Tools

DECIPHER-ing pathological genomic imbalances with DECIPHER

April 27 2022

At the opposite site of DGV (the Database of Genomic Variants, which contains only not pathogenic variations), there is DECIPHER, a useful database to retrieve pathogenic and plausibly pathogenic structural variations in humans. Completely free DECIPHER is an open-source database which contains data about a large amount of submicroscopic structural DNA variations (microdeletions, microduplications and other

GATK

April 24 2016

GATK: the Genome Analysis Toolkit The Genome Analysis Toolkit or more simply, GATK, is a software which is widely used to analyze high throughput sequencing data. GATK has been developed by the Data Science and Data Engineering group working at the Broad Institute. This specialized toolkit provides users with a broad selection tools and to focus on variant discovery, genotyping and data quality

CNVs databases

January 14 2016

STORING IMBALANCES Due to the amount and complexity of information relating to Copy Number Variations (CNVs), the scientific community felt the need to organize all available data, and future submissions, into open-source online repositories. Luckily, some of these resources are reciprocally synchronized, so that conflicting information is reduced to the minimum. The most important CNVs

ClinVar or HGMD?

December 3 2015

Which one is the best database? Genetic testing remains the most complex and difficult among all laboratory tests, both from the technical and the medical point of view. Since an excellent bioinformatic pipeline is fundamental to produce good data for the geneticist and because several bioinformatic tools are available today, it is necessary to choose well when establishing standard

MLPA: 10 questions and answers

November 30 2015

MLPA: Q&A MLPA is acronym for Multiplex Ligation Probe Amplification, which is a special molecular technique based on PCR. It is used to scan large deletions/duplications/multiplications which are not detectable by standard sequencing (either NGS or Sanger). The alternative to this technique is the qPCR (quantitative PCR). Is it necessary to always perform MLPA? No, it isn’t always indicated. Multiplex

Polyphen/Polyphen-2

November 16 2015

A tool to predict the effect of missense variants Polyphen, now available in its version Polyphen-2, predicts the impact of a missense variant (also referred to as nsSNP: non synonymous single nucleotide polymorphism) based on (1) protein sequence (2) phylogenetic information and (3) structural information. So Polyphen is able to do the so called functional annotation of missense variants.

dbVar: comprendere le variazioni strutturali

November 14 2015

QUESTA PAGINA È STATA TRASFERITA: CLICCARE QUI PER LA VERSIONE AGGIORNATA.

dbVar: understanding structural variations

November 13 2015

Besides DGV, DGVa and DECIPHER, there is another database that lists structural DNA variations: it’s dbVar, which we expect to be the most comprehensive one, based on its illustrious trademark: NCBI. What is a structural variation? Before going on, we just want to recall here that a genomic structural variation or variant is usually defined

The DGV database: non-pathological structural variations in humans

November 12 2015

There is an online database of which aim is to collect all DNA structural variations which can be considered as normal polymorphisms in humans (DGV – Database of Genomic Variants). The consultation of this database is particularly important because it allows to know whether a particular CNV (copy number variation) can be pathogenic or not.

The ExAC database: one of the most useful resources for the scientific community

November 9 2015

ExAC is acronym for Exome Aggregation Consortium, which is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects. As such, ExAC is also the name of the database that the consortium is feeding. In the ExAC database, which is currently in its beta version,

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Tools

DECIPHER-ing pathological genomic imbalances with DECIPHER

GATK

CNVs databases

ClinVar or HGMD?

MLPA: 10 questions and answers

Polyphen/Polyphen-2

dbVar: comprendere le variazioni strutturali

dbVar: understanding structural variations

The DGV database: non-pathological structural variations in humans

The ExAC database: one of the most useful resources for the scientific community

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RESEARCH

HIGH THROUGHPUT

ANCILLARY

CLASSICS

PROACTIVE

PREDICTIVE TESTING

EXOME PRO / GENOME PRO

Tools

Search

Categories

Research

Others

Registered office and Business

Main office & Laboratory

Feel free to call us to book your appointment

CONTACT FORM

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