{% extends "layout.html" %}
{% from "utils.html" import comments_panel, activity_panel, pedigree_panel %}
{% from "variants/utils.html" import compounds_table %}
{% block title %}
{{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }}
{% endblock %}
{% block top_nav %}
{{ institute.display_name }}
{{ case.display_name }}
{% if cancer %}
{{ variant.variant_type|capitalize }} cancer variants
{% else %}
{{ variant.variant_type|capitalize }} SNV and INDELs
{% endif %}
{{ variant.display_name|truncate(20, True) }}
{% endblock %}
{% block top_nav_right %}
{% if config['MAIL_USERNAME'] %}
{# Email setting must be setup #}
{{ sanger_button() }}
{% endif %}
{{ pin_button() }}
{{ causative_button() }}
{{ super() }}
{% endblock %}
{% block content_main %}
{% if variant.missing_data %}
Showing only first 30 genes!
{% endif %}
{{ matching_variants() }}
{{ panel_basics() }}
{{ panel_summary() }}
{{ transcript_overview() }}
{{ inheritance_panel() }}
{{ omim_phenotypes() }}
{{ frequency_list() }}
{{ severity_list() }}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{{ gtcall_panel() }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %}
{% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %}
{% if variant.compounds %}
{% endif %}
{{ overlapping_panel() }}
{{ genes_panel() }}
{{ transcripts_panel() }}
{{ proteins_panel() }}
{{ activity_panel(events|reverse) }}
{% if config['MAIL_USERNAME'] %}
{# Email setting must be setup #}
{{ modal_sanger() }}
{% endif %}
{% if config['MAIL_USERNAME'] %}
{# Email setting must be setup #}
{{ modal_cancel_sanger() }}
{% endif %}
{% endblock %}
{% macro sanger_button() %}
{% if variant.sanger_ordered %}
{% if variant.validation in ['True positive', 'False positive']%}
Sanger: {{ variant.validation }}
{% else %}
{% endif %}
{% else %}
{% endif %}
{% endmacro %}
{% macro sanger_form() %}
-
Case {{ case.display_name }}
{{ variant.display_name }}
-
HGNC symbols:
{{ variant.hgnc_symbols|join(', ') }}
-
Gene panels:
{{ variant.panels|join(', ') }}
- Amino acid changes
{% for gene in variant.genes %}
{% for transcript in gene.transcripts %}
{% if transcript.refseq_id %}
- {{ transcript.change_str }}
{% endif %}
{% endfor %}
{% endfor %}
- GT call
{% for individual in variant.samples %}
-
{{ individual.display_name }}: {{ individual.genotype_call }}
{% endfor %}
-
Ordered by:
{{ current_user.name }}
{% endmacro %}
{% macro pin_button() %}
{% if variant._id not in case.suspects %}
{% else %}
{% endif %}
{% endmacro %}
{% macro causative_button() %}
{% if variant._id in case.causatives %}
{% else %}
{% endif %}
{% endmacro %}
{% macro matching_variants() %}
Matching causatives from other cases
{% endmacro %}
{% macro panel_basics() %}
Basics
Position
{{ variant.chromosome }}:{{ variant.position }}
{% if variant.is_par %}
PAR
{% endif %}
|
Change
{{ variant.reference }} → {{ variant.alternative }}
|
{{ acmg_form(variant.acmg_classification.code if variant.acmg_classification) }}
Classify
{% if variant._id in case.suspects and not variant.clinvar_clinsig %}
Submit to ClinVar (BETA)
{% endif %}
{% if variant.clinvar_clinsig%}
Modify clinvar submission
{% endif %}
{% if evaluations %}
{% for evaluation in evaluations %}
{{ acmg_classification_item(evaluation) }}
{% endfor %}
{% endif %}
{% endmacro %}
{% macro panel_summary() %}
Summary
Rank
{{ variant.variant_rank }}
|
Rank score
{{ variant.rank_score }}
|
CADD score
{{ variant.cadd_score or '-' }}
|
Matches OMIM inhert.
