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Big Data in Genomics

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Julia Baptista

Genomic testing for acutely ill children with rare disease and the UK national rapid exome sequencing service

The Exeter Genomics Laboratory implemented a diagnostic rare disease exome pipeline in 2013 and in October 2019, it launched the new NHSE nationally-commissioned rapid exome sequencing service for acutely unwell children.


Children in neonatal or pediatric intensive care units or those with a likely monogenic disorder where a diagnosis was needed for immediate management decisions were eligible for this service. In its first year, 519 children were tested and a genetic diagnosis identified in 37% . With a focus on multidisciplinary team working, this service is a model of how translational medical research and close multidisciplinary working across the NHS can revolutionise patient care, improve patient outcomes and empower families by providing early diagnoses.



Shareef Nahas

System for delivery of rapid genome sequencing-enabled management of childhood genetic diseases

Genetic disease is a leading contributor to infant and childhood mortality in hospital intensive care units (ICU). Although the incidence of any single monogenetic disorder is low, there are more than 8000 single gene diseases with diverse presentations, frequently precluding a diagnosis prior to ICU admission. Identifying a genetic disease has implications for the patient’s medical management as well as prognosis. Moreover, 10% of children with severe chronic illness, often due to genetic disease, represent 70% of healthcare costs.


Recent publications have demonstrated that Rapid-Whole Genome Sequencing (rWGS) has emerged as a method of diagnosing genetic conditions in acutely ill neonates and has demonstrated high clinical utility rates in the neonatal intensive care unit (NICU). In this presentation, Dr. Nahas will present evidence of the diagnostic and clinical utility of rWGS within Intensive Care Units, and how an automated system for data integration can result in population-scale diagnosis and acute management guidance for genetic diseases.



Andreas Henschel

Genotype-Phenotype predictions using Genomic Data Science: Enabling Machine Learning for Understudied Populations

Data intensive Whole Genome Sequencing projects are central to the currently ongoing transformation in 21st century medicine. The challenge to utilize the collective genomic population data for personalized medicine in the UAE is threefold - lack of genomic data, capabilities to Big Genomic Data and finally to make sense of it. This presentation discusses scalable whole genome sequencing efforts to tackle the first challenge. For the latter two, we showcase the deployment of Big Data Technology.


Our Genomic Data Science framework will deploy and extend OpenCGA, a Hadoop/NoSQL based system for scalable genomic analysis. On this fundament, we show algorithmic approaches to formulate genotype-phenotype predictions for Complex Diseases as Machine Learning problems. To further tackle the issue of understudied populations, we demonstrate the use of Transfer Learning in order to utilize and adapt clinically relevant genetic knowledge from well-studied populations.

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Centre for Arab Genomic Studies
Level II, Al Nashwan Building , Al Mankhool Road, Bur Dubai

Khalifa University, UAE

Dr. Andreas Henschel earned his M.Sc. and PhD in Computer Science from Technical University Dresden, Germany in 2002 and 2008, respectively. He became Assistant Professor in 2011 at Masdar Institute, UAE. In 2018 he was announced Associate Professor at Khalifa University. He has published more than 50 peer reviewed journal papers and conference publications, mainly on the topics of Bioinformatics and Artificial Intelligence, which is also central to his post graduate teaching activities since 2012.

Exeter Genomics Laboratory, UK

Dr Julia Baptista is a scientist at the Exeter Genomics Laboratory leading the national exome service for NHS patients with rare genetic diseases.


Julia's work is focused on solving rare disease and ending the diagnostic odyssey for families. She is interested in how genomic testing, especially in early age, can improve outcomes for patients and their families and in how rare genomic variation impacts on human health and disease. A keen educator, Julia is a member of the European School of Genetic Medicine providing courses in genomics and cytogenetics to the international healthcare community and is an honorary lecturer in Genomic Medicine at the University of Exeter Medical School.


Julia is also the South West Genomic Laboratory Hub Rare Disease Scientific Lead for Genomic Education and has been elected a board member of the European Society of Human Genetics.

Rady Pediatric Genomic and Systems Medicine Institute

Shareef Nahas is a fellow of the American College of Medical Genetics and Genomics. He received his PhD in molecular toxicology and pathology laboratory medicine from the University of California, Los Angeles in 2008 and subsequently completed a postdoctoral fellowship in Clinical Molecular Genetics. He is currently the Chief Scientific Officer and Vice President Global Operations, Laboratory Services at Infinity BiologiX.


Prior to this, he was the Senior Director at the Rady Children’s Institute for Genomic Medicine, where he was responsible for managing and overseeing research and clinical diagnostic implementation of rapid Whole Genome Sequencing as well as the analysis, interpretation and delivery of results of genetic testing ordered for critically ill babies and children hospitalized in intensive care at Rady Children’s Hospital-San Diego and hospitals participating in RCIGM’s clinical trials.

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