How global data sharing helped uncover the cause of a rare genetic disorder

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Dina Zielinski

Dina Zielinski. DNA Land User Group Meeting. New York Genome Center. September 2016

Science

Yaniv Erlich14 September 2016 @dinazielinski
How global data sharing helped uncover
the cause of a rare genetic disorder
D ina Zielinski
As s oc iate Sc ientis t
Er lic h lab
A girl in Israel,
a cousin in Philly,
and a lab in Georgia

Yaniv Erlich14 September 2016 @dinazielinski
A girl in Israel
‫אריאלה‬Ariela

Yaniv Erlich14 September 2016 @dinazielinski
Goldenhar Syndrome
Hemifacial Microsomia: craniofacial disorder

Yaniv Erlich14 September 2016 @dinazielinski
High Throughput Sequencing

Yaniv Erlich14 September 2016 @dinazielinski
Sequencing data: 10s of millions of lines

Yaniv Erlich14 September 2016 @dinazielinski
Finding a causal mutation: a numbers game
Whole genome = 3.1billion base pairs
Exome = 30 million base pairs
Public databases
~20,000-30,000 variants
Causal mutation

Yaniv Erlich14 September 2016 @dinazielinski
Public data: filtering bystanders

Yaniv Erlich14 September 2016 @dinazielinski
Public databases
~20,000-30,000 variants
Familial variants

Yaniv Erlich14 September 2016 @dinazielinski
-1 in 5,600-20,000 births
-Highly heterogeneous
-Complex pathogenesis
Goldenhar Syndrome

Yaniv Erlich14 September 2016 @dinazielinski
Focus only on familial regions
chromosome
shared segments

Yaniv Erlich14 September 2016 @dinazielinski
Finding a causal mutation
Exome = 30 million base pairs
Public databases
~20,000-30,000 variants
Familial variants

Yaniv Erlich14 September 2016 @dinazielinski
“Happy families are all alike;
each unhappy family is
unhappy in its own way.”

Yaniv Erlich14 September 2016 @dinazielinski
Goldenhar Syndrome
8 shared mutations

Yaniv Erlich14 September 2016 @dinazielinski
Proband Grandmother Cousin
Exonic
mutations
23,175 22,252 22,746
Rare
mutations
660 591 646
Harmful 358 308 331
Shared 8 variations
A cousin in Philly
0 shared mutations

Yaniv Erlich14 September 2016 @dinazielinski
CNV: Copy Number Variant
duplication
deletion

Yaniv Erlich14 September 2016 @dinazielinski
Eureka! (in hindsight)
Ariela
1st cousin
grandmother
grandmother’s
cousin

Yaniv Erlich14 September 2016 @dinazielinski
128 Healthy Controls
10 labs in Israel and NY

Yaniv Erlich14 September 2016 @dinazielinski
A lab in Georgia

Yaniv Erlich14 September 2016 @dinazielinski
But what gene?

Yaniv Erlich14 September 2016 @dinazielinski
A mouse with HFM
Cousley et al. 2002
overlapping traits for the same
gene in mouse and human

Yaniv Erlich14 September 2016 @dinazielinski

Yaniv Erlich14 September 2016 @dinazielinski
Rank of gene expression in mouse

Yaniv Erlich14 September 2016 @dinazielinski
2010

Yaniv Erlich14 September 2016 @dinazielinski
Published 5/9/2014

Yaniv Erlich14 September 2016 @dinazielinski
29,000 genomes and counting!
genealogy
crowd sourcing
data sharing

Yaniv Erlich14 September 2016 @dinazielinski
If it takes a village to raise a child…
…it takes the world to help a child with
a genetic disorder

Yaniv Erlich14 September 2016 @dinazielinski
Acknowledgements
DNA Land
Yaniv Erlich
Joe Pickrell
Assaf Gordon
Jie Yuan
Tristan Hayeck
Richard Munoz
Mary Wahl
Kevin Shi
Nathan Pearson
Robert Aboukhalil Funding
Burroughs Wellcome Career Award
Broad Institute SPARC Award
Andria and Paul Heafy
Whitehead Institute
Goldenhar Syndrome
Barak Marcus
Mona Sheikh
Balaji Srinivasan
Clement Chu
Melissa Gymrek
Dror Aizenbud

