Liquid Biopsy NGS Assay
Liquid Biopsy NGS Assay

Overview


Cancer is one of the leading causes of death worldwide, yet many types still don’t have regular screening programs. Even when screening is available, many people at higher risk find the tests difficult or uncomfortable to follow. Newer blood-based tests, like liquid biopsies, are showing promise for early detection of cancers. Liquid biopsy is a method where circulating tumor DNA (ctDNA) shed from the tumor is extracted and sequenced. This unveils the necessary information regarding cancer causing mutations in the related genes enhancing clinicians to decide the best course of treatment.

Lung Cancer Care Through Liquid Biopsy:

Liquid biopsy, powered by Next-Generation Sequencing (NGS), is revolutionizing how lung cancer is detected and managed. Unlike traditional tissue biopsies, which are often invasive and sometimes difficult to perform, liquid biopsy works by analyzing tiny fragments of tumor DNA (ctDNA) or tumor cells (CTCs) that are released into the bloodstream. This non-invasive approach allows clinicians to uncover critical genetic information about the tumor, making it possible to guide treatment and monitor disease with greater ease and precision.

Actionable ctDNA Lung Cancer Genes and Therapy Options

Type of Cancer Gene Drug
Non–small cell lung cancer (NSCLC) ALK Alectinib,crizotinib, ceritinib, lorlatinib, dabrafenib+trametinib
Non–small cell lung cancer (NSCLC) BRAF Dabrafenib+trametinib
Non–small cell lung cancer (NSCLC) EGFR Erlotinib, Osimertinib, gefitinib, erlotinib, afatinib, mobocertinib, amivantamb
Non–small cell lung cancer (NSCLC) ERBB2 Fam-trastuzumab deruxtecan-nxki

Colorectal Cancer Care with Liquid Biopsy & NGS:

Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the second leading cause of cancer-related mortality worldwide. Liquid biopsy, particularly when combined with Next-Generation Sequencing (NGS), has emerged as a powerful non-invasive strategy for molecular profiling, therapy guidance, and disease monitoring in CRC.

CRC Panel: Critical Genes, Pathways, and Therapy Options

Type of Cancer Gene Drug
Colorectal Cancer EGFR Cetuximab, Panitumumab
Colorectal Cancer KRAS Cetuximab, Panitumumab

Breast Cancer Detection and Monitoring Powered by Liquid Biopsy and NGS


Breast cancer is characterized by the uncontrolled proliferation of malignant epithelial cells within the breast tissue, leading to tumor formation. Although rare in men, it remains predominantly a disease of women and represents a major global health burden. Breast cancer is represented by substantial heterogeneity, encompassing diverse genetic alterations and distinct histopathological subtypes. Despite advances in research, the precise molecular mechanisms driving its initiation and progression remain incompletely understood. The biggest risk factors include simply being female and increasing age. Other factors like family history, gene mutations, race/ethnicity, pregnancy history, breast feeding history and unhealthy lifestyle can also raise the likelihood of developing breast cancer. Research shows that inherited genetic factors contribute to about 5-10% of all breast cancer cases and follow an autosomal dominant inheritance pattern, but in women under 30, they may explain up to 25% of diagnoses. Among these, mutations in the BRCA1 and BRCA2 genes are the most well-recognized causes of hereditary breast cancer risk.

How Genes Affect Breast Cancer:

In breast cancer, cell-free circulating tumor DNA (ctDNA) is emerging as a powerful, noninvasive biomarker that may reduce the need for traditional tissue biopsies. Through liquid biopsy, ctDNA shed by tumors into the bloodstream can be analyzed to track genetic changes. Using next-generation sequencing (NGS), even very small amounts of ctDNA can be detected with high accuracy, enabling the identification of both specific gene mutations and broader, genome-wide alterations that drive breast cancer. This helps in guiding targeted therapies and personalized treatment choices.

Targetable Gene Alterations in the Breast Cancer Panel:

Type of Cancer Gene Drug
Breast cancer, Metastatic Castrate Resistant Prostate Cancer, Ovarian Cancer BRCA1 Olaparib, Rucaparib, Niraparib + Abiraterone acetate
Ovarian Cancer, Breast cancer BRCA2 Talazoparib
Breast Cancer ERBB2 Trastuzumab, Pertuzumab, Ado-trastuzumab emtansine
Breast Cancer ESR1 Elacestrant (Orserdu)

Key features and highlights


  • Focused Comprehensively Validated Panel: Covers all relevant genes with the ability to detect ultra-low VAF mutations, delivering clinical-grade precision you can trust.
  • Low Input: Process compatible with low input quality compromised samples.
  • Robust and Rapid Workflow: Hybridization enhancer technology and enzyme-based library preparation enables quick turnaround time.
  • Hassle-Free Data and Reporting: User-friendly software for data upload, automated and cloud-based analysis followed by report generation.
  • Optimized for Clinical Use: Designed to support personalized medicine and evidence-based care in lymphoid malignancies.

