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The Genome
CMECNE

Microarrays and Microdeletions: Key Concepts Summarized

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Learning Objectives and CME/Disclosure Information

This activity is intended for healthcare providers delivering care to women and their families.

After completing this activity, the participant should be better able to:

1. Relate the definition of a microdeletion
2. Discuss the differences between a CGH and SNP array

Estimated time to complete activity: 0.25 hours

Faculty:

Susan J. Gross, MD, FRCSC, FACOG, FACMG
President and CEO, The ObG Project

Disclosure of Conflicts of Interest

Postgraduate Institute for Medicine (PIM) requires instructors, planners, managers and other individuals who are in a position to control the content of this activity to disclose any real or apparent conflict of interest (COI) they may have as related to the content of this activity. All identified COI are thoroughly vetted and resolved according to PIM policy. PIM is committed to providing its learners with high quality CME activities and related materials that promote improvements or quality in healthcare and not a specific proprietary business interest of a commercial interest.

Faculty: Susan J. Gross, MD, receives consulting fees from Cradle Genomics, and has financial interest in The ObG Project, Inc.

Planners and Managers: The PIM planners and managers, Trace Hutchison, PharmD, Samantha Mattiucci, PharmD, CHCP, Judi Smelker-Mitchek, MBA, MSN, RN, and Jan Schultz, MSN, RN, CHCP have nothing to disclose.

Method of Participation and Request for Credit

Fees for participating and receiving CME credit for this activity are as posted on The ObG Project website. During the period from Dec 31 2017 through Dec 31 2021, participants must read the learning objectives and faculty disclosures and study the educational activity.

If you wish to receive acknowledgment for completing this activity, please complete the post-test and evaluation. Upon registering and successfully completing the post-test with a score of 100% and the activity evaluation, your certificate will be made available immediately.

For Pharmacists: Upon successfully completing the post-test with a score of 100% and the activity evaluation form, transcript information will be sent to the NABP CPE Monitor Service within 4 weeks.

Joint Accreditation Statement

In support of improving patient care, this activity has been planned and implemented by the Postgraduate Institute for Medicine and The ObG Project. Postgraduate Institute for Medicine is jointly accredited by the Accreditation Council for Continuing Medical Education (ACCME), the Accreditation Council for Pharmacy Education (ACPE), and the American Nurses Credentialing Center (ANCC), to provide continuing education for the healthcare team.

Physician Continuing Medical Education

Postgraduate Institute for Medicine designates this enduring material for a maximum of 0.25 AMA PRA Category 1 Credit(s)™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

Continuing Nursing Education

The maximum number of hours awarded for this Continuing Nursing Education activity is 0.2 contact hours.

Read Disclaimer & Fine Print

WHAT IS IT?

A microarray describes a newer technology that can identify small duplications or deletions of genetic material that previously could not be identified using conventional karyotyping alone. It has become a critical tool to help identify submicroscopic chromosomal deletions/duplications that underlie clinically significant syndromes in the prenatal period and throughout the lifespan.

Key Concepts

What is a Deletion?

  • A deletion describes a chromosomal break where genetic material is lost
Genetic Deletion

Credit: US National Library of Medicine

  • Deletions can be large or small, and can occur anywhere along a chromosome
    • Terminal deletion (end of a chromosome)
    • Interstitial (within the chromosome)
  • Duplication describes when additional material is gained

What is a Microdeletion?

  • Definition is based on size of missing DNA sequence
  • 1Mb (megabase) = 1 million base pairs
  • Conventional karyotype is based on light microscopy and can usually only detect deletions > 5 Mb
  • Microdeletions refer to deletions smaller than those that can be seen on karyotype – i.e., < 5 Mb

What is a CNV (copy number variant)?

  • Deletions or duplications are ≥ 1 kb (1000 base pairs) to many hundreds of Kb in size
  • Small CNVs are common and found in 5 to 10% of individuals in the general population
    • Only 1 to 2% will have CNVs > 1Mb
  • Most CNVs are simply a part of normal human variation
    • If CNVs delete or add sufficiently large number of genes or result in a breakpoint within a gene, they may have significant clinical consequences

Key Points:

CGH vs SNP arrays

CGH (Comparative genome hybridization)

  • The array is constructed with single short DNA sequences from the regions of interest
  • ‘Test’ and ‘control’ DNA are labelled with different fluorescent colors and then hybridized (annealed) to complementary sequences of interest on the array
  • The relative amounts of test vs control DNA can be measured
    • Excess control DNA signal color signifies a deletion in the test sample
    • Excess test DNA signal color signifies duplication in the test sample

SNP array

  • The array is constructed with short DNA sequences
    • Each region of interest will have two DNA sequences, representing the two possible alleles (versions) of known SNPs
  • Only ‘test DNA’ is labelled and hybridized to the allele specific probes within the array
  • Relative intensity of the hybridization signal is used to detect if DNA sequence is deleted or duplicated
    • Low/absent intensity signal signifies deletion
    • Excess signal signifies duplication

Additional capabilities of SNP array compared to CGH

  • Can detect triploidy, maternal cell contamination and mosacism
  • Can detect consanguinity and uniparental disomy (UPD) which can be associated with genetic syndromes
    • Rather than having one copy of each SNP allele, a region of identical SNPs, known as absence of heterozygosity (AOH), will be apparent
    • Labs may report AOH, raising concern for
      • Autosomal recessive disorders related to genes in that particular sequence or
      • UPD, depending on chromosome and region

Learn More – Primary Sources:

ACOG Committee Opinion 682: Microarrays and Next-Generation Sequencing Technology: The Use of Advanced Genetic Diagnostic Tools in Obstetrics and Gynecology

The use of chromosomal microarray for prenatal diagnosis

ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013

Yield of additional genetic testing after chromosomal microarray for diagnosis of neurodevelopmental disability and congenital anomalies: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG)

Practice guideline: joint CCMG-SOGC recommendations for the use of chromosomal microarray analysis for prenatal diagnosis and assessment of fetal loss in Canada

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Related ObG Topics:

The Use of Microarrays in the Prenatal and Postnatal Setting – Current Professional Guidelines
NIPS vs. Microarray for Pathogenic Results
Should Amniocentesis or Chorionic Villus Sampling Be Offered to All Pregnant Women?

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OBG Project CME requires a modern web browser (Internet Explorer 10+, Mozilla Firefox, Apple Safari, Google Chrome, Microsoft Edge). Certain educational activities may require additional software to view multimedia, presentation, or printable versions of their content. These activities will be marked as such and will provide links to the required software. That software may be: Adobe Flash, Apple QuickTime, Adobe Acrobat, Microsoft PowerPoint, Windows Media Player, or Real Networks Real One Player.

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This educational activity may contain discussion of published and/or investigational uses of agents that are not indicated by the FDA. The planners of this activity do not recommend the use of any agent outside of the labeled indications.

The opinions expressed in the educational activity are those of the faculty and do not necessarily represent the views of the planners. Please refer to the official prescribing information for each product for discussion of approved indications, contraindications, and warnings.

Disclaimer

Participants have an implied responsibility to use the newly acquired information to enhance patient outcomes and their own professional development. The information
presented in this activity is not meant to serve as a guideline for patient management. Any procedures, medications, or other courses of diagnosis or treatment discussed or suggested in this activity should not be used by clinicians without evaluation of their patient’s conditions and possible contraindications and/or dangers in use, review of any applicable manufacturer’s product information, and comparison with recommendations of other authorities.

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