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ereH stiH egdE dloF M I R A C A G E N E T I C S L A B O R A T O R I E S Global M A P S {Metabolomic Assisted Pathway Screen} 2450 Holcombe Boulevard Suite O-100, Houston, Texas 77021 1-800-411-GENE (4363) 713-798-6555 www.BMGL.com 8/2014 B A Y L O R Fold Edge Hits Here M etabolomic profiling is a large scale, semi-quantitative screening test that looks at perturbations in both individual analytes and pathways related to biochemical abnormalities. Using state-of-the-art LC-MS/ MS in positive and negative ion modes and GC/MS technologies, Global MAPS provides small molecule metabolic profiling to identify >1000 metabolites in human plasma, or CSF. Metabolites range in size from 50-1500 Da and include, but are not limited to, amino acids, organic acids, fatty acids, neurotransmitters, nucleotides, and bile acids, all identified in a single test. Global Metabolomic Assisted Pathway Screen Testing has the ability to identify amino acidopathies, organic acidemias, fatty acid oxidation disorders, vitamin cofactor disorders, pyrimidine biosynthesis, creatine biosynthesis, and urea cycle metabolism abnormalities, among other known disorders. A significant feature of this testing is the potential to combine the analysis with Proband WES data to assess the consequences of DNA variants in known or suspected metabolic pathways. The potential for discovery with this approach is considerable, including the identification of new inborn errors of metabolism and new regulatory factors for metabolic genes, as well as previously unknown metabolic associations/ perturbations with known disorders. Global MAPS offers a broad range of analyses in a single metabolic screen, requiring less sample volume from the patient and reducing the potential for sample mix-up due to multiple sample collection and standardization of results across the population. GLOBAL MAPS INDICATIONS FOR TESTING • Seizures • Autism spectrum disorder • Undifferentiated phenotype possibly related to perturbation in a biochemical pathway • Equivocal molecular test results in a gene known to be involved in small molecule metabolism Use of this test in combination with exome analysis may be most beneficial in more difficult cases or in cases where a small molecule inborn error of metabolism is suspected. S A M P L E I N F O R M A T I O N ee inserts or go to www.bcm.geneticlabs.org to view specific specimen S requirements and shipping conditions. S H I P P I N G A D D R E S S Baylor Miraca Genetics Laboratories 2450 Holcombe Grand Blvd. - Receiving Dock Houston, Texas 77021-2024 713-798-6555 • 1-800-411-gene (4363 www.BMGL.com 8/2014 • Developmental delay 8/2014 PROBAND PROBAND WHOLE EXOME SEQUENCING WHOLE EXOME SEQUENCING TEST INFORMATION TECHNICAL INFORMATION Indications for Testing Methodology The Proband Whole Exome Sequencing (WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when a patient’s medical history and physical exam findings strongly suggest that there is an underlying genetic etiology. In some cases, the patient may have had an extensive evaluation consisting of multiple genetic tests, without identifying an etiology. In other cases, a physician may opt to order the Proband Whole Exome Sequencing test early in the patient’s evaluation in an effort to expedite a possible diagnosis. See (FAQ) for additional details. Exome Capture and Next Generation Sequencing SAMPLE & SHIPPING INFORMATION Test Requisition Proband Whole Exome Sequencing Specimen Type Blood or other Requirements Draw blood in an EDTA (purple-top) tube(s). Send at least 5cc (children) or 10cc (adults). Shipping Conditions Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Sample must arrive within 48 hrs. Specimen Type Cultured Skin Fibroblast Requirements Send 2 T25 flasks at 80-100% confluence. Shipping Conditions: Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Specimen Type Purified DNA Requirements Send at least 20ug of purified DNA (minimal concentration of 50ng/uL; A260/A280 of ~1.7). Shipping Conditions Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Turn Around Time 15 weeks - Patient with undiagnosed genetic syndrome Note: Parental samples are required to interpret Proband WES results. See requisition for sample requirements and further details. PROBAND WHOLE EXOME SEQUENCING TEST DETAILS Test Code 1500 Special Notes The Proband Whole Exome Sequencing test is a highly complex test that is newly developed for the identification of changes in a patient’s DNA that are causative or related to their