Targeted Next-Generation Sequencing (NGS) Testing Services: Precision Genomic Analysis for Research & Clinical Applications

As an independent third-party sequencing service provider, we offer comprehensive targeted next-generation sequencing (NGS) for oncology, inherited disease research, pharmacogenomics, and translational medicine. Targeted NGS selectively amplifies and sequences specific genomic regions of interest – from a few hundred genes to custom panels covering the entire coding regions, actionable variants, or specific mutation hotspots. Compared to whole-genome or whole-exome sequencing, targeted NGS delivers higher coverage depth (typically 500‑5000×), enables detection of low‑frequency variants (down to 1% allele frequency), reduces sequencing cost per sample, and simplifies data analysis. Our accredited laboratory follows international guidelines (AMP/ACMG, CAP/CLIA, ISO 15189) using hybrid capture and amplicon‑based enrichment methods on Illumina and MGI platforms, combined with validated bioinformatics pipelines. This article outlines our targeted NGS testing capabilities – including scope, key test items, and standard methods – to help pharmaceutical companies, clinical research organizations, diagnostic developers, and academic researchers obtain high‑quality genomic data for variant detection, biomarker discovery, and patient stratification.

1. Our Testing Scope for Targeted NGS

We cover a wide range of gene panels, sample types, and application areas:

By panel type / content: Cancer hotspot panels (e.g., targeted regions of 50‑500 cancer‑associated genes, focusing on known driver mutations in solid tumors and hematologic malignancies); Comprehensive cancer panels (500‑1000+ genes covering entire coding regions of genes relevant to tumorigenesis, DNA damage repair, cell cycle, and signaling pathways); Inherited disease panels (custom or commercially available panels for cardiovascular, neurological, metabolic, ophthalmologic, and rare Mendelian disorders); Pharmacogenomics (PGx) panels – high‑coverage sequencing of key pharmacogenes (e.g., CYP2D6, CYP2C19, CYP2C9, VKORC1, DPYD, UGT1A1, TPMT, NUDT15) to guide drug dosing and predict adverse reactions; Custom panels (fully customizable – from a few genes to thousands of targets) – we design baits or primers for any genomic region of interest (coding exons, UTRs, promoters, known fusion breakpoints, intronic variants); Hotspot mutation panels (e.g., BRAF V600E, EGFR T790M, KRAS G12C, IDH1/2 R132, JAK2 V617F, CALR exon 9) – for fast screening of actionable variants in clinical research.

By sample type / input material: Fresh or frozen tissue (tumor biopsies, surgical resections); Formalin‑fixed, paraffin‑embedded (FFPE) tissue – optimized protocols for degraded DNA (as low as 10 ng input); Peripheral blood (whole blood, purified genomic DNA); Bone marrow aspirate and needle biopsy – for hematologic malignancies; Cell‑free DNA (cfDNA) / liquid biopsy – from plasma, urine, or cerebrospinal fluid (CSF) for non‑invasive detection of circulating tumor DNA (ctDNA); Saliva and buccal swabs – for germline genetic testing; Fine‑needle aspirate (FNA) – low‑input protocols available; Extracted DNA (≥ 10 ng for amplicon panels, ≥ 50 ng for hybrid capture).

By variant type detected: Single nucleotide variants (SNVs) and small insertions/deletions (indels) – detection at ≥ 5% allele frequency (standard) or down to 1% (with molecular barcodes / unique molecular identifiers – UMIs); Copy number variations (CNVs) – deletions and duplications of exons or whole genes (requires matched normal or specialized algorithms); Gene fusions / rearrangements – DNA‑based detection of common intronic breakpoints (e.g., ALK, ROS1, NTRK1/2/3, RET, FGFR2/3, MET exon 14 skipping); Large indels and complex structural variants – within targeted regions; Loss of heterozygosity (LOH) – for homologous recombination deficiency (HRD) assessment (by arrangement); Microsatellite instability (MSI) – using NGS‑based MSI calling from targeted panel data; Tumor mutational burden (TMB) – calculation from panel‑sequenced coding regions (requires panel size >0.5‑1.0 Mb).

By application area: Oncology (somatic mutation profiling for targeted therapy selection, immunotherapy response prediction, and resistance monitoring); Inherited disease diagnostics (confirming causal mutations, carrier screening, pre‑symptomatic testing); Pharmacogenomics (genotype‑guided drug selection and dosing); Liquid biopsy (monitoring minimal residual disease – MRD, tracking clonal evolution, detecting early relapse); Agrigenomics (custom panels for plant and animal breeding – by arrangement); Population genetics and GWAS follow‑up – targeted genotyping of identified risk loci.

