Periodic Reporting for period 4 - IndiGene (Genetics of Individuality)
Période du rapport: 2023-08-01 au 2025-07-31
Individuality is both the defining feature of us and an important factor that affects our well-being. Genetic, environmental and random variation must all be understood if we hope to realize personalized medicine and fully understand biological systems across species. Our central aim is to investigate the sources of variation that result in differences between individuals, focussed primarily on understanding the contribution and interactions between genetic, environmental and stochastic variation with respect to trait association mapping in Medaka fish.
This project makes use of the unique properties of medaka fish. Medaka can be fully inbred from the wild, are fertile and we have already sequenced a panel of 111 inbred medaka lines originating from a single natural population.
We will carry out in-depth profiling of these fish at multiple scales, ranging from molecular measurements to full organisms. We will analyse a number of traits in wild fish from the same source population, which will both increase our research potential and place our discoveries in the same context as human observational studies. A particular focus will be integrating this information across the cardiovascular systems, especially in comparison to human disease. A central strategy that we will use across most of our trait association mapping experiments is the full phenotyping across all MIKK panel lines followed by the design and selection of specific lines showing differential phenotype distributions for these traits to cross into F1 and F2 generations. Following the successful generation of large F2 populations all F2 offspring are then sequenced and phenotyped allowing genetic association mapping to be performed using techniques such as linear mixed models. Critically, this approach allows us to have a high level of control on all mentioned sources of variation and to explicitly test their interaction terms during association testing.
We will provide and distribute the inbred medaka lines to other research groups who can apply their own projects across the panel. This study will focus on the question of distinguishing between variation that occurs due to genetic, individual and environmental effects. This will lead to a more complete understanding of variation related to human disease and well-being.
This project makes use of the unique properties of medaka fish. Medaka can be fully inbred from the wild, are fertile and we have already sequenced a panel of 111 inbred medaka lines originating from a single natural population.
We will carry out in-depth profiling of these fish at multiple scales, ranging from molecular measurements to full organisms. We will analyse a number of traits in wild fish from the same source population, which will both increase our research potential and place our discoveries in the same context as human observational studies. A particular focus will be integrating this information across the cardiovascular systems, especially in comparison to human disease. A central strategy that we will use across most of our trait association mapping experiments is the full phenotyping across all MIKK panel lines followed by the design and selection of specific lines showing differential phenotype distributions for these traits to cross into F1 and F2 generations. Following the successful generation of large F2 populations all F2 offspring are then sequenced and phenotyped allowing genetic association mapping to be performed using techniques such as linear mixed models. Critically, this approach allows us to have a high level of control on all mentioned sources of variation and to explicitly test their interaction terms during association testing.
We will provide and distribute the inbred medaka lines to other research groups who can apply their own projects across the panel. This study will focus on the question of distinguishing between variation that occurs due to genetic, individual and environmental effects. This will lead to a more complete understanding of variation related to human disease and well-being.
The IndiGene project has resulted in several major achievements and scientific output throughout the course of the grant. There are at least 9 publications that are a direct result of the grant and numerous further publications and “spin off” studies that have been made possible by the resources we have generated and the experimental and computational techniques that we have developed.
We now have fully functioning experimental and computational pipelines to leverage the MIKK panel for gene to trait and gene to environment to trait mapping using large scale F2 cross designs. All of the datasets generated as part of the IndiGene project have or will be made publicly available via the EMBL-EBI service EGA and have already been used my multiple researchers to drive independent research. We have developed extensive computational workflows incorporating multiple analytical techniques to allow these resources to be used in an efficient and robust way most of which have been published in peer reviewed journals. We have also put in place safeguards to secure the MIKK panel breeding stocks into the future, having at least two locations where a copy of the full MIKK panel in maintained. Finally, we have developed extensive experimental and breeding protocols to allow crosses to be performed efficiently, being able to generate thousands of offspring, development and application of multiple high through put phenotyping assays and efficient tooling for mutagenisis experiments (experimental validation) at scale.
All together the IndiGene project has been a resounding success and resulted in many new scientific discoveries, peer reviewed publications and bot experimental and computational resources that will be high value to the community many years into the future.
We now have fully functioning experimental and computational pipelines to leverage the MIKK panel for gene to trait and gene to environment to trait mapping using large scale F2 cross designs. All of the datasets generated as part of the IndiGene project have or will be made publicly available via the EMBL-EBI service EGA and have already been used my multiple researchers to drive independent research. We have developed extensive computational workflows incorporating multiple analytical techniques to allow these resources to be used in an efficient and robust way most of which have been published in peer reviewed journals. We have also put in place safeguards to secure the MIKK panel breeding stocks into the future, having at least two locations where a copy of the full MIKK panel in maintained. Finally, we have developed extensive experimental and breeding protocols to allow crosses to be performed efficiently, being able to generate thousands of offspring, development and application of multiple high through put phenotyping assays and efficient tooling for mutagenisis experiments (experimental validation) at scale.
All together the IndiGene project has been a resounding success and resulted in many new scientific discoveries, peer reviewed publications and bot experimental and computational resources that will be high value to the community many years into the future.
We have sequenced to entire MIKK panel using Oxford nanopore (ONT) long read data. This will also us to build individual assemblies for all MIKK panel lines and to create a graph based 'pan genome' reference datasets for the MIKK panel.
This dataset also allow us to call methylation signatures across the entire panel in brain (the tissue that we sequenced) and we have been able to call both standard methylation (5mC) and hydroxymethylation (5hmC). Ongoing spin off project are underway to assess the levels of both 5mC and 5hmC genome wide in different tissues from lines of the MIKK panel, this work has already uncovered new discoveries related to 5hmC.
This dataset also allow us to call methylation signatures across the entire panel in brain (the tissue that we sequenced) and we have been able to call both standard methylation (5mC) and hydroxymethylation (5hmC). Ongoing spin off project are underway to assess the levels of both 5mC and 5hmC genome wide in different tissues from lines of the MIKK panel, this work has already uncovered new discoveries related to 5hmC.