medical concerns. In contrast to current sequencing tests that analyze one gene or small groups of related genes at a time, the Proband Whole Exome Sequencing test will analyze the exons or coding regions of thousands of genes simultaneously using next-generation sequencing techniques. The exome refers to the portion of the human genome that contains functionally important sequences of DNA that direct the body to make proteins essential for the body to function properly. These regions of DNA are referred to as exons. There are approximately 180,000 exons in the human genome which represents about 3% of the genome. These 180,000 exons are arranged in about 22,000 genes. It is known that most of the errors that occur in DNA sequences that then lead to genetic disorders are located in the exons. Therefore, sequencing of the exome is thought to be an efficient method of analyzing a patient’s DNA to discover the genetic cause of diseases or disabilities. Additionally, the Proband WES includes a mitochondrial genome sequencing. Mitochondria are structures within cells that convert the energy from food into a form that cells can use. Although most DNA is packaged in chromosomes within the nucleus, mitochondria also have a small amount of their own DNA. This genetic material is known as mitochondrial DNA or mtDNA. In humans, mitochondrial DNA represents a small fraction of the total DNA in cells. Many genetic conditions are related to changes in particular mitochondrial genes. The principle of the test is to sequence nucleotide by nucleotide, the human exome of an individual to a depth of coverage necessary to build a consensus sequence with high accuracy. This consensus sequence is then compared to standards and references of what is normal in the population and the result is interpreted by board-certified laboratory directors and clinicians. By sequencing the exome of a patient and comparing it to normal reference sequence, variations in an individual’s DNA sequence can be identified and related back to the individual’s medical concerns in an effort to discover the cause of the medical disorder. SHIPPING ADDRESS 2450 Holcombe, Grand Blvd. - Receiving Dock, Houston, Texas 77021-2024 BILLING INFORMATION List Price *For Insurance or Institutional Prices, please call. CPT Codes 81400x1, 81401x1, 81402x1, 81403x1, 81404x1, 81405x1, 81406x1, 81407x1 continued 1 1B PROBAND PROBAND WHOLE EXOME SEQUENCING WHOLE EXOME SEQUENCING TEST INFORMATION TECHNICAL INFORMATION Indications for Testing Methodology The Proband Whole Exome Sequencing (WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when a patient’s medical history and physical exam findings strongly suggest that there is an underlying genetic etiology. In some cases, the patient may have had an extensive evaluation consisting of multiple genetic tests, without identifying an etiology. In other cases, a physician may opt to order the Proband Whole Exome Sequencing test early in the patient’s evaluation in an effort to expedite a possible diagnosis. See (FAQ) for additional details. Exome Capture and Next Generation Sequencing SAMPLE & SHIPPING INFORMATION Test Requisition Proband Whole Exome Sequencing Specimen Type Blood or other Requirements Draw blood in an EDTA (purple-top) tube(s). Send at least 5cc (children) or 10cc (adults). Shipping Conditions Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Sample must arrive within 48 hrs. Specimen Type Cultured Skin Fibroblast Requirements Send 2 T25 flasks at 80-100% confluence. Shipping Conditions: Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Specimen Type Purified DNA Requirements Send at least 20ug of purified DNA (minimal concentration of 50ng/uL; A260/A280 of ~1.7). Shipping Conditions Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Turn Around Time 15 weeks - Patient with undiagnosed genetic syndrome Note: Parental samples are required to interpret Proband WES results. See requisition for sample requirements and further details. PROBAND WHOLE EXOME SEQUENCING TEST DETAILS Test Code 1500 Special Notes The Proband Whole Exome Sequencing test is a highly complex test that is newly developed for the identification of changes in a patient’s DNA that are causative or related to their medical concerns. In contrast to current sequencing tests that analyze one gene or small groups of related genes at a time, the Proband Whole Exome Sequencing test will analyze the exons or coding regions of thousands of genes simultaneously using next-generation sequencing techniques. The exome refers to the