{% extends "report_base.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% set affected = [] %} {% set printed_vars = [] %} {% block body %} {% block content_main %}

Scout case analysis report

- created on: {{report_created_at}}

{{ phenotype_panel() }}
{{ gene_panels_panel() }}
{{ causatives_panel() }}
{{ pinned_panel() }}
{{ classified_panel() }}
{{ tagged_panel() }}
{{ commented_panel() }}
{{ dismissed_panel() }} [END OF VARIANT REPORT]

{% if coverage_report %} {{ coverage_report|safe }}
{% endif %} http://www.clinicalgenomics.se/scout/
{% endblock %} {% endblock %} {% macro phenotype_panel() %}
Case {{ case.display_name }} - Phenotype Overview
{% if comments.count() %} {% else %} {% endif %}
{% if case.madeline_info and case.individuals|length > 1 %} {% if format == 'html' %} {{ case.madeline_info|safe }} {% else %} {% endif %} {% else %}

Single sample family. No pedigree available.

{% endif %}
Case created: {{case.created_at.strftime('%Y-%m-%d')}} Last updated: {{case.updated_at.strftime('%Y-%m-%d')}}

{% for ind in case.individuals %} {% endfor %}
Sample Sex Affected Sequencing Ancestry (pred.) Parenthood
{{ ind.display_name }} {{ ind.sex_human }} {% if ind.confirmed_sex %} {% endif %} {% if ind.phenotype==2 %} {% do affected.append(ind.display_name) %} YES {% else %} NO {% endif %} {{ ind.analysis_type|upper }} {{ ind.predicted_ancestry or 'N/A' }} {% if ind.confirmed_parent == True %} {% elif ind.confirmed_parent == False %} {% else %} N/A {% endif %}
Case status: {% if 'solved' in case.status%} {{case.status.upper()}} {% else %} {{case.status.upper()}} {% endif %}

{% if case.synopsis %} Synopsis: {{ case.synopsis|markdown }} {% endif %} Associated phenotypes:
{% if case.phenotype_terms %} {% else %} No phenotype terms associated. {% endif %}
Case-related comments
{% for comment in comments %} {% endfor %}
{{comment.created_at.strftime('%Y-%m-%d')}} {{comment.user_name}}: {{ comment.content }}
No comments left for this case.
{% endmacro%} {% macro gene_panels_panel() %}
Default gene panels
{% for panel in case.panels %} {% if panel.is_default %} {% endif %} {% else %} {% endfor %}
Panel Version Genes
{{ panel.display_name|truncate(75, True) }} {{ panel.version }} ({{ panel.updated_at.date() }}) {{ panel.nr_genes }}
No panels linked to case
{% endmacro%} {% macro causatives_panel() %}
Causative Variants
{% if causatives_detailed %} {% for causative in causatives_detailed|sort(attribute='variant_rank') %} {% do printed_vars.append(causative['_id']) %} {% if causative.category == 'snv' %} {{ sn_variant_content(causative, loop.index) }} {% else %} {{ sv_variant_content(causative, loop.index) }} {% endif %}
{% endfor %} {% else %} No causative variants available for this case {% endif %}
{% endmacro%} {% macro pinned_panel() %}
Pinned Variants
{% set duplicated_variants = [] %} {% if suspects_detailed %} {% for pinned in suspects_detailed|sort(attribute='variant_rank') %} {% if pinned['_id'] not in printed_vars %} {% do printed_vars.append(pinned['_id']) %} {% if pinned.category == 'snv' %} {{ sn_variant_content(pinned, loop.index) }} {% else %} {{ sv_variant_content(pinned, loop.index) }} {% endif %} {% else %} {% do duplicated_variants.append(pinned['_id']) %} {% endif %}
{% endfor %} {% else %} No pinned variants available for this case {% endif %} {% if suspects_detailed and duplicated_variants|length == suspects_detailed|length %} All pinned variants are described among the causative variants {% endif %}
{% endmacro %} {% macro classified_panel() %}
Other ACMG-classified Variants
{% set duplicated_variants = [] %} {% if classified_detailed %} {% for variant in classified_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {% if variant.category == 'snv' %} {{ sn_variant_content(variant, loop.index) }} {% else %} {{ sv_variant_content(variant, loop.index) }} {% endif %} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% else %} No ACMG-classified variants available for this case {% endif %} {% if classified_detailed and duplicated_variants|length == classified_detailed|length %} All ACMG-classified variants are already described in the previous views {% endif %}
{% endmacro %} {% macro tagged_panel() %}
Other Manual Ranked (Tagged) Variants
{% set duplicated_variants = [] %} {% if tagged_detailed %} {% for variant in tagged_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {% if variant.category == 'snv' %} {{ sn_variant_content(variant, loop.index) }} {% else %} {{ sv_variant_content(variant, loop.index) }} {% endif %} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% else %} No tagged variants for this case {% endif %} {% if tagged_detailed and duplicated_variants|length == tagged_detailed|length %} All tagged variants are already described in the previous views {% endif %}
{% endmacro %} {% macro commented_panel() %}
Other Commented Variants
{% set duplicated_variants = [] %} {% if commented_detailed %} {% for variant in commented_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {% if variant.category == 'snv' %} {{ sn_variant_content(variant, loop.index) }} {% else %} {{ sv_variant_content(variant, loop.index) }} {% endif %} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% else %} No commented variants for this case {% endif %} {% if commented_detailed and duplicated_variants|length == commented_detailed|length %} All commented variants are already described in the previous views {% endif %}
{% endmacro %} {% macro dismissed_panel() %}
Dismissed Variants
{% if dismissed_detailed %} {% for variant in dismissed_detailed|sort(attribute='variant_rank') %} {% if variant.category == 'snv' %} {% else %} {% endif %} {% endfor %}
Variant name Genes Dismissed description
#{{loop.index}}{{variant.display_name}}chr{{variant.chromosome}}:{{variant.position}}_{{variant.sub_category|upper}} {% for gene in variant.genes %} {{ gene.hgnc_symbol }} {{gene.region_annotation}}
{% endfor %} 		{% for reason in variant.dismiss_variant if not reason == "Select a tag" %}
  • {{dismissed_options[reason|int]['description']}} {% if reason == '2' and variant.category == 'snv'%}
    Frequency {% if variant.frequency == 'common' %} {{variant.frequency}} {% elif variant.frequency == 'uncommon' %} {{variant.frequency}} {% else %} {{variant.frequency}} {% endif %}
    {% 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 }} {% if not variant.max_thousand_genomes_frequency and not variant.thousand_genomes_frequency %} Not annotated {% endif %}
    ExAC {% if variant.max_exac_frequency %} {{ variant.max_exac_frequency|human_decimal }} (max) | {% endif %} {{ variant.exac_frequency|human_decimal if variant.exac_frequency }} {% if not variant.max_exac_frequency and not variant.exac_frequency %} Not annotated {% endif %}
    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 %}


