System Analyst (Data Integration)

About Hong Kong Genome Institute

The Hong Kong Genome Institute (HKGI), established and wholly owned by the Hong Kong SAR Government, commenced full operations in 2021.  With the vision “to avail genomic medicine to all for better health and well-being”and supported by the Health Bureau, HKGI works in close collaboration with the Department of Health, Hospital Authority, medical schools of local universities and other stakeholders to accelerate the development of genomic medicine in Hong Kong along four strategic foci: integrate genomics into medicine, advance research, nurture talents and enhance public genomic literacy.

As the first step towards achieving its vision, HKGI launched the Hong Kong Genome Project (HKGP) in 2021. As the city’s first large-scale genome sequencing project, HKGP serves as a catalyst to benefit patients and their families with more precise diagnosis and personalised treatment through whole genome sequencing. It also aims to establish genome database of the local population, testing infrastructure and talent pool to address the healthcare needs of Hong Kong in the long run.

For more information, please visit www.hkgp.org

System Analyst (Data Integration)

The System Analyst (Data Integration) will focus on integrating HKGI’s data lakehouse platform with internal systems and external partners.  The incumbent will be responsible for designing, implementing, and maintaining efficient data flows between HKGI’s data lakehouse and other systems while ensuring data quality, security, and compliance.  The incumbent will assume the following responsibilities:

Key Responsibilities:

• Design, develop, and maintain APIs and data transfer mechanisms (e.g., RESTful APIs, AWS S3 Upload) for seamless data exchange with external systems
• Design and implement strategies for data replication, failover, and disaster recovery to ensure high availability and data durability, leveraging clustering technologies (e.g., Kubernetes) and load balancing
• Establish and enforce data security policies, including access controls, encryption (data at rest and in transit), and audit logging, to protect sensitive genomic and clinical data
• Analyse system performance, identify bottlenecks, and implement optimisations to enhance data throughput, response times, and overall system efficiency
• Implement and monitor data validation processes, lineage tracking, and quality control checks to ensure the accuracy, consistency, and reliability of genomics data throughout its lifecycle
• Collaborate with bioinformaticians, software engineers, and stakeholders to design and implement data integration solutions for various genomics data types (e.g., FASTQ, BAM, VCF, short-reads, long-reads) and clinical data (FHIR, HL7)
• Perform any other duties assigned by senior officers

Requirements:

We are seeking a high-calibre candidate for the post of System Analyst (Data Integration)who possesses:

• A bachelor's degree in Computer Science or a related field
• At least 6 years of relevant hands-on working experience in data integration, software engineering, or a similar role
• Solid experience and deep understanding of data integration patterns within a hybrid environment
• Proven experience in the full lifecycle of RESTful API development, including design, implementation, testing, deployment, and maintenance
• Strong understanding and solid experience of API security best practices, including implementing authentication (e.g., OAuth, JWT), authorisation, encryption, and rate limiting
• Expertise in data serialisation formats (e.g., JSON) and API documentation tools (e.g., OpenAPI)
• Solid experience in implementing robust and resilient data transfer protocols (e.g., SFTP, HTTPS, AWS S3)
• Hands-on experience in developing microservices that interacts with enterprise messaging systems (e.g., Apache Kafka and RabbitMQ)
• Proven track record in designing and implementing data storage and management systems, demonstrating deep expertise in data modelling, database design (PostgreSQL, MySQL and MongoDB), and data warehousing principles
• Proficiency in at least one of these programming languages: NodeJS, Java or C++
• Hands-on experience with clustering technologies (e.g., Kubernetes) and good understanding of load balancing principles

Preferred Attributes

• Experience with healthcare interoperability standards, particularly FHIR and HL7.
• Knowledge of genomics data formats (e.g., FASTQ, BAM, VCF) and standards (e.g., CRAM)
• Prior experience in genomics is a plus

Office Location:
Hong Kong Science Park, Shatin

Remuneration:

Successful candidate will be offered attractive remuneration and be appointed on an initial two-year contract (subject to mutual agreement for contract renewal).
 

Application:

Interested parties should send full resume enclosing current and expected remuneration together with availability to HKGI on or before 3 September 2025. Only shortlisted candidates will be notified.

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