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DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.

Craig JM, Vena N, Ramkissoon S, Idbaih A, Fouse SD, Ozek M, Sav A, Hill DA, Margraf LR, Eberhart CG, Kieran MW, Norden AD, Wen PY, Loda M, Santagata S, Ligon KL, Ligon AH - PLoS ONE (2012)

Bottom Line: While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations.Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues.Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA).

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

ABSTRACT
Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.

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Related in: MedlinePlus

Overview of proposed methods for FSM ULS processing of FFPE specimens.Summary of methods and timeline for aCGH using the FSM method. Following DNA extraction, the workflow and protocol for preparation of fresh or frozen samples is identical to FFPE workflow shown.
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pone-0038881-g007: Overview of proposed methods for FSM ULS processing of FFPE specimens.Summary of methods and timeline for aCGH using the FSM method. Following DNA extraction, the workflow and protocol for preparation of fresh or frozen samples is identical to FFPE workflow shown.

Mentions: In summary, the use of FSM to match DNA fragment sizes (Figure 7) unveiled a hierarchy of factors that affect the performance of aCGH (Figure 8), and allow focused efforts to improve sample performance. Consequently, application of FSM expands the range of samples that can successfully be analyzed by aCGH.


DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.

Craig JM, Vena N, Ramkissoon S, Idbaih A, Fouse SD, Ozek M, Sav A, Hill DA, Margraf LR, Eberhart CG, Kieran MW, Norden AD, Wen PY, Loda M, Santagata S, Ligon KL, Ligon AH - PLoS ONE (2012)

Overview of proposed methods for FSM ULS processing of FFPE specimens.Summary of methods and timeline for aCGH using the FSM method. Following DNA extraction, the workflow and protocol for preparation of fresh or frozen samples is identical to FFPE workflow shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3376148&req=5

pone-0038881-g007: Overview of proposed methods for FSM ULS processing of FFPE specimens.Summary of methods and timeline for aCGH using the FSM method. Following DNA extraction, the workflow and protocol for preparation of fresh or frozen samples is identical to FFPE workflow shown.
Mentions: In summary, the use of FSM to match DNA fragment sizes (Figure 7) unveiled a hierarchy of factors that affect the performance of aCGH (Figure 8), and allow focused efforts to improve sample performance. Consequently, application of FSM expands the range of samples that can successfully be analyzed by aCGH.

Bottom Line: While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations.Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues.Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA).

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

ABSTRACT
Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.

Show MeSH
Related in: MedlinePlus