{% if variant.is_matching_inheritance %}
Yes
{% else %}
No
{% endif %}
|
Frequency
{{ variant.frequency }}
|
{% if variant.clinsig_human %}
CLINSIG |
Accession |
Revstat |
{% for clinsig in variant.clinsig_human %}
{{ clinsig.human }} |
{{ clinsig.accession }}
|
{{ clinsig.revstat }} |
{% else %}
No annotations
{% endfor %}
{% endif %}
Gene coverage
{% endmacro %}
{% macro transcript_overview() %}
Disease associated transcripts
{{ variant.disease_associated_transcripts|join(', ')
if variant.disease_associated_transcripts else '-' }}
Transcript overview
Gene |
Transcript |
HGVS Description |
{% for gene in variant.genes %}
{% for transcript in gene.primary_transcripts %}
{% for refseq_id in transcript.refseq_identifiers %}
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
{% if transcript.is_canonical %}
C
{% endif %}
|
{{ refseq_id }}({{ transcript.transcript_id }})
|
{{ (transcript.coding_sequence_name or '')|truncate(20, True) }}
{{ (transcript.protein_sequence_name or '')|url_decode }}
|
{% endfor %}
{% endfor %}
{% endfor %}
{% endmacro %}
{% macro frequency_list() %}
Frequency
-
{% if variant.dbsnp_id %}
1000G
{% else %}
1000G
{% endif %}
{% if variant.max_thousand_genomes_frequency %}
{{ variant.max_thousand_genomes_frequency|human_decimal }} (max) |
{% endif %}
{{ variant.thousand_genomes_frequency|human_decimal if variant.thousand_genomes_frequency }}
-
ExAC
{% if variant.max_exac_frequency %}
{{ variant.max_exac_frequency|human_decimal }} (max) |
{% endif %}
{{ variant.exac_frequency|human_decimal if variant.exac_frequency }}
-
gnomAD
{% if 'gnomad_frequency' in variant%}
{% if variant.max_gnomad_frequency %}
{{ variant.max_gnomad_frequency|human_decimal }}
(max) |
{% endif %}
{{ variant.gnomad_frequency|human_decimal if variant.gnomad_frequency }}
{% else %}
Not annotated
{% endif %}
-
Links
{% if variant.cosmic_link %}
COSMIC
{% else %}
COSMIC
{% endif %}
{% if config.LOQUSDB_SETTINGS %}
-
{{ observations.observations|default('N/A') }} obs.
{{ observations.homozygote|default('N/A') }} homo.
{{ observations.total }} tot.
{% if observations['cases'] %}
-
Cases
{% for data in observations['cases'] %}
{% if data.variant %}
{{ data.case.display_name }}
{% else %}
{{ data.case.display_name }}
{% endif %}
{% endfor %}
{% endif %}
Local observations (archive 2017-05-31)
-
{{ variant.local_obs_old or 'N/A' }} obs.
{{ variant.local_obs_hom_old or 'N/A' }} homo.
{{ variant.local_obs_total_old or 638 }} tot.
