New Results
PEDIA: Prioritization of Exome Data by Image Analysis
Tzung-Chien Hsieh, Martin Atta Mensah, Jean Tori Pantel, View ORCID ProfileKrawitz Peter, the PEDIA consortium, Dione Aguilar, Omri Bar, Allan Bayat, Luis Becerra-Solano, Heidi Beate Bentzen, Saskia Biskup, Oleg Borisov, Oivind Braaten, Claudia Ciaccio, Marie Coutelier, Kirsten Cremer, Magdalena Danyel, Svenja Daschkey, Hilda David-Eden, Koenraad Devriendt, Sandra Dölken, Sofia Douzgou, Dejan Đukić, Nadja Ehmke, Christine Fauth, Björn Fischer-Zirnsak, Nicole Fleischer, Heinz Gabriel, Luitgard Graul-Neumann, Karen W. Gripp, Yaron Gurovich, Asya Gusina, Nechama Haddad, Nurulhuda Hajjir, Yair Hanani, Jakob Hertzberg, Hoertnagel Konstanze, Janelle Howell, Ivan Ivanovski, Angela Kaindl, Tom Kamphans, Susanne Kamphausen, Catherine Karimov, Hadil Kathom, Anna Keryan, Salma-Gamal Khalil, Alexej Knaus, Sebastian Köhler, Uwe Kornak, Alexander Lavrov, Maximilian Leitheiser, J. Gholson Lyon, Elisabeth Mangold, Purificación Marín Reina, Antonio Martinez Carrascal, Diana Mitter, Laura Morlan Herrador, Guy Nadav, Markus Nöthen, Alfredo Orrico, Claus-Eric Ott, Kristen Park, Borut Peterlin, Laura Pölsler, Annick Raas-Rothschild, Nicole Revencu, Christina Ringmann Fagerberg, Peter Nick Robinson, Stanislav Rosnev, Sabine Rudnik, Gorazd Rudolf, Ulrich Schatz, Anna Schossig, Max Schubach, Or Shanoon, Eamonn Sheridan, Pola Smirin-Yosef, Malte Spielmann, Eun-Kyung Suk, Yves Sznajer, Christian Thomas Thiel, Gundula Thiel, Alain Verloes, Irena Vrecar, Dagmar Wahl, Ingrid Weber, Korina Winter, Marzena Wiśniewska, Bernd Wollnik, Ming Wai Yeung, Max Zhao, Na Zhu, Johannes Zschocke, Stefan Mundlos, Denise Horn
doi: https://doi.org/10.1101/473306
Tzung-Chien Hsieh
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Martin Atta Mensah
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
41Berlin Institute of Health (BIH), Anna-Louisa-Karsch 2, 10178 Berlin, Germany
Jean Tori Pantel
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
41Berlin Institute of Health (BIH), Anna-Louisa-Karsch 2, 10178 Berlin, Germany
Krawitz Peter
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- For correspondence: pkrawitz@uni-bonn.de
Dione Aguilar
3Monterrey Institute of Technology and Higher Education, Mexico
Omri Bar
4FDNA Inc., Boston Massachusetts, United States
Allan Bayat
5Rigshospitalet, Department of Neurology, Copenhagen, Denmark
Luis Becerra-Solano
6Unidad de Investigación Médica en Medicina Reproductiva, Mexico
Heidi Beate Bentzen
7University of Oslo, Oslo, Norway
Saskia Biskup
8CeGaT GmbH, Tübingen, Germany
Oleg Borisov
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
Oivind Braaten
7University of Oslo, Oslo, Norway
Claudia Ciaccio
9University of Milan, Milan, Italy
Marie Coutelier
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Kirsten Cremer
10Department of Human Genetics, University Hospital of Bonn, Bonn, Germany
Magdalena Danyel
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Svenja Daschkey
11Heinrich Heine University Düsseldorf, Düsseldorf, Germany
Hilda David-Eden
4FDNA Inc., Boston Massachusetts, United States
Koenraad Devriendt
12Catholic University Leuven, Leuven, Belgium
Sandra Dölken
13University of Hamburg, Hamburg, Germany
Sofia Douzgou
14University of Manchester, Manchester, United Kingdom
Dejan Đukić
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
Nadja Ehmke
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Christine Fauth
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Björn Fischer-Zirnsak
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Nicole Fleischer
4FDNA Inc., Boston Massachusetts, United States
Heinz Gabriel
16University of Tübingen, Tübingen, Germany
Luitgard Graul-Neumann
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Karen W. Gripp
17A. I. duPont Hospital for Children, Wilmington, United States
Yaron Gurovich
4FDNA Inc., Boston Massachusetts, United States
Asya Gusina
18National Research and Applied Medicine Centre “Mother and Child”, Belarus
Nechama Haddad
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Nurulhuda Hajjir
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Yair Hanani
4FDNA Inc., Boston Massachusetts, United States
Jakob Hertzberg
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Hoertnagel Konstanze
8CeGaT GmbH, Tübingen, Germany
Janelle Howell
19Lineagen, United States
Ivan Ivanovski
20Santa Maria Nuova Hospital, Italy
Angela Kaindl
21Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
Tom Kamphans
22GeneTalk, Bonn, Germany
Susanne Kamphausen
23University Hospital Magdeburg, Magdeburg, Germany
Catherine Karimov
24Children’s Hospital of Los Angeles, Los Angeles, United States
Hadil Kathom
25Medical University of Sofia, Sofia, Bulgaria
Anna Keryan
