NGS Platforms available at Genotypic:
Also available: SoLiD 5500XL for high accuracy genome closures and structural re-arrangment detection
Summary of the Platforms and Recommended Applications
||Number of Reads
||Peak Data Output
||2 × 150 bp
||400 M paired
||100 - 120 Gb
|| • Eukaryotic Whole Genome de novo*
• RNA-seq de novo*
• Whole Genome metagenome
• RNA-seq Reseq
|2 × 75 bp
||400 M paired
||50 - 60 Gb
|| • Eukaryotic Whole Genome reseq
• RNA-seq Reseq*
• ChIP-seq (histone modifications)
|1 × 75 bp
||25 - 30 Gb
|| • Small RNA Profiling*
• ChIP-seq *
||2 × 150 bp
||12 - 15 M paired
||4.5 - 5 Gb
|| • Targeted sequencing
|2 × 300 bp
||22 - 25 M paired V3
||13 - 15 Gb
|| • 16S rRNA metagenome sequencing*
• Bacterial Whole genome De novo*
• De novo transcriptome
• HLA typing*
• Genome Gap closures
||1 × 120 - 160 bp
||100 - 150 M
||10 - 12 Gb
|| • Whole Exome*
• RNA-seq reseq
• Bacterial Genome reseq
|Ion Torrent PGM
||1 × 300 - 400 bp
||0.1 - 10 M
||10 Mb - 1 Gb
|| • Targeted sequencing
• Viral genomes and plasmids*
|* Indicates the preferred platform for the application
To know more about library preparation capabilities of Genotypic,please click here.
Contact us to know about platform specific advantages and to choose the right platform suited for your research. You can reach us at genomicsatgenotypic.co.in or sequencingatnextgenseq.com.
Key features of Next Generation Sequencing Services at Genotypic
- All genomics solution under one roof
- Technical support from team of experts who have completed more than 1000 Next Generation Sequencing projects from project planning to data interpretation
- Quick turn-around-time
- Specialized (Customized) disease panels for SNP identification in known gene
- Variety of read-lengths (depending on platform) to cater to different sequencing output needs
- Ultra high depth and paired end sequencing
- Option of Multiplexing to save cost (i.e. more than one sample per lane)
- Provision for combining different platforms based on project needs- Hybrid Assembly Service
- Strict data confidentiality with secure data transfer through our high end server
Whole Genome Sequencing
Full service for all organisms from sample preparation to analysis.
- Draft sequence for any organism can be generated.
- No prior sequence information required.
- Customized approaches in library construction depending on genome size, available information and goal of the project.
Genotypic offers targeted re-sequencing services to
- Sequence selected genes / genomic regions in multiple samples using DNA Capture by Agilent’s SureSelect Technology - On-Array DNA Capture and In-Solution (Liquid) Capture.
- Sequence exons (coding regions) or whole exome
- Sequence mitochondria, chloroplast DNA (Kbs and Mbs instead of Gbs, cheaper to sequence and quicker to analyze) based on clients’ interest.
- Customize regions of interest for sequencing (custom array/bait designing)
|On-Array DNA Capture
||In-Solution (Liquid) Capture
|Up to 1 million bases, 1 sample or more
||For 100kb- 50Mb, >10 samples
|Optimal for detecting variations in targeted regions less than 6Mb
||Optimal for detecting variations in whole exome.
|Minimum input required is 10ug of DNA
||Minimum input required is 5ug of DNA.
|Splice variant detection among known genes
||Ideal for Human Exome
RNA sequencing by Next Generation Sequencing allows simultaneous sequencing and quantification of transcript levels. At Genotypic, we have successfully completed Transcriptome sequencing projects for both de novo
and known transcriptomes for a variety of species. We offer variety of read lengths (2X75 and 2X150 bp, 1X120+ bp) and multiplexing options to customers.
Highlights of Transcriptome Sequencing at Genotypic
- Identify novel transcripts
- Identify novel isoforms
- Identify alternative splice sites
- Allele specific expression
- Identify rare transcripts
- Directional paired end sequencing on Illumina
Digital gene expression
Genotypic provides digital gene expression services using various sequencing platforms which offer several advantages in providing in-depth coverage. Advantages include ultra high coverage to enable rare transcript discovery, highly accurate characterization of transcripts and quantitative data to enable accurate measurement of gene expression levels.
Applications of Digital Gene Expression
- Target discovery
- Disease classification
- Pathway studies
- Rare transcript detection
- Validation of microarray results
ChIP Seq is a widely used method to identify regions of genome associated with specific proteins. Based on our extensive experience, we have incorporated processes in our pipeline which ensures an initial QC certifying a sample suitable for ChIP-Seq. We have been successful in generating good libraries from ChIP DNA from a variety of sources including insects, cell culture etc. Since our protocols are well standardized we offer quick turn-around-time to our valuable clients.
