Case Studies | Healthcare & Life Sciences

A secure, compliant genomics foundation on AWS

HealthOmics Analysis Pipeline

About

A Healthcare & Life Sciences business working with Cloud Combinator on AWS. The client is anonymised at their request.

Challenge

The challenge had three focus areas.

A secure landing zone

Genomic patient data demands strong guardrails from day one. The client needed an AWS account with least-privilege IAM, single sign-on and transit-gateway networking across multiple availability zones, ready for regulated workloads.

Compliant cross-border transfer

Patient datasets of sixty to one hundred gigabytes each had to move from the partner lab's S3 bucket in India to the client's bucket in London, meeting GDPR and data-sovereignty needs, without runaway storage costs or transfer failures.

A validated analysis pipeline

The client needed the AWS HealthOmics ctDNA variant-calling workflow deployed, parameterised and validated on a pilot cohort, with outputs and run metadata organised so downstream analytics could build on them.

Solution

Patient sequencing data lands in the partner laboratory's Amazon S3 bucket in India. AWS DataSync performs cost-optimised, cross-account batch transfers into the client's S3 bucket in the London region, governed by cross-account bucket policies and default encryption, with AWS Lake Formation applied to the data and Amazon CloudWatch alarms watching for transfer failures. Lifecycle rules move data from Standard to Intelligent-Tiering and on to Glacier as access patterns change.

60-100 GB

Per-patient genomic dataset transferred lab to cloud

4-6 wks

Planned delivery window for the phase-one foundation

2 AZs

Multi-availability-zone VPC landing zone with least-privilege IAM

By the numbers:

  • 60-100 GB - Per-patient genomic dataset transferred lab to cloud
  • 4-6 wks - Planned delivery window for the phase-one foundation
  • 2 AZs - Multi-availability-zone VPC landing zone with least-privilege IAM
Changes

The engagement delivers a secure, compliant genomics foundation that unblocks patient-data ingestion and runs the client's ctDNA analysis end to end. Acceptance is defined against a production-ready landing zone, an automated cross-border transfer workflow and a validated HealthOmics pipeline. The timeline below is the planned delivery window for this phase.

  • Secure foundation — A landing zone with least-privilege IAM, single sign-on through IAM Identity Center and transit-gateway networking, built for regulated genomic workloads.
  • Compliant transfer — Cross-account, encrypted AWS DataSync transfers move large patient datasets from India to London in line with GDPR and data-sovereignty needs.
  • Cost control — S3 lifecycle rules tier data from Standard to Intelligent-Tiering to Glacier, and CloudWatch alarms flag any transfer failures.
  • Validated analysis — The AWS HealthOmics ctDNA workflow produces validated variant calls and QC outputs, with run metadata tracked in DynamoDB.
  • Handover — A landing-zone playbook, data-transfer runbook, pipeline configuration and a handover workshop leave the client ready to operate the platform.

With a secure, compliant foundation in place, the client is set up for its next steps, from bringing custom bioinformatics such as Snakemake onto AWS to evaluating Amazon Bedrock and a full Well-Architected review, ready to scale its genomics platform with confidence.

AWS Stack

AWS HealthOmics

For the managed ctDNA variant-calling genomics workflow.

AWS DataSync

For secure, cost-optimised cross-account data transfer.

Amazon S3

For tiered storage of raw and processed genomic data.

AWS Lake Formation

For governed access to the data lake.

AWS IAM Identity Center

For single sign-on and least-privilege access.

Amazon DynamoDB

For run metadata and traceability.

Amazon CloudWatch

For transfer-failure alarms and monitoring.

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