24Children’s Hospital of Los Angeles, Los Angeles, United States
Salma-Gamal Khalil
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Alexej Knaus
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
Sebastian Köhler
26Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, NeuroCure Clinical Research Center, Berlin, Germany
Uwe Kornak
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Alexander Lavrov
27Research Institute of Medical Genetics of Russian Academy of Medical Sciences, Russian Federation
Maximilian Leitheiser
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
J. Gholson Lyon
28Cold Spring Harbor Laboratory, Woodbury, United States
Elisabeth Mangold
29University of Bonn, Bonn, Germany
Purificación Marín Reina
30Hospital General Universitario De Valencia, Valencia, Spain
Antonio Martinez Carrascal
31Hospital General De Requena, Servicio Pediatría, Spain
Diana Mitter
32University Hospital Leipzig, Leipzig, Germany
Laura Morlan Herrador
33Hospital Universitario Miguel Servet, Spain
Guy Nadav
4FDNA Inc., Boston Massachusetts, United States
Markus Nöthen
10Department of Human Genetics, University Hospital of Bonn, Bonn, Germany
Alfredo Orrico
34Azienda Ospedaliera Universitaria Senese, Siena, Italy
Claus-Eric Ott
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Kristen Park
35Children’s Hospital Colorado, United States
Borut Peterlin
36Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
Laura Pölsler
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Annick Raas-Rothschild
37Sheba Medical Center, Israel
Nicole Revencu
38Université Catholique de Louvain, Bruxelles, Belgium
Christina Ringmann Fagerberg
39Odense University Hospital, Odense, Denmark
Peter Nick Robinson
40The Jackson Laboratory for Genomic Medicine, Farmington, United States
Stanislav Rosnev
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Sabine Rudnik
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Gorazd Rudolf
36Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
Ulrich Schatz
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Anna Schossig
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Max Schubach
41Berlin Institute of Health (BIH), Anna-Louisa-Karsch 2, 10178 Berlin, Germany
Or Shanoon
4FDNA Inc., Boston Massachusetts, United States
Eamonn Sheridan
42School of Medicine, University of Leeds, Leeds, United Kingdom
Pola Smirin-Yosef
43Ariel University, Ariel, Israel
Malte Spielmann
44Department of Genome Sciences, University of Washington, Seattle, United States
Eun-Kyung Suk
45Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
Yves Sznajer
46Cliniques universitaires Saint Luc UCL, Bruxelles, Belgium
Christian Thomas Thiel
47Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Erlangen, Germany
Gundula Thiel
45Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
Alain Verloes
48Hopital Robert Debré, Paris, France
Irena Vrecar
36Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
Dagmar Wahl
49Center for Human Genetics and Laboratory Diagnostics, Germany
Ingrid Weber
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Korina Winter
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Marzena Wiśniewska
50Poznañ University of Medical Sciences, Poznañ, Poland
Bernd Wollnik
51University Medical Center Göttingen, Göttingen, Germany
Ming Wai Yeung
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
Max Zhao
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Na Zhu
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Johannes Zschocke
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
Stefan Mundlos
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Denise Horn
2Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
Abstract
Phenotype information is crucial for the interpretation of genomic variants. So far it has only been accessible for bioinformatics workflows after encoding into clinical terms by expert dysmorphologists. Here, we introduce an approach, driven by artificial intelligence that uses portrait photographs for the interpretation of clinical exome data. We measured the value added by computer-assisted image analysis to the diagnostic yield on a cohort consisting of 679 individuals with 105 different monogenic disorders. For each case in the cohort we compiled frontal photos, clinical features and the disease-causing mutations and simulated multiple exomes of different ethnic backgrounds. With the additional use of similarity scores from computer-assisted analysis of frontal photos, we were able to achieve a top-10-accuracy rate for the disease-causing gene of 99 %. As this performance is significantly higher than without the information from facial pattern recognition, we make gestalt scores available for prioritization via an API.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted November 21, 2018.
