Table of Contents
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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
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Data files must be annotated with the following details:
For each of the following assays, data files must be annotated with the terms listed below to be staged for processing.
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 | AssayChoose between Bulk RNA Seq or Single Cell RNA Seq. | Whole Genome Sequencing |
| 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.Whole Exome Sequencing |
| 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
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| Note |
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Additional requirement:The |
...
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.
...
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. |