1
|
Li J, Greytak SR, Guan P, Engel KB, Goerlitz DS, Islam M, Varghese RS, Moore HM, Ressom HW. Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH. Biopreserv Biobank 2023; 21:407-416. [PMID: 36169416 PMCID: PMC10460690 DOI: 10.1089/bio.2022.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although molecular profiling of DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor specimens has become more common in recent years, it remains unclear how discrete FFPE processing variables may affect detection of copy number variation (CNV). To better understand such effects, array comparative genomic hybridization (aCGH) profiles of FFPE renal cell carcinoma specimens that experienced different delays to fixation (DTFs; 1, 2, 3, and 12 hours) and times in fixative (TIFs; 6, 12, 23, and 72 hours) were compared to snap-frozen tumor and blood specimens from the same patients. A greater number of regions containing CNVs relative to commercial reference DNA were detected in DNA from FFPE tumor specimens than snap-frozen tumor specimens even though they originated from the same tumor blocks. Extended DTF and TIF affected the number of DNA segments with a copy number status that differed between FFPE and frozen tumor specimens; a DTF ≥3 hours led to more segments, while a TIF of 72 hours led to fewer segments. Importantly, effects were not random as a higher guanine-cytosine (GC) content and/or a higher percentage of repeats were observed among stable regions. While limiting aCGH analysis to FFPE specimens with a DTF <3 hours and a TIF <72 hours may circumvent some effects, results from FFPE specimens should be validated against fresh or frozen specimens whenever possible.
Collapse
Affiliation(s)
- James Li
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA
| | | | - Ping Guan
- Biorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - David S. Goerlitz
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Rency S. Varghese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Helen M. Moore
- Biorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Habtom W. Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| |
Collapse
|
2
|
Gao GF, Oh C, Saksena G, Deng D, Westlake LC, Hill BA, Reich M, Schumacher SE, Berger AC, Carter SL, Cherniack AD, Meyerson M, Tabak B, Beroukhim R, Getz G. Tangent normalization for somatic copy-number inference in cancer genome analysis. Bioinformatics 2022; 38:4677-4686. [PMID: 36040167 PMCID: PMC9563697 DOI: 10.1093/bioinformatics/btac586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/28/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas, the Broad Institute Genome Characterization Center developed the Tangent normalization method to generate copy-number profiles using data from single-nucleotide polymorphism (SNP) arrays and whole-exome sequencing (WES) technologies for over 10 000 pairs of tumors and matched normal samples. Here, we describe the Tangent method, which uses a unique linear combination of normal samples as a reference for each tumor sample, to subtract systematic errors that vary across samples. We also describe a modification of Tangent, called Pseudo-Tangent, which enables denoising through comparisons between tumor profiles when few normal samples are available. RESULTS Tangent normalization substantially increases signal-to-noise ratios (SNRs) compared to conventional normalization methods in both SNP array and WES analyses. Tangent and Pseudo-Tangent normalizations improve the SNR by reducing noise with minimal effect on signal and exceed the contribution of other steps in the analysis such as choice of segmentation algorithm. Tangent and Pseudo-Tangent are broadly applicable and enable more accurate inference of SCNAs from DNA sequencing and array data. AVAILABILITY AND IMPLEMENTATION Tangent is available at https://github.com/broadinstitute/tangent and as a Docker image (https://hub.docker.com/r/broadinstitute/tangent). Tangent is also the normalization method for the copy-number pipeline in Genome Analysis Toolkit 4 (GATK4). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Galen F Gao
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Coyin Oh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gordon Saksena
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Davy Deng
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Barbara A Hill
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Reich
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La, Jolla, CA, USA
| | - Steven E Schumacher
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashton C Berger
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott L Carter
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Matthew Meyerson
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Barbara Tabak
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| |
Collapse
|
3
|
Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma. Diagnostics (Basel) 2022; 12:diagnostics12051219. [PMID: 35626372 PMCID: PMC9139996 DOI: 10.3390/diagnostics12051219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Recovery and amplification of nucleic acids from archived formalin-fixed tissue samples is the most developing field in retrospective genetic studies. We compared different deparaffinization methods and DNA isolation techniques, and intergroup comparisons were performed to evaluate the effectiveness of different storing methods for archival OSCC samples based on obtained mean DNA quantity, quality, and PCR amplification of the P53 gene. The study comprised 75 archival histologically diagnosed OSCC samples which were divided into Group I: Formalin-fixed paraffin-embedded tissue blocks and Group II: Long-term formalin-fixed tissue. A comparison of different deparaffinization methods showed that xylene deparaffinization is an efficient method to obtain suitable DNA. Comparing different DNA isolation techniques illustrated that the conventional phenol–chloroform method gives better integrity to DNA in contrast with the kit method. Comparison between FFPET and long-term FFT samples demonstrated that samples fixed in formalin overnight and embedded in wax yield better quality and quantity DNA in comparison with long-term samples fixed in formalin. To obtain suitable integrity of DNA, tissue samples should be stored by fixing in formalin overnight followed by preparation of paraffin tissue blocks, deparaffinization by xylene, and subjecting them to the conventional phenol–chloroform DNA isolation protocol.