PEDIA: Prioritization of Exome Data by Image Analysis
Tzung-Chien Hsieh, Martin Atta Mensah, Jean Tori Pantel, Krawitz Peter, the PEDIA consortium, Dione Aguilar, Omri Bar, Allan Bayat, Luis Becerra-Solano, Heidi Beate Bentzen, Saskia Biskup, Oleg Borisov, Oivind Braaten, Claudia Ciaccio, Marie Coutelier, Kirsten Cremer, Magdalena Danyel, Svenja Daschkey, Hilda David-Eden, Koenraad Devriendt, Sandra Dölken, Sofia Douzgou, Dejan Đukić, Nadja Ehmke, Christine Fauth, Björn Fischer-Zirnsak, Nicole Fleischer, Heinz Gabriel, Luitgard Graul-Neumann, Karen W. Gripp, Yaron Gurovich, Asya Gusina, Nechama Haddad, Nurulhuda Hajjir, Yair Hanani, Jakob Hertzberg, Hoertnagel Konstanze, Janelle Howell, Ivan Ivanovski, Angela Kaindl, Tom Kamphans, Susanne Kamphausen, Catherine Karimov, Hadil Kathom, Anna Keryan, Salma-Gamal Khalil, Alexej Knaus, Sebastian Köhler, Uwe Kornak, Alexander Lavrov, Maximilian Leitheiser, J. Gholson Lyon, Elisabeth Mangold, Purificación Marín Reina, Antonio Martinez Carrascal, Diana Mitter, Laura Morlan Herrador, Guy Nadav, Markus Nöthen, Alfredo Orrico, Claus-Eric Ott, Kristen Park, Borut Peterlin, Laura Pölsler, Annick Raas-Rothschild, Nicole Revencu, Christina Ringmann Fagerberg, Peter Nick Robinson, Stanislav Rosnev, Sabine Rudnik, Gorazd Rudolf, Ulrich Schatz, Anna Schossig, Max Schubach, Or Shanoon, Eamonn Sheridan, Pola Smirin-Yosef, Malte Spielmann, Eun-Kyung Suk, Yves Sznajer, Christian Thomas Thiel, Gundula Thiel, Alain Verloes, Irena Vrecar, Dagmar Wahl, Ingrid Weber, Korina Winter, Marzena Wiśniewska, Bernd Wollnik, Ming Wai Yeung, Max Zhao, Na Zhu, Johannes Zschocke, Stefan Mundlos, Denise Horn
bioRxiv 473306; doi: https://doi.org/10.1101/473306
PEDIA: Prioritization of Exome Data by Image Analysis
Tzung-Chien Hsieh, Martin Atta Mensah, Jean Tori Pantel, Krawitz Peter, the PEDIA consortium, Dione Aguilar, Omri Bar, Allan Bayat, Luis Becerra-Solano, Heidi Beate Bentzen, Saskia Biskup, Oleg Borisov, Oivind Braaten, Claudia Ciaccio, Marie Coutelier, Kirsten Cremer, Magdalena Danyel, Svenja Daschkey, Hilda David-Eden, Koenraad Devriendt, Sandra Dölken, Sofia Douzgou, Dejan Đukić, Nadja Ehmke, Christine Fauth, Björn Fischer-Zirnsak, Nicole Fleischer, Heinz Gabriel, Luitgard Graul-Neumann, Karen W. Gripp, Yaron Gurovich, Asya Gusina, Nechama Haddad, Nurulhuda Hajjir, Yair Hanani, Jakob Hertzberg, Hoertnagel Konstanze, Janelle Howell, Ivan Ivanovski, Angela Kaindl, Tom Kamphans, Susanne Kamphausen, Catherine Karimov, Hadil Kathom, Anna Keryan, Salma-Gamal Khalil, Alexej Knaus, Sebastian Köhler, Uwe Kornak, Alexander Lavrov, Maximilian Leitheiser, J. Gholson Lyon, Elisabeth Mangold, Purificación Marín Reina, Antonio Martinez Carrascal, Diana Mitter, Laura Morlan Herrador, Guy Nadav, Markus Nöthen, Alfredo Orrico, Claus-Eric Ott, Kristen Park, Borut Peterlin, Laura Pölsler, Annick Raas-Rothschild, Nicole Revencu, Christina Ringmann Fagerberg, Peter Nick Robinson, Stanislav Rosnev, Sabine Rudnik, Gorazd Rudolf, Ulrich Schatz, Anna Schossig, Max Schubach, Or Shanoon, Eamonn Sheridan, Pola Smirin-Yosef, Malte Spielmann, Eun-Kyung Suk, Yves Sznajer, Christian Thomas Thiel, Gundula Thiel, Alain Verloes, Irena Vrecar, Dagmar Wahl, Ingrid Weber, Korina Winter, Marzena Wiśniewska, Bernd Wollnik, Ming Wai Yeung, Max Zhao, Na Zhu, Johannes Zschocke, Stefan Mundlos, Denise Horn
bioRxiv 473306; doi: https://doi.org/10.1101/473306
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