Next-generation sequencing will be conducted in collaboration with NXTGNT, a reference center for sequencing, (epi-)genome and transcriptome analysis at Ghent University and a partner of ProGenTomics. Below a short overview of the possible next-generation sequencing services we can offer is given. For much more detailed information, please feel free to visit the NXTGNT website. All sequencing is performed with Illumina platforms, scalable to the need of your project: MiSeq, NextSeq 500 or HiSeq 3000 sequencers can be used.
Genomics
The most comprehensive method for analyzing the genome is by whole-genome sequencing. While whole-genome sequencing is commonly associated with sequencing human genomes, the scalable, flexible nature of next-generation sequencing (NGS) technology makes it equally useful for sequencing any species, such as agriculturally important livestock, plants, or disease-related microbes. Even when limited amounts of starting material are available, whole-genome amplification can be applied to obtain enough material for sequencing. However, not all the information entangled in the genomic code is always crucial in research. In such cases, exome sequencing, which is targeted to protein-coding regions only (about 1% of the human genome) can be performed. Or when even exome sequencing captures too much information, one can opt to perform targeted sequencing, in which only a few particular genes or gene regions are targeted during the sequencing.
Transcriptomics
Information at the genome or the DNA-level is transcribed to RNA transcripts, which in turn are usually translated to proteins. Transcriptomics (or expression profiling) is the study of the transcriptome – the complete set of RNA transcripts that are produced by specific cells or tissues under specific circumstances. Depending on your interest several different RNA transcripts, messenger RNAs (mRNA), micro RNAs (miRNA), long non-coding RNAs (lncRNA), etc can be profiled using RNA-seq. Limited starting material is no problem, as single-cell transcriptomics can be easily performed starting from the RNA available in one (human) cell. Also partly degraded or low quality RNA isolated from, for instance, formalin-fixed, or paraffin-embedded (FFPE) tissues pose no hurdle for transcriptome sequencing. Finally, we can sequence only RNA that is actively transcribed to proteins by ribo-profiling.
Epigenomics
Epigenetic research seeks to describe dynamic alterations in the transcriptional potential of a cell. Changes in the epigenome occur regularly and naturally, but can also be influenced by several factors including age, the environment/lifestyle, and disease state. Epigenomics is believed to be the link between the environment and gene expression. The main epigenetic mechanisms are DNA methylation, histone modification, and non-coding RNA-associated gene silencing. DNA-methylation can be profiled using a variety of techniques such as MBD sequencing or (h)MeDIP sequencing, (oxidative) reduced representation bisulfite sequencing or (oxidative) bisulfite sequencing. Histone modifications can be easily detected by ChIP-seq. Since non-coding RNA are a type of RNA, they can be characterized using RNA-seq.