Sebastià Franch | Researcher at Consorci Institut D'Investigacions Biomediques August Pi I Sunyer

Researcher • Doctorate/PhD

Consorci Institut D'Investigacions Biomediques August Pi I Sunyer • Barcelona, Spain

After my biochemistry degree, I shared my passion for computers, informatics and basic research. Therefore, I decided to enrol in the CIBERehd bioinformatics platform during my master degree, under Dr. J.J. Lozano supervision. I learned and improved my software coding skills and performed germline copy number variant identification through exome sequencing data analysis from hereditary colorectal cancer patients. Lately, I was employed by Genetic predisposition to colorectal cancer research group, led by Dr. Castellvi-Bel, where I began my PhD studies aiming to identify new predisposition variants to colorectal cancer.

During this period, I generated an annotation and filtration pipeline to prioritize those potential germline predisposition variants to colorectal cancer (R based), either single nucleotide variants or copy number variants, improving the past manual filtration workflow used by the group. I contributed to generate a shiny implemented web-based application for mutational profile extraction: MuSiCa. Moreover, I performed gene expression array data analysis to assess gene dosage in colorectal cancer affected families carrying validated germline copy number variants.

Recently, I have been working in the development of a second shiny app, CNApp, to perform copy number alterations analysis. It is crucial to characterize copy number tumor genomic profiles due to their correlation with oncogenic treatment outcomes. For that, comprehensive analysis integrating copy number alterations with molecular and clinical features are mandatory. CNApp web tool easily allows for that by generating genome-wide profiles and by computing focal, broad and global alterations scores, establishing associations with clinical and biological annotations. More information about CNApp can be found at http://bioinfo.ciberehd.org/CNApp.

Skills and expertise

Omics and technologies

Copy number alteration databases

Software tools and databases

CNVkit
CoNIFER
Control-FREEC
DELLY
DNAcopy
ExomeDepth
GATK
SAMtools
VarScan

Maths and IT

Bioinformatics
Data Analysis
Data Mining
Databases

Life Science

Biochemistry

Health Science

Translational Research

General Skills

Communication
Data curation
Public speaking
Scientific writing
Technical writing
Training

Programming languages

Python
R

Tools maintained

CNApp

Web

Desktop

CNApp / Copy Number Alteration Application

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Performs integrative analysis of copy number alterations (CNAs). CNApp is a web tool that allows assessment of CNAs and identification of relevant functional implications. This software uses…