754f88bccf3da4feb7cf1f988ddd13e692b0870e jnavarr5 Wed Aug 14 16:58:39 2024 -0700 Moving the Data Access and License sections to the bottom of the page. Making the 'Important' section to the top. Adding sections suggested by Anna, refs #27141 diff --git src/hg/makeDb/trackDb/human/spliceAI.html src/hg/makeDb/trackDb/human/spliceAI.html index 7859a07..d73d187 100644 --- src/hg/makeDb/trackDb/human/spliceAI.html +++ src/hg/makeDb/trackDb/human/spliceAI.html @@ -1,92 +1,109 @@ - - - - - - +

+Important: The SpliceAI data on the UCSC Genome Browser is directly from +Illumina (See Data Access below). However, since SpliceAI refers to the +algorithm, and not the computed dataset, the data on the Broad server or other sources may have +some differences between them. +

Description

SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a lookup tool -is provided by the Broad institute.

-Important: The SpliceAI data on the UCSC Genome Browser is directly from -Illumina (See Data Access below). However, since SpliceAI refers to the algorithm, and not the computed dataset, -the data on the Broad server or other sources may have some differences between them. +is provided by the Broad institute. +

+

Why are some variants not scored by SpliceAI?

+

+SpliceAI only annotates variants within genes defined by the gene +annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome +ends (5kb on either side), deletions of length greater than twice the input parameter -D, or +inconsistent with the reference fasta file. +

+ +

What are the differeneces between masked and unmasked tracks?

+

+The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites +and weakening unannotated splice sites, which are typically much less pathogenic than weakening +annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing +changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative +splicing analysis and masked tracks for variant interpretation.

Display Conventions and Interpretation

Variants are colored by their predicted effects: +

-Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), -location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this -information. +

+Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor +gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up +a table with this information.

The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs.

-

Data Access

-These data are not available for download from the Genome Browser. -The raw data can be found directly on -Illumina. -See below for a copy of the license restrictions pertaining to these data. -

- -

License

-

-FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are -made available by Illumina only for academic or not-for-profit research only. -By accessing the SpliceAI data, you acknowledge and agree that you may only -use this data for your own personal academic or not-for-profit research only, -and not for any other purposes. You may not use this data for any for-profit, -clinical, or other commercial purpose without obtaining a commercial license -from Illumina, Inc. -

-

Methods

The data were downloaded from Illumina. The spliceAI scores are represented in the VCF INFO field as SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31

Here, the pipe-separated fields contain

+

Since most of the values are 0 or almost 0, we selected only those variants -with a score equal to or greater than 0.02.

+with a score equal to or greater than 0.02. +

+

The complete processing of this track can be found in the makedoc.

+ +

Data Access

+These data are not available for download from the Genome Browser. +The raw data can be found directly on +Illumina. +See below for a copy of the license restrictions pertaining to these data. +

+ +

License

+

+FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are +made available by Illumina only for academic or not-for-profit research only. +By accessing the SpliceAI data, you acknowledge and agree that you may only +use this data for your own personal academic or not-for-profit research only, +and not for any other purposes. You may not use this data for any for-profit, +clinical, or other commercial purpose without obtaining a commercial license +from Illumina, Inc. +

+

References

Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. PMID: 30661751

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