    {% elif reason == '7' %} ( {% for model in variant.genetic_models|sort %} {{model}} {% else %} No models followed {% endfor %})

    {% elif reason== '23' %}
    {% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% endfor %}
    Sample Genotype (GT) Allele depth (AD) Genotype quality
    Ref. Alt.
    {{ sample.display_name }} {{ sample.genotype_call }}{{ number }}N/A N/A{{ sample.genotype_quality }}


    {% endif %}
{% endfor %}
{% else %} No dismissed variants for this case {% endif %}
{% endmacro %} {% macro sn_variant_content(variant, index) %}
# {{variant.display_name}}  SNV  {% if variant.sanger_ordered and variant.validation %} Verification:{{variant.validation}} {% elif variant.sanger_ordered %} Verification ordered {% endif %}
{% if variant.cytoband_start and variant.cytoband_end %} {% else %} {% endif %}
Coordinates Cytoband nucl. change dbsnp id Gene panels
chr{{variant.chromosome}}:{{variant.position}}-{{variant.end}}{{variant.cytoband_start}}-{{variant.cytoband_end}}-{{variant.reference}} → {{variant.alternative}} {% if variant.dbsnp_id %} {{variant.dbsnp_id}} {% else %} - {% endif %} {% for panel_id in variant.panels %} {{ panel_id }} {% endfor %}
{% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% endfor %}
Sample Genotype (GT) Allele depth (AD) Genotype quality (GQ)
Reference Alternative
{{ sample.display_name }} {{ sample.genotype_call }}{{ number }}N/A N/A{{ sample.genotype_quality }}
Frequency {% if variant.frequency == 'common' %} {{variant.frequency}} {% elif variant.frequency == 'uncommon' %} {{variant.frequency}} {% else %} {{variant.frequency}} {% endif %}
{% 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 }} {% if not variant.max_thousand_genomes_frequency and not variant.thousand_genomes_frequency %} Not annotated {% endif %}
ExAC {% if variant.max_exac_frequency %} {{ variant.max_exac_frequency|human_decimal }} (max) | {% endif %} {{ variant.exac_frequency|human_decimal if variant.exac_frequency }} {% if not variant.max_exac_frequency and not variant.exac_frequency %} Not annotated {% endif %}
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 %}
Scout Rank Scout score Manual rank CADD score Inheritance models ACMG classification
{{variant.variant_rank}} {{variant.rank_score}} {% if variant.manual_rank %} {{ manual_rank_options[variant.manual_rank]['label'] }} {% else %} - {% endif %} {{ variant.cadd_score or '-' }} {% for model in variant.genetic_models|sort %} {{ model }} {% else %} No models followed {% endfor %} {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %}
{% for gene in variant.genes %} {% endfor %}
Affected gene(s) Description Region annotation Transcript - HGVS - Protein OMIM phenotypes [inheritance]
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{gene.description|title}} {{gene.region_annotation}} {% set n_primary_transcripts = [] %}
    {% for transcript in gene.primary_transcripts %} {% do n_primary_transcripts.append(gene.primary_transcripts|length) %} {% if loop.index <= 5 or transcript.is_canonical or transcript.is_disease_associated %}
  • {{transcript.refseq_id}} - {{ (transcript.coding_sequence_name or '')|truncate(20, True) }} - {{ (transcript.protein_sequence_name or '')|url_decode }} {% if transcript.is_canonical %} C {% endif %} {% if transcript.is_disease_associated %} D {% endif %}
    • {% endif %} {% endfor %}
{% if n_primary_transcripts|sum > 5 %} .. other transcripts available for this variant are not shown.

