The development of several high throughput analytical approaches in molecular biology has revolutionized genomics. In particular, Next Generation Sequencing has wide application to many functional genomics settings. This course will introduce a range of these applications, focusing on the nature of data generated, its strengths and limitations as well as computational and statistical approaches used to analyse genomic and transcriptomic datasets in various contexts.
During the course, students will acquire: - A knowledge of the scope of bioinformatics in genomics and functional genomics - A detailed appreciation of the nature of Next Generation Sequencing data from different platforms, their characteristics, advantages and weaknesses - An understanding of fundamental aspects of experimental design in genomics and transcriptomics - An understanding of data quality checking and filtering approaches - An appreciation of theoretical considerations underlying data analytical approaches in genomics and transcriptomics (genome assembly and annotation, variant detection, gene annotation, quantitative analysis of gene expression, analysis of small non-coding RNAs) - The ability to critically interpret results of genome wide studies. - Experience in the evaluation and synthesis of results of genomics experiments through the preparation and presentation of a scientific poster.
Expected learning outcomes
Lesson period: First semester
(In case of multiple editions, please check the period, as it may vary)
1) Historical perspective and the role of bioinformatics in genomics 2) NGS technologies, read lengths, error profiles, base quality scores, data formats, data quality control. 3) Preparation of sequencing libraries, coverage biases and the impact of PCR, targetted resequencing, indexed libraries. 4) Variant discovery and structural variation between genomes 5) Di novo genome assembly 6) Annotation of genes, transcripts and alternative splicing 7) Quantitative transcriptomics 8) Analysis of small non-coding RNAs 9) Analysis of ChIP-Seq data 10) In silico promoter analysis 11) Innovative applications of NGS in genomics 12) Poster presentation sessions
REFERENCE MATERIAL Articles provided by the teacher.
PREREQUISITES AND EXAMINATION PROCEDURES Participants should posses a sound grasp of basic concepts in molecular biology (DNA replication, transcription, translation, the genetic code, PCR). The exam consists of 2 parts with equal wieght (50%) 1) A written exam (around 15 multiple choice questions and 3 or 4 open questions to which short answers must be provided. Multiple choice and open questions carry the same total weight (50%)). 2) The preparation and brief presentation to the class of a scientific poster, summarizing a relevant paper. These posters are produced by groups of 3 students and the choice of paper can be guided by the teacher.
TEACHING METHODS Frontal teaching with a high level of teacher interaction supported by projected teaching material which is available to students from a dedicated website. Extensive discussions to allow development of critical faculties and encourage constructive individual involvement in the teaching/learning process. Meetings with the teacher to discuss preparation of scientific posters
PROGRAM INFORMATION Additional information available through direct contact with the teachers