Maran Valentina

Posted on January 18, 2012 | Leave a comment

Focus to key Genomic regions – Agilent’s SureSelect Platform.

Agilent’s SureSelect platform allows you to focus your next-gen sequencing workflow on key genomic regions of interest while reducing cost per sample. This system uses an extremely efficient hybrid selection technique. One hundred twenty-mer RNA oligos provide reliable capture of more small and large variants, including SNPs, CNVs and Indels with unsurpassed allelic balance.

You can now achieve unparalleled efficiency in sequencing a statistically relevant number of samples, as well as enabling more powerful and cost-efficient studies of genetic diversity. SureSelect target enrichment has enabled researchers to identify mutations associated with more than 50 Mendelian diseases, 10 different types of cancer, and other complex ailments such as schizophrenia and Parkinson’s disease.

The SureSelect platform offers the most complete offering of catalog and custom capture kits (including comprehensive exome kits for human, mouse, and other model organisms, and flexible custom DNA or RNA target enrichment solutions) on all major next-generation sequencing platforms. The platform is easily scalable and automatable for large, high-throughput studies. As the cost of next gen sequencing continues to fall, using SureSelect only further enhances that cost-effectiveness, moving your studies of genomic variation forward very quickly and easily.

Maran Valentina – Agilent Technologies , Italy

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Reza Ghodssi

Posted on January 16, 2012 | Leave a comment

Integration of Biomaterials in Micro/Nano Systems for
Biological and Chemical Sensing.
Reza Ghodssi
Herbert Rabin Distinguished Professor,
Director, Institute for Systems Research and MEMS Sensors and Actuators Laboratory,
Electrical and Computer Engineering Department,
University of Maryland College Park, USA
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Integration of biological materials in micro/nano systems confers multiple advantages for biosensing.  Biological materials not only can provide the specificity required for targeted biosensing applications, but also can augment the fundamental performance of microfabricated sensors.
Our team has utilized the biomaterials chitosan and calcium alginate as interfaces between electromechanical microsystems and biological elements.  Electrodeposition of these materials onto electrodes enables biofunctionalization of microfabricated devices through conjugation or codeposition with proteins, DNA, cells, and other biological elements. 

We have integrated chitosan with several different types of microfabricated sensor systems, including a microcantilever DNA sensor and an optical waveguide sensor integrated with microfluidic sample delivery.  Chitosan and alginate together have been integrated with microfluidic systems and used to position cells in microenvironments that permit the study of interactions between different cell populations.
We have also used the Tobacco mosaic virus (TMV) to produce nanostructured microfabricated devices.  Genetic engineering of the virus coat allows for spatially selective deposition of the virus on metal surfaces, and also allows for electroless metal deposition over the high aspect ratio virus structure.  We have also developed the capability to use standard microfabrication techniques to pattern TMV on any type of substrate, allowing for nanostructuring a multitude of device surfaces. 

In addition to nanostructuring sensors to augment sensitivity through the increased surface area, the TMV virus can also be engineered to display surface peptides that specifically bind to biological and chemical molecules.  In this way, TMV can be used to create a highly selective sensor functionalization layer that can be patterned with high resolution for integration with microsensors. 
This presentation will cover the technologies we have developed to integrate the above biomaterials in microfabricated sensor platforms, and will discuss the advantages conveyed through this synergy. 

 

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Riccardo Velasco

Posted on January 13, 2012 | Leave a comment

Beyond plant genomes: which perspectives

Apple DNA sequences (around 13 billion sequenced nucleotides) were produced during 2007 and 2008, and in 2009 researchers assembled and reconstructed the gene content and order into the 17 apple chromosomes. The sequences equal a 17-fold coverage of the apple genome with over 82% of the genome assembled in the chromosomes and over 90% of the genes anchored to a precise position in the chromosomes.

Sequencing activity was performed using advanced technologies which demonstrated a growth rate unexpected until few years ago. In a decade, high throughput facilities moved from thousands of nucleotides per day to billions per hours, requiring an adequate growth of the related bioinformatics, not always able to keep similar speed, becoming then the real bottle neck.

