Low-Pass WGS

Low-Pass Whole Genome Sequencing

Low-pass or shallow whole genome sequencing involves sequencing the genome at low coverage, typically between 1x and 4x. Low-pass genome sequencing provides a broad overview of the genome, allowing for the detection of common variants in genome-wide association studies (GWAS) at a lower cost compared to deep sequencing.

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Application & Services

Our standard Variant Analysis service includes detection and annotation of germline single nucleotide polymorphism (SNPs), insertions and deletions (InDel).
Predicted genotypes for missing or low-confidence variants are imputed and provided in standard formats like VCF (Variant Call Format).
For optional DNA isolation service, please refer to our DNA isolation guide. We do not accept samples with higher biosafety level than S2. GMOs are only accepted with S1 level.

Highlights

Unique Dual Indexing (UDI) ensures high-quality data
Utilizes imputation methods to provide accurate variant calls
Cost-effective alternative to high-coverage sequencing
Low Coverage (1x-4x): Sequencing the genome at low coverage for broad variant detection
Fast Turnaround times
Data transfer via secure FTP
Optional DNA isolation service

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More details

Specifications for low-pass genome sequencing

QC of DNA quantity is performed
Illumina-compatible DNA library preparation using Unique Dual Indexing
Technology: Illumina NovaSeq 6000 or NovaSeq Xplus
Run type: paired-end
Read length: 2 x 150 bp
For human genome: on average 1x coverage (3 Gb) raw data per package, 10 Mio read pairs NovaSeq (2 x 150 bp), additional read packages can be ordered

Starting material for low-pass genome sequencing

Sample Type: Genomic DNA (RNA-free)
Minimum Amount: 600 ng
Volume: up to 200 µL
Concentration: >3 ng/µl
Purity (OD260/280): 1.8-2.0
Resuspension Buffer: Water, EB, or low TE (<0.1 mM EDTA)
Format: barcode labelled 1.5 ml Eppendorf safe-lock tubes; or for > 48 samples in Eppendorf twin.tec PCR Plate 96, full-skirted, leave position G12 & H12 empty
Shipment Method: room temperature

Deliverables for low-pass genome sequencing

Raw data as FASTQ files (.fastq.gz)
Aligned BAM file (.bam)
Imputed Genotype Data with predicted genotypes for missing or low-confidence variants (.vcf)
A detailed report summarizing the mapping quality, coverage, variant call quality, and accuracy statistics.
Details of the reference panel used for imputation, including population data and coverage specifics.
Statistical information on allele frequencies, variant distribution, and imputation success across different regions of the genome included in the VCF output.