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Developmental Biology - Transposons

Jumping Genes Can Cause Rare Child Disorders

Jumping genes can cause genetic changes in patients with undiagnosed neurodevelopmental disease...


The largest study of its kind into childhood developmental disorders has discovered that jumping genes cause genetic changes in some patients with undiagnosed neurodevelopmental diseases.

The research from the Wellcome Sanger Institute and its collaborators in the National Health Service (NHS) Regional Genetics services in the United Kingdom, enabled genetic diagnoses for three children with previously undiagnosed rare developmental diseases. All the children were enrolled in the Deciphering Developmental Disorders project and their diagnoses will help families access support and understand disease risks for any future children with such disorders. The research reported October 11th, 2019 in Nature Communications, is a step towards providing explanations for additional families with children with undiagnosed neurodevelopmental disorders.

Every year in the UK, thousands of babies are born with errors in their DNA that mean they do not develop normally. These genetic changes, or mutations, can lead to conditions such as intellectual disability, epilepsy, autism or heart defects. There are over 1,000 recognised genetic causes. However, many individual developmental disorders are so rare that genetic causes are not known.
Jumping genes, or transposons, are pieces of DNA that can jump from place to place in the genome. These genomic nomads sometimes land in the middle of genes and stop them from working. However, it wasn't known how often transposons lead to rare developmental disorders.

The Deciphering Developmental Disorders (DDD) project was launched in 2010 aiming to provide genetic diagnoses for families of children with severe undiagnosed developmental disorders. In this study, researchers studied genomes of nearly 10,000 children enrolled in the project, looking for jumping genes not present in their parents.

Researchers found jumping genes were likely to be the cause of developmental disorders in three previously undiagnosed patients. These transposons had jumped into different genes in each patient, preventing those genes from functioning properly. The damaged genes provided crucial genetic diagnoses for the three patients, allowing their families to understand their child's disorder better. The study also revealed a transposon in a fourth patient who had been diagnosed previously.
Diagnoses are extremely important for people as they allow families with the same genetic conditions to meet and access support. They also allow families to understand the risk for any further children they may have.

Eugene Gardner PhD, the first author from the Wellcome Sanger Institute, explains:
"This is the first time we have been able to estimate the contribution of jumping genes, transposons, in a large cohort sequencing rare developmental disorders. We found transposons were the likely cause of symptoms of four of the 9,738 patients, three of whom had not been previous diagnosed. These are significant diagnoses for the families involved, and another step on the path to understanding causes of developmental disorders."
To carry out this study, the scientists needed to develop and validate an analytic pathway that could quickly assess patient genomes at scale, looking for transposon-created variants. This software is openly available for academic use and can be used to help diagnose rare transposon events in future patients.

Matthew Hurles PhD, senior author from the Wellcome Sanger Institute:
"Diagnoses are extremely helpful for families, allowing them to access support. Previously, transposons in rare developmental disorders had been poorly understood. Now, we have developed a strategy to analyse patient genomes for transposons that cause their symptoms. Our study suggests routine clinical sequencing could assess patient genomes for damaging transposon events, which could allow more children to be diagnosed."

Abstract
Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient’s symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

Authors
Eugene J. Gardner, Elena Prigmore, Giuseppe Gallone, Petr Danecek, Kaitlin E. Samocha, Juliet Handsaker, Sebastian S. Gerety, Holly Ironfield, Patrick J. Short, Alejandro Sifrim, Tarjinder Singh, Kate E. Chandler, Emma Clement, Katherine L. Lachlan, Katrina Prescott, Elisabeth Rosser, David R. FitzPatrick, Helen V. Firth and Matthew E. Hurles.

About the Deciphering Developmental Disorders study:
The Deciphering Developmental Disorders (DDD) study aims to advance clinical genetic practice for children with developmental disorders. Children were recruited into the study between 2010 and 2015.

The DDD study is no longer recruiting new patients. If your child has an undiagnosed developmental disorder please speak with your paediatrician or GP about the most appropriate tests or referral into other studies.

The DDD team is absolutely committed to analysing and re-analysing all the genomic data from families in the study over the coming five years to try to find a diagnosis for as many children as possible.

More information about the DDD study can be found at http://www.ddduk.org

The software for identifying transposon events is available at http://melt.igs.umaryland.edu/


Acknowledgments
The authors wish to thank the Wellcome Sanger Institute sequencing facility staff for their assistance in preparing samples and performing sequencing experiments, all members of the DDD study for providing valuable comments during data analysis and the paper preparation, and the DDD families—this work would not be possible without their confidence and support. We also thank Panayiotis Constantinou for helping to curate known MEI-associated cases and for annotation of affected parents as well as Hilary Martin for constructive comments during manuscript preparation. We also wish to acknowledge Jeffrey Barrett and Caroline Wright for their leadership of the DDD. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number: HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number: WT098051]. The views expressed in this publication are those of the author(s), and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. This study makes use of DECIPHER [http://decipher.sanger.ac.uk]), which is funded by the Wellcome.

The Wellcome Sanger Institute
The Wellcome Sanger Institute is a world leading genomics research centre. We undertake large-scale research that forms the foundations of knowledge in biology and medicine. We are open and collaborative; our data, results, tools and technologies are shared across the globe to advance science. Our ambition is vast - we take on projects that are not possible anywhere else. We use the power of genome sequencing to understand and harness the information in DNA. Funded by Wellcome, we have the freedom and support to push the boundaries of genomics. Our findings are used to improve health and to understand life on Earth. Find out more at http://www.sanger.ac.uk or follow us on Twitter, Facebook, LinkedIn and on our Blog.

About Wellcome
Wellcome exists to improve health by helping great ideas to thrive. We support researchers, we take on big health challenges, we campaign for better science, and we help everyone get involved with science and health research. We are a politically and financially independent foundation. https://wellcome.ac.uk/


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Oct 15 2019   Fetal Timeline   Maternal Timeline   News  


Jumping Genes may creat child disorders

Transposons can be the origin of developmental disorders. This knowledge can help affected families understand as well as get assistance for epilepsy, autism or heart defects that may result.


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