program
draft program - shown in Central European Daylight Time: UTC + 2
program is draft - we may make some small changes
Schedule
Time shown is Central European Daylight Time. UTC +2. ON-DEMAND: Long Read Sequencing Approaches, WES Analysis.
Welcome & Introduction
Dr. Andreas Laner
Chair
Variants in the Genome: position and possible consequences
Jan is a Professor of Genetics, and Director of the Laboratory of Medical Genetics, Athens... More
Joanne Traeger-Synodinos
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 Ljublijana, Slovenia
Coffee Break
Gene variant databases & sharing information
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]).
EMQN - genomics quality assurance
Manchester Science Park, Manchester, UK
Lunch Break
HGVS Nomenclature - describing variants
WORKSHOP
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]).
Coffee 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
Coffee Break
The Ensembl Browser and its possibilities
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the... More
Aleena Mushtaq
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the Quadram Institute Biosciences, UK to pursue her PhD in the field of Molecular Biology. Her PhD investigated the molecular and microbial changes in the gut-liver axis in response to the high-fibre and low-fibre Western diets. Aleena joined EMBL-EBI as an Ensembl Outreach Officer in 2021 and delivers training on Ensembl resources.
The UCSC Browser and its possibilities
Robert is Associate Director of the UCSC Genome Browser, UC Santa Cruz Genomics Institute,... More
Robert Kuhn
Robert is Associate Director of the UCSC Genome Browser, UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
Robert Kuhn studied biology and biochemistry at the University of Wisconsin and University of Cincinnati. Following a masters degree in chemistry at the Oregon Health and Sciences University, he received his PhD in biochemistry and molecular biology at the University of California Santa Barbara, where he studied the centromeres of yeast. He then studied photoreceptor genes in plants at UC Berkeley and has taught biochemistry, genetics and molecular biology at UC Santa Cruz. Since joining the UCSC Genome Browser team in 2003, he has been instrumental in guiding the growth of the Browser and has shared the Browser in more than 300 presentations to scientists around the world.
Variant Effect Predictor
WORKSHOP
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the... More
Aleena Mushtaq
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the Quadram Institute Biosciences, UK to pursue her PhD in the field of Molecular Biology. Her PhD investigated the molecular and microbial changes in the gut-liver axis in response to the high-fibre and low-fibre Western diets. Aleena joined EMBL-EBI as an Ensembl Outreach Officer in 2021 and delivers training on Ensembl resources.
Integration of phenotypic and genomic data to diagnose patients with rare diseases (+ HPO intro)
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
Variants in the mitochondrial genome
Holger Prokisch, PhD, is head of the research group “Genetics of Mitochondrial... More
Holger Proksich
Holger Prokisch, PhD, is head of the research group “Genetics of Mitochondrial Disorders” at the Institute of Human Genetic of the Technical University Munich and of the Helmholtz Zentrum München. He has longstanding experience in the molecular analysis of mitochondrial disorders. His research focus seeks to understand genetic variation in both rare and common disorders leading to mitochondria-related dysfunction. He was very successful in integrating genomic approaches with detailed functional biochemical investigations. By applying WES, his group has contributed to the discovery of more than 50 novel disease genes and to the diagnosis of more than 1,000 patients. In his work, Dr. Prokisch undertakes genomic, proteomic, metabolomic, and transcriptomic studies and accomplishes computational analysis to produce a comprehensive picture of mitochondrial dysfunction. Dr. Prokisch coordinates two Eurasian networks for mitochondrial disorders (GENOMIT and PerMiM).
Coffee Break
ACMG grading - BASIC/GENERAL
WORKSHOP
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
Coffee Break
Variant Annotation Integrator
WORKSHOP
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.
Robert is Associate Director of the UCSC Genome Browser, UC Santa Cruz Genomics Institute,... More
Robert Kuhn
Robert is Associate Director of the UCSC Genome Browser, UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
Robert Kuhn studied biology and biochemistry at the University of Wisconsin and University of Cincinnati. Following a masters degree in chemistry at the Oregon Health and Sciences University, he received his PhD in biochemistry and molecular biology at the University of California Santa Barbara, where he studied the centromeres of yeast. He then studied photoreceptor genes in plants at UC Berkeley and has taught biochemistry, genetics and molecular biology at UC Santa Cruz. Since joining the UCSC Genome Browser team in 2003, he has been instrumental in guiding the growth of the Browser and has shared the Browser in more than 300 presentations to scientists around the world.
Lunch Break
UCSC Genome Browser
WORKSHOP
Robert is Associate Director of the UCSC Genome Browser, UC Santa Cruz Genomics Institute,... More
Robert Kuhn
Robert is Associate Director of the UCSC Genome Browser, UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
Robert Kuhn studied biology and biochemistry at the University of Wisconsin and University of Cincinnati. Following a masters degree in chemistry at the Oregon Health and Sciences University, he received his PhD in biochemistry and molecular biology at the University of California Santa Barbara, where he studied the centromeres of yeast. He then studied photoreceptor genes in plants at UC Berkeley and has taught biochemistry, genetics and molecular biology at UC Santa Cruz. Since joining the UCSC Genome Browser team in 2003, he has been instrumental in guiding the growth of the Browser and has shared the Browser in more than 300 presentations to scientists around the world.
Coffee Break
varvis genomics platform
SPONSORED WORKSHOP
The varvis® genomics platform is a cloud-based and standardized software solution for clinical genetics. It supports the entire NGS workflow from raw data processing and genomics data management to variant interpretation and includes clinically validated and automated CNV and SNV/Indel analysis. varvis® allows you to build your own comprehensive in-house variant database from the entire analysis history, but also leverages the variant data from all users to help solving even complex WES or WGS cases. Our services comprise first-class support, training, automated quality control and validation compliant with relevant international guidelines. varvis® is a registered CE-IVD device and as such specifically designed to aid in the diagnosis of patients.
Contact: info@varvis.com
Website: www.varvis.com
Break
Ensembl Genome Browser
WORKSHOP
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the... More
Aleena Mushtaq
Aleena studied Molecular and Biomedical Sciences at King’s College London. She joined the Quadram Institute Biosciences, UK to pursue her PhD in the field of Molecular Biology. Her PhD investigated the molecular and microbial changes in the gut-liver axis in response to the high-fibre and low-fibre Western diets. Aleena joined EMBL-EBI as an Ensembl Outreach Officer in 2021 and delivers training on Ensembl resources.
RNA analysis: expanding the Dx yield (practice)
Functional Testing (Protein plus RNA) / (Potential consequences on the Protein Level)
Epigenetics - beyond Mendel
Coffee Break
NGS in diagnostics: where things can go wrong
WORKSHOP
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]).
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.
Coffee Break
Integration of phenotypic and genomic data to diagnose patients with rare diseases (+ HPO intro)
WORKSHOP
Lunch Break
ACMG grading - ADVANCED
WORKSHOP
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
Coffee Break
Future Developments
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
Course Evaluation & Close
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