Collapse
|
4
|
Lahiri P, Mukherjee S, Ghosh B, Das D, Lahiri B, Varshney SK, Pal M, Paul RR, Chatterjee J. Comprehensive Evaluation of PAXgene Fixation on Oral Cancer Tissues Using Routine Histology, Immunohistochemistry, and FTIR Microspectroscopy. Biomolecules 2021; 11:biom11060889. [PMID: 34203873 PMCID: PMC8232633 DOI: 10.3390/biom11060889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022] Open
Abstract
The choice of tissue fixation is critical for preserving the morphology and biochemical information of tissues. Fragile oral tissues with lower tensile strength are challenging to process for histological applications as they are prone to processing damage, such as tissue tear, wrinkling, and tissue fall-off from slides. This leads to loss of morphological information and unnecessary delay in experimentation. In this study, we have characterized the new PAXgene tissue fixation system on oral buccal mucosal tissue of cancerous and normal pathology for routine histological and immunohistochemical applications. We aimed to minimize the processing damage of tissues and improve the quality of histological experiments. We also examined the preservation of biomolecules by PAXgene fixation using FTIR microspectroscopy. Our results demonstrate that the PAXgene-fixed tissues showed significantly less tissue fall-off from slides. Hematoxylin and Eosin staining showed comparable morphology between formalin-fixed and PAXgene-fixed tissues. Good quality and slightly superior immunostaining for cancer-associated proteins p53 and CK5/6 were observed in PAXgene-fixed tissues without antigen retrieval than formalin-fixed tissues. Further, FTIR measurements revealed superior preservation of glycogen, fatty acids, and amide III protein secondary structures in PAXgene-fixed tissues. Overall, we present the first comprehensive evaluation of the PAXgene tissue fixation system in oral tissues. This study concludes that the PAXgene tissue fixation system can be applied to oral tissues to perform diagnostic molecular pathology experiments without compromising the quality of the morphology or biochemistry of biomolecules.
Collapse
Affiliation(s)
- Pooja Lahiri
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
- Correspondence:
| | - Suranjana Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Biswajoy Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Debnath Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Basudev Lahiri
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Shailendra Kumar Varshney
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Mousumi Pal
- Guru Nanak Institute of Dental Sciences and Research (GNIDSR), Kolkata 700114, India;
| | - Ranjan Rashmi Paul
- Department of Oral & Dental Sciences, JIS University, Kolkata 700109, India;
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| |
Collapse
|
5
|
Van der Linden M, Raman L, Vander Trappen A, Dheedene A, De Smet M, Sante T, Creytens D, Lievens Y, Menten B, Van Dorpe J, Van Roy N. Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Arch Pathol Lab Med 2019; 144:974-981. [PMID: 31846367 DOI: 10.5858/arpa.2019-0010-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed. OBJECTIVE.— To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing. DESIGN.— We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material. RESULTS.— Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%. CONCLUSIONS.— Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
Collapse
Affiliation(s)
- Malaïka Van der Linden
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Lennart Raman
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Ansel Vander Trappen
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Annelies Dheedene
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Matthias De Smet
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Tom Sante
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - David Creytens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Yolande Lievens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Björn Menten
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Jo Van Dorpe
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Nadine Van Roy
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| |
Collapse
|
6
|
Early Hereditary Diffuse Gastric Cancer (eHDGC) is Characterized by Subtle Genomic Instability and Active DNA Damage Response. Pathol Oncol Res 2018; 25:711-721. [PMID: 30547291 DOI: 10.1007/s12253-018-0547-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/16/2018] [Indexed: 12/26/2022]
Abstract
Diffuse gastric cancer (DGC) is one of the two primary types of stomach cancer. Carriers of germline mutations in the gene encoding E-cadherin are predisposed to DGC. The primary aim of the present study was to determine if genomic instability is an early event in DGC and how it may lead to disease progression. Chromosomal aberrations in early intramucosal hereditary diffuse gastric cancer (eHDGC) were assessed using array comparative genomic hybridization (array CGH). Notably, no aneuploidy or other large-scale chromosomal rearrangements were detected. Instead, all aberrations affected small regions (< 4.8 Mb) and were predominantly deletions. Analysis of DNA sequence patterns revealed that essentially all aberrations possessed the characteristics of common fragile sites. These results and the results of subsequent immunohistochemical examinations demonstrated that unlike advanced DGC, eHDGCs is characterized by low levels of genomic instability at fragile sites. Furthermore, they express an active DNA damage response, providing a molecular basis for the observed indolence of eHDGC. This finding is an important step to understanding the pathology underlying natural history of DGC and supports a revision of the current definition of eHDGC as a malignant disease.
