Clinical sequencing: From raw data to diagnosis with lifetime value

Area of Science:

• Genetics
• Genomics
• Molecular Biology

Background:

• High-throughput sequencing (HTS) has transformed genetic variant detection at an unprecedented scale.
• Challenges remain in achieving complete genomic coverage and in analyzing/interpreting HTS data.
• The array of available HTS methods and tools can be overwhelming for researchers and clinicians.

Purpose of the Study:

• To review the comprehensive workflow of HTS from data generation to molecular diagnosis of Mendelian diseases.
• To highlight the advantages and limitations of current HTS technologies and analytical approaches.
• To address critical regulatory aspects including genetic counseling, reimbursement, and data management.

Main Methods:

• Review of current High-throughput sequencing technologies, including targeted, whole-exome, and whole-genome sequencing.
• Examination of key bioinformatic steps: read alignment, variant calling, and variant interpretation.
• Discussion of regulatory considerations for clinical implementation.

Main Results:

• Overview of short-read and long-read sequencing platforms and their applications.
• Analysis of the strengths and weaknesses of various data processing and interpretation tools.
• Identification of challenges in achieving comprehensive coverage and accurate variant detection.

Conclusions:

• HTS offers powerful capabilities for genetic variant discovery and disease diagnosis.
• Addressing challenges in coverage, data analysis, and interpretation is crucial for clinical utility.
• Navigating regulatory landscapes is essential for the successful integration of HTS into molecular diagnostics.