Genomic Data Processing - Data Eligibility Criteria (v-1.0)

Table of Contents

The NF-OSI is piloting a new initiative to uniformly process genomic and transcriptomic data that is shared on the NF Data Portal. All studies funded by the Neurofibromatosis Therapeutic Acceleration Program uploaded within the duration 2018 to 2023 are included in the scope of this initiative. The processing of high dimensional genomic and transcriptomic data will be done using standardized data processing pipelines.

The datatypes in the scope of processing include:

Whole Exome Sequencing
Whole Genome Sequencing
Bulk RNA Sequencing
Single cell RNA sequencing

The uniformly processed data will be shared on the NF Data Portal and will also be used to support the use of data from the NF Data Portal in other data analysis/exploration platforms.

Thanks to the generosity of the NF-OSI funders, a subset of the NF Data Portal data is currently eligible for reprocessing. If you have a dataset that you have shared on the NF Data Portal and would like to utilize the NF-OSI Processing pipelines, please reach out to us at nf-osi@sagebionetworks.org. We would be happy to assist you in a case-by-case basis.

Eligibility criteria for data files to be staged for processing

Data files must be annotated with the following details:

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

Availability of processing workflows:

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	✅	✅	❌	❌	✅	NA
WGS	✅	✅	✅	✅	✅	NA
Bulk RNAseq	NA	NA	NA	NA	NA	✅
Single Cell RNAseq	NA	NA	NA	NA	NA	✅

^{✅ 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.}

^NA^{The workflow is not applicable for this data type.}

Genomic Data Processing - Data Eligibility Criteria (v-1.0)

Eligibility criteria for data files to be staged for processing

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*

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

readPairOrientation*

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

Whole Exome Sequencing

Annotation term

Additional Details

fileFormat

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*

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

_{Annotation term}

_{Additional Details}