724
DKFZp779O175
DSG2
EIF2C2
ENO1
EVI5
EXOSC4
FABP5
FLJ13052
FLJ20489
FUCA1
GNG10
IFI16
ILF3
KIAA1754
KIF14
LARS2
LAS1L
LGALS1
LTBP1
MCLC
MGC15606
MGC4308
MGC57827
MPHOSPH1
OPN3
PAPD1
PARG1
PDHA1
PFN1
PNPLA4
PSMD4
RAD18
RAN
RFC4
RFP2
ROBO1
RUVBL1
SELI
SLCI19A1
SNX5
STK6
TAGLN2
TBRG4
TCOF1
TMPO
TRIM33
TRIP13
UBE2I
UBE2R2
WEE1
YWHAZ

15.1 Notes

The 70 genes listed above were identified as linked to early disease-related death.

Approximately 30% of these genes map to chromosome 1 (P < .001).

The risk score for each sample can be computed using gene expression data, though the exact methodology depends on your dataset and implementation.

15.2 References

Shaughnessy JD Jr, et al. (2007). A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1. Blood. PMID: 17105813.