=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut package Bio::EnsEMBL::Variation::Utils::Config; use base qw(Exporter); our @EXPORT_OK = qw( @ATTRIB_TYPES %ATTRIBS @ATTRIB_SETS @VARIATION_CLASSES @OVERLAP_CONSEQUENCES @FEATURE_TYPES $OVERLAP_CONSEQUENCE_CLASS $MAX_ATTRIB_CODE_LENGTH %SO_ACC_MAPPER ); our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence'; our $MAX_ATTRIB_CODE_LENGTH = 20; our @short_names = qw(hapmap ind_venter ind_watson fail_all fail_nonref fail_ambig fail_gt_fq fail_incons_map fail_mult_map fail_no_alleles fail_no_gt fail_no_map fail_no_seq fail_non_nt fail_mult_alleles fail_dbsnp_suspect ph_hgmd_pub ph_nhgri ph_omim ph_variants ph_uniprot ph_cosmic ph_ega hapmap_ceu hapmap_hcb hapmap_jpt hapmap_yri Affy_500K Affy_SNP6 Cardio-Metabo_Chip HumanOmni1-Quad Illumina_1M-duo Illumina_660Q Illumina_CytoSNP12v1 Human610_Quad HumanHap550 HumanHap650Y HumanOmni2.5 PorcineSNP60 esp_6500 clin_assoc all_chips Chicken600K EquineSNP50 BovineHD BovineLD BovineSNP50 phencode HumanOmni5 OvineSNP50 OvineHDSNP ExomeChip ImmunoChip HumanOmniExpress ClinVar MGP HumanCoreExome 1kg_3 1kg_3_afr 1kg_3_amr 1kg_3_eas 1kg_3_sas 1kg_3_eur 1kg_3_com 1kg_3_afr_com 1kg_3_amr_com 1kg_3_eas_com 1kg_3_sas_com 1kg_3_eur_com LSDB dbPEX HbVar Infevers KAT6BDB LMDD OIVD PAHdb ); our @dbsnp_clinical_significance_types = qw( unknown untested non-pathogenic probable-non-pathogenic probable-pathogenic pathogenic drug-response histocompatibility other ); our @clinvar_clinical_significance_types = ( 'uncertain significance', 'not provided', 'benign', 'likely benign', 'likely pathogenic', 'pathogenic', 'drug response', 'histocompatibility', 'other', 'confers sensitivity', 'risk factor', 'association', 'protective' ); our @dgva_clinical_significance_types = ( 'Not tested', 'Benign', 'Pathogenic', 'Uncertain Significance', 'likely benign', 'likely pathogenic', 'not provided', 'association', 'risk factor' ); our @evidence_statuses = ( 'Multiple_observations', 'Frequency', 'HapMap', '1000Genomes', 'Cited', 'ESP', 'Phenotype_or_Disease', 'ExAC', 'TOPMed', 'gnomAD' ); our @VARIATION_CLASSES = ( { SO_accession => 'SO:0001483', SO_term => 'SNV', display_term => 'SNP', somatic_display_term => 'somatic SNV', }, { SO_accession => 'SO:1000002', SO_term => 'substitution', }, { SO_accession => 'SO:0000667', SO_term => 'insertion', }, { SO_accession => 'SO:0000159', SO_term => 'deletion', }, { SO_accession => 'SO:1000032', SO_term => 'indel', }, { SO_accession => 'SO:0000705', SO_term => 'tandem_repeat', display_term => 'tandem repeat', }, { SO_accession => 'SO:0001059', SO_term => 'sequence_alteration', display_term => 'sequence alteration', }, { SO_accession => 'SO:0001645', SO_term => 'genetic_marker', display_term => 'genetic marker', }, # Structural variation classes { SO_accession => 'SO:0001537', SO_term => 'structural_variant', display_term => 'SV', type => 'sv', }, { SO_accession => 'SO:0001019', SO_term => 'copy_number_variation', display_term => 'CNV', type => 'sv', }, { SO_accession => 'SO:0000051', SO_term => 'probe', display_term => 'CNV_PROBE', type => 'sv', }, { SO_accession => 'SO:0001742', SO_term => 'copy_number_gain', display_term => 'gain', type => 'sv', }, { SO_accession => 'SO:0001743', SO_term => 'copy_number_loss', display_term => 'loss', type => 'sv', }, { SO_accession => 'SO:1000036', SO_term => 'inversion', type => 'sv', }, { SO_accession => 'SO:0001784', SO_term => 'complex_structural_alteration', display_term => 'complex alteration', type => 'sv', }, { SO_accession => 'SO:1000173', SO_term => 'tandem_duplication', display_term => 'tandem duplication', type => 'sv', }, { SO_accession => 'SO:0001837', SO_term => 'mobile_element_insertion', display_term => 'mobile element insertion', type => 'sv', }, { SO_accession => 'SO:0002066', SO_term => 'mobile_element_deletion', display_term => 'mobile element deletion', type => 'sv', }, { SO_accession => 'SO:0001873', SO_term => 'interchromosomal_breakpoint', display_term => 'interchromosomal breakpoint', type => 'sv', }, { SO_accession => 'SO:0001874', SO_term => 'intrachromosomal_breakpoint', display_term => 'intrachromosomal breakpoint', type => 'sv', }, { SO_accession => 'SO:0000199', SO_term => 'translocation', type => 'sv', }, { SO_accession => 'SO:1000035', SO_term => 'duplication', type => 'sv', }, { SO_accession => 'SO:0001838', SO_term => 'novel_sequence_insertion', display_term => 'novel sequence insertion', type => 'sv', }, { SO_accession => 'SO:0002060', SO_term => 'interchromosomal_translocation', display_term => 'interchromosomal translocation', type => 'sv', }, { SO_accession => 'SO:0002061', SO_term => 'intrachromosomal_translocation', display_term => 'intrachromosomal translocation', type => 'sv', }, { SO_accession => 'SO:0002063', SO_term => 'Alu_insertion', display_term => 'Alu insertion', type => 'sv', }, { SO_accession => 'SO:1000005', SO_term => 