Panel Specifications


Parameter
ctDNA Lung
ctDNA Colorectal
ctDNA Breast
No. of genes:
32
25
63 (14 DNA fusions)
Variant types:
SNV / InDels / CNV
SNV / InDels / CNV
SNV / InDels / CNV
Covered region:
Whole CDS
Whole CDS
Whole CDS
Target size:
110 Kb
75 Kb
440 Kb
Coverage Recommendations:
25000X
25000X
25000X
Data requirement (per sample):
3000 Mb
2000 Mb
11000 Mb
Sample type:
Blood / Plasma
Platform:
Illumina, MGI, Element Biosciences
Bioinformatics Support:
G2M CliSeq Interpreter
Primary Analysis: FASTQ to annotated VCF
Secondary Analysis: CNVs, SNVs, InDel, Fusions
Tertiary Analysis: Clinical interpretation

Assay performance


Features
Performance_Lung*
Performance_Colorectal*
Performance_Breast*
Coverage Uniformity (0.2X):
>99%
>99%
>99%
Reproducibility (%):
96
95.5
96.3
Sensitivity (%):
96
93.7
96
On Target Ratio (%):
70-85
70-85
70-85

*The panel’s performance is from the Illumina platform.

High-Fidelity Coverage for Confident Variant Detection

Allelic Discrimination Plot

Coverage profiles of critical genes (ESR1, BRCA1, PIK3CA, ERBB2, and GATA3) exhibit strong concordance between mean (solid line) and median (dashed line) depth, demonstrating uniform sequencing and minimal bias across all target regions. This alignment highlights the assay’s robust performance and reliability, ensuring confident results across diverse breast cancer samples.

Mutation Burden Landscape Across Breast Cancer Genes

Melting Curve

Distribution of variant allele frequencies (VAFs) in 158 breast cancer samples reveals distinct mutation patterns. Genes such as AR, CCND1, and FGFR1 exhibit higher median VAFs with broad variability, indicating a substantial mutation burden and potential influence on disease progression. Conversely, APC, EGFR, and KIT show lower, more uniform VAFs, suggesting a stable or limited role in the overall genomic architecture.

Efficient On-Target Capture for Liquid Biopsy Precision

Standard Curve

The ctDNA breast cancer panel consistently delivers more than 75% on-target alignment, reflecting its smart design and efficient target capture. This ensures reliable mutation detection from low-input samples, enabling early diagnosis, treatment monitoring, and scalable diagnostic utility.

Uniform BRCA1 Exon Coverage with G2M ctDNA Breast Cancer Panel

Standard Curve

The figure illustrates read coverage for BRCA1 exons 3, 4, and 5. The top panel highlights the BRCA1 target region (green), the middle panel displays per-base coverage depth achieved by the G2M ctDNA Breast Cancer Panel (blue), and the bottom panel represents the gene’s coding regions as annotated by RefSeq (orange). This visualization underscores uniform coverage across clinically significant exons, ensuring reliable variant detection.

Mutation Hotspots Driving Breast Cancer Genomics

Relative Quantification Analysis

Oncoplot showcasing the 12 most frequently mutated genes in ctDNA breast cancer samples. Missense mutations (green) dominate, followed by in-frame deletions (yellow), while multi-hit events (black) indicate multiple mutation types within the same gene. The right panel summarizes mutation frequency per gene.

Ordering Information


Commercial Name Cat No. Pack Size Platform
ctDNA Lung NGS Test Kit G710028-1 24 T Illumina
G710028-2 96 T Illumina
G710028-3 96 T – EZY Illumina – EZY
ctDNA Lung NGS Test Kit G710028-4 24 T MGI
G710028-5 96 T MGI
G710028-6 96 T – EZY MGI – EZY
ctDNA Lung NGS Test Kit G710028-7 24 T Aviti
G710028-8 96 T Aviti
G710028-9 96 T – EZY Aviti – EZY
ctDNA Lung NGS Test Kit G710028-10 24 T Thermo
G710028-11 96 T Thermo
G710028-12 96 T – EZY Thermo – EZY

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