portion of the human genome that contains functionally important sequences of DNA that direct the body to make proteins essential for the body to function properly. These regions of DNA are referred to as exons. There are approximately 180,000 exons in the human genome which represents about 3% of the genome. These 180,000 exons are arranged in about 22,000 genes. It is known that most of the errors that occur in DNA sequences that then lead to genetic disorders are located in the exons. Therefore, sequencing of the exome is thought to be an efficient method of analyzing a patient’s DNA to discover the genetic cause of diseases or disabilities. Additionally, the Proband WES includes a mitochondrial genome sequencing. Mitochondria are structures within cells that convert the energy from food into a form that cells can use. Although most DNA is packaged in chromosomes within the nucleus, mitochondria also have a small amount of their own DNA. This genetic material is known as mitochondrial DNA or mtDNA. In humans, mitochondrial DNA represents a small fraction of the total DNA in cells. Many genetic conditions are related to changes in particular mitochondrial genes. The principle of the test is to sequence nucleotide by nucleotide, the human exome of an individual to a depth of coverage necessary to build a consensus sequence with high accuracy. This consensus sequence is then compared to standards and references of what is normal in the population and the result is interpreted by board-certified laboratory directors and clinicians. By sequencing the exome of a patient and comparing it to normal reference sequence, variations in an individual’s DNA sequence can be identified and related back to the individual’s medical concerns in an effort to discover the cause of the medical disorder. SHIPPING ADDRESS 2450 Holcombe, Grand Blvd. - Receiving Dock, Houston, Texas 77021-2024 BILLING INFORMATION List Price *For Insurance or Institutional Prices, please call. CPT Codes 81400x1, 81401x1, 81402x1, 81403x1, 81404x1, 81405x1, 81406x1, 81407x1 continued 1 1B GLOBAL MAPS GLOBAL MAPS TEST INFORMATION Global MAPS is appropriate for individuals with: Test Requisition Global MAPS Specimen Type Plasma Cerebrospinal fluid - Developmental delay - Seizures - Autism spectrum disorder - Undifferentiated phenotype possibly related to perturbation in a biochemical pathway Indications for Testing - Equivocal molecular test results in a gene known to be involved in small molecule metabolism Use of this test in combination with exome analysis may be most beneficial in more difficult cases or in cases where a small molecule inborn error of metabolism is suspected. GLOBAL MAPS While this test may also enable the identification of new biomarkers associated with specific genetic conditions, as well as biomarkers associated with medications, disease status, and diet-related treatment, we will not report xenobiotics, plant biproducts, or microbial findings in this report. Requirements Draw blood in a EDTA (purple top) tube(s) and separate as soon as possible, freezing immediately. Send 1-2 cc of plasma. Store the specimen frozen at -20 C. Specimen may be stored frozen for up to 7 days. Whole blood stored for >1 hour or exposed to extreme temperatures is not appropriate for analysis. Send 1-2 cc of cerebrospinal fluid. Store the specimen frozen at -20 C. Specimen may be stored frozen for up to 7 days. Turn Around Time 21 Days SHIPPING ADDRESS 2450 Holcombe, Grand Blvd. - Receiving Dock, Houston, Texas 77021-2024 TEST DETAILS Test Code 4900 (plasma), 4902 (cerebrospinal fluid) TECHNICAL INFORMATION Metabolomic profiling is a large scale, semi-quantitative screening test that looks at perturbations in both individual analytes and pathways related to biochemical abnormalities, including but not limited to amino acid, organic acid, lipid, and nucleotide metabolism. This is a small molecule screen for compounds 50-1500 Da. It should be used only as a screening tool for individuals who have an undifferentiated phenotype or as supportive evidence in individuals with equivocal mutations in genes related to metabolic processes. It is NOT intended to supplant diagnostic testing for specific conditions nor is it intended for monitoring therapy. Abnormalities detected on the Global MAPS Profile should be confirmed by diagnostic biochemical or molecular testing. This test must be ordered by a physician and must be accompanied by detailed clinical information for the most informative interpretation. Patient should NOT be on TPN, special