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Cancer Research

Cancer research is a basic research into cancer to identify causes and develop strategies for prevention, diagnosis, treatment, and cure. Cancer research ranges from epidemiology, molecular bioscience to the performance of clinical trials to evaluate and compare applications of various cancer treatments. We provide a complete workflow for Cancer Research at the genomic and cellular level.

The DNA from an individual is a signature of their genome.  Cancer genomics is a field of study to evaluate the genome of a cancerous cell to identify changes due to genetic inheritance or environmental abuse and their role in carcinogenesis. Such changes can be identified in the DNA as Single Nucleotide Polymorphisms (SNP), Copy Number variation (CNV), insertion or deletions of bases.

These variations in genes result either in loss of function of proteins or in some cases gain of function where a normal quiescent cell now starts rapidly dividing turning into a malignancy.

Solutions from

Studies of cancers in individuals with familial history can provide gene signatures that are passed on through generations. One such example is the changes (mutations) in a gene called HER2. HER2 is a member of the epidermal growth factor and dysregulation of this protein has been observed in several breast cancers. An emerging field of cancer treatment, personalized medicine utilizes the knowledge from Cancer Genomics to selectively manufacture drugs killing cells with just the targeted mutation. Patients with HER2 positive breast or gastric cancer can now be treated with the drug Herceptin (trastuzumab) to only kill cancer cells. Such treatments are less toxic and more effective.

Our comprehensive genomic solutions for cancer provide of glimpse of DNA (targeted sequencing), RNA sequencing, and Whole exome sequencing. Newer methods of recovering cancer cells from tissue free biological samples such as Liquid Biopsy for early detection. Techniques for single cell analysis or segregating cancer cells (through Laser Capture Microdissection- LCM) are also covered.

Targeted Sequencing using PanelsRNA SequencingWhole Exome SequencingLiquid Biopsy for CFDNALaser Capture MicrodissectionSingle Cell Isolation from CTC using DEPArray technology

Targeted Sequencing using panels

Targeted sequencing is a powerful way to increase the cost-effectiveness of variant discovery and detection. With targeted resequencing, a subset of genes or regions of the genome are isolated and sequenced. Targeted approaches using next-generation sequencing (NGS) allow researchers to focus time, expense, and data analysis on specific areas of interest. IGB partnered with Thermofisher offers wide range of panels from a powerful ampliseq technology to boost your cancer research. AmpliSeq technology helps you achieve high uniformity of coverage across fragmented DNA frequently found in FFPE and fine needle aspirate (FNA) samples.

Ion Ampliseq Panels Oncomine Assays
  • Germ line mutation detection
  • FFPE Samples
  • Liquid Biopsy
  • Solid Tumor
  • FFPE
  • CTC
  • cfDNA

Ampliseq Panel

Ion Ampliseq Technology is a powerful tool to enhance your research in understanding the cancer genomics. Ion AmpliSeq panels consist of a pool of oligonucleotide primer pairs, each pair designed to amplify a specified genomic region. Each panel can be designed to interrogate all bases across a gene, or it can be focused on specific mutation hotspots. Choose  either the pre-design panel from the list or create your own custom Panel visiting website www.ampliseq.com.  Available Panels for cancer research are tabulated below:

Panel Name Number of genes Pools Input DNA/RNA Brochure
Ampliseq Hot Spot Cancer Panel V2 50 genes One 10ng
Ion AmpliSeq™ Comprehensive Cancer Panel 400 genes four 40ng
Ion AmpliSeq™ BRCA1 and BRCA2 Panel BRCA1 and 2 3 30ng
Ion AmpliSeq™ Colon and Lung Research Panel v2 22 1 10ng
Ion AmpliSeq™ TP53 Panel TP53 gene 2 20ng
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel Gene fusion detection 1 10ng
Ion AmpliSeq™ AML Research Panel 277 genes 4 40ng

Ion Ampliseq Complete Workflow

DNA/RNA Extraction Manual/Automated Ampliseq Library Preparation Template Preparation using OneTouch2 Or Ion Chef System Sequencing Using S5 PGM Data Analysis
MagMax Multi sample kit
MagMax FFPE kit		 Manual- Ion Ampliseq Library kit v 2.0
On Ion Chef- Ion Ampliseq Kit for Chef DL8		 One Touch 2
Ion Chef		 Ion PGM
S5		 Ion Reporter Server




Step1 DNA Extraction

Manual

Automated

Step2 DNA Quantitation Using Qubit

Step3 DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Automated Library Preparation using IC

Step4 Template Preparation

Automated Template and Chip loading using IC

Semi automated using TO2

Step5 Sequencing

PGM

S5 and S5XL

Step6 Data Analysis

Ion reporter Server

Oncomine Tumor Panels

The discovery of Genetic Biomarkers and their application in oncology is paving the way towards targeted therapy. As more and more gene and mutations are now discovered and their role is defined the clinicians are finding it easy to prescribed the treatment for a particular oncogene.