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How global data sharing helped uncover the cause of a rare genetic disorder

1. Yaniv Erlich14 September 2016 @dinazielinski How global data sharing helped uncover the cause of a rare genetic disorder D ina Zielinski As s oc iate Sc ientis t Er lic h lab A girl in Israel, a cousin in Philly, and a lab in Georgia

2. Yaniv Erlich14 September 2016 @dinazielinski A girl in Israel ‫אריאלה‬Ariela

3. Yaniv Erlich14 September 2016 @dinazielinski Goldenhar Syndrome Hemifacial Microsomia: craniofacial disorder

4. Yaniv Erlich14 September 2016 @dinazielinski High Throughput Sequencing

5. Yaniv Erlich14 September 2016 @dinazielinski Sequencing data: 10s of millions of lines

6. Yaniv Erlich14 September 2016 @dinazielinski Finding a causal mutation: a numbers game Whole genome = 3.1billion base pairs Exome = 30 million base pairs Public databases ~20,000-30,000 variants Causal mutation

7. Yaniv Erlich14 September 2016 @dinazielinski Public data: filtering bystanders

8. Yaniv Erlich14 September 2016 @dinazielinski Public databases ~20,000-30,000 variants Familial variants

9. Yaniv Erlich14 September 2016 @dinazielinski -1 in 5,600-20,000 births -Highly heterogeneous -Complex pathogenesis Goldenhar Syndrome

10. Yaniv Erlich14 September 2016 @dinazielinski Focus only on familial regions chromosome shared segments

11. Yaniv Erlich14 September 2016 @dinazielinski Finding a causal mutation Exome = 30 million base pairs Public databases ~20,000-30,000 variants Familial variants

12. Yaniv Erlich14 September 2016 @dinazielinski “Happy families are all alike; each unhappy family is unhappy in its own way.”

13. Yaniv Erlich14 September 2016 @dinazielinski Goldenhar Syndrome 8 shared mutations

14. Yaniv Erlich14 September 2016 @dinazielinski Proband Grandmother Cousin Exonic mutations 23,175 22,252 22,746 Rare mutations 660 591 646 Harmful 358 308 331 Shared 8 variations A cousin in Philly 0 shared mutations

15. Yaniv Erlich14 September 2016 @dinazielinski CNV: Copy Number Variant duplication deletion

16. Yaniv Erlich14 September 2016 @dinazielinski Eureka! (in hindsight) Ariela 1st cousin grandmother grandmother’s cousin

17. Yaniv Erlich14 September 2016 @dinazielinski 128 Healthy Controls 10 labs in Israel and NY

18. Yaniv Erlich14 September 2016 @dinazielinski A lab in Georgia

19. Yaniv Erlich14 September 2016 @dinazielinski But what gene?

20. Yaniv Erlich14 September 2016 @dinazielinski A mouse with HFM Cousley et al. 2002 overlapping traits for the same gene in mouse and human

21. Yaniv Erlich14 September 2016 @dinazielinski

22. Yaniv Erlich14 September 2016 @dinazielinski Rank of gene expression in mouse

23. Yaniv Erlich14 September 2016 @dinazielinski 2010

24. Yaniv Erlich14 September 2016 @dinazielinski Published 5/9/2014

25. Yaniv Erlich14 September 2016 @dinazielinski 29,000 genomes and counting! genealogy crowd sourcing data sharing

26. Yaniv Erlich14 September 2016 @dinazielinski If it takes a village to raise a child… …it takes the world to help a child with a genetic disorder

27. Yaniv Erlich14 September 2016 @dinazielinski Acknowledgements DNA Land Yaniv Erlich Joe Pickrell Assaf Gordon Jie Yuan Tristan Hayeck Richard Munoz Mary Wahl Kevin Shi Nathan Pearson Robert Aboukhalil Funding Burroughs Wellcome Career Award Broad Institute SPARC Award Andria and Paul Heafy Whitehead Institute Goldenhar Syndrome Barak Marcus Mona Sheikh Balaji Srinivasan Clement Chu Melissa Gymrek Dror Aizenbud

Editor's Notes

Our story starts in Israel with a girl named Ariela
`
The mutation was not found in 128 AJ controls from TAGC

How global data sharing helped uncover the cause of a rare genetic disorder

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