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All in One Application Note All In One Application Note Test kit for 21 samples REF: 800014 Store at -20°C For use with the NanoChip® 400 Instrument For Professional Use Only European Authorized Representative: Obelis s.a. Savyon Diagnostics Ltd. 3 Habosem St. Ashdod 7761003 Boulevard Général Wahis 53 ISRAEL 1030 Brussels, BELGIUM Tel.: +(972).8.8562920 Tel: +(32) 2. 732.59.54 Fax: +(972).8.8523176 Fax: +(32) 2.732.60.03 E-mail: E-Mail : [email protected] [email protected] 02-05.2016 AP800014E Page 2 of 42 Table of Contents Introduction ................................................................................................. 3 Intended Use ................................................................................................ 3 Background .................................................................................................. 3 Kit Contents ................................................................................................. 12 Storage ...................................................................................................... 12 Using NanoChip Cartridges .............................................................................. 12 NanoChip Cartridge Handling ...................................................................... 12 Materials and Equipment ................................................................................. 13 Materials Available from................................................................................... 13 Additional Materials Available from Savyon ............................................................ 13 Other Required Materials (not available from Savyon ) ............................................... 14 Required Equipment ....................................................................................... 14 Technical Assistance ...................................................................................... 14 Precautions ................................................................................................. 15 Performing Sample Amplification ....................................................................... 16 Extraction ................................................................................................... 16 Amplification ................................................................................................ 16 Preparing the Sample Plate .............................................................................. 19 Operating the NanoChip 400 System .................................................................... 20 Preparing Solutions for Use in the NanoChip 400 Instrument ....................................... 21 Preparing the NanoChip Cartridge and Instrument .................................................... 21 Creating a Protocol ........................................................................................ 22 Running the Assay ......................................................................................... 25 Analyzing the Data ......................................................................................... 27 Appendix A: All In One Assay Format .................................................................. 28 Appendix B: All In One Data Analysis Spreadsheet and Data Calculations ....................... 34 Appendix C: Legal Notices ............................................................................... 37 REFERENCES ................................................................................................ 38 02-05.2016 AP800014E Page 3 of 42 Introduction Intended Use The NanoChip® All In One Kit is used to detect and identify a panel of 35 different genetic diseases (91 mutations) that are associated with various genetic disorders of the Israeli population, based on the specific individual ethnic origin. For in vitro diagnostic use only. Background Israeli population comprised of many ethnic backgrounds. Different ethnic groups have a higher risk for specific disease-causing mutations than the general Israeli population. These diseases are inherited in an autosomal recessive pattern. Affected individuals have inherited two copies of the mutated gene, one from each parent. The All In One assay was designed to diagnose the following diseases: 3 Methyl Glutaconic Aciduria (3MGA), also known as Costeff Optical Atrophy, is characterized by degeneration (atrophy) of the optic nerves, which leads to visual acuity, within the first years of life. Other nervous system problems might occur, such as an inability to maintain posture, poor muscle tone, a gradual increase of involuntary jerking movements (choreiform movements), and a general decrease in brain function (cognitive deficit). The disorder is caused by mutations in the OPA3 gene encoding a protein whose function is unknown. Researchers have suggested that cells with a defective OPA3 protein are prematurely vulnerable to apoptosis. The incidence of 3-methylglutaconic aciduria type III is about 1 in 10,000 newborns in the Iraqi Jewish population. This disorder is extremely rare in all other populations. Carrier frequency in affected populations is estimated in 1 in 10 to 40 in Iraqi Jews and in 1 in 10 in Persian (Iranian) Jews (1-2). Alpha 1- Antitrypsin (AAT) deficiency is the most prevalent potentially lethal hereditary disease of Caucasians. It leads to jaundice in infants, liver disease in children and adults, and pulmonary emphysema in adults. AAT is a protease inhibitor (PI), which protects tissue structures from damage by degrading enzymes. The genetic defect in AAT deficiency results in a molecule that cannot be released from its production site in hepatocytes. Low serum levels of AAT result in low alveolar concentration, where the protein normally would serve as protection against proteases. Consequential protease excess destroys alveolar walls and causes obstructive lung disease. Moreover, unsecreted AAT self-aggregates in the liver and causes liver disease. Mutations in the PI locus, located on chromosome 14, are associated with AAT deficiency. The most common risk alleles are PiS whose worldwide carrier rate is 1:50 (1:9 to 1:12 in Caucasians) and PiZ, with a worldwide carrier rate of 1:162 (1:30 to 1:40 in Caucasians) (3-8). Ataxia Telangiectasia (AT), is an autosomal recessive disorder characterized by progressive difficulty with coordinating movements (ataxia) beginning in early childhood, usually before age 5. Affected children typically develop difficulty walking, problems with balance and hand coordination, involuntary jerking movements (chorea), muscle twitches (myoclonus), and disturbances in nerve function (neuropathy). The movement problems typically cause people to require wheelchair assistance by adolescence. People with this disorder also have slurred speech and trouble moving their eyes to look side-to-side (oculomotor apraxia). Small clusters of enlarged blood vessels called telangiectases, which occur in the eyes and on the surface of the skin, are also characteristic of this condition. People with ataxia-telangiectasia often have a weakened immune system, and many develop chronic lung infections. They also have an increased risk of developing cancer, particularly cancer of blood-forming cells (leukemia) and cancer of immune system cells (lymphoma). Affected individuals are very sensitive to the effects of 02-05.2016 AP800014E Page 4 of 42 radiation exposure, including medical x-rays. The life expectancy of people with ataxia-telangiectasia varies greatly, but affected individuals typically live into early adulthood. Complementation groups for the classic form of the disease map to chromosome 11q23 and are associated with mutations in the ATM gene. Ataxia-telangiectasia occurs in 1 in 40,000 to 100,000 people worldwide. Carrier frequency is particularly high among North African Jews estimated at 1 in 40 to 80 individuals (9). Bloom Syndrome is inherited in an autosomal recessive fashion. Bloom Syndrome patients are much smaller than average, and often have a high-pitched voice and characteristic facial features including a long, narrow face, small lower jaw, a prominent nose and ears. They tend to develop pigmentation changes and dilated blood vessels in the skin. Other features of the disorder may include learning disabilities, mental retardation, chronic lung problems and diabetes. Men with Bloom Syndrome usually do not produce sperm while women with the disorder generally experience menopause earlier than usual. Chromosomal instability in Bloom Syndrome results in a high risk of cancer in affected individuals. Mutations in the BLM gene (locus 15q26.1) cause Bloom Syndrome. The BLM gene provides instructions for producing a protein called the Bloom (BLM) Syndrome Protein, which is a member of the DNA helicase family The carrier frequency in individuals of Eastern European ancestry is about 1:100 (10-11). Canavan Disease is an autosomal recessive disorder that causes progressive damage to nerve cells in the brain. This disease is one of a group of genetic disorders called leukodystrophies. They are characterized by degeneration of myelin in the phospholipid layer insulating the axon of a neuron. The gene is located on chromosome 17. Canavan disease is caused by a defective ASPA gene which is responsible for the production of the enzyme aspartoacylase. Decreased aspartoacylase activity prevents the normal breakdown of N-acetyl aspartate, and the lack of breakdown somehow interferes with growth of the myelin sheath of the nerve fibers in the brain.
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