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Reanalysis of SNP Microarray Results: How Does Copy Number Variant Classification Change over Time?

Tomins, Kelly
http://orcid.org/0000-0002-1524-3051
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1649768796523289

Abstract Details

2022, MS, University of Cincinnati, Medicine: Genetic Counseling.
Genome-wide assessment of copy number variants (CNVs) by chromosomal microarray (CMA) is a first-line test offered to individuals with developmental delay, multiple congenital anomalies, autism spectrum disorder, and other indications. Exome reanalysis studies have demonstrated that reanalysis of genetic tests over time can yield additional diagnoses due to updates in genetic databases and the literature. Compared to exome reanalysis studies, there is limited data regarding the yield of microarray reanalysis. We conducted a manual reanalysis of 154 non-diagnostic patient SNP microarrays five years after they were initially performed in 2016. We found that 25/339 (7.4%) CNVs changed in classification after reanalysis with 24/154 (15.6%) patients having at least one variant that changed in classification. Of those variants that changed, 15/25 changed from benign to uncertain significance. However, only 2/154 patients (1.3%) had a diagnostic change, with a variant upgraded to likely pathogenic or pathogenic. The most common reasons variants changed in classification were changes in CNV classification standards, in particular the decoupling of patient phenotype to variant classification and new scoring guidelines. Overall, we demonstrate that while variants can be classified differently over time, SNP microarray reanalysis yields lower diagnostic rates compared to previously published exome reanalysis studies, if done within a relatively recent time-period of initial analysis (5-6 years).
Melanie Myers, Ph.D. (Committee Member)
Alyxis Coyan, M.S. (Committee Member)
Qiaoning Guan (Committee Member)
Wenying Zhang, M.D. Ph.D. M.B.A. (Committee Member)
Teresa Smolarek, Ph.D. (Committee Member)
Elizabeth Ulm, M.S. (Committee Member)
Jie Liu (Committee Member)
37 p.
Genetics
chromosomal microarray; variant classification; genetic testing; copy number variant; microarray reanalysis; diagnostic yield

Recommended Citations

Citations

  • Tomins, K. (2022). Reanalysis of SNP Microarray Results: How Does Copy Number Variant Classification Change over Time? [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1649768796523289

    APA Style (7th edition)

  • Tomins, Kelly. Reanalysis of SNP Microarray Results: How Does Copy Number Variant Classification Change over Time? 2022. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1649768796523289.

    MLA Style (8th edition)

  • Tomins, Kelly. "Reanalysis of SNP Microarray Results: How Does Copy Number Variant Classification Change over Time?" Master's thesis, University of Cincinnati, 2022. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1649768796523289

    Chicago Manual of Style (17th edition)

ucin1649768796523289
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This open access ETD is published by University of Cincinnati and OhioLINK.