Sequencing of the apple genome has allowed new discoveries to be made and increased our knowledge of the apple plant and its history. In particular:
- the cultivated apple was domesticated 3-4000 years ago from a recent wild progenitor, Malus sieversii, a species that is still widespread in the forests across Kazakhstan and China;
- the apple genome underwent duplication around 50 million years ago, bringing the number of chromosomes from 9 in the old American progenitor to the current 17;
- it has the highest number of genes, 57 thousand, of any plant genome studied to date. Of these, the publication identifies the complete set of 992 genes responsible for disease resistance, a potentially useful arsenal for genetic improvement;
- a list of three million genome positions (molecular markers) is available, which may serve as an orientation reference within the genome and to discover the functions of its genes;
- several families of genes which may be correlated with the development of the pome, the botanical name for the fruit of apple and its close relatives (e.g. pear, medlar), have been identified.

The data obtained will allow new varieties of apple to be developed more quickly than with conventional genetic improvement methods, resulting in plants with self-defence mechanisms against diseases and insects and which produce healthier and tastier fruits. The aim is to construct apple varieties requiring fewer agro-technical interventions, leading to more sustainable fruit cultivation, a research line that the Agricultural Institute of San Michele all’Adige has been following for several years. Sequencing of the apple genome has increased a thousand-fold our knowledge of this important agricultural plant, in particular its nutritional properties, environmental impact, exploration of biodiversity, philogenetic and evolutionary studies.

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Giorgia Girotto

Posted on January 13, 2012 | Leave a comment

Hereditary hearing loss in Italian and Qatari population: identification of new deafness genes using high throughput technologies
Giorgia Girotto1, Moza Alkowari2, Khalid Abdulhadi3, Savina Dipresa1, Diego Vozzi4, Danilo Licastro4, Emmanouil Athanasakis1, Rowa Siam2, Nihal Najjar2, Ramin Badii2 and Paolo Gasparini1
1Med Genet, IRCCS-Burlo Garofolo Children Hospital, Trieste Univ, Trieste, Italy
2 Molecular Genetics Laboratory, Hamad Medical Corporation, Doha, Qatar
3ENT Division, Hamad Medical Corporation, Doha, Qatar
4CBM scrl., Basovizza, Trieste, Italy

Hereditary Hearing loss (HLL) is a common disorder accounting for at least 60% of prelingual deafness. Most cases (70%) are non-syndromic (NSHHL) while the others (15-30%) are syndromic in which there are other clinical features in addition to the hearing impairment. GJB2 gene mutations, GJB6 deletion, and A1555G mitochondrial mutation play a major role worldwide and account for approximately 35% of Italian pathogenic alleles and almost no other common genes have been identified. Regarding the Qatari population, a molecular screening for these common genes/mutations on 126 Qatari patients clearly demonstrates that GJB2, GJB6 deletion and A1555G accounts for a minor proportion of NSHHL cases in this population.

Thus, these findings strongly suggest that many genes for NSHHL await identification and, until recently, linkage analysis was the first step in positional cloning approaches. Now, the availability of Next Generation Sequencing (NGS) technologies opens new perspectives in the search for causative genes. In this light, to increase our knowledge on the molecular bases of HHL in the Italian and Qatari populations, an extensive use of high throughput technologies such as High Density arrays (i.e for linkage data) and Next Generation Sequencing has been planned.
Six Italian families (dominant inheritance) and five Qatari families (recessive inheritance), all negative for the presence of mutations in the most common hearing genes, have been selected. High density SNPs arrays have been utilized to define a minimum number of candidate loci, to be applied in the filtering phase of NGS data. NGS protocols have been used to obtain whole exome data. After filtering (dbSNP and in-house database), some candidate genes have been identified in both populations. Results have been validated by Sanger sequencing and should be further investigated at the functional level. These results will definitely increase our knowledge of new deafness genes, and further confirm the importance of such new technologies for disease gene identification.

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Esposito Alessandro

Posted on January 12, 2012 | Leave a comment

Nanobiotechnologies meet Systems Biology

A large number of molecules cooperate in an intricate network of interactions for the maintenance of the structural integrity, the metabolism and the function of the living cell.

A challenge for engineering and physics in optical microscopy is to provide tools that could offer the highest spatio-temporal resolution with the capability to decode complex networks of molecular interactions by the development of technologies and methods that, at the same time, may provide cost-effective and user-friendly instruments.

Are current methods and technologies up to the challenge?

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C.Furlanello-M.Chierici

Posted on January 12, 2012 | Leave a comment

Computational tools for next generation sequencing: from nucleotides to functional genomics.

The aim of this tutorial is to make participants familiar with state-of-the-art bioinformatics methodologies for the analysis of deep sequencing data.

