ADSPM: Second Primary Malignancy Dataset

Background Story:

One day, I need to validate a SPM related files and ADSPM in a hematology study, I communicated with an experienced colleague many times and finally got the work done. Since each study has different data structure, there is  no standard SPM process  available for all. I will share my experience with SPM work, hopefully it is helpful in some way. 

SPM (Second Primary Malignancy) is a good indication to access safety analysis in hematology studies. In addition, it reflects the disease progression. SPM, such as DNA damage, cytotoxic chemotherapy agents, may occur months/years after the original (primary malignancy ) was diagnosed and treated. 

In Hematology studies, such as newly diagnosed multiple myeloma trials(NDMM), if an increased frequency SPM were reported in studies, we will generate an ADSPM dataset from multiple sources (AE, Death, Drug safety database)to capture the info. 

Key point:  SPM sequence
Since the SPM collected from multiple sources(AE, Death, SPM Safety track, MSAE) linked and combined, we need Clinical Scientist, Statistical programmer, and statistician closely work together.

SPM Related Work Process Flow:

Database Lock -> Study Analysis datasets(SPM Process)-> SPM Sequencing and Data Derivation -> ADSPM ->SPM TLG Development QC and Review

SPM TLG could include, but not limited to:

Tables: risk factor, univariate and multivariate, odds ratio, SPM free survival,
              SPM survival, time-dependent covariates

Listings: Medical History, prior cancer history

Figures: Competing risk, KM, forest plot, piecewise Cox regression

ADSPM

Source Data: ADSL, ADAE, Death Data, SPM Unique preferred term sheet, Reconcile File

Key variables: STUDY, SUBJID, AESEQ, SPMFL,EXCLRN,SPMPD, PTNM,SOCNM,CAT, CAT1, CAT2, CAT3

AESEQ:  SPM reconcile sequence (from AE)
AESTDT: AE start date
SPMFL:  SPM flag (yes, no)
EXCLRN: SPM excluded reason
SPMPD:  SPM recurrence/progression (Yes, No, missing)
PTNM:   SPM preferred term
SOCNM:  SPM system organ class
CAT:    SPM category
CAT1:   SPM category level1
CAT2:   SPM category level1
CAT3:   SPM category level1
  1. Select ADSL safety population
  2. Select SPM category and AEDECOD from ADAE 
  3. Import SPM related excel sheet (unique preferred term, reconcile file) as SPM
  4. Merge ADSL with SPM by subject ID 
  5. Modify the variable SPM Sequence 
  6. Repeat step 3-5 for Death and SPM AE 
  7. Merge three data (Death, AE, SPM AE) together

 

Sample ADSPM Output:

Thanks very much to Jason Zhang for guiding me through the process and sharing the precious SPM materials.

REF:

Jason Zhang

Allan JM, Travis LB Mechanism of therapy

Happy Studying!

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