🧩 Exploring Haplotype Assembly and Methylation
Pablo Angulo Lara enjoyed a fantastic opportunity to undertake a research secondment at Oxford Nanopore Technologies (ONT) from July to September 2024, under the guidance of Aino Järvelin.
My main objective? To design a pipeline for performing haplotype assembly at the full-chromosome level in samples affected by aneuploidy and to analyze methylation data obtained through gDNA sequencing using Nanopore, with the goal of investigating haplotype-specific regulation at the methylation level.
What I Learned 🎓
During my time at ONT, I gained hands-on experience in:
✅ Designing pipelines and workflows for analyzing genomic sequencing data from Nanopore.
✅ Methods for haplotype assembly and differential methylation analysis from Nanopore sequencing data.
✅ Analyzing sequencing data from samples affected by aneuploidy, dealing with high noise and unexpected results.
✅ Implementing new types of analysis and software, including tools like Modkit for methylation data.
The pipelines I developed during this experience will be crucial for my future research, particularly in haplotype assembly and genome-wide methylation analysis. The knowledge gained here will directly inform my thesis project and enhance the quality of the analyses I will conduct in the coming months.
Challenges and Takeaways 🧩
One of the main challenges was implementing new analytical techniques, especially when dealing with methylation data and using new software like Modkit. Additionally, analyzing real aneuploidy data presented unexpected results and a higher degree of noise than anticipated, but this only added to the learning process.
Impact 🔝
Beyond the technical training, this secondment allowed me to experience working in a company environment, offering valuable insight into the industry setting. It was also a rewarding personal journey, exploring a new city like Oxford, meeting new people, improving my language skills, and gaining exposure to new experiences.
This secondment has significantly shaped my future research goals, and I am excited to apply everything I’ve learned moving forward. I’m extremely grateful for the opportunity and support from Aino Järvelin and the ONT team.
Looking forward to future collaborations and applying these techniques to my thesis!