Collapse
|
7
|
Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
Collapse
Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
| |
Collapse
|
8
|
Jeong YJ, Park SH, Mun SH, Kwak SG, Lee SJ, Oh HK. Association between lysyl oxidase and fibrotic focus in relation with inflammation in breast cancer. Oncol Lett 2017; 15:2431-2440. [PMID: 29434955 DOI: 10.3892/ol.2017.7617] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 08/03/2017] [Indexed: 12/31/2022] Open
Abstract
We hypothesized that lysyl oxidase (LOX) contributes to the formation of fibrotic focus (FF) in association with inflammation and serves a significant role in breast carcinogenesis. In the present study, the association between the expression of LOX family members and FF with regards to with inflammation was analyzed, and the prognostic significance of LOX and FF in breast cancer was investigated. Immunohistochemical staining for LOX, LOX-like protein (LOXL) 1, LOXL2 and LOXL3 was performed in primary breast cancer tissues. The status of FF within the tumor was assessed, including size and grade. Levels of inflammatory markers, intratumoral and peritumoral lymphocyte infiltration were also evaluated. The clinicopathological characteristics were evaluated from the medical records of patients. In the present study, the expression of LOX family members was not associated with the presence of FF. FF was identified to be associated with intratumoral and peritumoral inflammation, tumor stage, larger tumor size, lymph node metastasis, high histologic grade, and p53 expression. LOX and LOXL3 were associated with intratumoral, and peritumoral inflammation. Furthermore, LOXL1 was associated with intratumoral inflammation and interleukin-4. In addition, LOX was associated with cluster of differentiation 8+ T cells. LOXL3 was associated with expression of ER and PR, and molecular subtype. In the survival analysis, overall survival time was statistically significantly longer in the FF-negative compared with that in the FF-positive group. In conclusion, it was demonstrated that FF and the expression of LOX family members were associated with inflammation in breast cancer. FF was associated with poor prognostic markers of breast cancer. Further studies are required to clarify the mechanisms underlying the association between the LOX family, FF and inflammation in breast cancer.
Collapse
Affiliation(s)
- Young Ju Jeong
- Department of Surgery, College of Medicine, Catholic University of Daegu, Daegu 705-718, Repulic of South Korea
| | - Sung Hwan Park
- Department of Surgery, College of Medicine, Catholic University of Daegu, Daegu 705-718, Repulic of South Korea
| | - Sung Hee Mun
- Department of Radiology, College of Medicine, Catholic University of Daegu, Daegu 705-718, Repulic of South Korea
| | - Sang Gyu Kwak
- Department of Medical Statistics, College of Medicine, Catholic University of Daegu, Daegu 705-718, Repulic of South Korea
| | - Sun-Jae Lee
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 705-718, Repulic of South Korea
| | - Hoon Kyu Oh
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 705-718, Repulic of South Korea
| |
Collapse
|
9
|
The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
Collapse
|
10
|
Tong YQ, Liu B, Fu CH, Zheng HY, Gu J, Liu H, Luo HB, Li Y. Genetic analysis of the PKHD1 gene with long-rang PCR sequencing. ACTA ACUST UNITED AC 2016; 36:758-766. [PMID: 27752906 DOI: 10.1007/s11596-016-1658-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/26/2016] [Indexed: 12/13/2022]
Abstract
PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease (ARPKD). However, it is inconvenient to detect the mutations by common polymerase chain reaction (PCR) because the open reading frame of PKHD1 is very long. Recently, long-range (LR) PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.
Collapse
Affiliation(s)
- Yong-Qing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Bei Liu
- Department of Pathology, Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, China
| | - Chao-Hong Fu
- Department of Clinical Laboratory, Dongfeng Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Hong-Yun Zheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hang Liu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hong-Bo Luo
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Yan Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| |
Collapse
|
11
|
CNARA: reliability assessment for genomic copy number profiles. BMC Genomics 2016; 17:799. [PMID: 27733115 PMCID: PMC5062840 DOI: 10.1186/s12864-016-3074-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/07/2016] [Indexed: 01/22/2023] Open
Abstract
Background DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing methods. Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA quality is sometimes observed in genome screening experiments and may lead to unreliable copy number profiles. Depending on the extent of these artefacts and the resulting misidentification of copy number alterations/variations (CNA/CNV), it may be desirable to exclude such samples from analyses or to adapt the downstream data analysis strategy accordingly. Results Here, we propose a method to distinguish reliable genomic copy number profiles from those containing heavy wave artefacts and/or large DLRS. We define four features that adequately summarize the copy number profiles for reliability assessment, and train a classifier on a dataset of 1522 copy number profiles from various microarray platforms. The method can be applied to predict the reliability of copy number profiles irrespective of the underlying microarray platform and may be adapted for those sequencing platforms from which copy number estimates could be computed as a piecewise constant signal. Further details can be found at https://github.com/baudisgroup/CNARA. Conclusions We have developed a method for the assessment of genomic copy number profiling data, and suggest to apply the method in addition to and after other state-of-the-art noise correction and quality control procedures. CNARA could be instrumental in improving the assessment of data used for genomic data mining experiments and support the reliable functional attribution of copy number aberrations especially in cancer research. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3074-7) contains supplementary material, which is available to authorized users.
Collapse
|
12
|
Ennaifer E, Salhi F, Laassili T, Fehri E, Ben Alaya N, Guizani I, Boubaker S. Type-Specific Human Papillomavirus Distribution in Invasive Squamous Cervical Carcinomas in Tunisia and Vaccine Impact. Asian Pac J Cancer Prev 2016; 16:6769-72. [PMID: 26434909 DOI: 10.7314/apjcp.2015.16.15.6769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High risk human papillomaviruses (HPVs) are the leading cause of cervical cancer (CC) and Pap smear screening has not been successful in preventing CC in Tunisia. HPV vaccination that targets HPV16 and 18 offers a new efficient prevention tool. Identification of HPV types in CC is thus essential to determine the impact of HPV vaccine implementation. The aim of this study is to provide specific data from Tunisia. MATERIALS AND METHODS A total of 89 histological confirmed paraffin embedded samples isolated from patients with CC diagnosed between 2001 and 2011 were collected from five medical centres from Northern and Southern Tunisia. HPV DNA was detected using a nested PCR (MY09/MY11-GP5+/GP6+) and genotyping was assessed using a reverse blot line hybridisation assay that enables the detection of 32 HPV types. RESULTS HPV DNA was detected in all samples. Twelve high risk types were detected; HPV16 and/or 18 were predominant, accounting together for 92.1% of all the CC cases (HPV16: 83.1%). Single infections accounted for 48.8% of the cases and were mostly linked to HPV 16 (32.6%) and less frequently to HPV 18 (2.4%). The other high risk HPV single infections were linked to HPV 35 (4.6%), 45 (4.6%), 58 (2.3%) and 59 (2.3%). Multiple infections with mixing of 2 to 4 genotypes predominately featrued HPV16 and/or 18 with HPV 35 and 45 (96.6 %) and less frequently with HPV 59, 40, 66, 73 and 58. There was no statistically significant variation in the relative distribution of HPV types with age. CONCLUSIONS These results strongly indicate that prophylactic HPV vaccines can have a major impact in preventing CC in Tunisia.
