Amir Naar

- Regular update of the variants database for Alamut products (ClinVar, dbSNP, Decipher, RefSeq, Ensembl)

- System redesign in Python of the ClinVar data integration in Alamut Visual (reference Genome Browser in the domain used by > 650 hospitals):

ClinVar is the most up-to-date and informative database that clinicians need to interpret Variant data and possible molecular therapy.

Due to outdated processes in C++, this catalog was not updated anymore and outdated data were available on the track of the Genome Browser. This involved decrypting the available processes in C++, understanding the functioning of all the different database involved internally due to a lack of process description, and the development from scratch in Python of a solution to ensure a regular update of ClinVar in Alamut Visual (1x/month fitting the availability of the ClinVar public data)

- MANE prioritization integration in SOPHiA DDM:

The Matched Annotation from NCBI and EMBL-EBI (MANE) project produces a matched set of high-confidence transcripts that are identically annotated between RefSeq and Ensembl/GENCODE. This enhancement provides a more comprehensive annotation by improving transcript mapping on the panel's target regions, without impacting the detection capabilities or accuracy of the big gene panel as SOPHiA Exome Solution.

- Major contribution to the refinement of the gene panels and the integration of MANE prioritization for large panel products. Among these products: CES_v3, Twist_HCExome, WES_v1

- Fast-track update in SOPHiA DDM with the migration of the release kit (each 2 weeks)

- Maintenance of the Genome Browser backend.

- Internal / External Support

Personalized cancer medicine (targeted treatments). NGS Data analysis.

- Development and maintenance of pipelines to treat and analyze different types of tumors in somatic and constitutional genetics for diagnosis: lung cancer, colon cancer, melanoma, glioma, hematological malignancies, breast / ovarian cancer in particular.

- Variant calling (GATK, samtools, FreeBayes), variant annotation (ANNOVAR, snpEff), reporting.

- Management of NGS data from different types of sequencers: MiSeq, NextSeq, NovaSeq, Vela, S5XL.

- Resolution of routine issues related to the activity of the Department of Biology and Medical Pathology.

- Involvement in accreditation procedures, quality documentation.

- Management, maintenance, development of analyzes in personalized medicine for translational research (MOSCATO, SAFIR, OncoMine, OncoLung ...).

- Php, MySQL, Perl, Html, JavaScript.

Personalized cancer medicine (targeted treatments)

- Analysis and management of NGS data.

- Pipeline developments to analyze various types of tumors: lung cancer, colorectal cancer, melanoma, glioma, hematologic malignancies, breast/ ovarian cancer in particular.

- Data processing: fastqc, cutadapt, bwa, samtools, picards, GATK, FreeBayes...

- Variant calling and annotation ; reports generation in pdf (LaTex), Excel, HTML...

- Unix/Linux OS, Windows

- Perl, Python, Bash, Java, Html, JavaScript