Hackett-PractGuide CYTO Micro Array 13July10

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CCMG Guidelines for Genomic Microarray Testing Submitted by: CCMG Cytogenetics Committee June, 2010 Approved by: CCMG Board of Directors July 13, 2010 Prepared by: James Stavropoulos and Mary Shago Hospital for Sick Children with contributions from the Canadian microarray user group: Bruyere H; Chan M; Chernos J; Chun K; Cote G; Craddock K; Dawson A; Duncan A; Eydoux P; Feuk L; Finzel R; Freeman V; George A; Gillan T; Halbgewachs J; Harrison K; Hrynchak M; Kolomietz E; Lavoie J; Lemyre E; Lu C;
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    CCMG Guidelines for Genomic Microarray Testing Submitted by:CCMG Cytogenetics CommitteeJune, 2010Approved by:CCMG Board of DirectorsJuly 13, 2010Prepared by:James Stavropoulos and Mary ShagoHospital for Sick Childrenwith contributions from the Canadian microarray user group:Bruyere H; Chan M; Chernos J; Chun K; Cote G; Craddock K; Dawson A; Duncan A;Eydoux P; Feuk L; Finzel R; Freeman V; George A; Gillan T; Halbgewachs J; HarrisonK; Hrynchak M; Kolomietz E; Lavoie J; Lemyre E; Lu C; Marshall C; McCready E;McGowan-Jordan J; Morash B; Mueller R; Parslow M; Pinto D; Scherer SW; Shetty S;Soucy J-F; Speevak M; Wang, J; Winsor E; Xu J.  2 TABLE OF CONTENTS Microarray – Suggestions for Practice Guideline Section Title Page1. Genomic Microarray – Capabilities 32. Genomic Microarray – Limitations 33. Indications-   Constitutional-   Prenatal-   Malignancies33444. Requisition Requirements 45. Specimen Requirements 46. Platform Requirements - Minimum 57. Reference DNA 58. Procedure 59. Monitoring of Analytic Standards-   Pre-analytic-   Analytic-   Post-analytic566610. Analysis of Microarray Data 611. Interpretation of Microarray Data 712. Validation and Reporting of Results 713. Turn Around Time 814. Documentation 915. Proficiency Testing 916. Suboptimal Specimens 917. Validation of Platform 918. Other Guidelines 919. References 10  3 1. Genomic Microarray -Capabilities ã   Array comparative genomic hybridization using platforms with bacterial artificialchromosomes (BAC) or non-polymorphic oligonucleotide probes can detect: o   Copy number gains and losses across the genome i.e. unbalancedmicroscopic and submicroscopic chromosome rearrangements. ã   Microarray platforms containing single nucleotide polymorphism (SNP) probescan detect: o   Copy number gains and losses across the genome i.e. unbalancedmicroscopic and submicroscopic chromosome rearrangements. o   Long contiguous stretches of homozygosity which may indicatehomodisomic uniparental disomy (UPD), identity by descent or loss of heterozygosity. Confirmation of UPD requires a trio haplotype analysis. ã   Resolution: o   Depends on probe size, number, and the placement of probes across thegenome. o   Is determined by the software algorithm and settings selected by the userto detect copy number alterations. 2. Genomic Microarray Limitations ã   Array comparative genomic hybridization using platforms with BAC or non-polymorphic oligonucleotide probes cannot detect: o   Balanced rearrangements, long contiguous stretches of homozygosity,low level mosaicism of unbalanced rearrangements/aneuploidy, andpolyploidy. ã   Microarray platforms containing SNP probes cannot detect:   o   Balanced rearrangements, low level mosaicism of unbalancedrearrangements/aneuploidy, and heterodisomic uniparental disomy.  3. Indications ã   For Constitutional Postnatal and Prenatal Indications – Practice guidelines shouldrefer to the Canadian College of Medical Geneticists (CCMG) Position Statementon the use of array genomic hybridization, developed by Clinical Practice,Cytogenetics, and Prenatal Diagnosis committees. ã   Constitutional Postnatal o   Idiopathic mental retardation/developmental delay/autism/multiplecongenital abnormalities. o   Apparently balanced inherited or de novo rearrangements in aphenotypically abnormal individual. o   The constitutional microarray assay which includes whole genomecoverage is not recommended for couples experiencing infertility/multiplespontaneous pregnancy losses.  4 ã   Prenatal: o   Fetal congenital abnormalities detected on ultrasound or magneticresonance imaging (MRI) that indicate a significant risk for an unbalancedchromosome abnormality. o   Apparently balanced inherited rearrangements in a fetus with fetalcongenital abnormalities. o   Apparently balanced de novo rearrangements identified by G-bandanalysis. o   Referral from a CCMG-accredited or equivalent Medical Geneticist isrequired to perform pre- and post-test counseling. o   Not recommended for pregnancies with low risk of chromosomeabnormalities including late maternal age, soft signs on ultrasound,previous pregnancy with a trisomy, positive maternal serum screen,positive integrated prenatal screen or positive first trimester screen. ã   Malignancies: o   The utility of microarrays designed for use in the analysis of bone marrow,soft and solid tumors, as well as paraffin embedded tissue is currentlybeing studied by the Cancer Cytogenomics Microarray Consortium(CCMC) Clinical trial group. 4. Requisition Requirements 1. Patient name and address2. Patient date of birth3. Patient sex4. Unique identifying number5. Name of physician or other authorized person requesting test6. Specimen source7. Specimen collection date8. Test requested9. Clinical indications for the test(s)10. Ethnicity – polymorphic CNV frequencies may differ between populations  5. Specimen Requirements DNA extracted from each tissue type must be validated at the discretion of the laboratorydirector, since performance characteristics and sensitivity may vary between DNAsamples extracted from different tissues. ã   Peripheral blood: o   Two specimens in appropriate anticoagulants – one for DNA extractionand when required, one for cytogenetic preparation to confirm or furthercharacterize positive findings by FISH/G-banding . ã   Tissue: o   Cultured primary fibroblasts with low passage number, saliva, or buccalswab.
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