Collapse
Affiliation(s)
- Emna Ennaifer
- HPV Research Unit, Laboratory of Molecular Epidemiology and Experimental Pathology Applied to Infectious Diseases, Pasteur Institute of Tunis, Tunis, Tunisia *E-mail : ,
| | | | | | | | | | | | | |
Collapse
|
13
|
Mathieson W, Marcon N, Antunes L, Ashford DA, Betsou F, Frasquilho SG, Kofanova OA, McKay SC, Pericleous S, Smith C, Unger KM, Zeller C, Thomas GA. A Critical Evaluation of the PAXgene Tissue Fixation System: Morphology, Immunohistochemistry, Molecular Biology, and Proteomics. Am J Clin Pathol 2016; 146:25-40. [PMID: 27402607 DOI: 10.1093/ajcp/aqw023] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To evaluate the PAXgene tissue fixation system. METHODS Clinical biospecimens (n = 46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS]). RESULTS PFPE protocol optimization was required in most cases and is described. RNA extracted from PFPE sections was considerably less degraded than that from FFPE sections but more degraded than that from FF blocks. Genomic-length DNA was extracted from PFPE and FF biospecimens, and methylation profiling showed PFPE and FF biospecimens to be almost indistinguishable. Only degraded DNA was extracted from FFPE biospecimens. PFPE sections yielded peptides that were slightly less amenable to LC-MS/MS analysis than FFPE sections, but FF gave slightly better results. CONCLUSIONS While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.
Collapse
Affiliation(s)
- William Mathieson
- From the Integrated Biobank of Luxembourg, Luxembourg
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | | | | | - David A. Ashford
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Fay Betsou
- From the Integrated Biobank of Luxembourg, Luxembourg
| | | | | | - Siobhan C. McKay
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Stephan Pericleous
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Colleen Smith
- Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom
| | - Kristian M. Unger
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Constanze Zeller
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Geraldine A. Thomas
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom
| |
Collapse
|
14
|
Hara K, Watanabe A, Matsumoto S, Matsuda Y, Kuwata T, Kan H, Yamada T, Koizumi M, Shinji S, Yamagishi A, Ishiwata T, Naito Z, Shimada T, Uchida E. Surgical Specimens of Colorectal Cancer Fixed with PAXgene Tissue System Preserve High-Quality RNA. Biopreserv Biobank 2015; 13:325-34. [DOI: 10.1089/bio.2014.0101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Keisuke Hara
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Atsushi Watanabe
- Department of Biochemistry and Molecular Biology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Satoshi Matsumoto
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Yoko Matsuda
- Department of Pathology and Integrative Oncological Pathology, Nippon Medical School Graduate School, Tokyo, Japan
| | | | - Hayato Kan
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Michihiro Koizumi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Seiichi Shinji
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Aya Yamagishi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Toshiyuki Ishiwata
- Department of Pathology and Integrative Oncological Pathology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Zenya Naito
- Department of Pathology and Integrative Oncological Pathology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Takashi Shimada
- Department of Biochemistry and Molecular Biology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Eiji Uchida
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| |
Collapse
|
15
|
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res 2014; 24:2022-32. [PMID: 25236618 PMCID: PMC4248318 DOI: 10.1101/gr.175141.114] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.
Collapse
|
16
|
Abstract
MOTIVATION Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses. METHOD We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes. RESULTS Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets. CONTACT lzhangli@mdanderson.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Liangcai Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA and Department of Biophysics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | | |
Collapse
|
17
|
Moore DA, Saldanha G, Ehdode A, Potter L, Dyall L, Bury D, Pringle JH. Accurate detection of copy number changes in DNA extracted from formalin-fixed, paraffin-embedded melanoma tissue using duplex ratio tests. J Mol Diagn 2013; 15:687-94. [PMID: 23810241 DOI: 10.1016/j.jmoldx.2013.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 04/16/2013] [Accepted: 04/24/2013] [Indexed: 11/29/2022] Open
Abstract
A minority of melanocytic lesions cannot confidently be classified as benign or malignant on histopathological examination, causing diagnostic uncertainty. DNA copy number changes can be used to distinguish nevi from melanoma, although the use of FFPE tissue can pose technical challenges. DNA copy number assays, called duplex ratio tests, have been developed with duplex real-time PCR, using a simple method with potential for high throughput. Five duplex ratio test assays targeting loci with common DNA copy number changes in melanoma were designed and tested using DNA extracted from FFPE samples microdissected from melanoma, common nevi, benign tonsil (10 each), and two melanoma cell lines. The assays proved accurate when DNA extracted from fresh and FFPE melanoma cell lines were compared (intraclass correlation coefficient, 0.99) and gave precise results when repeated on DNA from FFPE tissue (intraclass correlation coefficient range, 0.90 to 0.96). In combination, duplex ratio test values from three of the assays distinguished between the nevi and melanomas with 100% sensitivity (95% CI, 69.1% to 100%) and 100% specificity (95% CI, 69.1% to 100%). Duplex ratio test assays have been shown to be accurate and precise and can distinguish melanomas from common nevi using DNA from FFPE tissue. Appropriately designed assays could have value in assessment of other cancers.
