Hilmi Ozcelik, Xuejiang Shi, Martin C

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Presentation transcript:

Long-Range PCR and Next-Generation Sequencing of BRCA1 and BRCA2 in Breast Cancer Hilmi Ozcelik, Xuejiang Shi, Martin C. Chang, Eric Tram, Matt Vlasschaert, Nando Di Nicola, Anna Kiselova, Denise Yee, Aaron Goldman, Mark Dowar, Balram Sukhu, Rita Kandel, Kathy Siminovitch The Journal of Molecular Diagnostics Volume 14, Issue 5, Pages 467-475 (September 2012) DOI: 10.1016/j.jmoldx.2012.03.006 Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 A total of 17 long-range PCR amplicons spanning the complete genomic region of BRCA1 and BRCA2, including flanking regions. A: 17 long-range PCRs amplified the complete genomic regions of BRCA1 and BRCA2, including their flanking sequences. B: BRCA1 PCR8 and BRCA1 PCR6.1 performed under optimized cycling condition. C: 1-kb Plus DNA Ladder (Invitrogen). Picture was adapted to show the sizes of the corresponding bands. The Journal of Molecular Diagnostics 2012 14, 467-475DOI: (10.1016/j.jmoldx.2012.03.006) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Sensitivity analysis using different data size of short reads. Short reads of patient 7 from lane 7 and split data sets of lane 7 with sizes of 10.24, 20.52, and 40.8 Mb were mapped to the genomic reference sequence. The performance of the alignment is recorded and the data outputs were compared with respect to the corresponding mean coverage, percentage of reference genomic coverage, and numbers of variations detected. The saturation of the number of variation call along with the increase in the data size of the short reads is presented in Table 7. The Journal of Molecular Diagnostics 2012 14, 467-475DOI: (10.1016/j.jmoldx.2012.03.006) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Distribution of BRCA1 versus BRCA2 variants identified in 12 familial breast cancer patients. Deleterious mutation carriers were indicated for patients 2 (BRCA1 1479delAG), 3 (BRCA1 5154delC), 8 (BRCA1 5382insC), and 9 (BRCA1 5382insC). The data table below demonstrates the number of variants detected in BRCA1 and BRCA2. The Journal of Molecular Diagnostics 2012 14, 467-475DOI: (10.1016/j.jmoldx.2012.03.006) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Distribution of variants in exons, introns, and untranslated regions of BRCA1 (A) and BRCA2 (B), which were identified in 12 familial breast cancer patients. Deleterious mutation carriers were indicated for patients 2 (BRCA1 1479delAG), 3 (BRCA1 5154delC), 8 (BRCA1 5382insC), and 9 (BRCA1 5382insC). The data table below each chart demonstrates the number of variants detected in BRCA1 and BRCA2. The Journal of Molecular Diagnostics 2012 14, 467-475DOI: (10.1016/j.jmoldx.2012.03.006) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions