Test Overview
DNA is analyzed for the presence of a specific mutation, aberration or variation using an appropriate method; applicable methods include Sanger Sequencing, chromosomal microarray(CMA) or next-generation sequencing (NGS)
Sanger Sequencing Methodology: The regions of interest are amplified using specific primers, and bidirectionally sequenced using a fluorescent method (Sanger sequencing).
CMA Methodology: Targeted chromosomal microarray analysis (CMA) utilizes Illumina genome-wide Infinium Global Diversity Array (GDA) with Cytogenetics-8 v1.0 (Illumina, San Diego, CA), containing approximately 1.8 million probes. Patient DNA is isolated, amplified, fragmented, hybridized to microarray probes, and extended with tagged terminating nucleotides. The array is stained, washed, and scanned. By comparing to in-silico controls, probe intensities and single nucleotide polymorphism (SNP) genotypes are calculated and used to detect copy number variants (CNVs) and regions of homozygosity (ROH), with coordinates based on genome reference consortium human build 37 (GRCh37, hg19). The resolution for CNVs, using a window of 10 consecutive probes, is approximately 50 kilobases (Kb) in most non-repetitive regions and about 10 Kb in targeted areas. CNVs are analyzed and interpreted by searching the Database of Genomic Variants (DGV, http://dgv.tcag.ca/dgv/app/home), ClinGen Dosage Sensitivity Map (https://search.clinicalgenome.org/kb/gene-dosage), DECIPHER (https://www.deciphergenomics.org/), OMIM (https://www.omim.org/), published literature, and internal database. In general, deletions over 200 Kb, gains over 500 Kb, ROH over 5 megabases (Mb), genome wide ROH over 5% of autosomal genome, and potential uniparental disomy (UPD) in chromosomes associated with imprinting disorders, are reported. In addition, smaller known pathogenic CNVs will also be reported, while larger known benign CNVs will not. In general, CNV classification is based on ACMG/ClinGen standards (PMID: 31690835). This targeted analysis is only intended to determine the presence or absence of the familial CNVs in the current patient; CNVs and ROHs outside the targeted region, regardless of pathogenicity, are generally not analyzed nor reported.
NGS Methodology: All coding exons (plus 15 bp upstream and downstream of each coding exon) of the targeted gene(s) are captured, sequenced using NGS and aligned to the human reference genome. A minimum NGS coverage of 20X is achieved for all coding exons +/- 5 bp, and a minimum coverage of 10X an additional 10 bp from +/- 6 bp through +/- 15 bp. A minimum coverage of 10X is achieved for all clinically significant promoter regions. Regions which do not meet these coverage metrics are filled with targeted Sanger Sequencing. Variants in the targeted regions that are of potential clinical significance, based on the ACMG guidelines for interpretation of sequence variants (PMID: 25741868), will be reported. All reported variants of potential clinical significance not meeting the sequencing quality criteria will be confirmed by a different technology. Copy number variation is assessed by coverage depth within the targeted regions compared to a normalized reference file.
This assay can be used to detect and/or confirm the presence of a specific mutation, aberration or variation, in a family member of a patient previously tested in the MMGL Molecular Genetics Laboratory, or in another CAP/CLIA-certified clinical laboratory. This test pathway CANNOT be used to confirm a previous result obtained in a research laboratory.
Interpretive report provided.
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
This targeted analysis will not identify variants in other regions of the genome that are not included in this test. As new scientific information becomes available, the interpretation and classification of variants identified in this assay may change. This information reflects the current state of scientific understanding at the time of test completion. Test interpretation may be impacted by the presence of a hematologic malignancy or an allogenic bone marrow transplant.
Chromosomal microarray (CMA) may not detect low-level mosaicism and cannot detect chromosomal aberrations that do not result in net gains or losses of genomic material, such as balanced chromosomal rearrangements (balanced translocations, balanced insertions, and inversions), rearrangements in repeat sequences (short arms of acrocentric chromosomes and heterochromatic regions), point mutations, indels, and epigenetic alterations. CMA will not detect genomic imbalances in regions that are not represented on the array.
Test Details
4 weeks
- CLINICAL ID OF FAMILIAL MUT
- CLIFS
- CLIFSS
- Clin ID Familial Mut Shadow
Specimen Requirements
Physicians must contact the MMGL-MGL laboratory at 734-615-2429 prior to sending samples for new testing. Collect blood specimen in a EDTA lavender top tube. Send it within 24 hours if stored at room temperature or within 5 days if stored refrigerated. Alternatively, send 5-10 µg of gDNA (at a concentration of > or = 50 ng/µL) in buffer or water. DNA specimens must pass quality control analysis before use. If the previous testing of the proband was not performed by the MMGL laboratory, please also provide a copy of the clinical molecular genetics report issued by the CLIA-certified testing laboratory for the proband, patient or family member in which the variant was previously detected.
Fill out a MLabs Molecular test requisition (or place an e-order if applicable):
https://mlabs.umich.edu/media/166
Fill out a Clinical History Form for Insurance Prior Authorization (include all required documentation indicated at the bottom of this form):
https://mlabs.umich.edu/sites/default/files/2020-08/file/mlab11618clini…
Fill out a UMHS Request and Consent for Genetic Testing form:
https://mlabs.umich.edu/sites/default/files/2023-04/file/germline-conse…
Michigan State law requires the ordering provider to obtaining informed consent from the patient prior to prognostic or predictive genetic testing. Contact a MLabs Client Services Center at 800-862-7284 to request paper copies or to setup a client account.
Saliva kit (Oragene OGD-510), follow collection instructions.
gDNA
5-10 µg of gDNA
3 µg of gDNA
2-36°C for cheek swab or saliva kit
2-8°C for gDNA
Additional Information
Most insurance carriers require prior authorization for genetic testing. Testing will not begin until insurance prior authorization is received by the laboratory or it is confirmed that prior authorization is not required. The ordering health care provider can obtain the prior authorization or request the laboratory to submit it. To obtain BCN prior authorization call Joint Venture Hospital Laboratories (JVHL) at 800-445-4979; for all other insurances, contact the plan directly. By ordering this test the clinician acknowledges that informed consent, https://mlabs.umich.edu/sites/default/files/2023-04/file/germline-conse…, has been obtained from the patient as required by applicable state or federal laws and the ordering clinician has authorization from the patient permitting MLabs to report the test results to the ordering clinician. Test includes medical geneticist interpretation of results billed as a separate additional charge. This test is not available without interpretation.