Collapse
Affiliation(s)
- David A Moore
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
18
|
Non-formalin fixative versus formalin-fixed tissue: A comparison of histology and RNA quality. Exp Mol Pathol 2013; 94:188-94. [DOI: 10.1016/j.yexmp.2012.07.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
|
19
|
Salawu A, Ul-Hassan A, Hammond D, Fernando M, Reed M, Sisley K. High quality genomic copy number data from archival formalin-fixed paraffin-embedded leiomyosarcoma: optimisation of universal linkage system labelling. PLoS One 2012; 7:e50415. [PMID: 23209738 PMCID: PMC3510175 DOI: 10.1371/journal.pone.0050415] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/19/2012] [Indexed: 01/01/2023] Open
Abstract
Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment.
Collapse
Affiliation(s)
- Abdulazeez Salawu
- Department of Oncology, The University of Sheffield, Medical School, Sheffield, United Kingdom.
| | | | | | | | | | | |
Collapse
|
20
|
DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues. PLoS One 2012; 7:e38881. [PMID: 22719973 PMCID: PMC3376148 DOI: 10.1371/journal.pone.0038881] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 05/14/2012] [Indexed: 11/30/2022] Open
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.
Collapse
|
21
|
Tan YC, Michaeel A, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H. A novel long-range PCR sequencing method for genetic analysis of the entire PKD1 gene. J Mol Diagn 2012; 14:305-13. [PMID: 22608885 DOI: 10.1016/j.jmoldx.2012.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 02/12/2012] [Accepted: 02/22/2012] [Indexed: 12/20/2022] Open
Abstract
Genetic testing of PKD1 and PKD2 is useful for the diagnosis and prognosis of autosomal dominant polycystic kidney disease; however, analysis is complicated by the large transcript size, the complexity of the gene region, and the high level of gene variations. We developed a novel mutation screening assay for PKD1 by directly sequencing long-range (LR) PCR products. By using this method, the entire PKD1 coding region was amplified by nine reactions, generating product sizes from 2 to 6 kb, circumventing the need for specific PCR amplification of individual exons. This method was compared with direct sequencing used by a reference laboratory and the SURVEYOR-WAVE Nucleic Acid High Sensitivity Fragment Analysis System (Transgenomic) screening method for five patients with autosomal dominant polycystic kidney disease. A total of 53 heterozygous genetic changes were identified by LR PCR sequencing, including 41 (of 42) variations detected by SURVEYOR nuclease and all 32 variations reported by the reference laboratory, detecting an additional 12 intronic changes not identified by the other two methods. Compared with the reference laboratory, LR PCR sequencing had a sensitivity of 100%, a specificity of 98.5%, and an accuracy of 98.8%; compared with the SURVEYOR-WAVE method, it had a sensitivity of 97.1%, a specificity of 100%, and an accuracy of 99.4%. In conclusion, LR PCR sequencing was superior to the direct sequencing and screening methods for detecting genetic variations, achieving high sensitivity and improved intronic coverage with a faster turnaround time and lower costs, and providing a reliable tool for complex genetic analyses.
Collapse
Affiliation(s)
- Ying-Cai Tan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
Formalin is the most commonly used tissue fixative worldwide. While it offers excellent morphological preservation for routine histology, it has detrimental effects on nucleic acids. Most studies of nucleic acids have therefore used fresh frozen tissue, the collection and storage of which is resource intensive. The ability to use modern genomic, transcriptomic and epigenomic methods with nucleic acids derived from formalin-fixed, paraffin-embedded (FFPE) tissues would allow enormous archives of routinely stored tissues (usually with well-annotated clinical data) to be used for translational research. This paper outlines the effects of formalin on nucleic acids, describes ways of minimizing nucleic acid degradation and optimizing extraction, and reviews recent studies that have used contemporary techniques to analyse FFPE-derived nucleic acids (with a focus on malignant tissue sources). Simple tips are also offered to ensure the utility of your institution's samples for future studies, and broadly applicable guidelines are listed for those contemplating their own study using FFPE-derived material.