Whether you are working with DNA or RNA, formalin-fixed, paraffin-embedded (FFPE) tissue samples, or blood, Oncomine assays engender trust among clinical cancer researchers because:

  • Content includes cancer genes and is reviewed by experienced professionals to help ensure the highest relevancy.
  • Protocols and verification are based on analyses of clinical research samples to help ensure repeatable results
  • Assays are produced under enhanced manufacturing quality control to facilitate consistent analyses across large sample sets.
  • Specialized application support teams are available to help enable faster implementation in your lab.

Oncomine Solid tumor assays for Cancer Research

Panel Name No. of genes Pools Input DNA/RNA Brochure
Oncomine Solid tumor assay 23 1 10ng
Oncomine Focus assay 52 2 40ng
Oncomine Comprehensive assay V3 161 4 30ng
Oncomine BRCA research assay 10 1 10ng
Oncomine Lung cfDNA Assay 2 20ng
Oncomine Lung CfDNA kit 11 1 10ng
Oncomine™ Colon cfDNA Assay 14 1 10ng

Oncomine Complete Workflow

DNA/RNA Extraction Manual/Automated Ampliseq Library Preparation Template Preparation using OneTouch2 Or Ion Chef System Sequencing Using S5 PGM Data Analysis
MagMax Multi sample kit
MagMax FFPE kit		 Manual- Ion Ampliseq Library kit v 2.0
On Ion Chef- Ion Ampliseq Kit for Chef DL8		 One Touch 2
Ion Chef		 Ion PGM
S5		 Ion Reporter Server




Step1 DNA Extraction

Manual

Automated

Step2 DNA Quantitation Using Qubit

Step3 DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Automated Library Preparation using IC

Step4 Template Preparation

Automated Template and Chip loading using IC

Semi automated using TO2

Step5 Sequencing

PGM

S5 and S5XL

Step6 Data Analysis

Ion reporter Server

Ion Exome Workflow

Exome Sequencing provide a powerful tool to cancer researchers as most of the variant sequences which can alter the protein is situated in the exon region (which corresponds to 1% of the whole genome). By specifically targeting exons, whole exome sequencing is a simple and efficient approach to identify rare mutations and help discover new biomarkers. Our Exome workflow using S5XL and Ion Chef is the fastest solution available.

DNA/RNA Extraction Manual/Automated Ampliseq Library Preparation Template Preparation using OneTouch2 (Ion PGM Hi-Q OT2 Kit) Or Ion Chef System (Ion chef template kit) Sequencing Using S5 (540 chip) or PGM Data Analysis
MagMax Multi sample kit
MagMax FFPE kit		 Ampliseq Library Kit One Touch 2
Ion Chef		 S5 Ion Reporter Server


Step 1: DNA Extraction

Manual

Automated

Step 2: DNA Quantitation Using Qubit

Step 3: DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Step 4: Template Preparation

Automated Template and Chip loading using IC

Step 5: NGS Sequencing

S5 and S5XL

Step 6: Data Analysis

Ion reporter Server

RNA analysis

Cancer is characterized by a dazzling array of genetic lesions directly affecting genes, including point mutation, insertion, deletion, translocation, exon-skipping and gene fusion. If the mutant genes are transcribed, these lesions become detectable by RNA-Seq. At the same time, RNA-Seq measures the transcript abundance, thus revealing the expression levels of the mutant genes.82,83 RNA-Seq can thus identify biomarkers for cancer risks, subtypes and stages of progression, providing crucial insights into cancer diagnosis, prognosis and potential personalized therapies. Next-generation sequencing and advances in real-time PCR (qPCR) throughput have revolutionized the way differential gene expression is analyzed, including variability between gene alleles and differently spliced transcripts, non-coding RNAs, post-transcriptional mutations and editing, and gene fusions.

