Targeting specific regions in the genome is necessary when looking for variants or trying to identify rearrangements in diseased versus normal tissue. While whole genome (WGS) or whole exome sequencing (WES) can also identify variants, these methods are broad examinations of all DNA or all protein coding regions and do not focus on individual genes or target sequence. Broad approaches like WGS or WES can be insufficient when:

1. high sequencing depth is required.
2. SNPs are found in a gene, intron or intron/exon boundary not covered by existing exome capture hybridization probes.
3. identifying variants in a subset of genes is needed.
4. the focus is on individual genes, not the whole exome, such as in clinical applications.
5. off-target rates are too high to make exome-sequencing a reliable way to identify variants in a single or subset of genes.

If you need help deciding whether exome-seq or a specific gene panel is needed for your appcliation, contact us for recommendations.

See Genohub's up-to-date list of Amplicon and Hybrid Capture based Gene Panel Services

Broadly, there are two methods used when targeting specific regions in the genome:

1. Amplicon based approaches – PCR primers are designed upstream and downstream of the target region. Once amplified, sequencing adapters are ligated or added by a second PCR amplification. Sets of primers targeting several genes are pooled and sequenced together.
2. Hybridization based capture – Similar to the way exons are captured in exome capture kits, probes are designed to specific genes of interest and hybridized. These probes are typically biotinylated and bind to a solid support such as streptavidin beads, allowing captured regions to be pulled out from a genomic milieu. Targeted genes are then amplified and sequenced.

Below is a list of gene panels using both amplicon and hybrid based capture methods.

Gene Panels

Agilent ClearSeq and SureSelect Panels

ClearSeq panels use a hybridization based approach to capture somatic variants in solid tumors and hematological cancers. These panels enable the detection of mutations, indels and genes fusions from FFPE, blood and bone marrow samples.

SureSelect panels are also hybrid-capture based, pre-designed panels that focus on targeted gene sets, specifically inherited diseases, the kinome and X-chromosome. They are designed for targeting either genomic or transcriptomic regions.

Archer FusionPlex Panels

FusionPlex panels are specifically built for detecting gene fusions without a priori knowledge of fusion partners or breakpoints. The panels target enriches cDNA from RNA and nucleic acid extracted from FFPE samples. Fixed panels and services to customize unique panels are available.

Bioo Scientific’s NEXTflex™ Amplicon Panels

NEXTflex panels use an amplicon based targeting method. Custom panels are designed using proprietary software called Amplicon Studio and offer >90% base coverage at 0.2x mean coverage and >90% on-target reads. Custom panels consist of up to 2,000 amplicons, covering 1 – 500 kb regions.

IDT xGen Panels

AxGEN Lockdown panels use a hybridization based capture method, specifically 5’biotin probes to hybridize to target regions. After hybridization target reginos are pulled down with streptavidin coated magnetic beads. Up to 2,000 probes per pool can be designed, allowing enrichment of SNPs and indels.

Illumina TruSight Panels

TruSight panels use an amplicon based targeting strategy and focus on exonic regions with disease causing mutations. Evenness of coverage and regions targeted depend on the specific panel.

Nimblegen SeqCap Panels

SeqCap is a hybrid-capture based method for enriching target genes. Fixed and custom panels are available.

Qiagen GeneRead Panels

GeneRead panels are amplicon based and designed to cover 90% of targeted bases at 0.2x mean coverage. They use overlapping primer sets across exonic portions of target genes to enrich and improve target coverage.