Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis
Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis
Purpose
Genome sequencing (GS) for diagnosis of rare genetic disease is being introduced into the clinic, but the complexity of the data poses challenges for developing pipelines with high diagnostic sensitivity. We evaluated the performance of the Genomics England 100,000 Genomes Project (100kGP) panel-based pipelines, using craniosynostosis as a test disease.
Methods
GS data from 114 probands with craniosynostosis and their relatives (314 samples), negative on routine genetic testing, were scrutinized by a specialized research team, and diagnoses compared with those made by 100kGP.
Results
Sixteen likely pathogenic/pathogenic variants were identified by 100kGP. Eighteen additional likely pathogenic/pathogenic variants were identified by the research team, indicating that for craniosynostosis, 100kGP panels had a diagnostic sensitivity of only 47%. Measures that could have augmented diagnoses were improved calling of existing panel genes (+18% sensitivity), review of updated panels (+12%), comprehensive analysis of de novo small variants (+29%), and copy-number/structural variants (+9%). Recent NHS England recommendations that partially incorporate these measures should achieve 85% overall sensitivity (+38%).
Conclusion
GS identified likely pathogenic/pathogenic variants in 29.8% of previously undiagnosed patients with craniosynostosis. This demonstrates the value of research analysis and the importance of continually improving algorithms to maximize the potential of clinical GS.
2360-2368
Hyder, Zerin
b9e87dfa-5829-4d65-aa75-306e8fe731ea
Calpena, Eduardo
bad80457-ecc0-481a-8f9b-3cebc677d722
Pei, Yang
933fc229-1c3f-4225-8646-d47ce0c684f3
Tooze, Rebecca S
17084b0c-11e9-43ae-822b-c263e9348da4
Brittain, Helen
19411fbb-588d-49c3-93e8-f2926c8541e3
Twigg, Stephen R F
894d2681-a4c2-4571-825b-72577969617b
Cilliers, Deirdre
58d7fbc7-9f32-4ac5-bd04-d56b36e6afcd
Morton, Jenny E V
4404222b-195a-4d27-baec-3248e153e054
McCann, Emma
e86886b8-4f81-453f-a381-41003d14d699
Weber, Astrid
68f254cc-0a8b-483a-83ce-0f7cbd4a85d5
Wilson, Louise C
9ddd87d2-0e18-4ca8-b8a9-28ae1dfcc0ab
Douglas, Andrew G L
2c789ec4-a222-43bc-a040-522ca64fea42
McGowan, Ruth
a7f8dc75-9777-4366-b9c8-823e362170be
Need, Anna
149e1309-2447-45f9-b5a3-177584009b08
Bond, Andrew
94b1c5ea-ac6f-4062-9673-13064c82aeee
Tavares, Ana Lisa Taylor
730fb640-a84a-451f-815e-a3d7155e4938
Thomas, Ellen R A
659e19e1-db65-4097-ad3f-518138316823
Hill, Susan L
205c58b1-452d-466f-8f7f-c0459490a0ea
Deans, Zandra C
c0246abe-844c-4a2f-b668-2f31f73c2c52
Boardman-Pretty, Freya
b928cc82-f967-4ba2-a6f3-105090e3099c
Caulfield, Mark
2267d97b-b1ca-4902-ab87-d989374eb7f5
Scott, Richard H
19488755-f941-45d3-985b-dc0ab1e647d2
Wilkie, Andrew O M
7064a09e-66d9-4acf-92eb-cffad1ce3762
Genomics England Research Consortium
1 December 2021
Hyder, Zerin
b9e87dfa-5829-4d65-aa75-306e8fe731ea
Calpena, Eduardo
bad80457-ecc0-481a-8f9b-3cebc677d722
Pei, Yang
933fc229-1c3f-4225-8646-d47ce0c684f3
Tooze, Rebecca S
17084b0c-11e9-43ae-822b-c263e9348da4
Brittain, Helen
19411fbb-588d-49c3-93e8-f2926c8541e3
Twigg, Stephen R F
894d2681-a4c2-4571-825b-72577969617b
Cilliers, Deirdre
58d7fbc7-9f32-4ac5-bd04-d56b36e6afcd
Morton, Jenny E V
4404222b-195a-4d27-baec-3248e153e054
McCann, Emma
e86886b8-4f81-453f-a381-41003d14d699
Weber, Astrid
68f254cc-0a8b-483a-83ce-0f7cbd4a85d5
Wilson, Louise C
9ddd87d2-0e18-4ca8-b8a9-28ae1dfcc0ab
Douglas, Andrew G L
2c789ec4-a222-43bc-a040-522ca64fea42
McGowan, Ruth
a7f8dc75-9777-4366-b9c8-823e362170be
Need, Anna
149e1309-2447-45f9-b5a3-177584009b08
Bond, Andrew
94b1c5ea-ac6f-4062-9673-13064c82aeee
Tavares, Ana Lisa Taylor
730fb640-a84a-451f-815e-a3d7155e4938
Thomas, Ellen R A
659e19e1-db65-4097-ad3f-518138316823
Hill, Susan L
205c58b1-452d-466f-8f7f-c0459490a0ea
Deans, Zandra C
c0246abe-844c-4a2f-b668-2f31f73c2c52
Boardman-Pretty, Freya
b928cc82-f967-4ba2-a6f3-105090e3099c
Caulfield, Mark
2267d97b-b1ca-4902-ab87-d989374eb7f5
Scott, Richard H
19488755-f941-45d3-985b-dc0ab1e647d2
Wilkie, Andrew O M
7064a09e-66d9-4acf-92eb-cffad1ce3762