Program
All times are Central European Summer Time (CETS)
CEST = UTC + 2
Find the local time in your city here for the 8.00 am start on 21st Sept. We are using Paris as the home city for CEST.
Tuesday 21 Sept. 2021:
- Familiariasation with platform opens - 8.00
- Course Begins - 8.50
- End Day 1 - 16.00
Wednesday 22 Sept:
- Course continues 8.30 - 17.05
Thursday 23 Sept.:
- Course continues 8.30 - 16.30
- Course Ends 16.30
Core topics will be presented during the three-day course. Other topics will be available as on-demand content for six months.
Draft Program
ON-DEMAND: - Human Phenotype Ontology (HPO) - describing phenotypes (Lecture & Workshop). - WES analysis/ LOVD+ (Lecture & Workshop). - Others to be announced.
Platform Familiarisation
Familiarise yourself with the platform, view the sessions, poster selections, exhibitors and speakers and learn how to navigate before the event. Please login BEFORE the start day to setup your profile and if possible familiarise yourself with the platform to save you time at the beginning of the course and ensure you do not miss anything in case you have any problems with login. We will email you the login instructions approximately one week or slightly earlier before the course start.
Course Welcome
Dr Andreas Laner
Chair
Variants in the Genome: position and possible consequences
Jan Traeger-Synodinos, DPhil (Oxon) Jan is a Professor of Genetics, and Director of the... More
Joanne Traeger-Synodinos
Jan Traeger-Synodinos, DPhil (Oxon)
Jan is a Professor of Genetics, and Director of the Laboratory of Medical Genetics, Athens University, and has over 30 years of experience in molecular genetics. Originally from the UK, where she graduated with a BSc in Physiology and Biochemistry from Reading University and a Doctorate (DPhil) at Oxford University, (under Sir Professor David Weatherall), she moved to Greece in 1982 and since 1983 has worked in the university clinics (pediatrics and genetics) of the St. Sophia’s Children’s Hospital in Athens. In 2005 she became a member of Athens University Medical School, in the Laboratory of Medical Genetics. Jan has wide experience with molecular diagnostics for many monogenic diseases. She is an internationally recognized expert in the hemoglobinopathies and also preimplantation genetic diagnosis (PGD), and has contributed to publications on Best Practice Guidelines for both topics. Her main research activities focus on investigating the molecular genetics of monogenic diseases and also the development of methods for molecular diagnostics. She has also participated in an EU-funded project which focused on Introducing diagnostic applications of next-generation sequencing in human genetics. She has over 150 peer-reviewed publications in international journals and chapters in several books.
Jan is a long-term member of the European Society of Human Genetics (ESHG) and the European Society of Human Reproduction and Embryology (ESHRE), serving on the Steering Committee of the ESHRE PGD Consortium between 2004-2016, and as Chair between 2012-2014. She is also a member of the Special Advisory Group for External Quality Assessment for PGT through GenQA and The Haemoglobinopathy Expert Panel, recognised by the Clinical Genome Research (ClinGen).
NGS: what method to apply (gene panel, WES or WGS) and where technology fails
Institute of Medical Genetics - Ljubljana University Medical Centre, Ljublijana, Slovenia Bio... More
Ales Maver
Institute of Medical Genetics - Ljubljana University Medical Centre,
Ljublijana, Slovenia
Bio TBA
Break
HGVS Nomenclature - describing variants
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same... More
Johan T. den Dunnen
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same university he received his PhD in Molecular Biology for his work on the "Evolution of eye-lens crystallin genes". After his PhD he moved to the department of Human Genetics (Leiden University) and became involved in the search for the gene causing Duchenne/Becker muscular dystrophy. He is currently employed at the Center for Human and Clinical Genetics (Leiden University Medical Center, Leiden, Nederland), studying genetic disease in general and neuromuscular disorders (DMD/BMD, LGMD) in particular. As professor in "Medical Genomics" he focuses on the use of new high-throughput technology in research and diagnosis of genetic disease, in particular the development of methods to detect DNA variants and the application of next generation sequencing. To spread the laboratories knowledge on hereditary muscle disease he initiated the "Leiden Muscular Dystrophy pages" (http://www.DMD.nl). As part of these efforts he currently curates over 50 gene sequence variant databases. His group developed the freely available LSDB-in-a-Box software package LOVD, the Mutalyzer tool (HGVS sequence variant description) and he participates in the EU FP7 Gen2Phen project (WP leader for gene variant databases [LSDBs]).
