Dataset Information

Genotyping data of routinely processed matched primary/metastatic tumor samples.

ABSTRACT: Genotypic and phenotypic comparisons of tumors in multiple tissue samples from the same patient are important for understanding disease evolution and treatment possibilities. Panel NGS genotyping is currently widely used in this context, whereby NGS variant filtering and final evaluation constitute the basis for meaningful comparisons. Here, we present the genotype data used for genotype / phenotype comparisons between matched primary / metastatic colorectal tumors in the work by Chatzopoulos et al (doi: 10.1016/j.humpath.2020.10.009), as well as the process followed for obtaining these data. We describe key issues while processing routinely formalin-fixed paraffin-embedded (FFPE) tumors for genotyping, NGS application (Ion Torrent), a stringent variant filtering algorithm for genotype analyses in FFPE tissues and particularly in matched tumor samples, and provide the respective datasets. Apart from research, tumor NGS genotyping is currently applied for clinical diagnostic purposes in Oncology. The datasets and method description provided herein (a) are important for comprehending the peculiarities of FFPE tumor genotyping, which is still mostly based on principles of germline DNA genotyping; (b) can be used in pooled analyses, e.g., of primary / metastatic tumors for the investigation of tumor evolution.

SUBMITTER: Kotoula V

PROVIDER: S-EPMC7749371 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Genotyping data of routinely processed matched primary/metastatic tumor samples.

Kotoula Vassiliki V Chatzopoulos Kyriakos K Papadopoulou Kyriaki K Giannoulatou Eleni E Koliou Georgia-Angeliki GA Karavasilis Vasilios V Pazarli Elissavet E Pervana Stavroula S Kafiri Georgia G Tsoulfas Georgios G Chrisafi Sofia S Sgouramali Helen H Papakostas Pavlos P Pectasides Dimitrios D Hytiroglou Prodromos P Pentheroudakis George G Fountzilas George G

Data in brief 20201211

Genotypic and phenotypic comparisons of tumors in multiple tissue samples from the same patient are important for understanding disease evolution and treatment possibilities. Panel NGS genotyping is currently widely used in this context, whereby NGS variant filtering and final evaluation constitute the basis for meaningful comparisons. Here, we present the genotype data used for genotype / phenotype comparisons between matched primary / metastatic colorectal tumors in the work by Chatzopoulos et ...[more]

PMID: 33365374

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Project description:BackgroundObservations of recurrent somatic mutations in tumors have led to identification and definition of signaling and other pathways that are important for cancer progression and therapeutic targeting. As tumor cells contain both an individual's inherited genetic variants and somatic mutations, challenges arise in distinguishing these events in massively parallel sequencing datasets. Typically, both a tumor sample and a "normal" sample from the same individual are sequenced and compared; variants observed only in the tumor are considered to be somatic mutations. However, this approach requires two samples for each individual.ResultsWe evaluate a method of detecting somatic mutations in tumor samples for which only a subset of normal samples are available. We describe tuning of the method for detection of mutations in tumors, filtering to remove inherited variants, and comparison of detected mutations to several matched tumor/normal analysis methods. Filtering steps include the use of population variation datasets to remove inherited variants as well a subset of normal samples to remove technical artifacts. We then directly compare mutation detection with tumor-only and tumor-normal approaches using the same sets of samples. Comparisons are performed using an internal targeted gene sequencing dataset (n = 3380) as well as whole exome sequencing data from The Cancer Genome Atlas project (n = 250). Tumor-only mutation detection shows similar recall (43-60%) but lesser precision (20-21%) to current matched tumor/normal approaches (recall 43-73%, precision 30-82%) when compared to a "gold-standard" tumor/normal approach. The inclusion of a small pool of normal samples improves precision, although many variants are still uniquely detected in the tumor-only analysis.ConclusionsA detailed method for somatic mutation detection without matched normal samples enables study of larger numbers of tumor samples, as well as tumor samples for which a matched normal is not available. As sensitivity/recall is similar to tumor/normal mutation detection but precision is lower, tumor-only detection is more appropriate for classification of samples based on known mutations. Although matched tumor-normal analysis is preferred due to higher precision, we demonstrate that mutation detection without matched normal samples is possible for certain applications.

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Dataset Information

Genotyping data of routinely processed matched primary/metastatic tumor samples.

Publications

Genotyping data of routinely processed matched primary/metastatic tumor samples.

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