Observed Survival Interval: A Supplement to TCGA Pan-Cancer Clinical Data Resource

Abstract

To drive high-quality omics translational research using The Cancer Genome Atlas (TCGA) data, a TCGA Pan-Cancer Clinical Data Resource was proposed. However, there is an out-of-step issue between clinical outcomes and the omics data of TCGA for skin cutaneous melanoma (SKCM), due to the majority of metastatic samples. In clinical cases, the survival time started from the initial SKCM diagnosis, while the omics data were characterized at TCGA sampling. This study aimed to address this issue by proposing an observed survival interval (OBS), which was defined as the time interval from TCGA sampling to patient death or last follow-up. We compared the OBS with the usual recommended overall survival (OS) by associating them with both clinical data and microRNA sequencing data of TCGA-SKCM. We found that the OS of primary SKCM was significantly shorter than that of metastatic SKCM, while the opposite happened if OBS was compared. OS was associated with the pathological stage of both primary and metastatic SKCM, while OBS was associated with the pathological stage of primary SKCM but not that of metastatic SKCM. Five previously cross-validated survival-associated microRNAs were found to be associated with the OBS rather than OS in metastatic SKCM. Thus, the OBS was more appropriate for associating microRNA-omics data of TCGA-SKCM than OS, and it is a timely supplement to TCGA Pan-Cancer Clinical Data Resource.

Predicting the Risk of Melanoma Metastasis Using an Immune Risk Score in the Melanoma Cohort

“…The melanoma cohort in the TCGA database contains primary and metastatic samples. Specifically, TCGA did not always adopt the initially diagnosed melanoma samples for sequencing (Xiong et al, 2019). The majority of the primary samples submitted to sequence were initially diagnosed melanoma samples, and the majority of the metastatic samples for sequencing were from follow-up patients instead of initially diagnosed samples.…”

Survival between synchronous and non-synchronous multiple primary cutaneous melanomas—a SEER database analysis

“…Thus, the potential pathology of synchronous MPM needs to be illustrated in the future. Furthermore, many molecular events such as mutation (Demunter et al, 2001;Griewank et al, 2014), copy number variation (Rákosy et al, 2010;Gerami et al, 2011), epigenetic variation (Roh et al, 2016;Wouters et al, 2017), expression of genes (Brown et al, 2012;Schramm et al, 2012) and non-coding RNAs (Xiong, Bing & Guo, 2019;Yang, Xu & Zeng, 2018) were reported to be involved in the prognosis of CM. Further laboratory studies aimed to investigate the potential molecular mechanisms of synchronous MPM occurrence and its prognostic roles are also in need.…”

Peer Review #1 of "Survival between synchronous and non-synchronous multiple primary cutaneous melanomas—a SEER database analysis (v0.1)"

“…Thus, the potential pathology of synchronous MPM needs to be illustrated in the future. Furthermore, many molecular events such as mutation (Demunter et al, 2001;Griewank et al, 2014), copy number variation (Rákosy et al, 2010;Gerami et al, 2011), epigenetic variation (Roh et al, 2016;Wouters et al, 2017), expression of genes (Brown et al, 2012;Schramm et al, 2012) and non-coding RNAs (Xiong et al, 2019;Yang et al, 2018) were reported to be involved in the prognosis of CM. Further laboratory studies aimed to investigate the potential molecular mechanisms of synchronous MPM occurrence and its prognostic roles are also in need.…”