IAGVDHTS · Integrated approaches for genomic variation discovery using high throughput sequencing
FP7 — People (Marie Curie Actions)
- Duration
- 2012-04-01 → 2016-03-31
- EU contribution
- €100,000
- Participants
- 1
- Scheme
- MC-CIG
Lines connect the coordinator with its partners.
Results in brief
Integrated approaches for genomic variation discovery using high throughput sequencing
IAGVDHTS aimed to develop and improve methods to discover genomic variation using the high throughput sequencing (HTS) platforms. For this purpose, we proposed new algorithms and improve existing ones to enable the discovery of previously uncharacterized forms of genomic structural variation. Another aim of the IAGVDHTS project was to take advantage of different strengths of different sequencing platforms and different library construction methods. This project aimed to fill in the efficient analysis gap: through integrating detection approaches and building a single, “one stop” genome analysis package, we will reduce the computational workload for variant discovery. The proposed research is transformative of several fields of research because it will enable fast analysis of HTS data by minimizing computational overhead of using many different tools and read mappers for different classes of variation, which will hopefully lead to faster discoveries in science and medicine. During this project we worked on 1) algorithms to improve speed, accuracy, and sensitivity of read mapping tools, 2) algorithms to map reads from newer sequencing platforms, 3) tools to characterize copy number variation using data from different sequencing platforms, 4) algorithms to discover large genomic inversions using pooled clone sequencing data, and 5) a new tool to incorporate different sequence signatures for structural variation into a single package. The project resulted in one direct journal publication, one indirect journal publication, and one more indirect journal publication that is currently under review. We are also preparing one more direct journal publication to be submitted by the end of May 2016 to the Genome Biology journal, and the current preprint of this manuscript is already available on the preprint server bioRxiv. During the project, one M.Sc. student was supported, who graduated in August 2015, and continued as a PhD student. A new Ph.D. student joined the project at a late stage (March 2016), and he continues to work on problems in line with this project. We also supported one internship student from India and one from Iran was also supported for three months each in Summer 2014. The project website is available at http://donut.cs.bilkent.edu.tr/support-mc-cig.html
Data: CORDIS, © European Union
Project objective
The new sequencing technologies revolutionize genomics as they promise low-cost, high-throughput sequencing (HTS) of both new species and different individuals to better analyze the patterns of genetic variation. These “next-generation” platforms started to contribute our understanding of human genome diversity with the 1000 Genomes Project that employs the HTS methods to produce the most detailed map of human variation. Other large scale sequencing projects are being initiated to characterize genomes to assess characteristics of human genome diversity, to find genetic causes for disease, and infer the evolutionary history of species. Although we can now generate data at a rate previously unimaginable, the analysis of the data is proceeding at a slower pace as currently available algorithms to analyze HTS data show different biases against different classes of variation. There is a need to forge an alliance between computer science and genomics to devise better methods to use the massive amount of sequence data. Here we propose to develop novel algorithms to comprehensively and quickly discover all forms of genomic variants including point mutations, indel polymorphisms and structural variation while resolving inconsistencies among different variants to accurately identify normal and disease-causing variation. The proposed project, when completed, will help better make use of the data generated by the HTS platforms by enabling complete and accurate analysis of genomic variants in newly sequenced human individuals, and non-human organisms. Better analysis in a timely fashion also opens the way to discover more variants that might be medically relevant. Moreover, accurate and complete characterization of genomic variants within the most complex regions of the human genome may help solve the problem of “missing heritability” in complex disease that is not readily addressed by conventional genome-wide association studies.
Original text from CORDIS.
Participants
- BILKENT UNIVERSITESI VAKIF · Bilkent AnkaraCoordinatorTürkiye
Links
Data: CORDIS, © European Union