diet, dietary supplements, or drug therapies for most accurate results. Metabolites and biomarkers that fall out of the normal range will be reported relative to the general population. Individual absolute values will not be reported. This test is not intended to screen for lysosomal storage disorders, congenital disorders of glycosylation, mucopolysaccharidoses, mucolipidoses, or other similar large molecule disorders. Methodology Global MAPS will identify known metabolites in plasma, or cerebrospinal fluid. The test will analyze hundreds of compounds simultaneously using a combination of LC-MS/ MS and GC-MS technologies (>900 compounds are regularly detected in human plasma). Significant abnormalities in metabolic pathways and/or in selected single analytes may be identified. In these situations, we will recommend targeted follow-up testing (molecular and/or biochemical) for confirmation. continued 2a 2b GLOBAL MAPS GLOBAL MAPS TEST INFORMATION Global MAPS is appropriate for individuals with: Test Requisition Global MAPS Specimen Type Plasma Cerebrospinal fluid - Developmental delay - Seizures - Autism spectrum disorder - Undifferentiated phenotype possibly related to perturbation in a biochemical pathway Indications for Testing - Equivocal molecular test results in a gene known to be involved in small molecule metabolism Use of this test in combination with exome analysis may be most beneficial in more difficult cases or in cases where a small molecule inborn error of metabolism is suspected. GLOBAL MAPS While this test may also enable the identification of new biomarkers associated with specific genetic conditions, as well as biomarkers associated with medications, disease status, and diet-related treatment, we will not report xenobiotics, plant biproducts, or microbial findings in this report. Requirements Draw blood in a EDTA (purple top) tube(s) and separate as soon as possible, freezing immediately. Send 1-2 cc of plasma. Store the specimen frozen at -20 C. Specimen may be stored frozen for up to 7 days. Whole blood stored for >1 hour or exposed to extreme temperatures is not appropriate for analysis. Send 1-2 cc of cerebrospinal fluid. Store the specimen frozen at -20 C. Specimen may be stored frozen for up to 7 days. Turn Around Time 21 Days SHIPPING ADDRESS 2450 Holcombe, Grand Blvd. - Receiving Dock, Houston, Texas 77021-2024 TEST DETAILS Test Code 4900 (plasma), 4902 (cerebrospinal fluid) TECHNICAL INFORMATION Metabolomic profiling is a large scale, semi-quantitative screening test that looks at perturbations in both individual analytes and pathways related to biochemical abnormalities, including but not limited to amino acid, organic acid, lipid, and nucleotide metabolism. This is a small molecule screen for compounds 50-1500 Da. It should be used only as a screening tool for individuals who have an undifferentiated phenotype or as supportive evidence in individuals with equivocal mutations in genes related to metabolic processes. It is NOT intended to supplant diagnostic testing for specific conditions nor is it intended for monitoring therapy. Abnormalities detected on the Global MAPS Profile should be confirmed by diagnostic biochemical or molecular testing. This test must be ordered by a physician and must be accompanied by detailed clinical information for the most informative interpretation. Patient should NOT be on TPN, special diet, dietary supplements, or drug therapies for most accurate results. Metabolites and biomarkers that fall out of the normal range will be reported relative to the general population. Individual absolute values will not be reported. This test is not intended to screen for lysosomal storage disorders, congenital disorders of glycosylation, mucopolysaccharidoses, mucolipidoses, or other similar large molecule disorders. Methodology Global MAPS will identify known metabolites in plasma, or cerebrospinal fluid. The test will analyze hundreds of compounds simultaneously using a combination of LC-MS/ MS and GC-MS technologies (>900 compounds are regularly detected in human plasma). Significant abnormalities in metabolic pathways and/or in selected single analytes may be identified. In these situations, we will recommend targeted follow-up testing (molecular and/or biochemical) for confirmation. continued 2a 2b ereH stiH egdE dloF M I R A C A G E N E T I C S L A B O R A T O R I E S Global M A P S {Metabolomic Assisted Pathway Screen} 2450 Holcombe Boulevard Suite O-100, Houston, Texas 77021 1-800-411-GENE (4363) 713-798-6555 www.BMGL.com 8/2014 B A Y L O R