Question 1

What is the Sequins WGS Core Control Set?

Accepted Answer

The Sequins WGS Core Control Set is a comprehensive, pre-configured set of synthetic nucleic acid spike-in controls designed for whole genome sequencing. It provides internal standards that mirror naturally occurring genomic sequences so that variant detection, coverage and data quality can be benchmarked across a WGS workflow.

Question 2

Which variant classes are included in the WGS Core Control Set?

Accepted Answer

The WGS Core Control Set includes difficult variants; germline variants at simple repeats such as homopolymers and di-, tri- and quad-nucleotide repeats in low and high GC regions; structural variants including tandem duplications, deletions and inversions greater than 50 bp; a stable microsatellite; mitochondrial DNA sequences representing the full mitochondrial genome; and a panel of common genetic variants representative of background variation.

Question 3

How are Sequins used in a WGS workflow?

Accepted Answer

Sequins from the WGS Core Control Set are spiked into genomic DNA prior to library preparation, typically at around 1 percent of the total calculated gDNA input for a 250 ng library. They are carried through library preparation and sequencing alongside the sample and are distinguished during analysis using a Sequins-specific FASTA file concatenated with the reference genome.

Question 4

What performance metrics can the WGS Core Control Set help assess?

Accepted Answer

Because Sequins experience the same technical variables as the sample, the WGS Core Control Set can be used to assess accuracy and precision of variant calling, evaluate the impact of laboratory and bioinformatic variables, support workflow troubleshooting, and provide reference factors for standardizing results between samples, runs, users, instruments and laboratories.

Question 5

Is the WGS Core Control Set compatible with different sequencing platforms?

Accepted Answer

Yes. The WGS Core Control Set is designed against the hg38 reference genome and is compatible with hg19. Sequins have been used successfully with most sequencing technologies, including short- and long-read platforms, and with a range of PCR-free library preparation methods. The set has been validated with both Illumina and Oxford Nanopore Technologies workflows, demonstrating high precision and sensitivity within the Sequins target regions.

Question 6

What kit sizes and catalog numbers are available for the WGS Core Control Set?

Accepted Answer

The WGS Core Control Set is available in two kit sizes based on a 1 percent spike-in for a 250 ng library input: PN-10004, which provides material for 24 samples, and PN-10005, which provides material for 96 samples.

Variant Class	Count	Description
Difficult Variants	11	Germline variants at simple repeats: – Homopolymers (mono-nucleotide) repeats- Di-nucleotide repeats- Tri-nucleotide repeats – Quad-nucleotide repeats – Low and high %GC regions
Structural Variants	9	Tandem duplications, deletions, and inversions >50bp in size, long tandem repeats
Microsatellites	1	Stable microsatellite sequences
Mitochondrial DNA	4	Reference sequences representing the entire mitochondrial genome
Common genetic variants	58	Representative of general background genetic variation

Sequins WGS Core Control Set

Standardizing Whole Genome Sequencing

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Workflow Monitoring and Optimization

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Most Comprehensive WGS Control Set

Plug & Play Simplicity

Spike Sequins into samples

Prepare library

Sequence

Concatenate reference genome with Sequins decoy chromosome

Align FASTQ files to concatenated reference genome

Call variants

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Sequins WGS Core Control Set