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Brugada syndrome

Recommended panel testing at Breda Genetics for this condition: Brugada syndrome (CACNA1C, CACNB2, GPD1L, HCN4, KCNE3, SCN1B, SCN3B, SCN5A) Summary Ion channelopathies are diseases caused by dysfunctional ion channels that may lead to sudden death. These diseases can be either acquired or inherited. The main phenotypes of Brugada syndrome in patients carrying these heritable arrhythmia syndromes are congenital long QT syndrome, Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia,

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Arthrogryposis

Genetically heterogenous Arthrogryposis Multiplex Congenita (AMC) is a clinically and genetically heterogeneous condition characterized by multiple joint contractures at birth. The condition is generally defined by the presence of congenital joint contractures in two or more body areas, usually associated with hypoplastic muscles. Sometimes the term arthrogryposis multiplex is used to identify a clinical sign rather than a specific disease. When referring to arthrogryposis multiplex as disease, a

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Haploinsufficiency

Most human apparatuses operate under conditions of functional redundancy. Many biological systems have a functional reserve to offer a better chance of survival in case of illness or accident. In fact, men have two lungs, two kidneys, two eyes (but can survive even with only one), a liver function which can be satisfactorily maintained even after the removal of 75% of the liver parenchyma, a

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NGS for dummies

Few simple words to explain NGS After years of Sanger sequencing being adopted as the gold standard in molecular diagnostics, Next Generation Sequencing (NGS) is about to finally an completely take over. NGS is also known as high-throughput sequencing (high yield sequencing) as it allows to sequence many fragments in parallel (which is impossible by traditional Sanger sequencing). There are several NGS systems, which have been developed by different

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Coffin-Siris syndrome

Recommended panel testing at Breda Genetics for this condition: Coffin-Siris syndrome (ARID1A, ARID1B, ARID2, DPF2, SMARCA4, SMARCB1, SMARCE1, SOX11) The fifth digit syndrome Coffin-Siris syndrome (also known as fifth digit syndrome) is a very rare genetic syndrome. Even though the condition is highly variable, the main hallmarks are abnormalities of the fifth finger, developmental disability of variable grade, hirsutism and coarse facial features. Clinical features

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Mitochondrial complex IV deficiency (cytochrome c oxidase deficiency)

Recommended panel testing at Breda Genetics for this condition: Mitochondrial complex IV deficiency – cytochrome c oxidase deficiency (APOPT1, C12ORF62, COA3, COA5, COA6, COX10, COX14, COX15, COX20, COX6B1, FARS2, FASTKD2, LRPPRC, MTCO1, MTCO2, MTCO3, MTTL1, MTTS1, PET100, POLG, SCO1, SCO2, SURF1, TACO1) Summary Mitochondrial complex IV deficiency (also known as cytochrome c oxidase – COX – deficiency or simply complex IV deficiency) is a very rare

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Ataxias with oculomotor apraxias (AOAs)

Recommended panel testing at Breda Genetics for this condition: Ataxia-oculomotor apraxia (APTX, PIK3R5, SETX, PNKP) INVOLVING EYE MOVEMENTS Idiopatic oculomotor apraxia Oculomotor apraxia (OMA)  is the absence of,  or a defect in,  the control of voluntary purposeful eye movement.  Children with this condition have difficulty moving their eyes horizontally. Because of this, most patients  with OMA have to turn their head in order to follow

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Potocki-Lupski syndrome

OVEREXPRESSION OF RAI1 Recommended panel testing at Breda Genetics for this condition: MLPA analysis – RAI1 gene (TAT: 15 days); aCGH (TAT: 6 weeks); EXOME D (TAT: 4 weeks). Reciprocal to Smith-Magenis syndrome Potocki-Lupski syndrome (PTLS – OMIM 610883), also known as chromosome 17p11.2 duplication syndrome, is a developmental disorder characterized by hypotonia, failure to thrive, pervasive developmental disorders with mild-to-severe mental retardation with possible language and cognitive