{% endif %}
    {% for disease_term in gene.disease_terms %}
  • {{ disease_term.description }} {{ disease_term.inheritance }}
    • {% endfor %}
{% if variant.comments.count() %}
Variant-related comments
{% for comment in variant.comments %} {% endfor %}
{{comment.created_at.strftime('%Y-%m-%d')}} {{comment.user_name}}: {{ comment.content }}
{% endif %}
{% endmacro %} {% macro sv_variant_content(variant,index) %}
# chr{{variant.chromosome}}:{{variant.position}}_{{variant.sub_category|upper}}  SV
{% if variant.cytoband_start and variant.cytoband_end %} {% else %} {% endif %}
Variant type length Coordinates Cytoband Gene panels Callers
{{variant.sub_category|upper}} {{ variant.length }} {% if variant.chromosome == variant.end_chrom %} chr{{variant.chromosome}}:{{variant.position}}-{{variant.end}} {% else %} chr{{variant.chromosome}}:{{variant.position}}/{{'chr'+variant.end_chrom}}:{{variant.end}} {% endif %} {{variant.cytoband_start}}-{{variant.cytoband_end}}- {% for panel_id in variant.panels %} {{ panel_id }}
{% endfor %} 		{% if variant.callers %} {% for caller,call in variant.callers|sort %} {{ caller+':'+call }} {% endfor %} {% else %} - {% endif %}
{% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% endfor %}
Sample Genotype (GT) Allele depth (AD) Genotype quality (GQ)
Reference Alternative
{{ sample.display_name }} {{ sample.genotype_call }}{{ number }}N/A N/A{{ sample.genotype_quality }}
{% for freq_name, value in variant.frequencies %} {% endfor %}
Frequencies
{{ freq_name }} {% if value %} {{ value|human_decimal }} {% else %} Not annotated {% endif %}
Scout Rank Scout score Manual rank Inheritance models ACMG classification
{{variant.variant_rank}} {{variant.rank_score}} {% if variant.manual_rank %} {{ manual_rank_options[variant.manual_rank]['label'] }} {% else %} - {% endif %} {% for model in variant.genetic_models|sort %} {{ model }} {% else %} No models followed {% endfor %} {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %}
{% for gene in variant.genes %} {% endfor %}
Affected gene(s) Description Region annotation Transcript - HGVS - Protein OMIM phenotypes [inheritance]
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{gene.description|title}} {{gene.region_annotation}} {% set n_primary_transcripts = [] %}
    {% for transcript in gene.primary_transcripts %} {% do n_primary_transcripts.append(gene.primary_transcripts|length) %} {% if loop.index <= 5 or transcript.is_canonical %}
  • {{transcript.refseq_id}} - {{ (transcript.coding_sequence_name or '')|truncate(20, True) }} - {{ (transcript.protein_sequence_name or '')|url_decode }} {% if transcript.is_canonical %} C {% endif %}
    • {% endif %} {% endfor %}
{% if n_primary_transcripts|sum > 5 %} .. other transcripts available for this variant are not shown.

{% endif %}
    {% for disease_term in gene.disease_terms %}
  • {{ disease_term.description }} {{ disease_term.inheritance }}
    • {% endfor %}
{% if variant.comments.count() %}
{% for comment in variant.comments %} {% endfor %}
Variant-related comments
{{comment.created_at.strftime('%Y-%m-%d')}} {{comment.user_name}}: {{ comment.content }}
{% endif %}
{% endmacro %} {% block scripts %} {{ super() }} {% endblock %}