Matched Tumor Samples

A relatively simple schema for the analysis of matched tumor/normal samples from cancer studies. The assumed setting is as follows.

  • Each bio entity is a patient/donor.
  • Each donor gives one normal (bio) sample (e.g., blood or saliva) and at least one (bio) sample from the cancer (e.g., primary tumor or metastesis).
  • For each tumor and non-tumor sample, there is at least one DNA HTS library sequenced.
  • For each tumor sample, there can be RNA HTS libraries.
  • Only the first seen DNA/RNA library is considered for each sample (the “primary one”)


The requirement of one DNA HTS library for each sample and RNA only for tumor can be dropped in the future.

Matched Tumor Fields

The following fields must be present for matched tumor sample sheets.

  • BioSample
    • isTumor – a boolean defining whether the sample was taken from tumor cells

Matched Tumor TSV Schema

Additionally, there is an alternative to defining schemas in JSON format for matched tumor sample sheets. Instead, a TSV-based schema can be used.

Optionally, the schema can contain meta data, starting with [Metadata] INI-style section header (the data section has to start with [Data]).

schema	cancer_matched
schema_version	v1
title	Example matched cancer tumor/normal study
description	The study has two patients, P001 has one tumor sample, P002 has two


The schema and schema_version lines are optional.

If the file does not start with an INI-style section header, it starts with tab-separated column names. An example is shown below:

patientName	sampleName	isTumor	extractionType	libraryType	folderName
P001	N1	N	DNA	WES	P001-N1-DNA1-WES1
P001	T1	Y	DNA	WES	P001-T1-DNA1-WES1
P001	T1	Y	RNA	mRNA-seq	P001-T1-RNA1-mRNAseq1
P002	N1	N	DNA	WES	P001-N1-DNA1-WES1
P002	T1	Y	DNA	WES	P001-T1-DNA1-WES1
P002	T1	Y	DNA	WES	P001-T1-RNA1-RNAseq1
P002	T2	Y	DNA	WES	P001-T2-DNA1-WES1
P002	T2	Y	RNA	mRNA-seq	P001-T2-RNA1-mRNAseq1

They are as follows:

  1. patientName – name of the patient, used to identify the patient in the sample sheet. This value will be used as the secondary id of the BioEntity of the patient.
  2. sampleName – name of the sample, used to identify the sample for the patient in the sample sheet. The secondary ID of the BioSample will be generated from the patientName and sampleName.
  3. isTumor – a flag identifying a sample as being from tumor, one of {Y, N, 1, 0}
  4. extractionType – a valid extraction type as in the JSON schema, which is one of DNA, RNA or other. Based on the extractionType (and the secondary ID of the BioSample), the secondary ID of the TestSample will be generated.
  5. libraryType – a valid libraryType, as in the JSON schema, e.g., WES or mRNA-seq. Based on the libraryType (and the secondary ID of the TestSample), the secondary ID of the NGSLibrary will be generated.
  6. folderName – a folder name to search the library’s FASTQ files for. The list of base folders to search for is given in the configuration and this folder is searched for a folder with the name given here. Thus, no absolute path is given here, only the folder name.

Optionally, the following fields can be added:

  • seqPlatform can be one of Illumina and PacBio, default is Illumina