Collapse
Affiliation(s)
- Adam Frankel
- University of Queensland, Ipswich Road, Woolloongabba,Brisbane, Qld 4102, Australia.
| |
Collapse
|
23
|
Brosens RPM, Haan JC, Carvalho B, Rustenburg F, Grabsch H, Quirke P, Engel AF, Cuesta MA, Maughan N, Flens M, Meijer GA, Ylstra B. Candidate driver genes in focal chromosomal aberrations of stage II colon cancer. J Pathol 2010; 221:411-24. [PMID: 20593488 DOI: 10.1002/path.2724] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chromosomal instable colorectal cancer is marked by specific large chromosomal copy number aberrations. Recently, focal aberrations of 3 Mb or smaller have been identified as a common phenomenon in cancer. Inherent to their limited size, these aberrations harbour one or few genes. The aim of this study was to identify recurrent focal chromosomal aberrations and their candidate driver genes in a well-defined series of stage II colon cancers and assess their potential clinical relevance. High-resolution DNA copy number profiles were obtained from 38 formalin-fixed, paraffin-embedded colon cancer samples with matched normal mucosa as a reference using array comparative genomic hybridization. In total, 81 focal chromosomal aberrations were identified that harboured 177 genes. Statistical validation of focal aberrations and identification of candidate driver genes were performed by enrichment analysis and mapping copy number and mutation data of colorectal, breast, and pancreatic cancer and glioblastomas to loci of focal aberrations in stage II colon cancer. This analysis demonstrated a significant overlap with previously identified focal amplifications in colorectal cancer, but not with cancers from other sites. In contrast, focal deletions seemed less tumour type-specific since they also showed significant overlap with focal deletions of other sites. Focal deletions detected were significantly enriched for cancer genes and genes frequently mutated in colorectal cancer. The mRNA expression of these genes was significantly correlated with DNA copy number status, supporting the relevance of focal aberrations. Loss of 5q34 and gain of 13q22.1 were identified as independent prognostic factors of survival in this series of patients. In conclusion, focal chromosomal copy number aberrations in stage II colon cancer are enriched in cancer genes that contribute to and drive the process of colorectal cancer development. DNA copy number status of these genes correlates with mRNA expression and some are associated with clinical outcome.
Collapse
Affiliation(s)
- Rebecca P M Brosens
- Department of Surgery, VU University Medical Centre, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Bae JS, Choi JS, Baik SH, Park WC, Song BJ, Kim JS, Lim Y, Jung SS. Genomic alterations of primary tumor and blood in invasive ductal carcinoma of breast. World J Surg Oncol 2010; 8:32. [PMID: 20409316 PMCID: PMC2865462 DOI: 10.1186/1477-7819-8-32] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 04/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic alterations are important events in the origin and progression of various cancers, with DNA copy number changes associated with progression and treatment response in cancer. Array CGH is potentially useful in the identification of genomic alterations from primary tumor and blood in breast cancer patients. The aim of our study was to compare differences of DNA copy number changes in blood and tumor tissue in breast cancer. METHODS DNA copy number changes in blood were compared to those in tumor tissue using array-comparative genomic hybridization in samples obtained from 30 breast cancer patients. The relative degree of chromosomal changes was analyzed using log2 ratios and data was validated by real-time polymerase chain reaction. RESULTS Forty-six regions of gains present in more than 30% of the tissues and 70 regions of gains present in more than 30% of blood were identified. The most frequently gained region was chromosome 8q24. In total, agreement of DNA copy numbers between primary tumor and blood was minimal (Kappa = 0.138, p < 0.001). CONCLUSION Although there was only a slight agreement of DNA copy number alterations between the primary tumor and the blood samples, the blood cell copy number variation may have some clinical significance as compared to the primary tumor in IDC breast cancer patients.
Collapse
Affiliation(s)
- Ja Seong Bae
- Department of Surgery, The Catholic University, Seoul, Korea
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Silvestris N, Tommasi S, Santini D, Russo A, Simone G, Petriella D, Maiello E, Tonini G, Colucci G. KRAS mutations and sensitivity to anti-EGFR monoclonal antibodies in metastatic colorectal carcinoma: an open issue. Expert Opin Biol Ther 2010; 9:565-77. [PMID: 19368524 DOI: 10.1517/14712590902870394] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Cetuximab and panitumumab, mAbs targeting EGFR, are registered for metastatic colorectal carcinoma (mCRC) patients whose tumors express EGFR as determined by immunohistochemistry. However, this method is not predictive of treatment efficacy. KRAS, the human homolog of the Kirsten rat sarcoma-2 virus oncogene, encodes a small G-protein that functions downstream of EGFR-induced signalling. OBJECTIVE/METHODS To examine KRAS mutations as predictive factors of response to anti-EGFR mAbs using recently published data. RESULTS/CONCLUSIONS Several retrospective studies show that efficacy of these mAbs is confined to patients with wild type KRAS and genotyping of tumors should be considered before treatment. The absence of KRAS mutations does not guarantee an improved likelihood of response to cetuximab and panitumumab. Investigation of other genetic and epigenetic biomarkers will be useful to further refine the responder population. Prospective studies to test the efficacy of combined therapies simultaneously targeting EGFR and the RAS/RAF/MAPK signalling pathways for mCRC are warranted.
