Data Analysis Considerations for Detecting Copy Number Changes in Formalin-Fixed, Paraffin-Embedded Tissues

Copy Number Changes ◽

Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles

Clinical Genetics ◽

10.1111/j.1399-0004.2007.00882.x ◽

2007 ◽

Vol 72 (5) ◽

pp. 441-447 ◽

Cited By ~ 33

Author(s):

EA Mc Sherry ◽

A Mc Goldrick ◽

EW Kay ◽

AM Hopkins ◽

WM Gallagher ◽

...

Keyword(s):

Copy Number ◽

Array Cgh ◽

Formalin Fixed Paraffin ◽

Copy Number Changes ◽

Sample Processing Considerations for Detecting Copy Number Changes in Formalin-Fixed, Paraffin-Embedded Tissues

Cold Spring Harbor Protocols ◽

10.1101/pdb.ip071753 ◽

2012 ◽

Vol 2012 (11) ◽

pp. pdb.ip071753-pdb.ip071753

Author(s):

S. Jacobs

Keyword(s):

Copy Number ◽

Sample Processing ◽

Formalin Fixed Paraffin ◽

Copy Number Changes ◽

Detection of Copy Number Changes in DNA from Formalin Fixed Paraffin Embedded Tissues Using Paralogue Ratio Tests

Analytical Chemistry ◽

10.1021/ac200153j ◽

2011 ◽

Vol 83 (9) ◽

pp. 3484-3492 ◽

Cited By ~ 8

Author(s):

Gerald Saldanha ◽

Linda Potter ◽

Lovesh Dyall ◽

Danielle Bury ◽

Nisreen Hathiari ◽

...

Keyword(s):

Copy Number ◽

Formalin Fixed Paraffin ◽

Copy Number Changes ◽

Detection of Copy Number Changes at Multiple Loci in DNA Prepared from Formalin-Fixed, Paraffin-Embedded Tissue by Multiplex Ligation-Dependent Probe Amplification

Methods in Molecular Biology - Genomics Protocols ◽

10.1007/978-1-59745-188-8_7 ◽

2008 ◽

pp. 101-108 ◽

Cited By ~ 3

Author(s):

Minoru Takata

Keyword(s):

Copy Number ◽

Multiple Loci ◽

Formalin Fixed Paraffin ◽

Copy Number Changes ◽

Formalin Fixed ◽

Dependent Probe

Accurate Detection of Copy Number Changes in DNA Extracted from Formalin-Fixed, Paraffin-Embedded Melanoma Tissue Using Duplex Ratio Tests

Journal of Molecular Diagnostics ◽

10.1016/j.jmoldx.2013.04.008 ◽

2013 ◽

Vol 15 (5) ◽

pp. 687-694 ◽

Cited By ~ 7

Author(s):

David A. Moore ◽

Gerald Saldanha ◽

Abdlrzag Ehdode ◽

Linda Potter ◽

Lovesh Dyall ◽

...

Keyword(s):

Copy Number ◽

Accurate Detection ◽

Formalin Fixed Paraffin ◽

Copy Number Changes ◽

Melanoma Tissue ◽

Genome-Wide, High-Resolution Detection of Copy Number, Loss of Heterozygosity, and Genotypes from Formalin-Fixed, Paraffin-Embedded Tumor Tissue Using Microarrays

Cancer Research ◽

10.1158/0008-5472.can-06-3597 ◽

2007 ◽

Vol 67 (6) ◽

pp. 2544-2551 ◽

Cited By ~ 53

Author(s):

Sharoni Jacobs ◽

Ella R. Thompson ◽

Yasuhito Nannya ◽

Go Yamamoto ◽

Raji Pillai ◽

...

Keyword(s):

High Resolution ◽

Loss Of Heterozygosity ◽

Copy Number ◽

Tumor Tissue ◽

Copy Number Loss ◽

Genome Wide ◽

Formalin Fixed Paraffin ◽

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

Genome Medicine ◽

10.1186/s13073-016-0375-z ◽

2016 ◽

Vol 8 (1) ◽

Cited By ~ 18

Author(s):

Tanjina Kader ◽

David L. Goode ◽

Stephen Q. Wong ◽

Jacquie Connaughton ◽

Simone M. Rowley ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Tumor Tissue ◽

Whole Genome ◽

Copy Number Analysis ◽

Formalin Fixed Paraffin ◽

Low Coverage ◽

Copy number, loss of heterozygosity and amplification detection in formalin-fixed paraffin-embedded melanocytic lesions using molecular inversion probes

Cancer Genetics ◽

10.1016/j.cancergen.2011.08.010 ◽

2011 ◽

Vol 204 (8) ◽

pp. 473

Author(s):

Leslie R. Rowe ◽

Wells Chandler ◽

Mona Jahromi ◽

Joshua D. Schiffman ◽

Sarah T. South

Keyword(s):

Loss Of Heterozygosity ◽

Copy Number ◽

Copy Number Loss ◽

Melanocytic Lesions ◽

Formalin Fixed Paraffin ◽

Molecular Inversion Probes ◽

Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe–Based Single-Nucleotide Polymorphism Array

Journal of Molecular Diagnostics ◽

10.1016/j.jmoldx.2016.03.008 ◽

2016 ◽

Vol 18 (5) ◽

pp. 676-687 ◽

Cited By ~ 8

Author(s):

Rajesh R. Singh ◽

Meenakshi Mehrotra ◽

Hui Chen ◽

Alaa A. Almohammedsalim ◽

Ayesagul Sahin ◽

...

Keyword(s):

Copy Number ◽

Single Nucleotide Polymorphism Array ◽

Gene Copy Number ◽

Gene Copy ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Formalin Fixed Paraffin ◽

Molecular Inversion Probe ◽

Abstract 3734: Development of a nanostring copy number assay for a customized 55 gene panel using challenging formalin-fixed paraffin-embedded (ffpe) tumor samples

10.1158/1538-7445.am2014-3734 ◽

2014 ◽

Author(s):

Tingdong Tang ◽

Wenge Shi ◽

Loretta Hipolito ◽

Julie Mayer ◽

Jelveh Lameh ◽

...

Keyword(s):

Copy Number ◽

Gene Panel ◽

Formalin Fixed Paraffin ◽

Copy Number Assay ◽

Ffpe Tumor ◽