After a brief overview of current deep sequencing technologies and applications, participants will be introduced to alignment strategies and bioinformatics challenges on such ultra high-throughput data. We will show how to run a complete RNA-Seq analysis pipeline by using efficient tools such as Bowtie, BWA, SAMtools, BEDtools.

Hands-on examples will be given of short read alignment, quantification and visualization of gene or miRNA expression levels, identification of genetic polymorphisms, visualization on genome browsers. Participants will be enabled to apply complete pipelines for single- and paired-end data analyses and visualization. A Linux or Mac laptop is required to benefit most from this course.

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Daub Carsten

Posted on January 12, 2012 | Leave a comment

As sequencing technology becomes accessible an affordable for many researchers, the challenges in employing this technology to address scientific questions become more and more apparent.

With the dropping cost of data production, other factors are becoming limiting bottlenecks.
In this lecture, we will discuss various challenging aspects ranging from the computational infrastructure, broad range of sequencing technologies, sample and data management to data analysis skills and the collaboration between “wet” and “dry” researchers.

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Boveri Luca Bio-Rad

Posted on January 10, 2012 | Leave a comment

“Droplet Digital PCR: Molecular Biology in High Resolution”

The QX100 Droplet Digital PCR system is the third generation of PCR technology.
Droplet Digital PCR (ddPCR) system provides an absolute measure of target DNA molecules with unrivaled precision, accuracy, and sensitivity.
The QX100 droplet generator partitions samples into thousands of nanoliter-sized droplets.

After PCR on a thermal cycler, droplets are streamed in single file on the QX100 droplet reader to count positive and negative reactions.
The QX100 ddPCR system provides single copy PCR resolution to accelerate discoveries and new strategies for the research of inherited disorder, cancer and infectious disease. The QX100 system delivers an absolute count of the number of target sequences for applications that include copy number variation, mutation detection, and gene expression analysis.

Boveri Luca Bio-Rad

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Luca Beretta Illumina

Posted on January 4, 2012 | Leave a comment

“Next Generation Sequencing: now it’s for anybody!”

The development of Next Generation Sequencing technologies, and Illumina has always been the Golden Standard for, is helding to a double effect: from one side,the incredibly high throughput reached by the biggest solutions from Illumina (HiSeq2000, HiSeq1000, HiScanSQ, GAIIx) allows researchers to run research projects with excellent quality and reduced costs.

On the other side, the development of smaller, cheaper, cost-effective, simple, immediate solutions such as the MiSeq System is now allowing anybody to have access to Next Generation Sequencing and to transfer research and clinical-research protocols from traditional, longer and more expensive solutions (i.e. capillary electrophoresis) into new, faster and economical ones, reaching levels of sensitivity and accuracy never been possible before.

Luca Beretta
Territory Account Manager
Illumina Italy srl
Illumina Web Site: www.illumina.com

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Hans Scheffer

Posted on January 2, 2012 | 1 Comment

“Implementation of next generation sequencing in molecular diagnostics – strategic considerations”

Hereditary disorders can be explained by one or more mutations in any of the ~ 20,000 genes. In order to detect these mutations diagnostic laboratories strive to have a  DNA sequencing test for each gene known to be involved in a disorder. For genetic conditions explained by a single gene defect genetic testing is relatively simple. However, there are numerous conditions for which many genes are known. Apart from making the appropriate clinical diagnosis,  a physician / clinical geneticist faces the problem which of the genes need to be tested in the laboratory. Moreover, for many (heterogeneous) diseases the genes are still unknown.

A new technology called Next Generation Sequencing (NGS) has made it possible to sequence multiple loci in parallel in a single test, i.e. the genome or the exome of individuals (all exons with intron / exon transitions from the ~ 20,000 genes). The search for a causative mutation in genetic heterogeneous disorders is therefore likely to be more effective using NGS. Initially, this diagnostic method is used for a number of common heterogeneous disorders: unexplained intellectual disability, congenital deafness, hereditary blindness, hereditary movement disorders, inherited disorders of the energy metabolism, and hereditary bowl cancer. Important aspects of the implementation of NGS as a diagnostic tool will be addressed; the informed consent procedure, description into our quality system, the laboratory and data-analysis workflow, as well as reporting to referring clinicians. This will be followed by a discussion on results of our diagnostic exome sequencing analyses.

H. Scheffer, PhD
associate professor clinical molecular genetics
head division Genome Diagnostics
Human Genetics, division Genome Diagnostics
Radboud University Nijmegen Medical Centre
www.dnadiagnostieknijmegen.nl

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