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Just a few days ago we discussed difficulties encountered when investigating host-associated mycobiomes by a metabarcoding approach suggesting some solutions.

 

In our latest study we compared metagenomic profiles of different mozzarella cheeses.

Global agriculture under pressure: increasing output while minimizing environmental impact Incredible population growth (by the middle of the 21st century we will be over nine billion people) imposes an unprecedented demand on the planet’s resources and capabilities. Imbalance between the agricultural lands needed for food production and the boost urban development, needed to accommodate this population increase, goes at the expense of farm lands. Consider also climatic changes that are likely going to have a negative impact on both natural ecosystems and agricultural productivity. The picture is quite dramatic.

You have surely noticed by now that one of the most universal questions in NGS is:

Targeted capture is one of the most popular NGS applications. However, due to the often-limited amounts of tissue it is challenging to satisfy quality requirements and obtain 200 ng of input DNA still needed by most protocols.

Metabarcoding Identification and classification of eukaryotes increasingly depends on DNA sequences of standardized genetic markers, a concept known as DNA barcoding. Thus, molecular taxonomists continue to search for regions conserved enough to allow reliable priming but sufficiently variable to yield highly resolved and well-supported phylograms. The ideal characteristics include adequate species resolution, ease of amplification, absence of extreme length variation, the presence of only single copies and low intra-species variability.

ChIP-Seq is extensively used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins.

So proud to announce that we qualified above the mean and got a green label in the external quality assessment of NextGen DNA Sequencing by European Molecular Genetics Quality Network (EMQN).

WATBIO is a European Framework 7 funded collaborative research project focused on developing drought-tolerant biomass crops for Europe. IGATech is the leading SME partner in WATBIO and conducts all the next-generation sequencing work. A large proportion of the WATBIO DNA and RNA sequencing work is done on poplar, and the WATBIO project has enabled IGATech to drive significant innovation in the type of sequencing involved.

16S amplicons loaded on a single Illumina lane (regardless of platform type or sequencing length) use to suffer poor quality due to low base complexity. Each cluster on a flowcell starts with the same base (the primers used for amplification) and mostly continue in a low complexity region depending on the diversity of the microbial community (which is anyhow far from balanced base composition on each cycle of sequencing; Fig. 1A). This causes impairing in the cluster identification during first cycles of sequencing since all clusters will emit the same color and thus reduce the ability to discriminate those that juxtapose one another.

16S rRNA sequencing is the most common approach used to identify microbes without the need to sequence entire genome. It is fast, cost-effective and flexible; however the method suffers some inefficiencies.

IGATech is keeping active in the human genomics field. After the D.NAMICA project in which we applied Whole Exome Sequencing to better understand the genetic characteristics of patients suffering dilatative cardiomyopathy, hepatocellular carcinoma and spinal muscular atrophy, we are moving to the next level by implementing Whole Genome Sequencing to redefine the diagnosis in breast cancer and in patients with behavioral, cognitive and developmental disorders.

Our latest work addresses the need for a method specifically developed for mosaic structural variants (SV) detection from Next Gen sequencing (NGS) data.

We finally made it! A brand new - featured - website. We hope this will provide ease of access to all the relevant information regarding our services for loyal and future customers. We thank infoFACTORY for the patient support in the development of the website and graphic creations.