Dataset Information

Quantitative Analysis of mtDNA Content in Formalin-Fixed Paraffin-Embedded Muscle Tissue.

ABSTRACT: Quantification of mitochondrial DNA (mtDNA) content is an essential tool for the diagnosis of mtDNA depletion syndrome (MDS). Samples collected and processed for anatomopathology studies represent a unique source of archived biological material. Thus, the possibility to study mtDNA copy number in these specimens would be a useful way to screen for MDS. In this study, we designed and validated the methodology to determine mtDNA content by quantitative real-time polymerase chain reaction (qRT-PCR) in formalin-fixed paraffin-embedded (FFPE) muscle tissue. We studied 14 frozen muscle biopsies and compared the results with a portion of the same biopsy embedded in paraffin. Our results showed a similar variability among frozen and FFPE muscle biopsies. Patients with MDS detected in frozen muscle were also confirmed in their corresponding FFPE samples, which validate the usefulness of this approach. We conclude that the analysis of mtDNA copy number in FFPE muscle tissue by qRT-PCR is a useful method for the molecular screening of patients suspected to have MDS when frozen biopsies are not available. Analysis of these samples would facilitate retrospective studies and diagnostic procedures.

SUBMITTER: Font A

PROVIDER: S-EPMC3509826 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Quantitative Analysis of mtDNA Content in Formalin-Fixed Paraffin-Embedded Muscle Tissue.

Font Aida A Tort Frederic F Navarro-Sastre Aleix A Cusí Victòria V García-Villoria Judit J Briones Paz P Ribes Antonia A

JIMD reports 20110622

Quantification of mitochondrial DNA (mtDNA) content is an essential tool for the diagnosis of mtDNA depletion syndrome (MDS). Samples collected and processed for anatomopathology studies represent a unique source of archived biological material. Thus, the possibility to study mtDNA copy number in these specimens would be a useful way to screen for MDS. In this study, we designed and validated the methodology to determine mtDNA content by quantitative real-time polymerase chain reaction (qRT-PCR) ...[more]

PMID: 23430839

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Project description:BackgroundWe have developed a gene expression assay (Whole-Genome DASL), capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE) specimens.Methodology/principal findingsWe demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF) and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing the WG-DASL assay with an in vitro transcription-based labeling method yielded fold-change correlations of R(2) approximately 0.83, while fold-change comparisons with quantitative RT-PCR assays yielded R(2) approximately 0.86 and R(2) approximately 0.55 for intact and FFPE samples, respectively. Additionally, the WG-DASL assay yielded high self-correlations (R(2)>0.98) with low intact RNA inputs ranging from 1 ng to 100 ng; reproducible expression profiles were also obtained with 250 pg total RNA (R(2) approximately 0.92), with approximately 71% of the probes detected in 100 ng total RNA also detected at the 250 pg level. When FFPE samples were assayed, 1 ng total RNA yielded self-correlations of R(2) approximately 0.80, while still maintaining a correlation of R(2) approximately 0.75 with standard FFPE inputs (200 ng).Conclusions/significanceTaken together, these results show that WG-DASL assay provides a reliable platform for genome-wide expression profiling in archived materials. It also possesses utility within clinical settings where only limited quantities of samples may be available (e.g. microdissected material) or when minimally invasive procedures are performed (e.g. biopsied specimens).

Dataset Information

Quantitative Analysis of mtDNA Content in Formalin-Fixed Paraffin-Embedded Muscle Tissue.

Publications

Quantitative Analysis of mtDNA Content in Formalin-Fixed Paraffin-Embedded Muscle Tissue.

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