Supporting Nalagenetics in their product development and regulatory activities, including adoption of WGS for pharmacogenomics and disease risk prediction.

Joined GIS to deliver the National Precision Medicine Program (NPMP), which aims to sequence the genome of 100K Singaporeans.Details:• Designed, developed and implemented a pipeline for QC of WGS results (https://bit.ly/2WmhPjG).• Drove a project within GA4GH-GHIF to standardise metrics for QC of WGS results in population-scale initiatives (https://bit.ly/3DeFDHn).• Led internal and external collaborations, including with industry partners, to extend the reportable range of… Show more Joined GIS to deliver the National Precision Medicine Program (NPMP), which aims to sequence the genome of 100K Singaporeans.Details:• Designed, developed and implemented a pipeline for QC of WGS results (https://bit.ly/2WmhPjG).• Drove a project within GA4GH-GHIF to standardise metrics for QC of WGS results in population-scale initiatives (https://bit.ly/3DeFDHn).• Led internal and external collaborations, including with industry partners, to extend the reportable range of our analysis pipeline (SVs, CNVs, CYP2D6 haplotypes) and characterise the variant landscape in the three Asian populations local to Singapore.• Contributed to contract negotiations and planning for phase 2 (100K genomes). Show less

Volunteered in a GIS-driven effort to set up two laboratories for COVID-19 testing.Details:• Coordinated the set up of the PCR platform to deliver COVID-19 diagnostic tests based on Fortitude 2.1 and Bio-Rad CFX96, with capacity of 10,000 tests per day.• Developed the PCR and clinical reporting workflows, and successfully defended them in our recent PHMC audit.• Responsible for training volunteers assigned to the PCR platform and monitoring the platform once we go live.

Details:• Involved in the set up of our pilot PHMC-accredited laboratory, with capacity of 1,000 tests per day.• Documented LIMS procedures for the sample plating area and delivered training to volunteers assigned to that station.• Participated in clinical validation: responsible for data analysis and validation report writing.

Contributed to the delivery of the 100,000 Genomes Project, gained experience in clinical WGS and developed leadership skills.Details:• Led a team responsible for validating changes to the WGS pipeline of our ISO 15189 Medical Laboratory.• Provided technical guidance and performed reproducible data analysis to evaluate the impact of changes to our established WGS pipeline (e.g. adoption of new sequencing platforms and analysis workflows).• Designed and implemented… Show more Contributed to the delivery of the 100,000 Genomes Project, gained experience in clinical WGS and developed leadership skills.Details:• Led a team responsible for validating changes to the WGS pipeline of our ISO 15189 Medical Laboratory.• Provided technical guidance and performed reproducible data analysis to evaluate the impact of changes to our established WGS pipeline (e.g. adoption of new sequencing platforms and analysis workflows).• Designed and implemented documentation procedures to keep track of validation test cases and outcomes, in compliance with our QMS.• Aligned with wet lab teams to define experimental design and interpret results, and with product development teams to communicate requirements.• Coordinated participation in EQA schemes and interpretation of results.• Participated in UKAS audits to maintain ISO 15189 accreditation. Show less

Details:• Built on previous role and extended technical expertise to variant calling and benchmarking (germline and somatic).• Involved in data analysis activities to validate changes to the current production pipeline. • Established a procedure to report measurement uncertainty in WGS-based tests, based on the calculation of credible intervals for calling performance metrics (https://github.com/Illumina/happyCompare).• Involved in defining standards for benchmarking germline… Show more Details:• Built on previous role and extended technical expertise to variant calling and benchmarking (germline and somatic).• Involved in data analysis activities to validate changes to the current production pipeline. • Established a procedure to report measurement uncertainty in WGS-based tests, based on the calculation of credible intervals for calling performance metrics (https://github.com/Illumina/happyCompare).• Involved in defining standards for benchmarking germline small variants, in collaboration with GA4GH.• Provided analytical support to customer queries, and involved in regular interactions with the customer.• Presented project outcomes internally and externally. Show less

Details:• Involved in high throughput data analysis and delivery of WGS results for RUGD and cancer patients in an ISO 15189 laboratory (100,000 Genomes Project).• Experience with QMS activities: established competencies and work instructions, delivered training, raised NCs and CAPAs.• Developed a solid understanding of genome QC metrics.• Automated daily production tasks, e.g. reporting and sample tracking.

Received a fellowship to join the EMBL International PhD Programme and further developed skills in NGS data analysis.Details:• PhD thesis: RNA sequencing for the study of splicing (https://doi.org/10.17863/CAM.15986).• Investigated transcriptome diversity and the extent to which it relates to protein diversity.• Studied splicing alterations in renal cancer as part of an ICGC project (CAGEKID).• Developed a tool to visualise changes in splicing across conditions… Show more Received a fellowship to join the EMBL International PhD Programme and further developed skills in NGS data analysis.Details:• PhD thesis: RNA sequencing for the study of splicing (https://doi.org/10.17863/CAM.15986).• Investigated transcriptome diversity and the extent to which it relates to protein diversity.• Studied splicing alterations in renal cancer as part of an ICGC project (CAGEKID).• Developed a tool to visualise changes in splicing across conditions (https://github.com/mgonzalezporta/SwitchSeq).• Explored the role of splicing in cell cycle progression and applied innovative analysis strategies based on intronic reads.• Explored the integration of transcriptomics (RNA-seq) and proteomics (SWATH-MS) data for the validation of differential splicing events.• Delivered training in RNA-sequencing in multiple occasions (https://github.com/mgonzalezporta/TeachingMaterial).• Thesis supervisor: Dr. Alvis Brazma. Show less

Embarked on an additional research internship before starting my PhD and gained experience in NGS for the first time.Details:• Investigated differences in gene expression and alternative splicing in human populations by analysing RNA-seq data.• Project supervisor: Dr. Roderic Guigó.

Involved in a research internship in parallel to my studies which allowed me to venture into the field of Bioinformatics.Details:• Developed tools to determine the interplay between CpG islands and miRNAs in the regulation of gene expression in humans.• Project supervisor: Dr. Antoni Romeu.

Sought to expand my Bioinformatics skills during my BSc thesis project.Details:• BSc thesis: Evolutionary insights into metazoan miRNA expression and function.• Implemented scripts to expand an existing database (Bgee) with publicly available miRNA expression data from several species and technologies.• Analysed the new data to compare miRNA expression patterns across tissues and species.• Thesis supervisors: Dr. Julien Roux and Dr. Marc Robinson-Rechavi.