Shallow Whole Genome Sequencing

CD Genomics provides the accurate and cost-effective shallow whole genome sequencing service using Illumina or BGI DNBseq platforms to achieve genome-wide genetic variation for plants, animals and humans.

What is Shallow Whole Genome Sequencing

Shallow Whole Genome Sequencing (shallow WGS, also known as low pass whole genome sequencing) is a new and high-throughput technology to achieve genome-wide genetic variation accurately and cost-effectively with a broad range of species: cattle, pig, chicken, dog, cat, rat, mice, corn, rice, soybean and pea and humans. Based on shotgun sequencing, shallow WGS can be used to obtain whole genome sequence at a very low coverage (most frequently between 0.4x and 1x) with over 99% accurate variant calls. Shallow WGS returns more data, greater statistical power, and new rare variant discovery capabilities than traditional genotyping arrays and GBS method. Shallow WGS can be used in genome-wide association study (GWAS), evolutionary analysis, pharmacogenomics, molecular breeding, etc. In addition, Shallow WGS can be used to build a custom reference panel for a specific population.

Advantages of Shallow Whole Genome Sequencing

• More cost-effective than genotyping arrays and regular whole-genome sequencing
• More data, greater statistical power, and new rare variant discovery capabilities than traditional genotyping arrays
• Over 99% accurate variant calls across whole genome
• Flexible setup of new species or custom populations

Shallow Whole Genome Sequencing Workflow

CD Genomics provides the accurate and cost-effective shallow whole genome sequencing and bioinformatics analysis for plants, animals and humans. Our professional expert team executes quality management, following every procedure to ensure confident and unbiased results. The general workflow for shallow whole genome sequencing is outlined below.

Service Specifications

	Sample Requirements Sample types for genome DNA, saliva, blood, fresh frozen tissue, cultured cells and FFPE samples. Regular Samples: Intact genomic DNA ≥ 1 μg, Concentration ≥ 12.5 ng/μl; Low input Samples: Intact genomic DNA ≥ 200 ng, Concentration  ≥ 2.5 ng/μl True PCR-Free: Intact genomic DNA ≥ 1.5 μg, Concentration  ≥ 12.5 ng/μl Minimum sample volume: 15 μl Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
Click	Sequencing Strategies Illumina or BGI DNBseq platforms Both PCR and PCR-Free library can be constructed in the library preparation step 100bp and 150bp paired-end sequencing available More than 80% of bases with a ≥Q30 quality score
	Data Analysis We provide customized bioinformatics analysis including: Read alignment Variant calling by imputation (reference panel: 1000 Genomes Phase 3) Novel variant discovery Ancestry analysis Microbiome Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

CD Genomics provides full shallow whole genome sequencing service package including DNA extraction, library construction, sequencing, raw data quality control, and bioinformatics analysis. We can tailor this pipeline to your research interest. We can offer BAM and VCF data files for you. If you have additional requirements or questions, please feel free to contact us.

Deliverables

• The original sequencing data
• Experimental results
• Data analysis report
• Details in Shallow Whole Genome Sequencing for your writing (customization)

1. How long does it take to get my results back?

Typically, 30-40 working days from sample qualified acceptance to data analysis report availability.

2. Which sequencing machines do you use for low pass whole genome sequencing?

Illumina or BGI DNBseq platforms can be used for sequencing.

3. What are the advantages of low pass whole genome sequencing over traditional genotyping arrays?

Low pass whole genome sequencing can be used to obtain whole genome sequence at a very low coverage (most frequently between 0.4x and 1x) with over 99% accurate variant calls. Over 10x more data than genotyping arrays at a similar or lower cost. Moreover, low pass whole genome sequencing allows to discover new rare variants. All these suggest that low pass whole genome sequencing outperforms genotyping arrays.

Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival

Journal: Cancers

Impact factor: 6.575

Published: 6 June 2020

Background

The FGFR family exhibits diverse genomic alterations, with FGFR1 amplification linked to poor prognosis and resistance to therapy in breast cancer. Clinical trials face challenges in obtaining fresh tissue biopsies for molecular analysis, leading to reliance on archival tissue with limited representation of tumor heterogeneity. Gene amplification evolves during cancer progression, emphasizing the need for real-time molecular profiling. Shallow whole-genome sequencing (sWGS) emerges as a cost-effective method for detecting circulating tumor DNA (ctDNA), aiding in treatment monitoring and prognostication. This study utilizes sWGS to explore ctDNA as a surrogate for FGFR1 amplification in metastatic breast cancer, correlating ctDNA levels with patient survival.

Methods

Results

Twenty cases, including ten FGFR1-amplified and ten control cases, were analyzed for ctDNA using mFAST-SeqS, followed by sWGS irrespective of mFAST-SeqS results. Although mFAST-SeqS cannot detect FGFR1 amplification, sWGS identified amplifications down to 1%. A good correlation was observed between mFAST-SeqS z-scores and ichorCNA estimates. Cases with ctDNA allele fractions (AF) above 3% accurately identified FGFR1 amplification, but cases with low ctDNA AFs still detected amplification, highlighting the challenges in establishing detection thresholds. Correlation between log2ratio and tumor fraction was observed for amplified cases, with hypothetical copy numbers correlating with Oncoscan but not FISH results. The detection of FGFR1 amplification in plasma depends on both gene copy number and tumor fraction, making a generalized threshold challenging to establish.

Fig 1. Heat-map of selected plasma samples with different values of genome-wide z-scores.

Fig 2. Copy number status of chromosome 8 of cell-free DNA (cfDNA) samples established with shallow whole-genome sequencing (sWGS).

This study evaluated tumor fraction using ichorCNA with ULP-WGS in metastatic breast cancer. Stratification based on median genome-wide z-score (>2.2) and tumor fraction (>4.6) revealed significantly reduced overall survival (OS). Conversely, total cfDNA quantity showed no discernible relevance in OS discrimination.

Fig 3. Kaplan–Meier analysis curves for the overall survival of metastatic breast cancer patients.

Conclusion

In summary, this study highlights the utility of shallow whole-genome sequencing (sWGS) for detecting clinically relevant somatic copy number alterations (SCNA), like FGFR1 amplification, in plasma of metastatic breast cancer patients. sWGS offers a valuable screening tool when fresh biopsies are unavailable, enabling reassessment of amplification status using archived samples. Additionally, both mFAST-SeqS and sWGS show promise for estimating tumor fraction and monitoring tumor dynamics in advanced cancer patients.

Reference:

1. Bourrier C, Pierga J-Y, Xuereb L et al. Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival. Cancers. 2020; 12(6):1481.