'complex_substitution', display_term => 'complex substitution', type => 'sv', }, { SO_accession => 'SO:0002096', SO_term => 'short_tandem_repeat_variation', display_term => 'short tandem repeat variation', type => 'sv', }, { SO_accession => 'SO:0001786', SO_term => 'loss_of_heterozygosity', display_term => 'loss of heterozygosity', type => 'sv', }, ); our @OVERLAP_CONSEQUENCES = ( { SO_accession => 'SO:0001060', SO_term => 'sequence_variant', display_term => 'SEQUENCE_VARIANT', rank => '39', tier => '4', description => 'A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration', label => 'sequence variant', impact => 'MODIFIER', include => { within_feature => 0 }, }, { SO_accession => 'SO:0001628', SO_term => 'intergenic_variant', display_term => 'INTERGENIC', rank => '38', tier => '4', description => 'A sequence variant located in the intergenic region, between genes', label => 'intergenic variant', is_default => 1, impact => 'MODIFIER', include => { within_feature => 0 }, }, { SO_accession => 'SO:0001631', SO_term => 'upstream_gene_variant', display_term => 'UPSTREAM', feature_SO_term => 'transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '24', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::upstream', description => 'A sequence variant located 5\' of a gene', label => 'upstream gene variant', impact => 'MODIFIER', include => { within_feature => 0 }, }, { SO_accession => 'SO:0001632', SO_term => 'downstream_gene_variant', display_term => 'DOWNSTREAM', feature_SO_term => 'transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '25', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::downstream', description => 'A sequence variant located 3\' of a gene', label => 'downstream gene variant', impact => 'MODIFIER', include => { within_feature => 0 }, }, { SO_accession => 'SO:0001575', SO_term => 'splice_donor_variant', display_term => 'ESSENTIAL_SPLICE_SITE', NCBI_term => 'splice-5', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '3', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::donor_splice_site', description => 'A splice variant that changes the 2 base region at the 5\' end of an intron', label => 'splice donor variant', impact => 'HIGH', include => { intron_boundary => 1 }, }, { SO_accession => 'SO:0001574', SO_term => 'splice_acceptor_variant', display_term => 'ESSENTIAL_SPLICE_SITE', NCBI_term => 'splice-3', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '3', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::acceptor_splice_site', description => 'A splice variant that changes the 2 base region at the 3\' end of an intron', label => 'splice acceptor variant', impact => 'HIGH', include => { intron_boundary => 1 }, }, { SO_accession => 'SO:0001630', SO_term => 'splice_region_variant', display_term => 'SPLICE_SITE', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '13', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::splice_region', description => 'A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron', label => 'splice region variant', impact => 'LOW', include => { intron_boundary => 1 }, }, { SO_accession => 'SO:0001627', SO_term => 'intron_variant', display_term => 'INTRONIC', NCBI_term => 'intron', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '21', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_intron', description => 'A transcript variant occurring within an intron', label => 'intron variant', impact => 'MODIFIER', include => { intron => 1, } }, { SO_accession => 'SO:0001623', SO_term => '5_prime_UTR_variant', display_term => '5PRIME_UTR', NCBI_term => 'untranslated_5', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '18', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_5_prime_utr', description => 'A UTR variant of the 5\' UTR', label => '5 prime UTR variant', impact => 'MODIFIER', include => { utr => 1, exon => 1, } }, { SO_accession => 'SO:0001624', SO_term => '3_prime_UTR_variant', display_term => '3PRIME_UTR', NCBI_term => 'untranslated_3', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '19', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_3_prime_utr', description => 'A UTR variant of the 3\' UTR', label => '3 prime UTR variant', impact => 'MODIFIER', include => { utr => 1, exon => 1, } }, { SO_accession => 'SO:0001819', SO_term => 'synonymous_variant', display_term => 'SYNONYMOUS_CODING', NCBI_term => 'cds-synon', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '15', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::synonymous_variant', description => 'A sequence variant where there is no resulting change to the encoded amino acid', label => 'synonymous variant', impact => 'LOW', include => { coding => 1, } }, { SO_accession => 'SO:0001583', SO_term => 'missense_variant', display_term => 'NON_SYNONYMOUS_CODING', NCBI_term => 'missense', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '12', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::missense_variant', description => 'A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved', label => 'missense variant', impact => 'MODERATE', include => { coding => 1, increase_length => 0, decrease_length => 0, } }, { SO_accession => 'SO:0001821', SO_term => 'inframe_insertion', display_term => 'NON_SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '10', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_insertion', description => 'An inframe non synonymous variant that inserts bases into in the coding sequence', label => 'inframe insertion', impact => 'MODERATE', include => { coding => 1, insertion => 1, } }, { SO_accession => 'SO:0001822', SO_term => 'inframe_deletion', display_term => 'NON_SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '11', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_deletion', description => 'An inframe non synonymous variant that deletes bases from the coding sequence', label => 'inframe deletion', impact => 'MODERATE', include => { coding => 1, deletion => 1, } }, { SO_accession => 'SO:0001587', SO_term => 'stop_gained', display_term => 'STOP_GAINED', NCBI_term => 'nonsense', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '4', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_gained', description => 'A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript', label => 'stop gained', impact => 'HIGH', include => { coding => 1, } }, { SO_accession => 'SO:0001578', SO_term => 'stop_lost', display_term => 'STOP_LOST', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '6', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_lost', description => 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript', label => 'stop lost', impact => 'HIGH', include => { coding => 1, } }, { SO_accession => 'SO:0001567', SO_term => 'stop_retained_variant', display_term => 'SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '15', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_retained', description => 'A sequence variant where at least one base in the terminator codon is changed, but the terminator remains', label => 'stop retained variant', impact => 'LOW', include => { coding => 1, } }, { SO_accession => 'SO:0002012', SO_term => 'start_lost', display_term => 'NON_SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '7', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::start_lost', description => 'A codon variant that changes at least one base of the canonical start codon', label => 'start lost', impact => 'HIGH', include => { coding => 1, } }, { SO_accession => 'SO:0002019', SO_term => 'start_retained_variant', display_term => 'SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '15', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::start_retained_variant', description => 'A sequence variant where at least one base in the start codon is changed, but the start remains', label => 'start retained variant', impact => 'LOW', include => { coding => 1, } }, { SO_accession => 'SO:0001589', SO_term => 'frameshift_variant', display_term => 'FRAMESHIFT_CODING', NCBI_term => 'frameshift', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '5', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::frameshift', description => 'A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three', label => 'frameshift variant', impact => 'HIGH', include => { coding => 1, snp => 0, } }, { SO_accession => 'SO:0001626', SO_term => 'incomplete_terminal_codon_variant', display_term => 'PARTIAL_CODON', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '14', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::partial_codon', description => 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed', label => 'incomplete terminal codon variant', impact => 'LOW', include => { coding => 1, } }, { SO_accession => 'SO:0001621', SO_term => 'NMD_transcript_variant', display_term => 'NMD_TRANSCRIPT', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '22', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_nmd_transcript', description => 'A variant in a transcript that is the target of NMD', label => 'NMD transcript variant', impact => 'MODIFIER', include => { within_feature => 1, nonsense_mediated_decay => 1, } }, { SO_accession => 'SO:0001619', SO_term => 'non_coding_transcript_variant', display_term => 'WITHIN_NON_CODING_GENE', feature_SO_term => 'ncRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '23', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_non_coding_gene', description => 'A transcript variant of a non coding RNA gene', label => 'non coding transcript variant', impact => 'MODIFIER', include => { within_feature => 1, protein_coding => 0, } }, { SO_accession => 'SO:0001792', SO_term => 'non_coding_transcript_exon_variant', display_term => 'WITHIN_NON_CODING_GENE', feature_SO_term => 'ncRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '20', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::non_coding_exon_variant', description => 'A sequence variant that changes non-coding exon sequence in a non-coding transcript', label => 'non coding transcript exon variant', impact => 'MODIFIER', include => { within_feature => 1, protein_coding => 0, exon => 1, } }, { SO_accession => 'SO:0001620', SO_term => 'mature_miRNA_variant', display_term => 'WITHIN_MATURE_miRNA', feature_SO_term => 'miRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '17', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_mature_miRNA', description => 'A transcript variant located with the sequence of the mature miRNA', label => 'mature miRNA variant', impact => 'MODIFIER', include => { within_feature => 1, protein_coding => 0, nonsense_mediated_decay => 0, } }, { SO_accession => 'SO:0001580', SO_term => 'coding_sequence_variant', display_term => 'CODING_UNKNOWN', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '16', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::coding_unknown', description => 'A sequence variant that changes the coding sequence', label => 'coding sequence variant', impact => 'MODIFIER', include => { coding => 1, } }, { SO_accession => 'SO:0001566', SO_term => 'regulatory_region_variant', display_term => 'REGULATORY_REGION', feature_SO_term => 'regulatory_region', feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '36', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_regulatory_feature', description => 'A sequence variant located within a regulatory region', label => 'regulatory region variant', impact => 'MODIFIER', }, { SO_accession => 'SO:0001782', SO_term => 'TF_binding_site_variant', display_term => 'REGULATORY_REGION', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '30', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_motif_feature', description => 'A sequence variant located within a transcription factor binding site', label => 'TF binding site', impact => 'MODIFIER', }, ## NEW FOR 68 ############# { SO_accession => 'SO:0001893', SO_term => 'transcript_ablation', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '1', tier => '1', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', description => 'A feature ablation whereby the deleted region includes a transcript feature', label => 'transcript ablation', impact => 'HIGH', include => { deletion => 1, complete_overlap => 1, } }, { SO_accession => 'SO:0001889', SO_term => 'transcript_amplification', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '8', tier => '1', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', description => 'A feature amplification of a region containing a transcript', label => 'transcript amplification', impact => 'HIGH', include => { increase_length => 1, complete_overlap => 1, }, }, # { # SO_accession => 'SO:0001886', # SO_term => 'transcript_fusion', # feature_SO_term => 'mRNA', # feature_class => 'Bio::EnsEMBL::Transcript', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '2', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_fusion', # description => 'A feature fusion where the deletion brings together transcript regions', # label => 'transcript fusion', # }, # { # SO_accession => 'SO:0001883', # SO_term => 'transcript_translocation', # feature_SO_term => 'mRNA', # feature_class => 'Bio::EnsEMBL::Transcript', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '9', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_translocation', # description => 'A feature translocation where the region contains a transcript', # label => 'transcript translocation', # }, { SO_accession => 'SO:0001895', SO_term => 'TFBS_ablation', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '26', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', description => 'A feature ablation whereby the deleted region includes a transcription factor binding site', label => 'TFBS ablation', impact => 'MODERATE', include => { deletion => 1, complete_overlap => 1, } }, { SO_accession => 'SO:0001892', SO_term => 'TFBS_amplification', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '28', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', description => 'A feature amplification of a region containing a transcription factor binding site', label => 'TFBS amplification', impact => 'MODIFIER', include => { increase_length => 1, complete_overlap => 1, }, }, # { # SO_accession => 'SO:0001888', # SO_term => 'TFBS_fusion', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '27', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_fusion', # description => 'A fusion where the deletion brings together transcription factor binding sites', # label => 'TFBS fusion', # }, # { # SO_accession => 'SO:0001885', # SO_term => 'TFBS_translocation', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '29', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_translocation', # description => 'A feature translocation where the region contains a transcription factor binding site', # label => 'TFBS translocation', # }, { SO_accession => 'SO:0001894', SO_term => 'regulatory_region_ablation', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '31', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', description => 'A feature ablation whereby the deleted region includes a regulatory region', label => 'regulatory region ablation', impact => 'MODERATE', include => { deletion => 1, complete_overlap => 1, } }, { SO_accession => 'SO:0001891', SO_term => 'regulatory_region_amplification', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '33', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', description => 'A feature amplification of a region containing a regulatory region', label => 'regulatory region amplification', impact => 'MODIFIER', include => { increase_length => 1, complete_overlap => 1, }, }, # { # SO_accession => 'SO:0001887', # SO_term => 'regulatory_region_fusion', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '32', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_fusion', # description => 'A fusion where the deletion brings together regulatory regions', # label => 'regulatory region fusion', # }, # { # SO_accession => 'SO:0001884', # SO_term => 'regulatory_region_translocation', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '34', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_translocation', # description => 'A feature translocation where the region contains a regulatory region', # label => 'regulatory region translocation', # }, { SO_accession => 'SO:0001907', SO_term => 'feature_elongation', feature_SO_term => 'sequence_feature', feature_class => 'Bio::EnsEMBL::Feature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '36', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_elongation', description => 'A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence', label => 'feature elongation', impact => 'MODIFIER', include => { increase_length => 1, sv => 1, }, }, { SO_accession => 'SO:0001906', SO_term => 'feature_truncation', feature_SO_term => 'sequence_feature', feature_class => 'Bio::EnsEMBL::Feature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '37', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_truncation', description => 'A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence', label => 'feature truncation', impact => 'MODIFIER', include => { decrease_length => 1, sv => 1, }, }, { SO_accession => 'SO:0001818', SO_term => 'protein_altering_variant', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '12', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::protein_altering_variant', description => 'A sequence_variant which is predicted to change the protein encoded in the coding sequence', label => 'protein altering variant', impact => 'MODERATE', include => { coding => 1, }, }, ); our @FEATURE_TYPES = ( { SO_accession => 'SO:0000234', SO_term => 'mRNA', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_feature_subtype => 'protein_coding', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000673', SO_term => 'transcript', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000185', SO_term => 'primary_transcript', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000655', SO_term => 'ncRNA', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000276', SO_term => 'miRNA', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0005836', SO_term => 'regulatory_region', ens_feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::RegulatoryFeatureVariation', }, { SO_accession => 'SO:0000409', SO_term => 'binding_site', ens_feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::MotifFeatureVariation', }, { SO_accession => 'SO:0005836', SO_term => 'regulatory_region', ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation', ens_feature_subtype => 'VISTA enhancer set', }, { SO_accession => 'SO:0000409', SO_term => 'binding_site', ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation', ens_feature_subtype => 'cisRED motif', }, { SO_accession => 'SO:0005836', SO_term => 'regulatory_region', ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation', ens_feature_subtype => 'miRanda miRNA target', }, { SO_accession => 'SO:0000110', SO_term => 'sequence_feature', ens_feature_class => 'Bio::EnsEMBL::Feature', ens_variant_class => 'Bio::EnsEMBL::Variation::StructuralVariationFeatureOverlap', }, ); # attrib_types are specified as hashrefs in the @ATTRIB_TYPES array. Each hashref should have a value for the key 'code' and optionally values for the keys 'name' and 'description' our @ATTRIB_TYPES = ( { code => 'SO_accession', description => 'Sequence Ontology accession', }, { code => 'SO_term', description => 'Sequence Ontology term', }, { code => 'display_term', description => 'Ensembl display term', }, { code => 