Molecular Inversion Probe Array for the Genetic Evaluation of Stillbirth Using Formalin- Fixed, Paraffin-Embedded Tissue Leslie R. Rowe, Harshwardhan.

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Molecular Inversion Probe Array for the Genetic Evaluation of Stillbirth Using Formalin- Fixed, Paraffin-Embedded Tissue Leslie R. Rowe, Harshwardhan M. Thaker, John. M. Opitz, Joshua D. Schiffman, Zaid M. Haddadin, Lance K. Erickson, Sarah T. South The Journal of Molecular Diagnostics Volume 15, Issue 4, Pages 466-472 (July 2013) DOI: 10.1016/j.jmoldx.2013.03.006 Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 MIP assay. A: The ends of the probe anneal to the target. A one-nucleotide gap remains in the probe at the SNP of interest. B: The gap is filled by adding DNA polymerase and dNTPs. C: The probe undergoes ligation and becomes circular. D: Exonuclease removes unreacted probes and any remaining linear DNA. E: The probe is cleaved and released from the genomic DNA. The captured genomic target becomes part of the internal segment of the probe. F: Universal primers amplify the barcode tag sequence. G: The amplified barcode tag is hybridized to a high-density array containing sequences complementary to the tag. The Journal of Molecular Diagnostics 2013 15, 466-472DOI: (10.1016/j.jmoldx.2013.03.006) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 A: Case 164: nexus chromosome 4 detail view. Previous fetal karyotype was 46,XY. The y axis of the upper plot represents the hybridization intensity of sample compared with reference DNA, with a value around zero interpreted as equal copy number between sample and reference for that segment of DNA. A cluster of probes with higher values is consistent with a gain in the sample DNA and a cluster of probes with lower values is consistent with a loss in the sample DNA. The upper plot shows a 14.96-Mb gain of 4qter. The y axis of the lower plot is B allele frequency. B allele frequency value near 0.5 indicates a heterozygous genotype (AB), whereas 0 and 1 indicate homozygous genotypes (AA and BB, respectively). In a normal diploid situation there is a mix of AA, AB, and BB genotypes. A region of nonmosaic heterozygous copy number gain will show only BAFs near 0 (AAA), 1 (BBB), 0.33 (AAB), and 0.67 (BBA), whereas an area of nonmosaic heterozygous loss will show only one BAF near 0 (A) and one BAF near 1 (B). The x axis is the chromosome. The lower plot shows B allele frequency values near 0, 1, 0.33, and 0.67 consistent with a nonmosaic heterozygous copy number gain. B: Case 164: nexus chromosome 13 detail view. The upper plot shows a 15.8-Mb loss of 13qter. The B allele frequency plot confirms the heterozygous loss with one BAF near 0 (A) and one BAF near 1 (B). The Journal of Molecular Diagnostics 2013 15, 466-472DOI: (10.1016/j.jmoldx.2013.03.006) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Case 138: nexus chromosome 17 detail view showing 1.8-Mb deletion of q12, highlighted by the oval. The previous karyotype was 46,XY. The Journal of Molecular Diagnostics 2013 15, 466-472DOI: (10.1016/j.jmoldx.2013.03.006) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Case 101: nexus whole genome view showing trisomy 18, highlighted by the oval. The fetus presented with multiple anomalies consistent with Nager acrofacial dysostosis, the most common condition to consider in the differential diagnosis of trisomy 18. The previous karyotype was not performed. The Journal of Molecular Diagnostics 2013 15, 466-472DOI: (10.1016/j.jmoldx.2013.03.006) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions