PittsburghV1, Ncbi, Curation, bibRecord, 001946

High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip

Identifieur interne : 001946 ( Ncbi/Curation ); précédent : 001945; suivant : 001947

High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip

Auteurs : Yan P. Yu [États-Unis] ; Amantha Michalopoulos [États-Unis] ; Ying Ding [États-Unis] ; George Tseng [États-Unis] ; Jian-Hua Luo [États-Unis]

Source :

PLoS ONE [ 1932-6203 ] ; 2014.

RBID : PMC:3974686

Descripteurs français

English descriptors

KwdEn :
- Chromosome Aberrations, DNA Copy Number Variations (genetics), DNA, Neoplasm (genetics), Formaldehyde (chemistry), Gene Expression Profiling, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Lymphoma (genetics), Oligonucleotide Array Sequence Analysis, Paraffin Embedding (methods), Proto-Oncogene Proteins B-raf (genetics), Repressor Proteins (genetics), Tissue Fixation, Trans-Activators (genetics).
MESH :
- chemical , chemistry : Formaldehyde.
- chemical , genetics : DNA, Neoplasm, Proto-Oncogene Proteins B-raf, Repressor Proteins, Trans-Activators.
- genetics : DNA Copy Number Variations, Lymphoma.
- methods : Paraffin Embedding.
- Chromosome Aberrations, Gene Expression Profiling, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Oligonucleotide Array Sequence Analysis, Tissue Fixation.

Abstract

Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974686

DOI: 10.1371/journal.pone.0092820
PubMed: 24699316
PubMed Central: 3974686

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Le document en format XML

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<front><div type="abstract" xml:lang="en"><p>Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.</p>
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<author><name sortKey="Dierssen, Jw" uniqKey="Dierssen J">JW Dierssen</name>
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<author><name sortKey="Van Eijk, R" uniqKey="Van Eijk R">R van Eijk</name>
</author>
<author><name sortKey="Oosting, J" uniqKey="Oosting J">J Oosting</name>
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<author><name sortKey="Israeli, D" uniqKey="Israeli D">D Israeli</name>
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<author><name sortKey="Haan, Jc" uniqKey="Haan J">JC Haan</name>
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<author><name sortKey="Van Essen, Hf" uniqKey="Van Essen H">HF van Essen</name>
</author>
<author><name sortKey="Smeets, Sj" uniqKey="Smeets S">SJ Smeets</name>
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<biblStruct><analytic><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name>
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<author><name sortKey="Cottman, M" uniqKey="Cottman M">M Cottman</name>
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<author><name sortKey="Schiffman, Jd" uniqKey="Schiffman J">JD Schiffman</name>
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<author><name sortKey="Ul Hassan, A" uniqKey="Ul Hassan A">A Ul-Hassan</name>
</author>
<author><name sortKey="Hammond, D" uniqKey="Hammond D">D Hammond</name>
</author>
<author><name sortKey="Fernando, M" uniqKey="Fernando M">M Fernando</name>
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<author><name sortKey="Reed, M" uniqKey="Reed M">M Reed</name>
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   |area=    PittsburghV1
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   |type=    RBID
   |clé=     PMC:3974686
   |texte=   High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip
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High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip

High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip

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