200+bridging the gap between biology and technologies

200+bridging the gap between biology and technologies

200+bridging the gap between biology and technologies

200+bridging the gap between biology and technologies

200+bridging the gap between biology and technologies

g e n o m i c s s i m p l i f i e d

Gopalakrishna Ramaswamy, Sriram Parameswaran, Chellappa Gopalakrishnan, Sudha Narayana Rao and Raja Mugasimangalam

Genotypic Technology (P) Ltd., Bangalore, India

Presenting Author email: gopalakrishna.r@genotypic.co.in

Case Studies in Plant and Animal Genomics: Technologies and Applications, a Genotypic Experience

Abstract:

Genomic Technologies - NGS, Microarrays, low volume PCRs are increasingly being applied in basic research of plants and animals and has found a wide variety of practical applications in Plant breeding and Animal husbandry. More than 500 well annotated plant and animal transcriptomes and > 100 large genomes are published in the last 2 years. From olives to tea and groundnuts; from eucalyptus to palms; from cattle to rabbits, Genomics is being applied to understand the functional connections between pathways and metabolites functions / traits and sequence variations. We will be describing the recent developments in NGS Technologies & microarrays and cases studies and publications from Genotypic and collaborators on applications in plant and animal genetics. The applications include expression profiling, small RNA, metagenomics, exome, whole genome sequencing & resequencing, GBS, amplicon sequencing, SNP validations and assays. The NGS data analysis and interpretation challenges and workflows relevant to plant/animal genomics will also be addressed.

Introduction:

Genotypic Technology Private Limited is the first Genomics Company in India and is emerging from a cutting edge service provider to a technology hub. As a technology hub Genotypic partners with companies & Institutions on their technology needs in the field of genomics by providing access to a multitude of cutting edge technology platforms & skilled personnel. We provide high quality microarray, NGS and bioinformatics services and solutions to both domestic as well as international Pharma and Biotech companies and academia. We are an ISO 9001:2008 certified company with more than 500 clients across the Globe citing our services in more than 200 publications. Genotypic in partnership with technology companies like Agilent, Illumina, life Technologies and Qiagen is a pioneer in simplifying genomics.

Next Generation Sequencing

Whole Genome Sequencing

De novo or reference-based alignment

mRNA and small RNA profiling

Coding variants in the genome

Target capture or amplicons

ChIP-seq, MedIP-seq and BS-seq

16S rRNA and whole genome metagenome

Transcriptome Sequencing

Whole Exome Sequencing

Targeted Genes Sequencing

Epigenetics applications

Metagenomics Profiling

Custom Designs to support NGS

• Custom capture panel using Agilent SureSelect

Targeted genes, mitochondria, chloroplast Exome capture kits for non-model systems Cross-organism panels

• Agilent Haloplex Panels for human DNA

Custom diagnostic panels up to 5 Mb target size

• Custom Genotypic ampliseq panels for targeted sequencing

• Ion ampliSeq

Have you tried BioInterpreter ?

The web-based tool from Genotypic that extracts the biology from your gene expression data. Write to us for a free trial license.

Cannot make sense of GB’s of NGS data?

Try out Genotypic’s Informatics services for Assembly, Annotation and Analysis of NGS Data. Get biological interpretation of your data using our optimized pipelines and supervised annotation with multiple databases.

Microarrays beyond Gene Expression

Technologies at Genotypic

Next Gen Sequencing Microarray qPCR Platforms

• Illumina NextSeq 500 Ultra-fast sequencer

3 mammalian genomes or 20 transcriptomes in a day

• Ion ProtonFlexible throughput sequencer

2 human exomes in less than a day

• Illumina MiSeqUltra-long readlengths

Ideal for targeted sequencing, Diagnostic Panel

• Life Tech Ion Torrent PGMAffordable sequencing for small genomes, targeted sequencing

• ABI 3130 Capillary SequencerTraditional Sanger sequencing direct long reads

• Agilent Microarray PlatformsCustomized array content at minimal additional cost, robustness of 60mer oligo proven technology and choice of array configuration to suit any throughput

• Stratagene/Agilent Mx3005P

• Roche LC480Quick detection with 96-384 samples per run

E-Array Custom Designs - for any organism

• Nearly 1200 ready-to-order designs covering 300+ organisms – human, mouse, rat and other mammals, bacteria, insects, virus and plants

• Conversion from other formats to Agilent

• Custom designs from unpublished RNA-seq data

• Designs for any organism, any application

Agri-Genomics Solutions

Genetic diversity Assessment

• Polymorphic markers using NGS

Genotype to functions / traits association

• Functional SNPs by Transcriptome sequencing

• Genome wide SNPs by Whole genome sequencing

Tilling for mutations/markers

• Targeted re-sequencing to identify SNPs

Validation of SNPs

• By SNP microarrays or qPCR

Ready to order Microarrays for over 20 crops

Molecular Diagnostics Platform

Clinician-referred tests for

• HLA Typing

• Pre- and post-natal screening Chromosomal abnormalities

• Muscular Dystrophy

• Cancer Hotspot Mutation Profiling

• Mutations associated with Cardiomyopathy

• Mutation associated with inherited disorder

• Risk factors for colorectal cancer

• Testing for Maturity Onset Diabetes

• Exome mutations

Genotypic’s Integrated Data Analysis

It includes analysis of massive and disparate data from various technologies- NexGenSeq and Microarray and as well as from different applications-WGS, Exome Sequencing, ChIP, miRNA, Transcriptome sequencing with quick TAT

Gene Expression Profiling

Unique SNP Array Design

Methylation and Promoter Arrays

Any organism with available sequences

Cost-effective tool to study gene regulations

Chromosomal aberrations and re-arrangements

Array CGH

Microarray Applications

miRNA arrays

A proprietary workflow to address genotyping 100 samples for few thousands custom SNPs. Most cost effective solution in the market

Best choice to study host-pathogen mixed

populations

Genotypic Technology Private Limited #259, “Apurva” 4th Cross, 80 Feet Road, R.M.V. 2nd Stage,Bangalore-560094, India. Ph: +91 80 40538300I, +91 990 003 5744, USA Ph: +1 408 844 3940 I Fax: +91 80 23516555 Email: genomics@genotypic.co.in. Web: www.genotypic.co.in, linkedin https://www.linkedin.com/company/genotypic-technology, facebook https://www.facebook.com/Genotypic, twitter https://twitter.com/GenotypicTech

More than 200 publications citing Genotypic’s work from customers and collaborators across the Globe http://www.genotypic.co.in/Whats-New/2/Publications.aspx

DSIR Certified R&D facility