Page Title

Platform

Options marked with the icon are parsers

Name

Comment

Label all excluded regions as Overwrite existing labels

Log ratio to copy number thresholds

restore default thresholds

For autosomal and PAR regions

Homozygous deletion (CN = 0) <

Deletion (CN = 1) <

Duplication (CN = 3) ≥

Multiplication (CN > 3) ≥

For non-PAR regions

Homozygous deletion (CN = 0) <

Non-PAR Duplication (CN = 2) ≥

Non-PAR Multiplication (CN > 2) ≥

Platform cm

Label all excluded regions as Overwrite existing labels

Name

Comment

Log ratio to copy number thresholds

restore default thresholds

For autosomal and PAR regions

Homozygous deletion (CN = 0) <

Deletion (CN = 1) <

Duplication (CN = 3) ≥

Multiplication (CN > 3) ≥

For non-PAR regions

Homozygous deletion (CN = 0) <

Non-PAR Duplication (CN = 2) ≥

Non-PAR Multiplication (CN > 2) ≥

Name

Category

Comment

For autosomal and PAR regions

By unique HUGO gene name or Ensembl ID

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By chromosomal locations (for GRCh37/hg19)

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Mask regions extension size (bp)

Conditions of Allelic Frequency

The Allelic Frequency filter allows to select variant positions based on allele frequency, either by specifying a frequency range or by specifying a minimal or maximal deviation from the allele frequency of a variant present in another lab result. All variant positions that match the specified conditions will be put in the MATCH box, all others will go to the NO MATCH box. Variant positions for which no frequency information is available or for which the allele frequency deviation with a variant position in the selected lab results can not be established, will be put in the UNKNOWN output.

Allele frequency filter

Enable the Allele frequency filter

≤ Allele frequency ≥

The Allelic Frequency filter allows to select variant positions based on allele frequency, either by specifying a frequency range or by specifying a minimal or maximal deviation from the allele frequency of a variant present in another lab result.

Comparative analysis

Enable Comparative analysis

Comparative analysis of

Patient lab results

Parent lab results

select all	Patient	Filename	Sample ID
select row	Value	Value	Value

Match of the sets selected above

Allele frequency deviation cutoff %

Id	1
Name	My Hospital example with logo
Language	en
Created on	Jun 29, 2011
Last update on	Dec 12, 2013
Created by	gthijs
Last updated on	Nov 27, 2013 10:45 AM
Last updated by	gthijs

Summary

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Description

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Confirmed Classification

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Include In Report

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Sanger Validated

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Validation Info

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Comments

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Export Variants

Export to

Excel file Tab-separated text file

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Include annotations:

select all	Annotation	Annotation Source
select row	Transcript	System
select row	Classification	System
select row	Confirmed Classification	System
select row	dbSNP	System
select row	OMIM refs	System
select row	OMIM Morbid refs	System
select row	Allele Frequency	DataFile
select row	Allelic Depth	DataFile
select row	Read depth (infoDP)	DataFile
select row	Call quality (quality)	DataFile
select row	Genotype quality (infoGQ)	DataFile
select row	Mapping quality (infoMQ)	DataFile
select row	Filter status (filter)	DataFile
select row	Gene (gene)	VariantFunction
select row	Gene (ensemblGene)	VariantFunction
select row	Transcript (transcript)	VariantFunction
select row	Type (varType)	VariantFunction
select row	Location (varLocation)	VariantFunction
select row	Location (varLocationMito)	VariantFunction

Report Template

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Name

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Click 'Add Files' to select files to upload from your local file system. A maximum of 24 files of 400 MB can be uploaded at once.
Please make sure to select the correct file type. All files in the upload must have the same file type.

Please consult the file format specifications in the User Documentation for detailed information on variant encoding in the various supported file formats.

File Type

Add files...

Filename

Size

Status

Progress / Warnings

Actions

Click 'Next' to continue with associating the samples in the files to patient records. If you do not want to associate the files and samples at this time, click 'Finish'.

Search query

Clear search

Number of results found: 4

Approved Symbol: ACOX2 Approved Name: acyl-CoA oxidase 2, branched chain Location: 3p14.3 Other Symbols: BRCACOX,BRCOX,THCCox
Approved Symbol: ARID4B Approved Name: AT rich interactive domain 4B (RBP1-like) Location: 1q42.1-q43 Other Symbols: BCAA,BRCAA1,SAP180, RBP1L1
Approved Symbol: BRCA1 Approved Name: breast cancer 1, early onset Location: 17q21.31 Other Symbols: RNF53,BRCC1,PPP1R53
Approved Symbol: BRCA2 Approved Name: breast cancer 2, early onset Location: 13q12-q13 Other Symbols: FAD,FAD1,BRCC2, FANCD1,FACD,FANCD

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Name

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Users

Available users

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Granted users

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Name

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Domain cm

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Description

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Manual entry of loci (genes/regions)

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From file

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Gene

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5 results are available, use up and down arrow keys to navigate.

Transcript

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Enter or paste the list of region to be added to the target panel.

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Regions originating from a BED file

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Proposed change

Submitted by	sraspoet

Submitted on	Jan 17, 2013 2:55 PM

Analysis	A_Inflammasome

Comments

Update 5bis

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New variant

Position	5:40,852,451
Gene	CARD6
Transcript	NM_032587.3
c.	c.1017C>G

Ref	C
Alt	G
Type	snp
Location	exonic

Exon	3
Effect	synonymous
p.	p.T339T

Classification

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Variant info

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Use the status and version selections on the available annotation sources and the status selections on the individual annotations per source to select a source for each variant annotation. Once saved, the configuration is immediately active for all newly created Analyses.

Name

Status

Version

Description

Info

1000Genomes

1000 Genomes Phase1 release v3.20101123

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Annotations

Category	Name	Display Name
Population	1000Gp1_FreqAll	1000 genomes phase 1 allele frequency all
Population	1000Gp1_FreqAFR	1000 genomes phase 1 allele frequency African
Population	1000Gp1_FreqEUR	1000 genomes phase 1 allele frequency European
Population	1000Gp1_FreqAMR	1000 genomes phase 1 allele frequency American
Population	1000Gp1_FreqASN	1000 genomes phase 1 allele frequency Asian

DataFile

Annotations derived from the input datafile records.

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dbNSFP

dbNSFP v2.0: Database of functional predictions for non-synonymous SNPs

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dbSNP

dbSNP build 137

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ESP6500

Variants in the ESP6500SI-V2 dataset of the exome sequencing project (ESP), annotated with SeattleSeqAnnotation137.

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HGMDProfessional

HGMD® Professional Database 2013.2

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HGMDPublic

HGMD® Public Database 2013.2

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Following variant annotations have no source identified. These annotations will not be populated in new Analyses and therefore not be available for visualization or triage & classification. This does not prevent the configuration from being saved.

Annotation	Available in
hgmdConfidence	HGMDProfessional
hgmdMatch	HGMDProfessional
hgmdVariantType	HGMDProfessional