Download Global MAPS Metabolomic Assisted Pathway Screen

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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