Collapse
Affiliation(s)
- Nicola Silvestris
- Scientific Institute for Research and Treatment of Cancer Giovanni Paolo II, Medical and Experimental Oncology Unit, Bari, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Mangold KA, Wang V, Weissman SM, Rubinstein WS, Kaul KL. Detection of BRCA1 and BRCA2 Ashkenazi Jewish founder mutations in formalin-fixed paraffin-embedded tissues using conventional PCR and heteroduplex/amplicon size differences. J Mol Diagn 2009; 12:20-6. [PMID: 19959799 DOI: 10.2353/jmoldx.2010.090023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In many families with histories suggestive of BRCA1- or BRCA2-related disease, the proband is deceased. Reliable assessment of archived tissue blocks not amenable to full gene sequencing would be helpful. In this study, a polymerase chain reaction (PCR) assay using primers that bracket the BRCA mutation site and microfluidics-based detection of heteroduplex/amplicon size differences was developed to circumvent artifacts associated with low quality DNA from formalin-fixed paraffin-embedded (FFPE) tissue. Genomic DNA was extracted from 100 FFPE specimens from patients that had previously undergone BRCA gene sequence analysis on blood specimens. Conventional PCR amplification products were differentiated using the Agilent 2100 Bioanalyzer. One FFPE specimen failed to amplify the wild-type alleles for all three sites and was therefore called indeterminate. All 62 FFPE specimens with known Ashkenazi Jewish founder mutations had both the wild-type and the correct mutated allele amplified, including one specimen that failed to amplify the mutant allele in other real-time PCR assays. Appropriately, 21 FFPE specimens known to have other BRCA1/2 mutations and 16 without any mutation had only the wild-type allele correctly amplified for each target. Therefore, by changing the primer location and detecting amplicons via heteroduplexes formed by size differences, we identified mutations from FFPE tissues missed using real-time methods.
Collapse
Affiliation(s)
- Kathy A Mangold
- Department of Pathology & Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201, USA.
| | | | | | | | | |
Collapse
|
27
|
Zon G, Barker MA, Kaur P, Groshen S, Jones LW, Imam SA, Boyd VL. Formamide as a denaturant for bisulfite conversion of genomic DNA: Bisulfite sequencing of the GSTPi and RARβ2 genes of 43 formalin-fixed paraffin-embedded prostate cancer specimens. Anal Biochem 2009; 392:117-25. [DOI: 10.1016/j.ab.2009.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 05/28/2009] [Accepted: 06/02/2009] [Indexed: 12/20/2022]
|
28
|
Chan LW, Choy KW, Leung TY, Lau TK. Prenatal diagnosis by array-comparative genomic hybridization. ACTA ACUST UNITED AC 2009; 3:649-57. [DOI: 10.1517/17530050903222247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
29
|
Lennon PA, Zhuang Y, Pierson D, Zhang X, Williams C, Perez C, Lin P. Bacterial artificial chromosome array-based comparative genomic hybridization using paired formalin-fixed, paraffin-embedded and fresh frozen tissue specimens in multiple myeloma. Cancer 2009; 115:345-54. [PMID: 19109814 DOI: 10.1002/cncr.24021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Multiple myeloma (MM) is a neoplasm of malignant plasma cells that often harbors many chromosomal aberrations. Currently, fresh frozen tissues (FT) are considered the most reliable for molecular genetic analysis; however, formalin-fixed, paraffin-embedded (FFPE) tissues are easily retrievable. Compared with conventional cytogenetics, bacterial artificial chromosome (BAC) array-comparative genomic hybridization (CGH) allows more sensitive detection of chromosomal abnormalities. METHODS The authors analyzed 7 paired FT and FFPE samples of bone marrow aspirate materials obtained from patients with MM in parallel to determine the efficacy of BAC array-CGH using FFPE. RESULTS Thirty-four aberrations were identified, including 29 that were observed in both sample types, yielding 85% concordance. Nonrandom anomalies, including gains on 7q, 9q, 15q, and 19p and losses on 8p and 13q, were observed in paired samples from at least 2 patients. To verify these results, fluorescence in situ hybridization (FISH) was performed using probes specific for 7q and 15q, and gains were observed in the 4 samples that were examined. Furthermore, 1 of 3 samples from patients who had monoclonal gammopathy of undetermined significance that were tested also carried gain on 7q, suggesting that this aberration may be an early transforming event. CONCLUSIONS The current results indicated that BAC array-CGH can be effective using FFPE samples and is a sensitive method for the identification of nonrandom chromosomal aberrations in MM.
Collapse
Affiliation(s)
- Patrick A Lennon
- School of Health Sciences, Department of Hematopathology, the University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Cukier HN, Pericak-Vance MA, Gilbert JR, Hedges DJ. Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays. Anal Biochem 2009; 386:288-90. [DOI: 10.1016/j.ab.2008.11.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 11/25/2008] [Accepted: 11/26/2008] [Indexed: 01/10/2023]
|
31
|
Wang Y, Carlton VEH, Karlin-Neumann G, Sapolsky R, Zhang L, Moorhead M, Wang ZC, Richardson AL, Warren R, Walther A, Bondy M, Sahin A, Krahe R, Tuna M, Thompson PA, Spellman PT, Gray JW, Mills GB, Faham M. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. BMC Med Genomics 2009; 2:8. [PMID: 19228381 PMCID: PMC2649948 DOI: 10.1186/1755-8794-2-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 02/19/2009] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (approximately 40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. RESULTS Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. CONCLUSION MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
Collapse
Affiliation(s)
| | | | | | | | - Li Zhang
- MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Robert Warren
- University of California San Francisco, San Francisco, CA, USA
| | - Axel Walther
- Cancer Research UK, London Research Institute, London, UK
| | | | | | - Ralf Krahe
- MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Joe W Gray
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | |
Collapse
|
32
|
Mojica WD. Importance of cell-procurement methods in transforming personalized cancer treatment from concept to reality. Per Med 2009; 6:33-43. [PMID: 29783382 DOI: 10.2217/17410541.6.1.33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The much-anticipated promise of personalized cancer care is to deliver therapies best suited for a patient based on the knowledge of that individual's genetics and tumor characteristics. This transformative approach will require many changes in the scientific and medical community, one of the most fundamental being the direct study of human tissue biospecimens. Biospecimens will be integral to the elucidation of biomarkers that will help identify and serve as potential diagnostic, prognostic and therapeutic targets in cancer. Despite the vast repositories of fixed-tissue biospecimens that are in existence, a number of flaws exist that hinder their reliable use as instruments from which to enable personalized cancer research and clinical care. A new view of biospecimen worth in the future will mandate that the molecules within its cells are reflective of their in vivo state, and not altered by external variables introduced during the excision and processing of the biospecimen. Research on biospecimen collection is a legitimate field of study that will be necessary for personalized cancer care to become a reality.
