The underlying genetic basis of ophthalmology disorders involves a wide and growing

number of clinical entities.

Recent technologies, particularly Next Generation Sequencing (NGS) allows fast,

accurate and valuable diagnostic tests.

For ophthalmology, CGC Genetics has an extensive list of genetic tests for detection

of molecular alterations, with the integrated support of our Medical Geneticists.

Medical Genetics is an essential tool for your clinical practice.

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This technology provides a breakthrough in genetic diagnostic yield, reducing

turnaround time and cost.

However, please note that not all options available on the market offer the same

coverage and, therefore, the same diagnostic yield. In order to understand the current

diagnostic capability it is essential to keep in mind concepts such as coverage and

depth of coverage.

The coverage represents the percentage of evaluated target regions. A coverage of

100% means that it is possible to detect a mutation in any of the gene’s target

regions. If the coverage is less than 100%, not all the regions of the gene will be

analyzed.

Depth of coverage represents the number of times that a specific target region is

sequenced. NGS is performed through a multiple reading system, i.e., each region is

sequenced multiple times. In order to be able to detect a single mutation in

heterozygosity, at least a 20x depth of coverage is required. Below this number of

readings, several mutations may go undetected. The greater depth of coverage,

greater detection ability there will be.

Therefore, the ideal condition is to have an average depth of coverage of 100x

(minimum 20x) with a 100% coverage of gene coding sequences (exons) and intronic

flanking regions (splicing sites).

All NGS Panels available at CGC Genetics are custom-designed by our team, with an

average depth of coverage of 100x and 100% coverage of gene coding regions, leading

to a strong diagnostic capability.

NGS panels are constantly updated, always following clinical criteria.

CGC Genetics may also consider the possibility of creating panels that include a group

of genes suggested by the physician.

For ophthalmology specialty, CGC Genetics has available several NGS panels:

Albinism

Bardet-Biedl syndrome

Cataracts

Ciliopathies

Cone-rod dystrophy

Exome Sequencing

Leber congenital amaurosis

Marfan and Loeys-Dietz syndromes

Marfan and Loeys-Dietz syndromes and aortic aneurysm

Microphthalmia

Neurofibromatosis type 1 and type 2 and Schwannomatosis

Retinitis pigmentosa

Retinitis pigmentosa, AD and X-linked

Retinite pigmentosa, AR and X-linked

Senior-Loken syndrome

Stargardt disease and macular dystrophy

Stickler syndrome

Usher syndrome

combines the highest resolution available in the

market with the clinical interpretation and integration by our specialized Medical

Team.

Human genome is composed of over 20 000 genes, of which only about 5 000 are

related to known medical disorders. The Exome is the set of all exons together,

equivalent to 1-2% of the human genome.

is a very efficient strategy to study most exons of a patient

genome, unraveling mutations possibly associated with specific disorders or

phenotypes. With this diagnostic strategy, patients can be studied with a significantly

reduced turnaround time and cost, when compared to single gene or gene panel

sequencing.

CGC Genetics has available two Exome Sequencing options, to best fit with patient’s

individual needs:

, which analyzes the entire exome with sequencing of

about 20 000 genes;

, which analyzes about 5 000 clinically-relevant

genes.

Whole Exome Sequencing (WES) entails the sequencing or “reading” of all genomic

coding regions, i.e., the exons.

WES purpose is to obtain the highest possible amount of genetic information of a

patient, using the most advanced technology currently available.

Genetic variants are searched throughout the 20 000 genes that make up the exome.

Nonetheless, variants established as responsible for genetic disorders are known in

only about 5 000 of these genes.

In order to overcome this limitation, CGC Genetics recommends , i.e.,

performing WES in both the patient and its parents.

This way, it is possible that both parents serve as a reference for filtering benign

variants, making WES an effective diagnostic method in detecting recessive

Mendelian diseases and de novo variants.

New or de novo variants may be either detected in genes related with defined clinical

conditions or in genes whose association with disease has not been yet described.

Maximum diagnostic capability available at this moment

Clinical phenotype expansion through the identification of new genes with clinical

significance

Detection of new variants not yet described

Confirmation of possible variants with Sanger Sequencing

WES has an average depth of coverage of 100x, with more than 90% coverage of

coding regions.

Disease Exome by CGC Genetics is one of the biggest sequencing panels available

which includes approximately 5 000 clinically relevant genes.

Disease Exome panel has a particular focus on coding regions (exons) and in flanking

regions (splicing sites) and is based on the following databases:

Human Gene Mutation Database (HGMD) (www.hgmd.cf.ac.uk/ac/index.php)

Online Mendelian Inheritance in Man (OMIM) (www.omim.org)

GeneTests (www.genetests.org)

Illumina TruSight Sequencing Panels (www.illumina.com/trusight)

Other sequencing panels available in the market

Targeted at clinically relevant genes;

High diagnostic capability

Confirmation of possible variants with Sanger Sequencing

Report with clinical integration and interpretation

Solving complex diagnostic cases

Reduced cost compared with whole exome sequencing (WES)

Requires only the patient sample (no parent sample needed)

is designed to produce an average depth of

coverage of 100x and minimum 20x in more than 95% coverage of coding regions. This

entails a very thorough study of coding sequences analyzed with high diagnostic

capability in most regions.

In exome sequencing only nuclear DNA is analyzed, excluding mitochondrial DNA.

Mitochondrial DNA contains 37 genes involved in several mitochondrial disorders.

Mutations in mitochondrial DNA are a common cause of eye diseases such as Leber

hereditary optic neuropathy or mitochondrial disorders with ophthalmic symptoms.

CGC Genetics offers a , which includes

complete sequencing analysis by NGS of the 37 mitochondrial genes.

Founded in 1992, CGC Genetics is one of the main European clinical genetics

laboratories and leader in medical genetic tests in Portugal. CGC Genetics, with

headquarters in Porto, reinforced its investment in Lisbon, USA (Newark) and Spain

(Madrid) and, receives samples for genetic testing from all over the world, including

hospitals, national and international, public and private, medical clinics, insurance

companies and universities.

Using vanguard technologies and strict quality policies, CGC Genetics has a clinical

department with 7 Medical Genetics Specialists. In addition, more than 80 highly

qualified Geneticists are divided into 5 different laboratory areas: Clinical Genomics,

Molecular Diagnostics, Cytogenetics, Prenatal screening and Pathology, offering more

than 3 400 genetic tests for prenatal diagnostic and screening, hematology, oncology,

neurology, ophthalmology, cardiology, preventive medicine, common and rare

diseases, pharmacogenetics/clinical trials. It has wide experience in Array CGH, NGS

panels, Disease Exome and Whole Exome Sequencing, analyzed and interpreted with

high clinical integration.

The great investment in research and development of new and unique tests,

positioned CGC Genetics as an international reference center (with more than 3 000

entries in different directories of genetic tests), being the exclusive diagnostic test

provider for some disorders.

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