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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
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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
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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
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Krawitz Peter
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  • ORCID record for 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
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Omri Bar
4FDNA Inc., Boston Massachusetts, United States
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Allan Bayat
5Rigshospitalet, Department of Neurology, Copenhagen, Denmark
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Luis Becerra-Solano
6Unidad de Investigación Médica en Medicina Reproductiva, Mexico
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Heidi Beate Bentzen
7University of Oslo, Oslo, Norway
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Saskia Biskup
8CeGaT GmbH, Tübingen, Germany
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Oleg Borisov
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
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Oivind Braaten
7University of Oslo, Oslo, Norway
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Claudia Ciaccio
9University of Milan, Milan, Italy
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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
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Kirsten Cremer
10Department of Human Genetics, University Hospital of Bonn, Bonn, Germany
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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
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Svenja Daschkey
11Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Hilda David-Eden
4FDNA Inc., Boston Massachusetts, United States
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Koenraad Devriendt
12Catholic University Leuven, Leuven, Belgium
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Sandra Dölken
13University of Hamburg, Hamburg, Germany
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Sofia Douzgou
14University of Manchester, Manchester, United Kingdom
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Dejan Đukić
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
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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
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Christine Fauth
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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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
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Nicole Fleischer
4FDNA Inc., Boston Massachusetts, United States
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Heinz Gabriel
16University of Tübingen, Tübingen, Germany
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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
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Karen W. Gripp
17A. I. duPont Hospital for Children, Wilmington, United States
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Yaron Gurovich
4FDNA Inc., Boston Massachusetts, United States
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Asya Gusina
18National Research and Applied Medicine Centre “Mother and Child”, Belarus
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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
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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
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Yair Hanani
4FDNA Inc., Boston Massachusetts, United States
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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
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Hoertnagel Konstanze
8CeGaT GmbH, Tübingen, Germany
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Janelle Howell
19Lineagen, United States
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Ivan Ivanovski
20Santa Maria Nuova Hospital, Italy
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Angela Kaindl
21Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
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Tom Kamphans
22GeneTalk, Bonn, Germany
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Susanne Kamphausen
23University Hospital Magdeburg, Magdeburg, Germany
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Catherine Karimov
24Children’s Hospital of Los Angeles, Los Angeles, United States
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Hadil Kathom
25Medical University of Sofia, Sofia, Bulgaria
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Anna Keryan
24Children’s Hospital of Los Angeles, Los Angeles, United States
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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
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Alexej Knaus
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
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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
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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
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Alexander Lavrov
27Research Institute of Medical Genetics of Russian Academy of Medical Sciences, Russian Federation
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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
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J. Gholson Lyon
28Cold Spring Harbor Laboratory, Woodbury, United States
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Elisabeth Mangold
29University of Bonn, Bonn, Germany
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Purificación Marín Reina
30Hospital General Universitario De Valencia, Valencia, Spain
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Antonio Martinez Carrascal
31Hospital General De Requena, Servicio Pediatría, Spain
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Diana Mitter
32University Hospital Leipzig, Leipzig, Germany
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Laura Morlan Herrador
33Hospital Universitario Miguel Servet, Spain
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Guy Nadav
4FDNA Inc., Boston Massachusetts, United States
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Markus Nöthen
10Department of Human Genetics, University Hospital of Bonn, Bonn, Germany
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Alfredo Orrico
34Azienda Ospedaliera Universitaria Senese, Siena, Italy
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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
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Kristen Park
35Children’s Hospital Colorado, United States
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Borut Peterlin
36Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Laura Pölsler
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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Annick Raas-Rothschild
37Sheba Medical Center, Israel
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Nicole Revencu
38Université Catholique de Louvain, Bruxelles, Belgium
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Christina Ringmann Fagerberg
39Odense University Hospital, Odense, Denmark
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Peter Nick Robinson
40The Jackson Laboratory for Genomic Medicine, Farmington, United States
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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
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Sabine Rudnik
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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Gorazd Rudolf
36Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Ulrich Schatz
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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Anna Schossig
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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Max Schubach
41Berlin Institute of Health (BIH), Anna-Louisa-Karsch 2, 10178 Berlin, Germany
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Or Shanoon
4FDNA Inc., Boston Massachusetts, United States
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Eamonn Sheridan
42School of Medicine, University of Leeds, Leeds, United Kingdom
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Pola Smirin-Yosef
43Ariel University, Ariel, Israel
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Malte Spielmann
44Department of Genome Sciences, University of Washington, Seattle, United States
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Eun-Kyung Suk
45Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
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Yves Sznajer
46Cliniques universitaires Saint Luc UCL, Bruxelles, Belgium
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Christian Thomas Thiel
47Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Erlangen, Germany
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Gundula Thiel
45Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
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Alain Verloes
48Hopital Robert Debré, Paris, France
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Irena Vrecar
36Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Dagmar Wahl
49Center for Human Genetics and Laboratory Diagnostics, Germany
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Ingrid Weber
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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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
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Marzena Wiśniewska
50Poznañ University of Medical Sciences, Poznañ, Poland
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Bernd Wollnik
51University Medical Center Göttingen, Göttingen, Germany
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Ming Wai Yeung
1Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
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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
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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
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Johannes Zschocke
15Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
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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
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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
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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.

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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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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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