Download Pruitt - Mouse Genome Informatics

The Consensus CoDing Sequence
(CCDS) Database
Kim D. Pruitt
Mouse Genome Annotation Summit Meeting
March 12-13, 2008
National Center for Biotechnology Information
Why is the CCDS project needed?
The Problem:
Annotation of the genome sequence is essential
– but beware of different interpretations!
• The availability of the human and mouse genome sequence has
had a significant impact on disease and health research.
• Most scientists rely on annotation information when designing,
interpreting, and evaluating research results.
• Inconsistencies in annotation results among the main public
resources hampers use of this important data.
• Researchers may not realize that a different annotation result is
available elsewhere – possibly leading to erroneous or incomplete
interpretations.
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CCDS - A collaborative project
• Initiated by the main public annotation/browser groups to address
concerns by the scientific community about inconsistencies in the
human and mouse genome annotation.
• Built by consensus among the collaborating members, which include:
European Bioinformatics Institute (EBI)
National Center for Biotechnology Information (NCBI)
University of California, Santa Cruz (UCSC)
Sanger Institute (WTSI)
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What is the CCDS project?
• Project Goals
– identify a core set of protein-coding genes that are consistently
annotated and of high quality
– support convergence toward a standard set of gene annotations
• Scope:
– Human and mouse protein coding regions
• Update frequency
– Variable
– Depends on frequency of genome annotation updates
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Process flow – calculating updates
NCBI (computational)
Havana (manual) Ensembl (computational)
RefSeq (manual)
Compare
CDS
(Annotation
+
Sequence)
Ensembl
merged
annotation
QA
Identical
Similar
Novel
Existing CCDS Retain
Retain
Lost
New match
Out of scope
Out of scope
New CCDS ID
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Assessing Quality
CCDS status is conservatively applied:
• Annotated CDS coordinates are identical
• Annotation is of high quality and passes QA tests, or curator review
• Existing CCDS proteins can be flagged for review by the collaborating
members
• Updates and removals are by consensus agreement.
Quality assessment tests include:
–
–
–
–
–
–
–
–
Consensus splice sites ("GY..AG" or "AT..AC")
Valid start and stop codons with no internal stops
NMD
QA test results are reviewed by curators
Low complexity
Over-rides are set to retain supported CDSs
Repeat-containing
Insufficient protein homology
Genome conservation
Putative pseudogene
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CCDS Counts
Date
Build
CDS IDs
GeneIDs
Mar-05 Hs35.1
14,795
13,142
Feb-07 Hs36.2
18,290
16,008
Oct-06 Mm36.1
13,374
13,014
Nov-07 Mm37.1
17,707
16,893
Step
Source
Annotation
NCBI
Annotation
Ensembl
Matching CDS
QA & curation rejections 1331
Accepted rejections
Final CCDS ID
Genes Proteins
24765
27209
18185
1350
1292
16893
26851
39941
19048
1341
17707
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Curation – how are updates curated and coordinated?
•
Any member of the collaboration can flag a CCDS for review
– Update the CDS definition (alter N-terminus extent internal splice site)
– Withdraw the CCDS ID (insufficiently supported, or non-protein coding)
•
NCBI provides a collaboration web site to coordinate this review
•
All collaborators must agree with a change to finalize a decision
•
Withdrawal of a CCDS may happen between genome annotation updates
•
An update to a CCDS is indicated by:
– Status change: a status of ‘pending update’ is reported when there is
collaborative agreement that a change is needed
– Version change: The CCDS version number is incremented once the change
is reflected in public annotation. This only occurs after a genome annotation
update and CCDS analysis has taken place.
CCDS curation is fully integrated with RefSeq curation
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CCDS update & curation stats
Curation-based changes:
name
human
human
human
human
mouse
mouse
mouse
mouse
action
update
update
withdraw
withdraw
update
update
withdraw
withdraw
Mouse: ~5200 curated CCDS genes
status
pending
agreed
pending
agreed
pending
agreed
pending
agreed
count
366
923
557
189
709
519
185
242
57
16
24
8
Annotation pipeline-based changes:
name build status
count
human 35.1 Withdrawn, inconsistent annotation 133
human 36.2 Withdrawn, inconsistent annotation
29
mouse 36.1 Withdrawn, inconsistent annotation
29
mouse 37.1 Withdrawn, inconsistent annotation
4
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Curation considerations
•
•
•
•
•
•
Alignments
Track low quality sequences (‘kill list’)
Protein conservation
Publications
Personal communications
QA measures
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Access – How do I know if an annotation has a CCDS ID?
• Genome browser displays
– NCBI
– UCSC
• Gene reports
– Ensembl
– NCBI
– UCSC
– Vega
• Other:
– RefSeq annotation (NCBI)
– CCDS web site
– FTP
http://www.ncbi.nlm.nih.gov/CCDS/
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NCBI Map Viewer (chr.5)
Link to
CCDS Browser
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UCSC Browser
chr5:30270000-30650000
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UCSC Browser – Tyms gene
CCDS Browser
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Access of CCDS data at NCBI
•CCDS Database & Browser interface
•Project Description
•Query support
•Reports attributes of the CCDS
•Location data
•Sequence members
•Status
•FTP reports
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CCDS Browser
History
Find all CCDSs for the Gene
Entrez Gene
View CCDS Details
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CCDS Browser
•Mouse-over highlights codon
•Click to highlight codon and
corresponding amino acid
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Biology is complex – some CCDS curation examples
• 1 vs 2 vs ‘n’ genes
• translation start site
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1 vs. 2 vs. ‘n’ genes
Curation Considerations:
– Nomenclature
– History (scientific use, publications, etc.)
– Different (but similar) products vs. distinct products
– Shared promoters
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carnitine palmitoyltransferase 1b,
choline kinase beta
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1 vs. 2 vs. ‘n’ genes
Current RefSeq representation of the region
- two protein coding loci
- one non-coding loci for the non-coding
transcript product (a read-through transcript)
Chkb (CCDS27750.1)
Cpt1b (CCDS27749.1 )
Chkb-cpt1b (PMID:12761301 )
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Translation start site
• Curation Considerations
– Publication reports (CDS begins at ‘n’)
– Other cDNA sequencing reveals the ORF can be extended
further upstream
– Evaluate:
• Genome conservation
• Literature reports for the protein
• Putative Kozak signals
• Presence of in-frame upstream stop codon
• INSDC submissions from an experimental lab source that do
have the longer ORF extent annotated.
• Consult with an expert
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Internal CCDS browser (restricted access)
Jmjd2d jumonji domain containing 2D (chr 19)
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Update is agreed on
by all parties
Resulting in a
258 aa N-terminal
extension
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Examples – no CCDS ID
EBI+WTSI and NCBI transcript annotation
may differ even though the gene includes
annotations with CCDS IDs
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Examples –no CCDS ID
EBI/WTSI
NCBI
EBI/WTSI
NCBI
Reasons:
•not found by one group
•different CDS length
•different splice sites
•different internal exon
•Curation removal
EBI/WTSI
NCBI
EBI/WTSI
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NCBI
Acknowledgements
Donna Maglott
Josh Cherry
Keith Oxenride
Craig Wallin
Andrei Shkeda
Collaborators at Ensembl, UCSC, Vega
Jen Ashurst & Vega curator group
Rachel Harte
Mark Diekhans
Steve Searle
RefSeq Curators
NCBI Genome Annotation Group
NCBI Map Viewer Group
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Ensembl – Tyms gene
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Vega browser Tyms gene (chromosome 5 30388989-30404404)
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