VARIANT ANNOTATION. Vivien Deshaies.
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1 VARIANT ANNOTATION Vivien Deshaies
2 Goal Add meta-information on variant to facilitate interpretation
3 Location TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
4 Location? TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
5 Location?? TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
6 Location??? TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
7 Location???? TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
8 Location????? TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
9 Location?????? TSS Exon Intron Exon Intron Exon 5 3 upstream Donor Acceptor downstream
10 Location?????? TSS Exon Intron Exon Intron Exon 5 3 upstream Regulatory element TFBS mirna binding Histone mark Donor Acceptor downstream
11 Location?????? TSS Exon Intron Exon Intron Exon 5 3 upstream Regulatory element TFBS mirna binding Histone mark Donor Acceptor downstream Databases : RefSeq, ensembl, encode, motif
12 Known variant? dbsnp : Database of nucleotide variant for 39 species Clinvar Relationship between variant and human phenotype COSMIC Catalogue of somatic mutation in cancer
13 Frequency in population Rare variant : allele frequency in population < 5% 1000 Genome project : 2500 individuals 26 populations Exome Sequencing Project (ESP) : ~6500 Exomes 2 populations Exome Aggregation Consortium (ExAC) : ~60000 Exomes 7 populations
14 Functionnal impact Impact on protein : synonymous / non synonymous Active domain Protein-protein interaction Structure Splicing : Exon skipping Intron retension Alternative Transcript expression : Transcription factor binding mirna binding Chromatin conformation Pathway
15 Annotation tools Annovar Ensembl variant_effect_predictor snpeff / SnpSift
16 Snpeff databases pre-compiled databases species : Downloadable with snpeff download snpeff compile : Possibility to compile your own database from a fasta file and a gff
17 Get data In galaxy shared data import : Variant_annotation - Files
18 Launch snpeff
19 Snpeff output (1/2) ANN field in vcf INFO Allele : A, T, C, G, C-chr1:123456_A>T Annotation : missense_variant, synonymous,_ Annotation_Impact : MODIFIER, LOW, MODERATE, HIGH Gene_Name : HGNC term example : KDM5A Gene_ID : ensembl id (example : ENSG ) Feature_Type : transcript, motif, mirna Feature_ID : ENST Transcript_BioType : protein_coding, noncoding Rank : Intron or exon rank / total number of introns or exons (eg. 19/28) HGVS.c : c.2594t>c HGVS.p : p.met865thr cdna.pos / cdna.length : 2957/10763 CDS.pos / CDS.length : 2594/5073 AA.pos / AA.length : 865/1690 ERRORS / WARNINGS / INFO
20 Snpeff ouput (2/2) Distance : Up/Downstream: Distance to first / last codon Intergenic: Distance to closest gene Distance to closest Intron boundary in exon (+/up/downstream) Distance to closest exon boundary in Intron (+/up/downstream) Distance to first base in MOTIF Distance to first base in mirna Distance to exon-intron boundary in _ or _region ChipSeq peak: Distance to summit (or peak center) Histone mark / Histone state: Distance to summit (or peak center)
21 Cohort pedigree
22 Launch snpsift CaseControl This tool add 2 info : Number of variants in cases: Hom, Het, Count Number of variants in controls: Hom, Het, Count
23 Snpsift filter Allow variant filtering with all info fields using boolean expressions All variant that pass previous filters : (FILTER = 'PASS') And quality > 30 (FILTER = 'PASS') & (QUAL > 30) Or quality >= 20 for indels (FILTER = 'PASS') & ((QUAL > 30) (( exists INDEL ) & (QUAL >= 20)))
24 SnpSift filter magic functions ANN field filter : (ANN[0].EFFECT has 'frameshift_variant ) (ANN[*].EFFECT has 'frameshift_variant ) Genotype field : (ishom( GEN[0] ) & isvariant( GEN[0] ) & isref( GEN[ samplex ])) More info at :
25 Filter variants
26 Launch snpsift dbnsfp Annotate with : Uniprot_id Interpro_domain Ensembl_geneid Ensembl_transcriptid MetaSVM_pred MetaLR_pred Reliability_index Cadd_phred 1000Gp1_AF 1000Gp1_EUR_AF ESP6500_EA_AF ExAC_AF ExAC_NFE_AF Clinvar_rs Clivar_clnsig Clinvar_trait
27 dbnsfp Database of non-synonymous variant functional prediction in human 83,422,341 pre-annotated SNV 17 functional predictions algorithms 6 conservation scores Allele frequency in populations
28 SnpSift Extract fields CHROM POS ID REF ALT ANN[*].GENE ANN[*].GENEID ANN[*].FEATURE ANN[*].FEATUREID ANN[*].EFFECT ANN[*].IMPACT ANN[*].BIOTYPE ANN[*].RANK ANN[*].HGVS_C ANN[*].HGVS_P ANN[*].DISTANCE ANN[*].ERRORS dbnsfp_uniprot_id dbnsfp_clinvar_rs dbnsfp_clinvar_clnsig dbnsfp_clinvar_trait dbnsfp_exac_af dbnsfp_exac_nfe_af dbnsfp_1000gp1_af dbnsfp_1000gp1_eur_af dbnsfp_esp6500_ea_af dbnsfp_ensembl_geneid dbnsfp_metasvm_pred dbnsfp_metalr_pred dbnsfp_reliability_index dbnsfp_cadd_phred dbnsfp_ensembl_transcriptid dbnsfp_interpro_domain GEN[*].GT
29 Conclusion snpeff / snpsift : very versatile tools A lot of annotation source for human Choose wisely Other organism No population allele frequency Less annotation
30 Thank you for your attention
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Investigating Inherited Diseases The purpose of these exercises is to introduce bioinformatics databases and tools. We investigate an important human gene and see how mutations give rise to inherited diseases.
PrimePCR Assay Validation Report
Gene Information Gene Name Gene Symbol Organism Gene Summary Gene Aliases RefSeq Accession No. UniGene ID Ensembl Gene ID protein kinase N1 PKN1 Human The protein encoded by this gene belongs to the protein