Targeted & Exome Sequencing Services

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Expertise that drives your insights

With a broad array of hybridization and capture platforms and the experience to choose the right technology for your project needs, HudsonAlpha Discovery’s Exome and Targeted and Exome Sequencing Services advance your studies with reliable, reproducible genomic data.

We support projects spanning the full range of research phases, including basic, discovery, translational, and clinical, and have the infrastructure to deliver rapid turnaround times for even large-scale studies.

Highlights

Enabling a wide range of targeted sequencing projects for moderate to high variant allele frequency (VAF) sensitivity across both tissue- (e.g., FFPE) and liquid- (e.g. plasma) based applications.

Multiple hybridization and capture technologies

including IDT, Twist, Roche, Agilent capture platforms

50x, 100x, 300x, and custom coverage options

Multiple Illumina TruSight panels

Applications

  • Genomic variant and biomarker analysis
    • Single nucleotide variants (SNV)
    • Insertions and deletions (InDels)
    • Copy number variation (CNV)
    • Tumor Mutation Burden (TMB)
    • Additional analyses— ask us to learn more »
  • Tumor mutation burden (TMB)
  • Biomarker profiling
  • Disease research
  • Personalized medicine
  • All research phases and activities
    • Basic discovery
    • Translational and pre-clinical
    • Clinical

Highlights of our targeted and exome sequencing service

Our experienced scientists will work with you to design an efficient and effective targeted moderate to high sensitivity sequencing approach including nucleic acid extraction
Nucleic acid extraction and library preparation
  • Optimized extraction protocols for nearly any sample type
  • Optimized protocols for working with ultra-low amounts of nucleic acid
  • Dual concurrent RNA-DNA extraction from challenging sample types such as FFPE tissue— read the white paper »
Multiple capture platforms and custom probe spike-in options
  • IDT
  • Twist
  • Agilent
Cancer sequencing panels
  • Illumina TruSight Tumor 170
  • Illumina TruSight Oncology 500
    • Solid Tumor FFPE TSO500
    • High-Throughput
    • Plasma ctDNA TSO500
  • Illumina TruSight Myeloid Panel
  • Qiagen QiaSeq Multimodal Oncology Panels
  • Additional off-the-shelf options and validation services
Sequencing depth
  • 50x coverage for identifying disease-associated genotypes
  • 100x coverage for most germline or matched normal variant detection applications
  • 300x coverage for tumor somatic mutation detection and identifying variants with low VAF
  • Tumor-only or tumor with matched normal tumor mutation burden (TMB)
  • Custom
Read length
Bioinformatics analysis and data storage
  • Tier 1: Raw BCL and FASTQ file output
  • Tier 2: Standard application-specific and quality report outputs (BCL, FASTQ, aligned BAM files and sequencing QC reports
  • Tier 3: Standard output plus variant calling (VCF, g-VCF) and genomic interpretation reports
  • Additional custom reporting options including Ingenuity Variant Analysis (Qiagen) consolidated variant reports as well as options for genomic variant annotation
  • Flexible data delivery and storage options
  • 90 days storage included with service pricing
  • Long term storage available

The HudsonAlpha Discovery Difference

Whole exome sequencing, targeted sequencing
Regular, frequent review and optimization of hybridization techniques to increase capture efficiency and ensure even coverage across targeted regions
Flexible and creative problem solving with expert scientific guidance
Optimized protocols and automated workflows that reduce technical bias
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Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results
Massive scale with 10 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs
A decade of proven experience spanning thousands of projects and hundreds of publications
See Recent Publications

Featured Paper

Exome sequencing for disease research

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7 encoding a heat-shock protein

Farhan SMK, et al. Nat Neurosci. 2019 Nov 25. 22: 1966–1974. PMCID: PMC6919277.

In this study, completed when the HudsonAlpha Discovery lab was still the HudsonAlpha Institute Genomic Services Lab, our exome sequencing services contributed to a larger, multi-center effort aimed at uncovering novel genes involved in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease. The total number of exomes sequenced by all centers was 11,703—3,864 ALS patients and 7,839 ancestry-matched controls.

Their findings: “We observed a significant excess of rare protein-truncating variants among ALS cases, which was concentrated in constrained genes,”1 including DNAJC7, a heat shock protein 40 (HSP40) family member.

The significance of this work: Through exome sequencing of a large cohort of patients and ancestry-matched controls, the authors identified a novel gene involved in ALS as well as an unexpected excess of protein-truncating variants.

Recent Publications
  1. Farhan SMK, et al. Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein. Nat Neurosci. 2019 Nov 25. 22: 1966–1974. PMCID: PMC6919277.
  2. Bishop MR, et al. A research-based gene panel to investigate breast, ovarian and prostate cancer genetic risk. PLoS One. 2019; 14(8): e0220929. PMCID: PMC6695138.
  3. Thompson ML, et al. Genomic sequencing identifies secondary findings in a cohort of parent study participants. Genet Med. 2018 Dec; 20(12): 1635–1643. PMCID: PMC6185813.

Get more information about our DNA and RNA sequencing services

Download the One-Sheet

Propel Your Research

Leverage the power of the HudsonAlpha Discovery division; contact us today!