'NCBI_term', description => 'NCBI term', }, { code => 'feature_SO_term', description => 'Sequence Ontology term for the associated feature', }, { code => 'rank', description => 'Relative severity of this variation consequence', }, { code => 'polyphen_prediction', description => 'PolyPhen-2 prediction', }, { code => 'sift_prediction', description => 'SIFT prediction', }, { code => 'short_name', name => 'Short name', description => 'A shorter name for an instance, e.g. a VariationSet', }, { code => 'dbsnp_clin_sig', name => 'dbSNP/ClinVar clinical significance', description => 'The clinical significance of a variant as reported by ClinVar and dbSNP', }, { code => 'dgva_clin_sig', name => 'DGVa clinical significance', description => 'The clinical significance of a structural variant as reported by DGVa', }, { code => 'clinvar_clin_sig', name => 'ClinVar clinical significance', description => 'The clinical significance of a variant as reported by ClinVar', }, { code => 'prot_func_analysis', name => 'Protein function analysis ', description => 'The program used to make protein function predictions', }, { code => 'associated_gene', name => 'Associated gene', description => 'ID of gene(s) linked by phenotype association', }, { code => 'risk_allele', name => 'Risk allele', description => 'Risk allele in phenotype association', }, { code => 'p_value', name => 'P-value', description => 'P-value denoting significance of an observed phenotype annotation', }, { code => 'variation_names', name => 'Variation names', description => 'Variant ID(s) linked with a phenotype association', }, { code => 'sample_id', name => 'Sample ID', description => 'Sample ID for source of phenotype association', }, { code => 'strain_id', name => 'Strain ID', description => 'Strain ID for source of phenotype association', }, { code => 'lod_score', name => 'LOD score', description => 'Log Of Odds score', }, { code => 'variance', name => 'Variance', description => 'Variance statistic', }, { code => 'inheritance_type', name => 'Inheritance type', description => 'Inheritance type of a trait', }, { code => 'external_id', name => 'External ID', description => 'External identifier for an entity', }, { code => 'odds_ratio', name => 'Odds ratio', description => 'Odds ratio used to denote significance of an observed phenotype annotation', }, { code => 'beta_coef', name => 'Beta coefficient', description => 'Beta coefficient (or standardized coefficient) used to denote significance of an observed phenotype annotation', }, { code => 'allele_symbol', name => 'Allele symbol', description => 'Allele symbol linked with phenotype association', }, { code => 'allele_accession_id', name => 'Allele accession ID', description => 'Allele accession ID linked with phenotype association', }, { code => 'marker_accession_id', name => 'Marker accession ID', description => 'Marker ID linked with phenotype association', }, { code => 'evidence', name => 'Variant evidence status', description => 'Evidence status for a variant', }, { code => 'sequence_number', name => 'Number of sequences in alignment', description => 'Number of protein sequences in the alignment use to make a protein impact prediction', }, { code => 'based_on', name => 'Evidence type used for protein impact prediction', description => 'Evidence type used for a PolyPhen protein impact prediction', }, { code => 'conservation_score', name => 'Sift conservation score', description => 'Median conservation value in an alignment used to make a Sift prediction', }, { code => 'review_status', name => 'ClinVar review_status', description => 'ClinVar review_status for assertation', } ); # attribs are specified in the %ATTRIBS hash, having the attrib_type code as hash key and a listref containing the attribs that will be loaded as value our %ATTRIBS = ( 'short_name' => \@short_names, 'dbsnp_clin_sig' => \@dbsnp_clinical_significance_types, 'dgva_clin_sig' => \@dgva_clinical_significance_types, 'clinvar_clin_sig' => \@clinvar_clinical_significance_types, 'polyphen_prediction' => ['probably damaging', 'possibly damaging', 'benign', 'unknown'], 'sift_prediction' => ['tolerated', 'deleterious', 'tolerated - low confidence', 'deleterious - low confidence'], 'prot_func_analysis' => [qw(sift polyphen_humvar polyphen_humdiv)], 'evidence' => \@evidence_statuses, ); # attrib sets are specified by putting a hashref in the @ATTRIB_SETS array having the attrib_type code as key and the attrib as value. new attrib entries will be inserted as necessary our @ATTRIB_SETS = ( @VARIATION_CLASSES, @OVERLAP_CONSEQUENCES, @FEATURE_TYPES ); # Used for the feature_so_acc functionality implemented by Bio::EnsEMBL::Feature our %SO_ACC_MAPPER = ( 'Bio::EnsEMBL::Variation::VariationFeature' => { acc => 'SO:0001060', term => 'sequence_variant', }, 'Bio::EnsEMBL::Variation::StructuralVariationFeature' => { acc => 'SO:0001537', term => 'structural_variant', } ); 1;