Reduced Representation Library sequencing
Reduced Representation Library (RRL) minimizes the target genome size by removing the repetitive sequences and also decreasing the complexity of the genome. This approach does not require prior knowledge of genome sequence of the particular organism. Identical region from different species can be selected and subjected to deep sequencing. This technology is ideal, cost effective and quick strategy for SNP discovery. Other applications of RRL sequencing include gene discovery, methylation analysis and genomic characterization of repetitive genomes. At Genotypic, we offer this customized service based on the client’s needs.
Epigenome / Methylome sequencing
Methylated CpG sites in the genome can be identified in a variety of ways such as MethylC-seq (Whole genome bisulfite sequencing), MethylCap-seq, MBD-seq, MeDIP-seq. Each of these approaches can be performed at Genotypic based on client’s requirements for specific projects.
Small RNA sequencing
At Genotypic we offer short read lengths suited for small RNA sequencing coupled with ultra high depth of sequencing for quantification. Our latest protocols are tailored to address nuances in bacterial and plant small RNA sequencing projects, where conventional methods of miRNA enrichment may not work efficiently. We have successfully sequenced small RNA populations from samples such as serum and urine- enabling biomarker discovery.
CLIP- Seq is used to study interaction between particular RNA species and specific RNA binding proteins. It employs UV-cross-linking between RNA and the protein, followed by immuno-precipitation with antibodies for the protein, fragmentation and sequencing. Preparation of Libraries for Next generation sequencing of such samples which can be very limited in quantity is challenging and offered by few Service providers around the world
Service includes preparation of libraries from CLIP samples and sequencing of varied lengths depending on the projects needs.
Amplicon sequencing involves deep sequencing of PCR products using Next generation sequencing platforms like Ion Torrent and MiSeq for analyzing variation. It replaces traditional Sanger Sequencing and provides higher sensitivity at ultra low cost per mutation detection.
It is possible to pool several individual samples in a single sequencing reaction by bar-coding them uniquely, thus lowering costs. Genotypic offers ultra high depth of sequencing that enables accurate and very low frequency variant identification. Applications include
- Detection of mutations/variants in disease
- Purity testing of GM crops and food products
- Detection of ultra low frequency variants in vaccine production
- Detection of ultra low frequency variants in Biopharma production
Mate pair library
Genotypic offers Mate pair library sequencing using Illumina GAIIX and SOLiD 5500xl platforms with applications in de novo sequencing of large genomes as well as to identify large genomic rearrangements in diseases like cancer. We offer construction of mate pair libraries of insert sizes varying from 1-5 kb. Based on the requirement of the project, status of existing genome sequence data if any, etc. we guide the decision for making a mate pair library with the appropriate insert size.
Human Exome Sequencing
We offer Human exome capture and sequencing on Ion Proton (using Ion/Agilent SureSelect exome capture) and Illumina NextSeq 500 (using Agilent SureSelect exome capture). For human exome, the called variants are mapped to databases such as dbSNP, COSMIC, 1000 genomes and SIFT/PolyPhen.platforms.
Single Sequence Repeats (SSRs) or microsatellites are genetic markers which exhibit a high degree of polymorphism due to the mutation affecting the number of repeat units. This hyper variability among related organisms makes them excellent markers for various applications such as genotype identification, analysis of genetic diversity, phenotype mapping, marker assisted selection of crop plants and wide range of molecular ecology and diversity studies. Genotypic recommends long read lengths using Illumina Miseq/Ion Torrent PGM for accurate characterization of Single Sequence Repeats.
Suppression subtractive hybridization sequencing / Selective subtractive hybridization sequencing is used to characterize uniquely expressed transcripts in any sample by sequencing the library generated using SSH protocols. This approach saves time and informative alternative to traditional methods involving cloning and sequencing individual transcripts from SSH libraries
- Identification of differentially expressed mRNA
- Identification of differentially expressed ncRNA
- Identification of DNA sequences specific to one taxon or the other
Identification of mutants by TILLING:
TILLING: (Targeting Induced Local Lesions IN Genomes), TILLING is a reverse genetic technique that uses traditional chemical mutagenesis methods to create libraries that are later subjected to high-throughput sequencing for the discovery of mutations. Observed phenotypes can be correlated with specific genotypes determined by sequencing.
TILLING by sequencing involves applying high throughput deep sequencing of target genes amplified from multi-dimensionally pooled templates. Barcoding or indexing by unique tags allows parallel processing of sequencing libraries and provides flexibility in terms of number and pooling arrangement of targeted genes, species and pooling schemes.