Research services

NewGene is a leading provider of R&D support to the NHS, academic community and industry.

NewGene's technology platforms combined with the expertise of its team offer exciting opportunities for clients with specific research projects.

Whether you are an academic department, government organisation, or work in industries as diverse as pharmaceutical, biotechnology or agriculture, NewGene’s sequencing team has the experience and expertise to help successfully accomplish your DNA sequencing and genotyping project.

NewGene services include:

• Extraction of DNA
• Next generation sequencing
• Genotyping on the Agena platform
• Real time PCR
• Bioinformatics analysis

NewGene provides a flexible approach to research services; its capability and expertise is applied to sequencing tasks, while customers can select the supporting activities they would like to include in the NewGene service. To discuss your research project in detail, please contact NewGene via the online enquiry form.

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Next Generation Sequencing Services

Illumina MiSeq

The MiSeq system enables a broad range of applications including targeted gene sequencing, metagenomics, small genome sequencing and expression analysis.

Illumina provide the option of optimised sample preparation kits or we can work with you to cater to your sequencing needs. The following table shows the current MiSeq workflows available and their output file format:

Workflow	File format
Assembly	contigs.fa
Custom Amplicon	.bam, .vcf
FASTQ only	fastq.gz
Library QC	.bam
Metagenomics	.txt.gz
PCR Amplicon	.bam, .vcf
Resequencing	.bam, .vcf
Small RNA	.contam, .genome, .mirna, .rna

Samples can be prepared for sequencing using commercial sequence capture kits or custom designed assays. Following sequencing, variant calling and sequencing alignment can take place directly on the instrument or using Illumina’s genomic analysis cloud platform – Base Space. Sequencing can take from as little as 4 hours, with DNA from template to result within only 1 day.

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Roche 454 FLX+

The Roche 454 GS FLX+ System combines long read lengths, accuracy and high-throughput sequencing. The technique is based upon emulsion PCR and pyrosequencing and enables full DNA sequencing of clonally amplified targets. The use of multiplex identifier tags (MIDs) enables efficient use of sequencing runs.

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Genotyping on the Agena Mass ARRAY 4 Platform

The Agena MassARRAY 4 is a highly accurate MALDI-TOF mass spectrometry based platform providing specificity and sensitivity for studies of genetic variation including somatic mutation detection in heterogeneous samples.

The technology is able to identify SNPs and other stretches of DNA sequence that differ by one, or a small number of bases via an extension reaction. From this the genotype is determined.

• 384 well footprint
• Agena CE marked kit based systems such as OncoCarta are available
• Agena EpiTYPER kit for methylation and epigenetic studies.

For more information, click here to visit the Agena Bioscience website.

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Support services

Extraction of DNA

NewGene can extract DNA from a wide range of clinical and research samples including; whole tissue, blood, buccal swabs and saliva samples, FFPE blocks or cut curls and cell pellets.

Extraction techniques focus on manual extraction including the COBAS system and robotic extraction of blood samples using the Roche M96 and Qiagen QIAsymphony platforms.

Manual extraction of RNA from blood collected in PAXgene tubes.

Real Time PCR

Real time PCR (RT-PCR) or quantitative real time PCR (qPCR) enables the real time detection of DNA amplification and quantification of the target molecule.

NewGene works closely with customers to develop bespoke RT-PCR assays for the detection of their gene of interest, and this service can be used for example to support the generation of regulatory data or routine testing.

Bioinformatics

NewGene accesses a number of Bioinformatics tools in order to support the analysis of clinical samples. These include the mutation databases DMuDB that is curated by the National Genetic Reference Laboratory at Manchester and the Leiden open source database LOVD, in addition to the Alamut software.

The results of research and development programmes will be provided in an appropriate format. If you have more complex Bioinformatic requirements a comprehensive service for analysis of next generation sequencing across a number of platforms is available from the Bioinformatics Support Unit of Newcastle University.

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