Ion Ampliseq Transcriptome Gene Expression Panel

Ion AmpliSeq™ technology-based gene expression survey designed to interrogate the collection of all human RefSeq transcripts. The kit Enables low input amounts & FFPE – 10ng total RNA input and no enrichment or selection required. An Application-specific plugin on Torrent Suite simplifies analysis.

DNA/RNA Extraction Manual/Automated Ampliseq Library Preparation Template Preparation using Ion Chef System Sequencing Using S5 on 530 or 540 chip Data Analysis
MagMax Multi sample kit
MagMax FFPE kit		 Manual- Ion Ampliseq Library kit v 2.0
On Ion Chef- Ion Ampliseq Kit for Chef DL8		 Ion Chef S5 Ion Reporter Server & Partek Software


Step1 DNA Extraction

Manual

Automated

Step2 DNA Quantitation Using Qubit

Step3 DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Automated Library Preparation using IC

Step4 Template Preparation

Automated Template and Chip loading using IC

Step5 Sequencing

S5 and S5XL

Step6 Data Analysis

Ion reporter Server

Partek Software

Targeted RNA Sequencing

Targeted RNA sequencing is an excellent tool for selecting and sequencing specific transcripts of Interest. Our RNA-Seq workflows simplify the entire process, from library preparation to data analysis and biological interpretation. The technology based on powerful Ampliseq panel will provide you high coverage of RNA transcript from variety of RNA samples including FFPE. Furthermore, targeted RNA sequencing can be used to detect fusion transcripts from chromosomal rearrangements, which are critical initiating steps of tumorigenesis. Two powerful Panels (tabulated below) are available for performing the RNA sequencing.

DNA/RNA Extraction Manual/Automated Ampliseq Library Preparation
Manual- Ion Ampliseq Lib kit v 2.0
Ion Chef- Ion Ampliseq kit for chef DL8		 Template Preparation using OneTouch2 Or Ion Chef System Sequencing Using S5 510, 520, 530 or 540 chip) or PGM (314,316 or 318 chip) Data Analysis
Manual
KingFisher		 Manual
Ion Chef		 One Touch 2
Ion Chef		 Ion PGM
Ion S5		 Ion reporter server




Panel Name No. of genes Pools Input DNA/RNA
Ion AmpliSeq™ RNA Apoptosis Panel 267 1 10ng
Ion AmpliSeq™ RNA Cancer Panel 50 1 500pg-5ng

Step1 DNA Extraction

Manual

Automated

Step2 DNA Quantitation Using Qubit

Step3 DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Automated Library Preparation using IC

Step4 Template Preparation

Automated Template and Chip loading using IC

Semi automated using TO2

Step5 Sequencing

PGM

S5 and S5XL

Step6 Data Analysis

Ion reporter Server

Whole Transcriptome analysis

Transcriptome sequencing, or RNA sequencing (RNA-Seq), provides fundamental insights into how genomes are organized and regulated—giving us valuable information about the internal state of cells and how altered expression of genetic variants contributes to complex disease research. Transcriptome sequencing relies on next-generation sequencing (NGS) methodology and techniques. We offer a complete RNA sequencing solution for gene expression research from sample prep to analysis. Furthermore, the results can be validated by downstream qPCR analysis.

DNA/RNA Extraction Manual/Automated Library Prepration using Ion Total RNA seq Kiit v2.0 Template Preparation using Ion Chef System and Ion Template Kit Sequencing Using S5 (530, 540 chip) Data Analysis
MagMax Multi sample kit
MagMax FFPE Kit		 Manual Ion Chef Ion S5 Ion Reporter Server & Partek Software

Step1 DNA Extraction

Manual

Automated

Step2 DNA Quantitation Using Qubit

Step3 DNA Amplification and Library Preparation

Library preparation kit

Step4 Template Preparation

Automated Template and Chip loading using IC

Step5 Sequencing

S5 and S5XL

Step6 Data Analysis

Ion reporter Server

Partek Software

Liquid Biopsy Workflow for Cancer

Tissue biopsy is currently the standard of care for the molecular diagnosis of cancer. Despite the informative nature of solid tumor biopsies, tumor heterogeneity and clonal evolution present significant challenges in designing effective treatment strategies based on tissue biopsies alone. Molecularly targeted, personalized cancer therapies are dependent on serial monitoring of cancer genetics. Performing consecutive biopsies to capture a tumor’s spatial and temporal heterogeneity during tumor evolution is often difficult, risky, expensive and often times unachievable. Therefore, the need for novel approaches that could efficiently detect tumor heterogeneity in the course of cancer system treatments has arisen.  Recent progress in genomic analysis of blood samples for CTC, cfDNA, cfRNA has made possible a real-time, affordable and non-invasive liquid biopsy approach for cancer detection and monitoring.