2. Key Test Items & Measurements We Perform

Our targeted NGS services deliver comprehensive genomic reports with validated variant calls and clinically relevant annotations.

2.1 Single Nucleotide Variants (SNVs) & Small Indels

We identify and report all non‑reference sequence changes within the targeted regions, including missense, nonsense, splice‑site, synonymous, and non‑coding variants. For each variant, we provide: genomic position (hg19/hg38), transcript identifier, cDNA and protein changes (e.g., c.2573T>G, p.Leu858Arg), zygosity (heterozygous/homozygous for germline; variant allele frequency – VAF for somatic), sequencing depth and quality metrics (total depth, allele depth, GQX, VQSR status). For somatic variants, we report VAF with a call confidence score (e.g., “high confidence”, “low confidence – verify by orthogonal method”).

Limits of detection: For research and clinical research assays, we routinely detect SNVs/indels down to 5% VAF (tissue, FFPE, blood) with ≥500× depth. For liquid biopsy (ctDNA) and ultra‑deep clinical applications, we use UMI‑based error correction (molecular barcodes) to achieve ≤1% VAF detection (or 0.5% for pre‑validated hotspots) at ≥10,000× effective depth. For germline (constitutional) variants, the detection of heterozygous calls is standard at 20‑40% VAF.

2.2 Copy Number Variations (CNVs)

We detect exon‑level and whole‑gene deletions/duplications using read‑depth analysis. For amplicon‑based panels, CNV calling requires internal normalization to reference genes. For hybrid capture panels, we use algorithms such as CNVkit, ExomeDepth, or VarScan2 (copy number mode). The report includes copy number ratio (log2 ratio), copy number state (0 = homozygous deletion, 1 = heterozygous deletion, 2 = normal, 3 = gain, ≥4 = amplification), and confidence interval. CNV detection is most reliable for alterations spanning at least 3 consecutive exons or >100‑200 bp. For high‑level amplifications (>10 copies), we can also confirm by droplet digital PCR (ddPCR) upon request.

2.3 Gene Fusions & Structural Variants (DNA‑Based)

For targeted DNA panels that include intronic capture probes spanning common breakpoints, we detect gene fusions such as ALK, ROS1, RET, NTRK1/2/3, FGFR2/3, NRG1, and MET exon 14 skipping. Fusion calls are validated by the presence of split‑reads or discordant read pairs. For each fusion, we report the specific partner gene, breakpoint coordinates (when within targeted introns), and the predicted protein consequence (e.g., EML4‑ALK fusion, EML4 exon 13 to ALK exon 20). For rare or novel fusions, we can confirm by RNA‑based NGS (fusion panel) upon request.

2.4 Tumor Mutation Burden (TMB) & Microsatellite Instability (MSI)

For comprehensive cancer panels (≥0.5‑1.0 Mb coding region), we compute TMB as the total number of non‑synonymous somatic mutations per megabase (mut/Mb) after filtering out germline variants. The TMB score is categorized as low, intermediate, or high according to pre‑defined cut‑offs (e.g., TMB‑high ≥10 mut/Mb). MSI status is determined by analyzing the distribution of homopolymer lengths at microsatellite loci; we report MSI‑high (MSI‑H), MSI‑low (MSI‑L), or microsatellite stable (MSS). Both TMB and MSI are reported as qualitative (positive/negative) and quantitative (TMB value) where applicable.

2.5 Pharmacogenomic (PGx) Star Allele Calling

For pharmacogenomics panels, we genotype key pharmacogenes and report the diplotypes and predicted phenotypes (e.g., CYP2D6 *1/*1 – normal metabolizer; CYP2C19 *2/*3 – poor metabolizer). The report includes actionable guidance: e.g., “For CYP2C19 poor metabolizers, consider reducing clopidogrel dose or using alternative antiplatelet therapy”.

3. Standard Methods & Workflow

All targeted NGS tests are performed according to validated protocols with strict quality control at each step.

3.1 Library Preparation & Enrichment

We offer two main enrichment strategies based on project needs:

Hybrid capture (probe‑based) – Uses biotinylated oligonucleotide probes to capture desired genomic regions. Suitable for large panels (>500 kb) and for detecting CNVs, fusions, and intronic variants. Input DNA: 50‑200 ng (FFPE: 100‑500 ng). Workflow: DNA shearing, end repair, adapter ligation, PCR amplification, hybridization with custom or commercial probe pools (overnight), streptavidin bead capture, post‑capture PCR, and indexing. Recommended for comprehensive cancer panels, inherited disease panels, and liquid biopsy (with UMI addition).