WORKSHOP: HGVS Nomenclature - describing variants
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same... More
Johan T. den Dunnen
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same university he received his PhD in Molecular Biology for his work on the "Evolution of eye-lens crystallin genes". After his PhD he moved to the department of Human Genetics (Leiden University) and became involved in the search for the gene causing Duchenne/Becker muscular dystrophy. He is currently employed at the Center for Human and Clinical Genetics (Leiden University Medical Center, Leiden, Nederland), studying genetic disease in general and neuromuscular disorders (DMD/BMD, LGMD) in particular. As professor in "Medical Genomics" he focuses on the use of new high-throughput technology in research and diagnosis of genetic disease, in particular the development of methods to detect DNA variants and the application of next generation sequencing. To spread the laboratories knowledge on hereditary muscle disease he initiated the "Leiden Muscular Dystrophy pages" (http://www.DMD.nl). As part of these efforts he currently curates over 50 gene sequence variant databases. His group developed the freely available LSDB-in-a-Box software package LOVD, the Mutalyzer tool (HGVS sequence variant description) and he participates in the EU FP7 Gen2Phen project (WP leader for gene variant databases [LSDBs]).
Break
CNV calling/ analysis: applications and challenges
Centro Nacional de Análisis Genómico (CNAG-CRG), Barcelona, Spain. Bio coming... More
Steven Laurie
Centro Nacional de Análisis Genómico (CNAG-CRG), Barcelona, Spain.
Bio coming soon...
WORKSHOP: Variant interpretation & reporting: what’s best for your lab? Standalone databases or a decision support tool
Sponsored Workshop
QIAGEN Advanced Genomics, Manchester, UK
Break
SNV calling/ analysis: applications and challenges
Anna is head of the Development and Technology Transfer department at the Munich Medical... More
Anna Benet-Pages
Anna is head of the Development and Technology Transfer department at the Munich Medical Genetics Centre since 2011. Anna moved from Barcelona to Munich in the year 2000 where she obtained her PhD in molecular biology by the Ludwig Maximilian University of Munich in the year 2005. As a post-doc she worked at the Helmholtz German Research Centre for Environmental Health in the Human Genetics Institute of Prof. Dr. Thomas Meitinger, where she managed the laboratory unit of the next-generation sequencing core facility. Her primary research area was genetic identification and molecular characterization of rare Mendelian diseases. As specialist in high-throughput sequencing and data analysis, she focuses her professional career at MGZ on the interdisciplinary management of laboratory technology, bioinformatics, and scientific development. In particular the application of next generation sequencing and the development of bioinformatics methods to detect genomic variations for the diagnosis of genetic disease. She aims to achieve Best Practices for high-throughput sequencing data analysis depending on the type of variation of interest and the technology employed. Anna has contributed to publications on guidelines for utilization of next-generation sequencing approaches in genetic testing and she is also assessor of the External Quality Assessment scheme for Charcot-Marie-Tooth disease within the European Genetics Quality Network (EMQN) framework.
Fast Forward Poster Presentations
Gene variant databases (LSDBs) / DNA diagnostics = sharing data
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same... More
Johan T. den Dunnen
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same university he received his PhD in Molecular Biology for his work on the "Evolution of eye-lens crystallin genes". After his PhD he moved to the department of Human Genetics (Leiden University) and became involved in the search for the gene causing Duchenne/Becker muscular dystrophy. He is currently employed at the Center for Human and Clinical Genetics (Leiden University Medical Center, Leiden, Nederland), studying genetic disease in general and neuromuscular disorders (DMD/BMD, LGMD) in particular. As professor in "Medical Genomics" he focuses on the use of new high-throughput technology in research and diagnosis of genetic disease, in particular the development of methods to detect DNA variants and the application of next generation sequencing. To spread the laboratories knowledge on hereditary muscle disease he initiated the "Leiden Muscular Dystrophy pages" (http://www.DMD.nl). As part of these efforts he currently curates over 50 gene sequence variant databases. His group developed the freely available LSDB-in-a-Box software package LOVD, the Mutalyzer tool (HGVS sequence variant description) and he participates in the EU FP7 Gen2Phen project (WP leader for gene variant databases [LSDBs]).
Genome Browsers - Ensembl
more speakers to be confirmed - watch this space!
WORKSHOP: Genome Browsers - Ensembl
more speakers to be confirmed - watch this space!
