by Sanjay Singh
Introduction
The human genome is vast, containing over 3 billion base pairs of double-stranded DNA, where each strand is composed of nucleotides represented by the letters A, C, G, and T. Advances in sequencing technology now allow the generation of massive genomic datasets in a short time, revolutionizing fields like genetic disease research, personalized medicine, and evolutionary biology. However, with this rapid growth comes the challenge of managing, archiving, and effectively communicating this data to enhance human health through clinical interventions. Without structured systems, genomic data can become overwhelming, leading to inefficiencies and missed opportunities.
This primer introduces genomics data concepts tailored for data engineers, highlighting their implications and applications. A follow-up blog post will explore personalized treatment plans and large-scale studies enabled by these innovations.
Background
The Human Genome Project (HGP) was a groundbreaking, collaborative effort involving over 2,000 researchers from around the world. This ambitious initiative sequenced the human genome, consisting of 23 chromosomes, to create the first ~3 billion base pair reference sequence. Notably, only about 2% of the genome, known as the exome, encodes proteins and has direct implications for diseases. The reference genome established by the HGP remains a cornerstone for genomic studies and diagnostics.
Sequencing technologies have evolved significantly since HGP’s completion. While precise, capillary sequencing (Sanger sequencing) is inefficient for large-scale studies. Next-generation sequencing (NGS) technologies have transformed genomic research, enabling the efficient analysis of millions to billions of base pairs.
Population-level genomic studies leveraging NGS technologies have revealed variations in individual genomes compared to the reference sequence. These variations, such as single-nucleotide polymorphisms (SNPs), have been linked to traits like eye color and drug responses. The Genome Reference Consortium (GRC) now maintains and updates the reference genome, which is used universally as a coordinate system for mapping individual sequences.
Types of NGS-based tests
NGS-based diagnostic tests are widely accepted in clinical settings. These tests utilize various human samples, such as blood, tumor tissue, cerebrospinal fluid, or reproductive cells, and involve DNA extraction, fragmentation, and sequencing.
Key applications include:
- Targeted Gene Panels: Focus on specific genes related to a phenotype, such as hypertrophic cardiomyopathy. These guide diagnoses, clinical management, and family screening.
- Somatic Mutation Profiling is crucial in oncology for identifying mutations, such as in the KRAS gene, to inform treatment decisions like anti-EGFR therapy. These tests often require a high sequencing depth (e.g., >1000×).
- Whole Exome Sequencing (WES): Targets the protein-coding regions of ~20,000 genes (~2% of the genome) to diagnose patients with complex phenotypes. WES is efficient and cost-effective.
- Whole Genome Sequencing (WGS): Examines the entire genome, including regulatory elements, offering unparalleled diagnostic insights. However, it remains cost-prohibitive for routine use.
File Formats
NGS experiments generate vast amounts of data, stored in standardized formats to support downstream analysis and clinical applications. The key formats include:
- FASTQ
- A text-based format consisting of sequenced bases (reads) and associated quality scores (base quality score, BQS) for each base.
- Quality scores in FASTQ files are encoded using ASCII characters representing PHRED scores, which indicate the probability of an incorrect base call (e.g., a PHRED score of 30 corresponds to a 1 in 1,000 error probability).
- Sequencing depth—the number of times a specific nucleotide is read—is critical for detecting rare variants. For instance, some cancer studies require >1000× depth for precision.
- FASTQ files are typically large, with whole-genome sequencing (WGS) outputs reaching up to 200 GB. In cancer studies, smaller segments of DNA may require extremely high sequencing depth, generating files of several gigabytes.
- SAM/BAM
- SAM (Sequence Alignment/Map): A tab-delimited text format that maps sequence reads to a reference genome (e.g., GRCh37 or GRCh38).
- BAM: A binary, compressed version of SAM that reduces file sizes while preserving data integrity (~120 GB for a human genome).
- SAM files consist of a header section (denoted by @ lines) and an alignment section. The alignment section stores details like chromosomal position, flags indicating read alignment status (e.g., paired-end, reverse strand), and mismatches relative to the reference genome.
- Softwares like bwa and bowtie are commonly used to align sequences to the reference genome, ensuring high accuracy and efficiency.
- Unmapped reads (those not aligning to the reference genome) are stored separately for additional analysis.
- BAM files use BGZF compression, enabling faster queries and efficient storage.
- VCF (Variant Call Format)
- Represents genetic variants (e.g., SNPs, insertions/deletions, structural variations) as differences from the reference genome.
- A VCF file includes:
- Header Section: Metadata such as the reference genome version and annotations (e.g., allele frequencies, dbSNP IDs).
- Variant Call Records: Tab-delimited data for each variant, including chromosome position, reference allele, observed allele(s), quality scores, and zygosity information.
- VCF files are compact, with WGS results reduced to a few megabytes by representing only differences rather than the entire genome sequence.
- Annotation and Clinical Reporting
- Tools like GATK (Genome Analysis Toolkit) use VCF files for variant calling and annotation, linking genomic variants to clinical relevance.
- Annotated VCF data is often shared with clinicians as PDFs through electronic health records (EHRs). However, these unstructured reports limit their usability for analytics and decision support systems.
- These reports typically provide only a point-in-time snapshot of key variants, and as knowledge advances, they can quickly become outdated.
Efforts are ongoing to replace unstructured outputs with standardized, interoperable formats like those defined by HL7 FHIR resources. Such advancements aim to enable more dynamic and reusable genomic data for research and clinical applications.
Challenges and Opportunities
Current genomic data practices face several challenges:
- Data Volume: Managing and storing vast datasets efficiently.
- Dynamic Knowledge Base: Rapid advancements in genetic research necessitate frequent reanalysis of data.
- Lack of Standardization: Unstructured formats like PDFs hinder interoperability and analytics.
To address these issues, large-scale efforts are underway to standardize genomic data through HL7 messaging and FHIR resources. These frameworks aim to harness the full potential of genomics for clinical and research applications.
The Role of kipi.ai in Genomics Data Management
Kipi.ai’s Health DataHub leverages Snowflake’s native capabilities to transform and manage healthcare data, including genomics data, using HL7 FHIR standards. Key features include:
- FHIR Server Enablers: Facilitate rapid deployment of FHIR-based systems.
- Bundle FHIR Pack: Streamlines data integration.
- JSON Flattener: Simplifies dynamic flattening of FHIR REST response data.
- Native Streamlit Applications: Enhance data visualization and usability.
These tools empower organizations to implement HL7 FHIR standards efficiently, enabling seamless interoperability and improved clinical outcomes.
Conclusion
Genomics is reshaping healthcare, offering transformative possibilities for personalized medicine and population studies. However, its integration into clinical workflows requires robust data management systems and standardized interoperability frameworks. By leveraging tools like Kipi.ai’s Health DataHub, data engineers can unlock the full potential of genomic data, driving better health outcomes and advancing the frontiers of medicine.
Stay tuned for our next post, where we’ll explore the future of personalized medicine and population-wide genomic studies.
About kipi.ai
Kipi.ai is a leading analytics and AI services provider, specializing in transforming data into actionable insights through advanced analytics, AI, and machine learning. As an Elite Snowflake Partner, we are committed to helping organizations optimize their data strategies, migrate to the cloud, and unlock the full potential of their data. Our deep expertise in the Snowflake AI Data Cloud enables us to drive seamless data migration, enhanced data governance, and scalable analytics solutions tailored to your business needs. At kipi.ai, we empower clients across industries to accelerate their data-driven transformation and achieve unprecedented business outcomes