Amplicon‑based (multiplex PCR) – Uses thousands of primer pairs to directly amplify target regions. Suitable for smaller panels (<500 kb), rapid turnaround, and high depth. Input DNA: 10‑50 ng (FFPE: 20‑100 ng). Workflow: multiplex PCR in a single tube (typically 2 pools to reduce primer‑dimer), enzymatic cleanup, adapter ligation, indexing PCR. Faster (library prep in 4‑6 hours) and more cost‑effective for hotspot panels. Less optimal for CNV detection and not recommended for fusion detection.

3.2 Sequencing Platforms

We operate Illumina (NovaSeq 6000, NextSeq 2000, MiSeq) and MGI (DNBSEQ‑T7) platforms. Sequencing parameters: paired‑end reads (2×75 to 2×150 bp), target coverage depth 500‑2000× (standard) or >5000× (ultra‑deep for ctDNA), with optional UMI incorporation for error correction.

3.3 Bioinformatics Pipeline

Raw sequencing data is processed through an internally validated pipeline:

Primary analysis: Demultiplexing, adapter trimming (cutadapt), quality filtering (FastQC, multiQC).

Read alignment: BWA‑MEM to hg19 or hg38 reference genome (or custom reference for non‑human species).

Post‑alignment processing: Mark duplicates (Picard), base quality score recalibration (BQSR – for DNA‑seq), realignment around indels (GATK).

Variant calling: For somatic (tumor‑only): Mutect2, VarScan2, or LoFreq (with matched normal if provided). For germline: GATK HaplotypeCaller, DeepVariant, or FreeBayes. For low‑frequency detection with UMIs: UMI‑aware caller (e.g., fgbio, smCounter2, or in‑house script).

Annotation: Variants are annotated using Ensembl VEP, ANNOVAR, or SnpEff with multiple databases (dbSNP, ClinVar, COSMIC, gnomAD, 1000 Genomes). Functional impact predictions (SIFT, PolyPhen, CADD, REVEL) are included.

3.4 Quality Control Metrics

Every sequencing run and sample must pass predefined QC thresholds: Average on‑target rate ≥60% (hybrid capture) or ≥90% (amplicon); Uniformity (percentage of target bases covered at 20% of mean depth) ≥90%; Coverage depth: mean depth >500×, and % target bases covered at 100× >95%; Q30 score ≥80% for the run; Contamination check (VerifyBAMID) with contamination <2%; Sample swapping verification via fingerprint SNPs.

4. Why Choose Our Third‑Party Targeted NGS Testing Services?

As an independent laboratory, we provide unbiased, accurate, and high‑quality genomic data. Our strengths include:

ISO/IEC 17025 accreditation – Our NGS laboratory is CNAS/CMA accredited, with regular participation in proficiency testing (e.g., CAP NGS‑A, UK NEQAS, EMQN).

Flexible panel design – We can design custom panels (hybrid capture or amplicon) for any set of genes or regions, with flexible sizing from 10 kb to >10 Mb.

Low input and FFPE optimization – Our workflows are validated for degraded DNA (e.g., FFPE, cfDNA) with input as low as 10 ng for amplicon panels.

Ultra‑deep detection with UMIs – For liquid biopsy and minimal residual disease monitoring, we offer UMI‑based error correction to detect variants down to 0.1‑0.5% VAF.

Comprehensive bioinformatics – We provide a full report including variant summary table, alignment metrics, QC statistics, and clinical annotations (ClinVar, OncoKB, PharmGKB). For research projects, we deliver raw FASTQ, BAM, and VCF files.

Fast turnaround – Standard hybrid capture panel (100 samples, 500 genes) completed in 2‑3 weeks; amplicon hotspot panel in 5‑7 business days.

Confidentiality – Full protection of your genetic data, patient information, and research objectives.

Consultative support – Our bioinformaticians and geneticists assist with panel design, assay validation, data interpretation, and regulatory submissions (for companion diagnostic development).

Whether you need to screen a cohort for somatic mutations in a clinical trial, develop a custom pharmacogenomics panel for drug response prediction, monitor ctDNA dynamics in cancer patients, or genotype hundreds of inherited disease genes, our targeted NGS testing experts are ready to deliver reliable, high‑quality genomic data.

Get Started with Your Targeted NGS Project

Contact our team with your region of interest (gene list or genomic coordinates), sample type (FFPE, blood, cfDNA), required coverage depth, and expected turnaround time. We will provide a detailed quotation, panel design recommendations, and a sample submission guideline. Let us help you unlock the power of targeted high‑throughput sequencing for your research or clinical application.

This article provides an overview of our targeted next‑generation sequencing capabilities. For specific panel design, sample quantity, and pricing, please request a tailored service proposal.