Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop...

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Hands-on Workshop

Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics

Ruth Burton PhD. – Clinical Applications Specialist ([email protected])

QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 1

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Agenda

• Introduction to the portfolio

• Getting started with IVA

• Filtering a whole exome sample

• Somatic analysis in QCI I

• Working with a trio

• Hereditary analysis in QCI I

• Uploading and sharing samples

• Working with your own data

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Introduction to the portfolio

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Getting started with IVA

Log-on

https://www.qiagenbioinformatics.com/product-login/

See your sheet for number!

Login name:

[email protected]

Password: variant123

https://www.qiagenbioinformatics.com/product-login/

mailto:[email protected]

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IVA Workshop


Logging on

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IVA Workshop


Welcome screen

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IVA Workshop


Welcome screen, may see other info such as T&Cs or a sample is waiting to be imported…

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IVA Workshop


Find the demo sample, the default view is analysis – we need to find the sample

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IVA Workshop


Change to samples and search for “WEX”

Highlight sample and click “Analyze”

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IVA Workshop


A series of options follows, guiding you through the analysis

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IVA Workshop



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Can wait for the email or press “Refresh”

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IVA Workshop


When active can open analysis and review the filtering steps

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IVA Workshop


A filtering cascade has been applied… let’s look at the filters in order

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IVA Workshop



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As well as filtering IVA provides a wealth of information…

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What can you do with your filtered list?

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To export to QCI I you need a QCI I account

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QCI I Demo


To export to QCI I you need a QCI I account

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QCI I Demo


Choose your workflow

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QCI I Demo


Add in patient meta data

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QCI I Demo


The software will “learn” from your classifications…

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QCI I Demo


Further meta data…

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QCI I Demo


Option for customized report…

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QCI I Demo


Go to results…

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QCI I Demo


The list of variants…

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QCI I Demo


Two views… a lot of information is already given about the variant

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QCI I Demo


ACMG Guidelines are used for classification

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QCI I Demo


Variant details provide supporting evidence for classification

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QCI I Demo



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QCI I Demo


Key step is creating a report

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QCI I Demo



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IVA Workshop


Trio Analysis, highlight and click “Open”

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IVA Workshop


Here we have a different set up and filters, click on the top of the filter cascade…

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While the same principles are used as with the single sample here we can use the parental samples to detect de novo variants in the child…

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After the genetic analysis filter only variants unique to the proband remain

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Refine this further using phenotype information…

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Phenotype-driven Ranking Algorithm

• Enter a phenotype (free text or HPO)

• KB returns matches – 44,000 variants current associated with phenotypes

• Evidence from KB connects variants with phenotypes/ disease

• The relevance of the connection “graded” by a score

• Consideration given to overall occurrence of the phenotype in the KB

• Allows the score to be adjusted for specificity and confidence improving accuracy

Mapping of phenotypes to variants

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Scoring algorithm

Nd = number of diseases connected to the phenotype (the more diseases the lower the specificity)

N = number of links between phenotype and variant (the greater the number of links the lower the confidence)

High scores achieved for variants with few diseases connecting directly to a phenotype

Specificity

Confidence

Score

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IVA

Disease-gene pair ranked by the score generated using phenotype-disease relationship

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IVA

Each connection displayed as a network showing Gene-Disease-Phenotype relationship

Variant containing gene

Disease / syndrome

Phenotypes

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The result is a list of variants prioritized by the relationship with the patients phenotype

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Can view the key genes and variants…

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Loading your own data…

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There are two options for large files the datastream is better…

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Just drag and drop your files…

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Sharing samples, ideal if you want to create your own account

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Any questions?

Come and visit us at our stand

[email protected]

www.qiagenbioinformatics.com

mailto:[email protected]

Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop...

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