Collapse
Affiliation(s)
- Wilfrido D Mojica
- University at Buffalo, State University of New York, Department of Pathology, 100 High Street, Buffalo NY 14203, USA.
| |
Collapse
|
33
|
Coe BP, Lockwood WW, Chari R, Lam WL. Comparative genomic hybridization on BAC arrays. Methods Mol Biol 2009; 556:7-19. [PMID: 19488868 DOI: 10.1007/978-1-60327-192-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Alterations in genomic DNA are a key feature of many constitutional disorders and cancer. The discovery of the underlying regions of gene dosage has thus been essential in dissecting complex disease phenotypes and identifying targets for therapeutic intervention and diagnostic testing. The development of array comparative genomic hybridization (aCGH) using bacterial artificial chromosomes (BACs) as hybridization targets has facilitated the discovery and fine mapping of novel genomic alterations allowing rapid identification of target genes. In BAC aCGH, DNA samples are first labeled with fluorescent dyes through a random priming reaction with 100-400 ng of genomic DNA. This probe is then co-hybridized to an array consisting of BAC clones, either tiling the genome (approximately 50 kbp resolution) or spaced at intervals (e.g., 1 Mbp resolution). The resulting arrays are then imaged and the signal at each locus is compared between a reference and test sample to determine the copy number status. The DNA samples to be analyzed may be derived from either fresh, frozen, or formalin-fixed paraffin-embedded material, and sample requirements are currently significantly lower than those for oligonucleotide platforms due to the high probe-binding capacity of BAC clone targets (approximately 150 kbp) compared to oligonucleotides (25-80 bp). In this chapter, we describe in detail the technical procedure required to perform copy number analysis of genomes with BAC aCGH.
Collapse
|
34
|
Neutering affects mRNA expression levels for the LH- and GnRH-receptors in the canine urinary bladder. Theriogenology 2009; 71:239-47. [DOI: 10.1016/j.theriogenology.2008.06.093] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 06/17/2008] [Accepted: 06/18/2008] [Indexed: 11/21/2022]
|
35
|
Zhang X, Chen J, Radcliffe T, Lebrun DP, Tron VA, Feilotter H. An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samples. J Mol Diagn 2008; 10:513-9. [PMID: 18832457 DOI: 10.2353/jmoldx.2008.080077] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that suppress gene expression at the posttranscriptional level via an antisense RNA-RNA interaction. miRNAs used for array-based profiling are generally purified from either snap-frozen or fresh samples. Because tissues found in most pathology departments are available only in formalin-fixed and paraffin-embedded (FFPE) states, we sought to evaluate miRNA derived from FFPE samples for microarray analysis. In this study, miRNAs extracted from matched snap-frozen and FFPE samples were profiled using the Agilent miRNA array platform (Agilent, Santa Clara, CA). Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. Seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling, and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results; technical replicates showed high correlations with one another (Kendall tau, 0.722 to 0.853; Spearman rank correlation coefficient, 0.891 to 0.954). Our results showed consistent high correlations between matched frozen and FFPE samples (Kendall tau, 0.669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling.
Collapse
Affiliation(s)
- Xiao Zhang
- Department of Pathology and Molecular Medicine, Queen's Laboratory for Molecular Pathology, Kingston, ON, Canada
| | | | | | | | | | | |
Collapse
|
36
|
Das K, Mohd Omar MF, Ong CW, Abdul Rashid SB, Peh BK, Putti TC, Tan PH, Chia KS, Teh M, Shah N, Soong R, Salto-Tellez M. TRARESA: a tissue microarray-based hospital system for biomarker validation and discovery. Pathology 2008; 40:441-9. [DOI: 10.1080/00313020802198101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
37
|
Garnis C. Diagnostic methods of lung cancer and its subtypes by comparative genomic hybridization. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2007; 1:541-544. [PMID: 23496360 DOI: 10.1517/17530059.1.4.541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Comparative genomic hybridization technologies have been applied to study genome-wide detection of copy number alterations in virtually all commonly diagnosed cancer types and several other diseases. The patent under evaluation describes a tool that can be used in principle to produce genome signatures with diagnostic and prognostic utility in lung cancer. Specific regions of genomic alterations correlate with either disease subtype, patient age or overall survival. The ability to characterize these phenotype-associated genome alterations in a clinical setting would presumably facilitate more robust disease diagnosis and also have potential for tailoring treatment strategies.
Collapse
Affiliation(s)
- Cathie Garnis
- Massachusetts Institute of Technology Center for Cancer Research, Room E17 529, 77 Massachusetts Avenue, Cambridge MA 02139, USA
| |
Collapse
|