Technologies

DNA and RNA extraction is routinely performed at IGATech, providing support to our customers directly from raw material. Relying on automated systems and consolidated protocols we can help you in accelerating the path to analyzed data. We also work with non standard substrates, such as plants and food. Our expertise in the isolation of high molecular weigth DNA for long-molecule sequencing applications will also be a specialized complement for de novo applications. Pleas enquire to obtain further details.

The whole genome sequence as the most comprehensive overview of its composition. Identify most of the variability accounted by SNPs, CNVs, PAVs, insertions, deletions, translocations along with its functional impact on the genetic code an organism. Dedicated technologies are applied for de novo reconstruction of personal genomes to an affordable price, providing an unbiased method to depict each individual human (and non-human) genome. See de novo - whole genome resequencing.

Providing the same type of information that can be yield from a whole genome sequencing, but focusing only on the coding part of a genome. Most of the phenotypically relevant variants reside on the coding regions or their nearby regions. Further enrichment can be carried out on a very limited set of genes: this is useful to reduce costs but also to produce very high coverage on such genes, providing adequate depth to detect somatic variations in tumor samples. See Exome sequencing.

Reducing the complexity of genomes has enabled NGS to pursue massive genotyping experiments with very competitive costs. One system relies on the cleavage of the genomic DNA by means of two restriction enzymes (ddRAD). Another approach, known as RRBS-Seq, utilizes reduced-representation libraries to perform survey of the methylation states of genomes in relevant regions. See ddRAD - RRBS-Seq.

In order to sequence only an exome, a limited set of genes, or any defined panel of loci, the template DNA must be enriched for fragments derived from them. One way to accomplish such task is to use a set of probes (ssDNA or RNA) to capture by hybridization the regions of interest. Probes, usually attached to biotin moieties, are pulled down with biotin-coated metal beads. See Exome sequencing - target genotyping - clinical genotyping.

As an alternative to hybridization-based enrichment, single-primer extension enrichments provides a very convenient system to enrich for target regions. The main advantage of such system is a much quicker workflow coupled with a higher performance in the enrichment efficiency (i.e. reads that belongs to the desired target). See  target genotyping - clinical genotyping.

NGS platforms have become the most convenient platforms to perform accurate quantification of transcripts. Moreover, relying on sequencing information, it is possible to obtain non-trivial information such as mutation in coding regions, alternative splicing with isoforms expression levels, allelic-specific expression, intron retention, etc. Also, when performing de novo reconstruction of a genome, RNA-Seq data will be one of the major drivers for gene prediction and modeling. See RNA-Seq - smallRNA-Seq.

Leveraging massive single-cell partitioning and barcoding with the Chromium platform it is possible to profile trascription patterns for up to tens of thousands of cells simultaneusly, with no lower limit on cells amount. Cell sorting and library preparation are perfomed in one day. The same technology can also be used to profile the immune system V(D)J repertoire of T-cells. 

Regular short reads generated after library preparation on the Chromium system. Reads carrying the same barcode originate from the few long molecules of DNA, each coming from a single allele. Sequences can be mapped against a reference genome to phase all the SNP and indel variants with long contiguity. On a de novo assembly graph, this method allows to disentangle ambiguous parts along with the ability to generate a reference sequence for each of the two haplotypes. See de novo.

The area of research which investigates the taxonomical composition and activity of complex biological substrates. While traditional sequencing of cultured microorganisms could not provide a picture of the diversity of natural substrates, shotgun sequencing has opened the possibility of an unbiased fingerprinting and metabolic activity profiling of diverse communities, ranging from soil samples to the human intestinal flora. Several techniques provide scalable solutions. See metagenomics - metabarcoding.

Chromatin immunoprecipitation is a technique that allows to enrich the genomic DNA for those fragments involved in specific interaction with some proteins. By comparing coverage profiles with non-enriched DNA, it is possible to detect peaks of enrichment which characterize where the protein has the most of its affinity. See ChIP-Seq.

An alternative way to pursue genotyping/classification experiment is carried to a very low coverage per individual. This technique is adopted in several applications such as metagenomics, allele/SNP mining, Pop-Seq, Pool-Seq. Haplotype/organism identification will rely on a ‘horizontal’ coverage rather than a ‘vertical’ coverage. This analysis does not have sufficient information to detect structural variation, but dramatically reduces costs in large genotyping and metagenomics experiments. See metagenomics - bioinformatics.

Bisulfite treatment allows to explore methylation levels of genomic DNA. Non-methylated cytosine are converted to uracil and then to thymine. Sequencing and mapping to adequate read depth allows to detect the level of 5mC (5-methylcytosine) on DNA molecules either on CpG, CHG or CHH contexts for both strands of the DNA molecules. See BS-Seq - RRBS-Seq.

With NGS increasing read length and base quality, amplification of one or many loci can be adopted as sequencing template. Whether interested to analyze the diversity of a single amplification product or to discover variability on limited set of interesting genes, Amplicon-Seq is a system that can provide adequate resolution and flexibility while maintaining a very affordable price to cope with large scale experiments/surveys. See Metabarcoding - Metagenomics - Clinical Genotyping

Long reads are empowering many applications by the ability to analyze DNA and RNA molecules with virtually no limitation on their size. This is of particular importance when the goal is to reconstruct complex genomes where short reads fail to resolve hard-to-sequence or repetitive regions. Also, direct RNA sequencing and full-length cDNA sequencing are providing unprecedented insight into the real strucure and abundance of transcripts isoforms.

Chromatin interactions are knonw to play an important role in trans-regulatory mechanisms of transcription and chromosome organization. Beside the biologically relevant signals acquired by HiC data (deviation from expected), the proximity contact matrix (expected) has become a state of-the-art technique to assemble genome at chromosome scale and possibly to phase alterantive alleles to the same extent to delivery complete diploid genome assemblies.