Among other molecular insights, this novel diagnostics method provides important complementary information on therapeutic targets and drug resistance mechanisms in patients that are afflicted with cancer. Our complete workflow starts with Isolating CTC, cfDNA/cfRNA, performing NGS for mutation detection and data analysis using Oncomine Knowledge software.

Liquid Biopsy Blood Collection kit
Remove 0.2mL blood to isolate WBC cfDNA Extraction CTC Enrichment
Ion Ampliseq Library Preparation Ion Ampliseq Library Preparation Ion Ampliseq Library Preparation
Sequencing
Data Analysis

Step 1: Liquid Biopsy

Step 2: DNA/RNA Extraction

Manual

Automated

Step 3: Ampliseq Panel/Oncomine panel

Oncomine Panel

Step 4: DNA Quantitation Using Qubit

Step 5: DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Automated Library Preparation using IC

Step 6: Template Preparation

Automated Template and Chip loading using IC 

Semi automated  using TO2

Step 7: NGS Sequencing

PGM

S5 and S5XL

Step 8: Data Analysis

Ion reporter Server

Oncomine Knowledge Reporter Software

Laser Capture Microdissection (LCM) Workflow for Cancer

Cancer have heterogeneous cellular population. A very small percentage of the cell population represent the tumor cells. Biopsy sample represent normal and tumor cell together with the high percentage of normal cell. Extracting the DNA from the Heterogeneous population leads to false negative results for the mutation detection.

Laser capture microdissection allows selection of the cancer cells from a heterogenous mixture of tumor and normal cells. Thus, only the enriched tumor cells can be processed downstream using the MagMax kit and Ion torrent NGS platform to identify mutations or the gene fusion.

Laser Dissection of the Cell Using LCM DNA/RNA Extraction Manual/Automated Ion Ampliseq Panel Oncomine Panel Ampliseq Library Preparation
Manual on Ion Ampliseq Lib Kit v 2.0
Ion Chef- Ion Ampliseq Kit		 Template Preparation using IC or OT2 Sequencing Using S5 (510,520,530, 540 chip) or PGM 314 or 316 or 318 chip Data Analysis
Arcturus LCM Manual – MagMax Multi sample kit
KingFisher – MagMax FFPE Kit		 Manual
Ion Chef		 One Touch 2
Ion Chef		 Ion PGM
Ion S5		 Ion reporter server Data Analysis




 

Step 1: Laser Dissection of Tissues

Step 2: DNA/RNA Extraction

Manual

Automated

Step 3: Ampliseq Panel/Oncomine panel

Oncomine Panel

Step 4: DNA Quantitation Using Qubit

Step 5: DNA Amplification and Library Preparation

Ion Ampliseq Library preparation kit

Automated Library Preparation using IC

Step 6: Template Preparation

Automated Template and Chip loading using IC

Semi automated  using TO2

Step 7: NGS Sequencing

PGM

S5 and S5XL

Step 8: Data Analysis

Ion reporter Server

Oncomine Knowledge Reporter Software

Single cell technology workflow

Recent Development in the technology for isolating the Circulating Tumor Cells (CTCs) and characterization of these cells have paved many advances in the cancer research and therapies. However, two major obstacles have limited the exploitation of CTC analysis, first the isolation of individual tumor cells to purity without contaminating white blood cells (WBCs) and second, the ability to comprehensively analyze single cell genomes or phenotypes for diagnostic purposes. The DEPArray technology overcomes these obstacles by isolating the Single cell from the population of a suspension of enriched cells. After isolation the single cell can be amplified using Ampli1 WGA kit and combined with the power of Ampliseq Panels to sequence the Cancer cells.

Single cell sorting Single cell amplification Sequencing using Ion torrent Technology Data analysis using Ion Reporter SW
DEPArray™Nxt Instrument Ampli1™ WGA Kit Ion Torrent® S5 /S5 xl Ion Reporter

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