{% endif %}
{% endmacro %}
{% macro severity_list() %}
Severity
-
Sift
{{ variant.sift_predictions|join(', ') }}
-
Polyphen
{{ variant.polyphen_predictions|join(', ') }}
-
SPIDEX
{{ variant.spidex_human }}
Conservation
-
PHAST
{{ variant.phast_conservation|join(', ') or '-' }}
-
GERP
{{ variant.gerp_conservation|join(', ') or '-' }}
-
phyloP
{{ variant.phylop_conservation|join(', ') or '-' }}
{% endmacro %}
{% macro inheritance_panel() %}
Gene annotations
-
Variant inheritance models
{% for model in variant.genetic_models|sort %}
{{ model }}
{% else %}
No models followed
{% endfor %}
{% if variant.azlength %}
Autozygous region
Length
{{ variant.azlength }}
|
Qual
{{ variant.azqual }}
|
{% endif %}
Gene models
Gene |
Inheritance |
Penetrance |
OMIM |
Manual |
OMIM |
Manual |
{% for gene in variant.genes %}
{{ gene.hgnc_symbol }} |
{% for model in gene.omim_inheritance %}
{{ model }}
{% endfor %}
|
{% for model in gene.manual_inheritance %}
{{ model }}
{% endfor %}
|
{% if gene.omim_penetrance %}
yes
{% else %}
no
{% endif %}
|
{% if gene.manual_penetrance %}
yes
{% else %}
no
{% endif %}
|
{% endfor %}
{% endmacro %}
{% macro omim_phenotypes() %}
{% endmacro %}
{% macro gtcall_panel() %}
GT call
{% if variant.is_par %}
PAR
{% endif %}
Sample |
Genotype (GT) |
Allele depth (AD) |
Genotype quality (GQ) |
Reference |
Alternative |
{% for sample in variant.samples %}
{{ sample.display_name }} |
{{ sample.genotype_call }} |
{% if sample.allele_depths %}
{% for number in sample.allele_depths %}
{{ number }} |
{% endfor %}
{% else %}
N/A |
N/A |
{% endif %}
{{ sample.genotype_quality }} |
{% endfor %}
{% endmacro %}
{% macro compounds_panel() %}
Compounds (top 20)
{{ compounds_table(institute, case, variant.compounds[:20]) }}
{% endmacro %}
{% macro rankscore_panel() %}
Rank score results
{% for result in variant.rank_score_results %}
{{ result.category|replace('_', ' ') }} |
{% endfor %}
{% for result in variant.rank_score_results %}
{{ result.score }}
|
{% endfor %}
{% endmacro %}
{% macro overlapping_panel() %}
Overlapping SVs
Variant |
Gene |
Type |
Combined score |
Rank score |
Length |
Region |
Function |
{% for sv_variant in overlapping_svs %}
{{ sv_variant.display_name|truncate(20, True) }}
|
{{ sv_variant.hgnc_symbols|join(', ')|truncate(40, True) }} |
{{ sv_variant.sub_category|upper }} |
{{ variant.rank_score + sv_variant.rank_score }} |
{{ sv_variant.rank_score }} |
{{ sv_variant.length }} |
{{ sv_variant.region_annotations|join(', ')|truncate(40, True) }} |
{{ sv_variant.functional_annotations|join(', ')|truncate(40, True) }} |
{% else %}
No overlapping SVs found |
{% endfor %}
{% endmacro %}
{% macro genes_panel() %}
{% endmacro %}
{% macro transcripts_panel() %}
Gene |
Transcript |
RefSeq |
Biotype |
Mutation type |
Strand |
Exon |
Intron |
cDNA |
Amino acid |
{% for gene in variant.genes %}
{% for transcript in gene.transcripts %}
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
|
{{ transcript.transcript_id }}
{% if transcript.is_canonical %}
C
{% endif %}
|
{{ transcript.refseq_identifiers|join(',') }}
|
{{ transcript.biotype or '' }} |
{{ transcript.functional_annotations
|join(', ')
|truncate(20, True) }}
|
{{ transcript.strand }} |
{{ transcript.exon or '' }} |
{{ transcript.intron or '' }} |
{{ (transcript.coding_sequence_name or '') }} |
{{ (transcript.protein_sequence_name or '')|url_decode }} |
{% endfor %}
{% endfor %}
{% endmacro %}
{% macro proteins_panel() %}
{% endmacro %}
{% macro modal_sanger() %}
{% endmacro %}
{% macro modal_cancel_sanger() %}
{% endmacro %}
{% macro external_links() %}
{% for gene in variant.genes %}
External links: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
{% endfor %}
{% endmacro %}
{% macro acmg_form(selected=None) %}
{% endmacro %}
{% macro acmg_classification_item(data) %}
{% set current_variant = (data.variant_specific == variant._id) %}
{{ data.classification.label }}
{{ data.classification.short }}
{% if not current_variant %}
{{ data.case.display_name }}
{% endif %}
{% endmacro %}
{% block scripts %}
{{ super() }}
{% endblock %}