hands-on workshop clinical genomics - interpretation and ... · sample to insight hands-on workshop...
TRANSCRIPT
![Page 1: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/1.jpg)
Sample to Insight
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
![Page 2: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/2.jpg)
Sample to Insight
Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 2
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
![Page 3: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/3.jpg)
Sample to Insight
Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 3
Introduction to the portfolio
![Page 4: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/4.jpg)
Sample to Insight
Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 4
Introduction to the portfolio
![Page 5: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/5.jpg)
Sample to Insight
Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 5
Introduction to the portfolio
![Page 6: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/6.jpg)
Sample to Insight
Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 6
Getting started with IVA
Log-on
https://www.qiagenbioinformatics.com/product-login/
See your sheet for number!
Login name:
Password: variant123
![Page 7: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/7.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 7
Logging on
![Page 8: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/8.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 8
Logging on
![Page 9: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/9.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 9
Welcome screen
![Page 10: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/10.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 10
Welcome screen, may see other info such as T&Cs or a sample is waiting to be imported…
![Page 11: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/11.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 11
Find the demo sample, the default view is analysis – we need to find the sample
![Page 12: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/12.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 12
Change to samples and search for “WEX”
Highlight sample and click “Analyze”
![Page 13: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/13.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 13
A series of options follows, guiding you through the analysis
![Page 14: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/14.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 14
A series of options follows, guiding you through the analysis
![Page 15: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/15.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 15
A series of options follows, guiding you through the analysis
![Page 16: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/16.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 16
A series of options follows, guiding you through the analysis
![Page 17: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/17.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 17
A series of options follows, guiding you through the analysis
![Page 18: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/18.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 18
A series of options follows, guiding you through the analysis
![Page 19: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/19.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 19
Can wait for the email or press “Refresh”
![Page 20: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/20.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 20
When active can open analysis and review the filtering steps
![Page 21: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/21.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 21
When active can open analysis and review the filtering steps
![Page 22: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/22.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 22
A filtering cascade has been applied… let’s look at the filters in order
![Page 23: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/23.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 23
A filtering cascade has been applied… let’s look at the filters in order
![Page 24: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/24.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 24
A filtering cascade has been applied… let’s look at the filters in order
![Page 25: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/25.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 25
A filtering cascade has been applied… let’s look at the filters in order
![Page 26: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/26.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 26
A filtering cascade has been applied… let’s look at the filters in order
![Page 27: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/27.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 27
A filtering cascade has been applied… let’s look at the filters in order
![Page 28: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/28.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 28
A filtering cascade has been applied… let’s look at the filters in order
![Page 29: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/29.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 29
As well as filtering IVA provides a wealth of information…
![Page 30: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/30.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 30
As well as filtering IVA provides a wealth of information…
![Page 31: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/31.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 31
As well as filtering IVA provides a wealth of information…
![Page 32: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/32.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 32
As well as filtering IVA provides a wealth of information…
![Page 33: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/33.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 33
As well as filtering IVA provides a wealth of information…
![Page 34: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/34.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 34
What can you do with your filtered list?
![Page 35: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/35.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 35
To export to QCI I you need a QCI I account
![Page 36: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/36.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 36
To export to QCI I you need a QCI I account
![Page 37: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/37.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 37
Choose your workflow
![Page 38: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/38.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 38
Add in patient meta data
![Page 39: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/39.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 39
Add in patient meta data
![Page 40: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/40.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 40
The software will “learn” from your classifications…
![Page 41: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/41.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 41
Further meta data…
![Page 42: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/42.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 42
Further meta data…
![Page 43: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/43.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 43
Option for customized report…
![Page 44: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/44.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 44
Go to results…
![Page 45: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/45.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 45
The list of variants…
![Page 46: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/46.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 46
Two views… a lot of information is already given about the variant
![Page 47: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/47.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 47
ACMG Guidelines are used for classification
![Page 48: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/48.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 48
Variant details provide supporting evidence for classification
![Page 49: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/49.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 49
Variant details provide supporting evidence for classification
![Page 50: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/50.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 50
Variant details provide supporting evidence for classification
![Page 51: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/51.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 51
Key step is creating a report
![Page 52: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/52.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 52
Key step is creating a report
![Page 53: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/53.jpg)
Sample to Insight
QCI I Demo
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 53
Key step is creating a report
![Page 54: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/54.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 54
Trio Analysis, highlight and click “Open”
![Page 55: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/55.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 55
Here we have a different set up and filters, click on the top of the filter cascade…
![Page 56: Hands-on Workshop Clinical Genomics - Interpretation and ... · Sample to Insight Hands-on Workshop Clinical Genomics - Interpretation and Reporting with QIAGEN Bioinformatics Ruth](https://reader036.vdocuments.site/reader036/viewer/2022070800/5f02526b7e708231d403b23f/html5/thumbnails/56.jpg)
Sample to Insight
IVA Workshop
QIAGEN Sample to Insight | www.qiagenbioinformatics.com | www.qiagen.com 56
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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Disease-gene pair ranked by the score generated using phenotype-disease relationship
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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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Sharing samples, ideal if you want to create your own account
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Any questions?
Come and visit us at our stand
www.qiagenbioinformatics.com