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CNVs: pathogenic mechanisms

AFFECTING GENES AND OTHER SEQUENCES CNVs may be clinically neutral or pathogenic. Because they typically lead to imbalances of large genomic tracts, which often include more than one gene or regulatory region, when CNVs are pathogenic they usually cause severe or very severe diseases. Gene deletions, duplications or multiplications as caused by CNVs may be pathogenic through one of the following mechanisms (CNVs: pathogenic mechanisms): Direct

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CNVs: non-homologous recombination

During DNA synthesis To further deepen the topic of CNVs formation: beyond evolution, we’ll now go into non-homologous recombination. Non-homologous recombination is a DNA repair mechanism which is not based on homology principles. There are two types of non-homologous recombination: replicative and non-replicative. Non-homologous recombination is the basis of non-recurrent CNVs. Most pathogenic microduplications and microdeletions are rare non-recurrent CNVs. Non-recurrent CNVs are: preferentially located in microhomology sites (2-15 bp). Microhomology sites are too small

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CNVs: NAHR (Non Allelic Homologous Recombination)

ON DIFFERENT ALLELES Expanding the topic about CNVs formation: beyond evolution, it is necessary to talk about NAHR: NAHR (Non Allelic Homologous Recombination) Homologous recombination (HR) guides the exchange of genomic material during the meiosis contributing to human inter individual variation. HR takes place between two allelic homologous regions (e.g. between two regions located at the same locus on two homologous chromosome, e.g. between a certain

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Work with us

Dear Candidate, many thanks for your interest in the positions we are offering. To ease your application and help us identifying key factors, we kindly request you to fill-out the form below. Your time is highly appreciated. For any further inquiries, please do not hesitate to contact us at info@bredagenetics.com.

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CNVs formation: beyond evolution

BEYOND EVOLUTION LCRs/DSs cause CNVs Mechanisms of DNA replication and repair are the basis for the formation of CNVs. CNVs formation is also strictly dependent from the action of some particular genomic regions called low copy repeats (LCRs) or segmental duplications (SDs). LCRs/SDs are tracts of duplicated DNA which are comprised between 1 and 400 Kb in size and of which sequence identity is not

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CNVs: detection methods

WHOLE & NOT Molecular diagnostics at present can be subdivided in “whole” approach (Whole Exome or Whole Genome) and “targeted” approach (single gene or single panel testing). Methods for the detection of CNVs vary significantly on the desired type of approach. Here below a guide to the right choice (and the techniques we have chosen). “WHOLE” APPROACHES Microarray technology (array-CGH and SNP-array) The microarray technology is

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CNVs databases

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 databases are: dbVar  This database is managed by the NCBI

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Multi-allelic CNVs (mCNVs)

mCNVs: YET TO BE DISCOVERED Several hundreds of human genomic traits (and maybe even more) show CNVs (Copy Number Variations) within a very large range of alleles. Such CNVs are also called multi-allelic CNVs (mCNVs). Non-Allelic Homologous Recombination (NAHR) mCNVs can evolve with mechanism of non-allelic homologous recombination (NAHR) at a much higher mutational rate than SNPs (Single Nucletoide Polymorphisms). Because of NAHR events, mCNVs may show

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CNVs: a universe of variations

Defning CNVs Genetic variants of the human genome can differ very much in size. From the smallest ones (variants affecting on single nucleotide: Single Nucleotide Variations – SNVs) to the largest ones (variants affecting the shape and number of an entire chromosome), everything can stay in the middle. Variants comprised between 1,000 bp (1Kb) and 1,000,000 bp (1Mb) are usually referred to as Structural Variations

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ClinVar or HGMD?

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 operating protocols for variant filtering and annotation. During the bioinformatic and

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MLPA: 10 questions and answers

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 Ligation Probe Amplification is usually indicated whenever large deletions/duplications have

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Tuberous sclerosis: catching mosaicism and intronic mutations

Recommended testing at Breda Genetics for this condition (also to test for mosaicism): Tuberous sclerosis (TSC1, TSC2) If negative: MLPA analysis (TSC1, TSC2 gene). If negative: Exonic ultra-deep sequencing (600x) and SNaPshot analysis Summary Tuberous Sclerosis Complex (TSC), also called Bourneville syndrome, is a multisystem disorder with variable expressivity characterized by hamartomas in multiple organ systems. It mainly affects the brain and the skin, with

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