Break
Variant Classification - ACMG Recommendations
Andreas Laner, PhD Head of Genomics Program Areas of Specialization Genetics of hereditary... More
Andreas Laner
Andreas Laner, PhD
Head of Genomics Program
Areas of Specialization
- Genetics of hereditary cancer syndromes
- Next-generation sequencing applications
- Interpretation and classification of sequence variants
Education & Experience
- Diploma in Biology, Ludwig Maximilian University, Munich
- PhD, Ludwig Maximilian University, Munich
Professional affiliations
- MGZ Munich, Head of Genomics Applications
- Member, European Society of Human Genetics
- Curator, Leiden Open Variation Database
- Organizational Committee, Variant Effect Prediction Training Course, Crete 2016
- Scientific Program Committee, 14th International Symposium on Variants in the Genome, Santiago de Compostela 2017
WORKSHOP: Variant Classification - ACMG Recommendations
To be advised
Andreas Laner, PhD Head of Genomics Program Areas of Specialization Genetics of hereditary... More
Andreas Laner
Andreas Laner, PhD
Head of Genomics Program
Areas of Specialization
- Genetics of hereditary cancer syndromes
- Next-generation sequencing applications
- Interpretation and classification of sequence variants
Education & Experience
- Diploma in Biology, Ludwig Maximilian University, Munich
- PhD, Ludwig Maximilian University, Munich
Professional affiliations
- MGZ Munich, Head of Genomics Applications
- Member, European Society of Human Genetics
- Curator, Leiden Open Variation Database
- Organizational Committee, Variant Effect Prediction Training Course, Crete 2016
- Scientific Program Committee, 14th International Symposium on Variants in the Genome, Santiago de Compostela 2017
Break
Annotating Variants: VEP
more speakers to be confirmed - watch this space!
WORKSHOP: To be Announced
Topic to be announced
more speakers to be confirmed - watch this space!
Break
When do I have enough evidence to link a (new) gene with a disease?
more speakers to be confirmed - watch this space!
Genome Browsers - UCSC
Associate Director UCSC Genome Browser UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA... More
Robert Kuhn
Associate Director UCSC Genome Browser
UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
WORKSHOP: Genome Browsers - UCSC
Associate Director UCSC Genome Browser UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA... More
Robert Kuhn
Associate Director UCSC Genome Browser
UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
Potential consequences on the RNA Level (theory)
Andreas Laner, PhD Head of Genomics Program Areas of Specialization Genetics of hereditary... More
Andreas Laner
Andreas Laner, PhD
Head of Genomics Program
Areas of Specialization
- Genetics of hereditary cancer syndromes
- Next-generation sequencing applications
- Interpretation and classification of sequence variants
Education & Experience
- Diploma in Biology, Ludwig Maximilian University, Munich
- PhD, Ludwig Maximilian University, Munich
Professional affiliations
- MGZ Munich, Head of Genomics Applications
- Member, European Society of Human Genetics
- Curator, Leiden Open Variation Database
- Organizational Committee, Variant Effect Prediction Training Course, Crete 2016
- Scientific Program Committee, 14th International Symposium on Variants in the Genome, Santiago de Compostela 2017
RNA analysis: expanding the Dx yield (practice)
Bio coming
Functional Testing (Protein plus RNA) / (Potential consequences on the Protein Level)
more speakers to be confirmed - watch this space!
Break
WORKSHOP: NGS in diagnostics: where things can go wrong
Anna is head of the Development and Technology Transfer department at the Munich Medical... More
Anna Benet-Pages
Anna is head of the Development and Technology Transfer department at the Munich Medical Genetics Centre since 2011. Anna moved from Barcelona to Munich in the year 2000 where she obtained her PhD in molecular biology by the Ludwig Maximilian University of Munich in the year 2005. As a post-doc she worked at the Helmholtz German Research Centre for Environmental Health in the Human Genetics Institute of Prof. Dr. Thomas Meitinger, where she managed the laboratory unit of the next-generation sequencing core facility. Her primary research area was genetic identification and molecular characterization of rare Mendelian diseases. As specialist in high-throughput sequencing and data analysis, she focuses her professional career at MGZ on the interdisciplinary management of laboratory technology, bioinformatics, and scientific development. In particular the application of next generation sequencing and the development of bioinformatics methods to detect genomic variations for the diagnosis of genetic disease. She aims to achieve Best Practices for high-throughput sequencing data analysis depending on the type of variation of interest and the technology employed. Anna has contributed to publications on guidelines for utilization of next-generation sequencing approaches in genetic testing and she is also assessor of the External Quality Assessment scheme for Charcot-Marie-Tooth disease within the European Genetics Quality Network (EMQN) framework.
