Required Annotations for Genomic Processing

Datatypes eligible for processing

Whole Exome Sequencing

^{A technique that focuses on sequencing only the exons, which are the coding regions of the genome, of an individual's DNA. WES is used to identify genetic variations in these regions that may be associated with certain diseases or traits.}

Whole Genome Sequencing

^{A technique that involves sequencing the entire genome of an individual. This includes both the coding regions and the non-coding regions of DNA. WGS is used to identify genetic variations throughout the entire genome that may be associated with certain diseases or traits.}

Bulk RNA Sequencing

^{A technique that involves sequencing the transcriptome of a bulk population of cells. This technique provides information on the gene expression levels of all genes in the sample and is commonly used to compare gene expression profiles between different samples or conditions.}

Single cell RNA sequencing

^{A technique that involves sequencing the transcriptome of individual cells. This technique provides information on the gene expression levels of each cell and is commonly used to study cell heterogeneity and identify rare cell populations.}

Assay-specific workflow availability

The table below shows the availability of processing workflows for different data files generated through various ‘omics assays.

Assay	Germline SNV	Somatic SNV	Copy Number Variation (CNV)	Structural variants (SV)	Microsatellite Instability (MSI)	Raw counts
WES	✅	✅	✖️	✖️	✅
WGS	✅	✅	✅	✅	✅
Bulk RNAseq						✅
Single Cell RNAseq						✅

✅ The workflow is available for this datatype

✖️ The workflow is available for this data type, but the NF-OSI will not provide this processing. This decision follows from the recommendation of scientists and engineers at Sage who have worked with these data modalities and have noted various problems in interpretation of processed data from these workflows during downstream analysis.

The workflow is not applicable for this data type.

Required annotations for data files to be staged for processing

For each of the following assays, data files must be annotated with the terms listed below.

Bulk and Single Cell RNA Sequencing

	Annotation term	Additional Details
1	fileFormat	Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.
2	individualID	Individual IDs are necessary to create the sample sheets.
3	specimenID	specimen IDs are necessary to interpret the analysis.
4	Assay	Choose between Bulk RNA Seq or Single Cell RNA Seq.
5	Species	The corresponding genome requires knowledge of the species.
6	libraryPreparationMethod	This refers to the name of the library preparation, such as KAPA Hyper PCR 3.
7	Platform	This refers to the name of the platform used, for example, illumina.
8	readPair	Specify whether the read pair is 1 or 2.
9	specimenPreparationMethod	Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.
10	tumorType	If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type.
11	isStranded*	This answer should be either "yes" or "no."
12	readPairOrientation*	Indicate the read pair orientation, such as forward or reverse.

^{* optional but recommended}

Whole Genome Sequencing

	Annotation term	Additional Details
1	fileFormat	Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.
2	individualID	Individual IDs are necessary to create the sample sheets.
3	specimenID	specimen IDs are necessary to interpret the analysis.
4	Assay	Choose between Bulk RNA Seq or Single Cell RNA Seq.
5	Species	The corresponding genome requires knowledge of the species.
6	libraryPreparationMethod	This refers to the name of the library preparation, such as KAPA Hyper PCR 3.
7	Platform	This refers to the name of the platform used, for example, illumina.
8	readPair	Specify whether the read pair is 1 or 2.
9	specimenPreparationMethod	Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.
10	tumorType	If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing.
11	isStranded*	This answer should be either "yes" or "no."
12	readPairOrientation*	Indicate the read pair orientation, such as forward or reverse.

^{* optional but recommended}

Whole Exome Sequencing

	Annotation term	Additional Details
1	fileFormat	Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing. Note: WES files are not eligible for variant calling if BED file is not available
2	individualID	Individual IDs are necessary to create the sample sheets.
3	specimenID	specimen IDs are necessary to interpret the analysis.
4	Assay	Choose between Bulk RNA Seq or Single Cell RNA Seq.
5	Species	The corresponding genome requires knowledge of the species.
6	libraryPreparationMethod	This refers to the name of the library preparation, such as KAPA Hyper PCR 3.
7	Platform	This refers to the name of the platform used, for example, illumina.
8	readPair	Specify whether the read pair is 1 or 2.
9	specimenPreparationMethod	Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.
10	tumorType	If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing.
11	isStranded*	This answer should be either "yes" or "no."
12	readPairOrientation*	Indicate the read pair orientation, such as forward or reverse.

^{* optional but recommended}

Additional requirement:

The BED file associated with the library preparation method for each WES dataset is required to be uploaded and available to the NF-OSI Sage Team for the dataset to be eligible for processing.

Required Annotations for Genomic Processing

Datatypes eligible for processing

Assay-specific workflow availability

Assay

Germline SNV

Somatic SNV

Copy Number Variation (CNV)

Structural variants (SV)

Microsatellite Instability (MSI)

Raw counts

WES

✅

✅

✖️

✖️

✅

WGS

✅

✅

✅

✅

✅

Bulk RNAseq

✅

Single Cell RNAseq

✅

✅ The workflow is available for this datatype

The workflow is not applicable for this data type.

Required annotations for data files to be staged for processing

Bulk and Single Cell RNA Sequencing

Annotation term

Additional Details

fileFormat

Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.

individualID

Individual IDs are necessary to create the sample sheets.

specimenID

specimen IDs are necessary to interpret the analysis.

Assay

Choose between Bulk RNA Seq or Single Cell RNA Seq.

Species

The corresponding genome requires knowledge of the species.

libraryPreparationMethod

This refers to the name of the library preparation, such as KAPA Hyper PCR 3.

Platform

This refers to the name of the platform used, for example, illumina.

readPair

Specify whether the read pair is 1 or 2.

specimenPreparationMethod

Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.

tumorType

If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type.

isStranded*

This answer should be either "yes" or "no."

readPairOrientation*

Indicate the read pair orientation, such as forward or reverse.

Whole Genome Sequencing

Annotation term

Additional Details

fileFormat

Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.

individualID

Individual IDs are necessary to create the sample sheets.

specimenID

specimen IDs are necessary to interpret the analysis.

Assay

Choose between Bulk RNA Seq or Single Cell RNA Seq.

Species

The corresponding genome requires knowledge of the species.

libraryPreparationMethod

This refers to the name of the library preparation, such as KAPA Hyper PCR 3.

Platform

This refers to the name of the platform used, for example, illumina.

readPair

Specify whether the read pair is 1 or 2.

specimenPreparationMethod

Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.

tumorType

If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing.

isStranded*