Whole Genome Sequencing at Admera Health: A Superior, End-to-End Workflow

Whole genome sequencing (WGS) offers comprehensive insight across the entire genome, allowing researchers the ability to investigate a broad range of variant types in a single-assay¹. The ability to sequence both coding and non-coding regions with improved sensitivity, makes WGS a first-tier tool for any researcher². Still, the cost of onboarding the specialized equipment and the extensive wet-lab and computational knowledge required, can make WGS prohibitive for some labs³. At Admera Health, we are leaders in next-generation sequencing (NGS) and bioinformatic services, working with a wide range of clients in academia and industry. Our quality research-use-only (RUO) WGS workflow operates in a CLIA/CLEP certified and CAP accredited environment to provide a superior end-to-end service. In this post, we will explore how Admera Health’s WGS workflow can elevate researchers’ ability to investigate variant types in rare and complex diseases⁴, explore potential targets in drug discovery⁵, or used in genomic analysis of non-model organisms⁶.  

Keywords: WGS, NGS, library construction, bioinformatics 

What is WGS? 

Admera Health’s WGS workflow provides clients with a complete end-to-end service from initial extraction, library construction and sequencing, to downstream data analysis & delivery. We also offer expert input on experimental design, initial pilot testing, and can run the workflow in a modular format, for clients who require only portions of the workflow. We’ve optimized our lab techniques handling a variety of sample types and provide our clients with rapid turnaround times. Clients interested in submitting samples for processing can learn more on our Sample Submission Guidelines page. 

·         Genomic Extraction: Admera’s WGS workflow begins with sample collection and extraction. Our dedicated scientists have extensive experience in extractions across a range of tissues, blood, and cell types; from low-quality samples (e.g. FFPE, formalin-fixed paraffin embedded) to high-molecular weight extractions. Our lab uses numerous high-throughput and automated systems to provide our clients with robust quality check (QC) measures evaluating sample concentration and quality. Following extraction, clients receive an Initial Quality Check (QC) Report detailing the results of the extraction, empowering researchers with the choice which samples to proceed.

·         Library Construction: Our WGS workflow constructs sequencing libraries over a wide range of inputs (1ng – 1µg) and qualities. Briefly, a typical WGS sample uses a PCR-free (or minimal PCR) approach, to avoid potential amplification bias⁷, where samples are fragmented to the required insert size and ligated with full-length, unique dual index (UDI) adapters that facilitate sample multiplexing and mitigate any potential “index hopping” phenonemna⁸ during sequencing. For lower input samples or for projects that require faster turnaround times, we also offer rapid tagmentation-based library preparation workflows. Following library construction, samples undergo a Final Library QC check to verify the library quantity and quality required for sequencing.  

·         NGS Sequencing: A typical human WGS project at Admera utilizes Illumina’s NovaSeq X Plus, for high-throughput NGS of 2x150 bp paired-end (PE) reads with coverage depths ranging from 30-100x. In PE sequencing, both strands of the DNA insert are read which improves genomic coverage, read mapping accuracy, and can aid in detection of gene fusion events⁹. The true benefit of Admera’s WGS workflow is the ability to sequence the genome once for current analysis, and use again for potential future work¹⁰. 

·         Data Analysis & Delivery: Admera’s expert bioinformaticians utilize custom and commercially available scripts to give clients extensive data analysis and delivery options. Generally, the sequencing data is processed using computational tools to assess initial sequencing quality, read alignment to a reference genome (if available), and finally to identification of somatic & germline variants, among other steps, to create publication ready plots for our clients. We also offer customized options for clients who require more in-depth and advanced analyses. Our bioinformatics team provides seamless data delivery options using BaseSpace, FTP or AWS. Check out example WGS reports here.  

The Admera Difference 

Admera Health’s WGS workflow is designed to provide researchers with a quality, untargeted approach to probe a broad range of variant types in a single-assay. Our WGS workflow offers researchers full end-to-end support from genomic extraction, library construction, NGS sequencing, downstream data analysis and delivery. Our extensive expertise of NGS and bioinformatic services provides researchers’ the flexibility to work across numerous sample types, sequence a variety of cover depth options, and obtain industry leading turnaround times. Check out more of our genomics services, including whole exome sequencing and targeted sequencing. We also offer an extensive catalog of transcriptomic, epigenomic, and single-cell sequencing services. Whether exploring variants involved with disease, obtaining de novo assemblies from non-modal organisms, or used as a part of drug discovery, Admera’s superior WGS workflow elevates researchers’ ability to uncover impactful insights across the entire genome. 

References 

1.      Austin-Tse, C.A. et al. Best Practices for the Interpretation and Reporting of Clinical Whole Genome Sequencing. Nature Genomic Medicine (2022). https://doi.org/10.1038/s41525-022-00295-z 

2.      Lionel, A.C. et al. Improved Diagnostic Yield Compared with Targeted Gene Sequencing Panels Suggests a Role for Whole-Genome Sequencing as a First-Tier Genetic Test. Genetics in Medicine (2017). https://doi.org/10.1038/gim.2017.119 

3.      Taylor, J.C. et al. Factors Influencing Success of Clinical Genome Sequencing Across a Broad Spectrum of Disorders. Nature Genetics (2015). https://doi.org/10.1038/ng.3304 

4.      Bick, D. et al. Case for Genome Sequencing in Infants and Children With Rare, Undiagnosed or Genetic Diseases. Journal of Medical Genetics (2019). https://doi.org/10.1136/jmedgenet-2019-106111 

5.      Spreafico, R. et al. Advances in Genomics for Drug Development. Genes (2020). https://doi.org/10.3390/genes11080942

6.      Xu. S/ et al. Whole Genome Sequencing Reveals the Genomic Diversity, Taxonomic Classification, and Evolutionary Relationships of the Genus Nocardia. PLOS Neglected Tropical Diseases (2021). https://doi.org/10.1371/journal.pntd.0009665 

7.      Zhou, G. et al. Performance Characterization of PCR-free Whole Genome Sequencing for Clinical Diagnosis. Medicine (Baltimore) (2022). https://doi.org/10.1097/MD.0000000000028972 

8.      MacConaill, LE. et al. Unique, Dual-Indexed Sequencing Adapters with UMIs Effectively Eliminate Index Cross-Talk and Significantly Improve Sensitivity of Massively Parallel Sequencing. BMC Genomics (2018). https://doi.org/10.1186/s12864-017-4428-5 

9.      Larson, N.B. et al. A Clinician’s Guide to Bioinformatics for Next-Generation Sequencing. Journal of Thoracic Oncology (2022). https://doi.org/10.1016/j.jtho.2022.11.006 

10.  Costain, G. et al. Periodic Reanalysis of Whole-Genome Sequencing Data Enhances the Diagnostic Advantage Over Standard Clinical Genetic Testing. European Journal of Human Genetics (2018). https://doi.org/10.1038/s41431-018-0114-6