Break
Integration of phenotypic and genomic data to diagnose patients with rare diseases (+ HPO intro)
Leslie Matalonga obtained a PhD in Biomedicine (University of Barcelona) and worked at a... More
Leslie Matalonga
Leslie Matalonga obtained a PhD in Biomedicine (University of Barcelona) and worked at a clinical Group in Hospital Clínic de Barcelona for 7 years. Since 2017, Leslie joined the CNAG-CRG Bioinformatics Unit as Clinical Genomics Specialist. She works in the analysis and interpretation of genomic data from patients with rare diseases. She works in collaboration with the developer team of the RD-Connect GPAP (https://platform.rd-connect.eu/ ) and coordinates part of the new features to be added. She has been involved in several national and internal projects towards rare disease genomic diagnostics and research such as URD-Cat, NAGEN 1000G and Solve-RD, where she is leading a working group on exome re-analysis through APIs. She is also a member of the ELIXIR Rare Disease Community and is an author of 21 international publications.
WORKSHOP: Integration of phenotypic and genomic data to diagnose patients with rare diseases (+ HPO intro)
Leslie Matalonga obtained a PhD in Biomedicine (University of Barcelona) and worked at a... More
Leslie Matalonga
Leslie Matalonga obtained a PhD in Biomedicine (University of Barcelona) and worked at a clinical Group in Hospital Clínic de Barcelona for 7 years. Since 2017, Leslie joined the CNAG-CRG Bioinformatics Unit as Clinical Genomics Specialist. She works in the analysis and interpretation of genomic data from patients with rare diseases. She works in collaboration with the developer team of the RD-Connect GPAP (https://platform.rd-connect.eu/ ) and coordinates part of the new features to be added. She has been involved in several national and internal projects towards rare disease genomic diagnostics and research such as URD-Cat, NAGEN 1000G and Solve-RD, where she is leading a working group on exome re-analysis through APIs. She is also a member of the ELIXIR Rare Disease Community and is an author of 21 international publications.
Break
UCSC recommended track sets
Associate Director UCSC Genome Browser UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA... More
Robert Kuhn
Associate Director UCSC Genome Browser
UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
Future Developments
Prof Makrythanasis received his Medical Degree from the University of Athens, Medical School,... More
Periklis Makrythanasis
Prof Makrythanasis received his Medical Degree from the University of Athens, Medical School, Greece and got his PhD from the same University in the field of Human Genetics. He got specialized in Medical Genetics in Geneva Switzerland and received his Privat Docent from the University of Geneva for his research in the identification of novel genes responsible for monogenic disorders through the study of consanguineous families. After his return in Greece he worked at the Greek Genome Center of the Biomedical Research Foundation of the Academy of Athens, before joining the Medical School of the University of Athens, where he currently holds the position of Assistant Professor in Medical Genetics.
Course Evaluation
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same... More
Johan T. den Dunnen
Johan den Dunnen studied biology at the Catholic University Nijmegen (Nederland). In the same university he received his PhD in Molecular Biology for his work on the "Evolution of eye-lens crystallin genes". After his PhD he moved to the department of Human Genetics (Leiden University) and became involved in the search for the gene causing Duchenne/Becker muscular dystrophy. He is currently employed at the Center for Human and Clinical Genetics (Leiden University Medical Center, Leiden, Nederland), studying genetic disease in general and neuromuscular disorders (DMD/BMD, LGMD) in particular. As professor in "Medical Genomics" he focuses on the use of new high-throughput technology in research and diagnosis of genetic disease, in particular the development of methods to detect DNA variants and the application of next generation sequencing. To spread the laboratories knowledge on hereditary muscle disease he initiated the "Leiden Muscular Dystrophy pages" (http://www.DMD.nl). As part of these efforts he currently curates over 50 gene sequence variant databases. His group developed the freely available LSDB-in-a-Box software package LOVD, the Mutalyzer tool (HGVS sequence variant description) and he participates in the EU FP7 Gen2Phen project (WP leader for gene variant databases [LSDBs]).
Andreas Laner, PhD Head of Genomics Program Areas of Specialization Genetics of hereditary... More
Andreas Laner
Andreas Laner, PhD
Head of Genomics Program
Areas of Specialization
- Genetics of hereditary cancer syndromes
- Next-generation sequencing applications
- Interpretation and classification of sequence variants
Education & Experience
- Diploma in Biology, Ludwig Maximilian University, Munich
- PhD, Ludwig Maximilian University, Munich
Professional affiliations
- MGZ Munich, Head of Genomics Applications
- Member, European Society of Human Genetics
- Curator, Leiden Open Variation Database
- Organizational Committee, Variant Effect Prediction Training Course, Crete 2016
- Scientific Program Committee, 14th International Symposium on Variants in the Genome, Santiago de Compostela 2017
