Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders

S.K. Westbury, E. Turro, D. Greene, C. Lentaigne, A.M. Kelly, T.K. Bariana, I. Simeoni, X. Pillois, A. Attwood, S. Austin, S.B.G. Jansen, T. Bakchoul, A. Crisp-Hihn, Wendy Erber, R. Favier, N. Foad, M. Gattens, J.D. Jolley, R. Liesner, S. Meacham & 20 others C.M. Millar, A.T. Nurden, K. Peerlinck, D.J. Perry, P. Poudel, S. Schulman, H. Schulze, J.C. Stephens, B. Furie, P.N. Robinson, C. Van Geet, A. Rendon, K. Gomez, M.A. Laffan, M.P. Lambert, P. Nurden, W.H. Ouwehand, S. Richardson, A.D. Mumford, K. Freson

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Abstract

© 2015 Westbury et al. Background: Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases. Methods: We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results: We show that 60% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician. Conclusions: These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.
Original languageEnglish
Pages (from-to)1-15
JournalGenome Medicine
Volume7
Issue number1
DOIs
Publication statusPublished - 2015

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Cluster Analysis
Blood Platelets
Hemorrhage
Phenotype
Inborn Genetic Diseases
Genetic Heterogeneity
Pedigree
Rare Diseases
Nervous System
Genes

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Westbury, S.K. ; Turro, E. ; Greene, D. ; Lentaigne, C. ; Kelly, A.M. ; Bariana, T.K. ; Simeoni, I. ; Pillois, X. ; Attwood, A. ; Austin, S. ; Jansen, S.B.G. ; Bakchoul, T. ; Crisp-Hihn, A. ; Erber, Wendy ; Favier, R. ; Foad, N. ; Gattens, M. ; Jolley, J.D. ; Liesner, R. ; Meacham, S. ; Millar, C.M. ; Nurden, A.T. ; Peerlinck, K. ; Perry, D.J. ; Poudel, P. ; Schulman, S. ; Schulze, H. ; Stephens, J.C. ; Furie, B. ; Robinson, P.N. ; Van Geet, C. ; Rendon, A. ; Gomez, K. ; Laffan, M.A. ; Lambert, M.P. ; Nurden, P. ; Ouwehand, W.H. ; Richardson, S. ; Mumford, A.D. ; Freson, K. / Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. In: Genome Medicine. 2015 ; Vol. 7, No. 1. pp. 1-15.
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abstract = "{\circledC} 2015 Westbury et al. Background: Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases. Methods: We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results: We show that 60{\%} of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician. Conclusions: These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.",
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Westbury, SK, Turro, E, Greene, D, Lentaigne, C, Kelly, AM, Bariana, TK, Simeoni, I, Pillois, X, Attwood, A, Austin, S, Jansen, SBG, Bakchoul, T, Crisp-Hihn, A, Erber, W, Favier, R, Foad, N, Gattens, M, Jolley, JD, Liesner, R, Meacham, S, Millar, CM, Nurden, AT, Peerlinck, K, Perry, DJ, Poudel, P, Schulman, S, Schulze, H, Stephens, JC, Furie, B, Robinson, PN, Van Geet, C, Rendon, A, Gomez, K, Laffan, MA, Lambert, MP, Nurden, P, Ouwehand, WH, Richardson, S, Mumford, AD & Freson, K 2015, 'Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders' Genome Medicine, vol. 7, no. 1, pp. 1-15. https://doi.org/10.1186/s13073-015-0151-5

Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. / Westbury, S.K.; Turro, E.; Greene, D.; Lentaigne, C.; Kelly, A.M.; Bariana, T.K.; Simeoni, I.; Pillois, X.; Attwood, A.; Austin, S.; Jansen, S.B.G.; Bakchoul, T.; Crisp-Hihn, A.; Erber, Wendy; Favier, R.; Foad, N.; Gattens, M.; Jolley, J.D.; Liesner, R.; Meacham, S.; Millar, C.M.; Nurden, A.T.; Peerlinck, K.; Perry, D.J.; Poudel, P.; Schulman, S.; Schulze, H.; Stephens, J.C.; Furie, B.; Robinson, P.N.; Van Geet, C.; Rendon, A.; Gomez, K.; Laffan, M.A.; Lambert, M.P.; Nurden, P.; Ouwehand, W.H.; Richardson, S.; Mumford, A.D.; Freson, K.

In: Genome Medicine, Vol. 7, No. 1, 2015, p. 1-15.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders

AU - Westbury, S.K.

AU - Turro, E.

AU - Greene, D.

AU - Lentaigne, C.

AU - Kelly, A.M.

AU - Bariana, T.K.

AU - Simeoni, I.

AU - Pillois, X.

AU - Attwood, A.

AU - Austin, S.

AU - Jansen, S.B.G.

AU - Bakchoul, T.

AU - Crisp-Hihn, A.

AU - Erber, Wendy

AU - Favier, R.

AU - Foad, N.

AU - Gattens, M.

AU - Jolley, J.D.

AU - Liesner, R.

AU - Meacham, S.

AU - Millar, C.M.

AU - Nurden, A.T.

AU - Peerlinck, K.

AU - Perry, D.J.

AU - Poudel, P.

AU - Schulman, S.

AU - Schulze, H.

AU - Stephens, J.C.

AU - Furie, B.

AU - Robinson, P.N.

AU - Van Geet, C.

AU - Rendon, A.

AU - Gomez, K.

AU - Laffan, M.A.

AU - Lambert, M.P.

AU - Nurden, P.

AU - Ouwehand, W.H.

AU - Richardson, S.

AU - Mumford, A.D.

AU - Freson, K.

PY - 2015

Y1 - 2015

N2 - © 2015 Westbury et al. Background: Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases. Methods: We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results: We show that 60% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician. Conclusions: These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.

AB - © 2015 Westbury et al. Background: Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases. Methods: We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results: We show that 60% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician. Conclusions: These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.

U2 - 10.1186/s13073-015-0151-5

DO - 10.1186/s13073-015-0151-5

M3 - Article

VL - 7

SP - 1

EP - 15

JO - Genome Medicine

JF - Genome Medicine

SN - 1756-994X

IS - 1

ER -