Case studies

Transforming Clinical Diagnostics: Migrating Excel-Based NGS Workflows to a Scalable Web Platform

Overview

Excelra partnered with a leading biotech company to modernize its Genomic Variant Analysis workflow. By replacing manual, Excel-based processes with a scalable web platform, the solution reduced manual effort by 70%, improved turnaround time by 50%, and ensured 100% data integrity and zero compliance gaps. This transformation enabled higher diagnostic accuracy, better team collaboration, and faster, audit-ready operations.

Our client

Our client

A leading biotech company specializing in clinical genetic testing and Next-Generation Sequencing (NGS). Known for delivering actionable insights for patient care, the client needed a modern, scalable solution to improve the accuracy, compliance, and throughput of its diagnostics workflow.

Client’s challenge

Client’s challenge

  • Relied on error-prone, Excel-based genomic variant analysis workflows.
  • Faced high manual effort and limited scalability.
  • Lacked end-to-end audit trails and traceability.
  • Experienced delays due to fragmented, manual annotation and review.
Client’s goals

Client’s goals

  • Eliminate manual inefficiencies via automation.
  • Improve data accuracy and reduce human error.
  • Ensure full auditability and compliance readiness.
  • Enable collaboration and faster decision-making via a unified platform.

Our approach

Excelra took a consultative and phased approach to solution delivery, ensuring that both technical and clinical considerations were addressed:

  1. Discovery & Workflow Mapping: Conducted stakeholder interviews to map current workflows and identify key pain points.
  2. Requirements Consolidation: Captured functional, data, and compliance needs to define a future-ready blueprint.
  3. Logic Extraction & Translation: Converted Excel macros and rules into scalable backend logic for the web application.
  4. Phased Development & Testing: Rolled out features incrementally for faster feedback and smooth adoption.
  5. User Enablement & Change Management: Delivered training, manuals, and live support for seamless onboarding.

Our solution

Building a scalable, audit-ready diagnostics platform

To address the client’s challenges and goals, we implemented comprehensive three-tiered architecture designed to streamline the genomic variant analysis workflow, enhance data accuracy, and improve operational efficiency. The solution included the following key components:

Tier 1: Web application

  • Centralized variant review, project tracking, and collaboration.
  • Real-time auditability and submission status visibility.
  • Intuitive interface for faster variant annotation and approval.

Tier 2: Data ingestion & curation

  • Automated JSON ingestion to eliminate manual entry.
  • Applied client-defined scripts for preprocessing and validation.
  • Used Apache Event Hub for audit trail logging and monitoring.

Tier 3: MS SQL database

  • Structured SNV/CNV and variant library storage.
  • Full audit trail capture for every workflow step.
  • Fast, reliable access to curated diagnostic data.

Implementation highlights

  1. Mapped and customized workflows through collaborative sessions.
  2. Deployed incrementally to minimize disruption.
  3. Trained users with tailored modules to drive adoption.
Technical-Architecture-scalable-ngs-diagnostics-platform

Figure: Technical architecture

Impact and results

  • 70% reduction in manual interventions
  • 50% faster variant classification turnaround
  • 100% data integrity through SQL-based validation
  • 0 compliance gaps with real-time auditability
scalable-ngs-diagnostics-platform-value

Conclusion

Collaboration improved dramatically as all stakeholders worked within a unified platform, setting a new standard for operational efficiency, accuracy, and scalability.