ArticleBMC research notes2011
Laser capture microdissection (LCM) and whole genome amplification (WGA) of DNA from normal breast tissue --- optimization for genome wide array analyses.
Article in BMC research notes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- From morphology to single-cell molecules: high-resolution 3D histology in biomedicine.Molecular cancer · 2025Review
- Low-input and single-cell methods for Infinium DNA methylation BeadChips.Nucleic acids research · 2024Article
- Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans.Nucleic acids research · 2023Article
- Single-Cell Analysis of Foot-and-Mouth Disease Virus.Frontiers in microbiology · 2020Review
- A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides.BMC microbiology · 2018Article
- Expression of CMIP in podocytes is restricted to specific classes of lupus nephritis.PloS one · 2018Article
- Endometriosis research using capture microdissection techniques: Progress and future applications.Biomedical reports · 2016Article
- Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations.Molecular cancer research : MCR · 2016Article
- Impact of upfront cellular enrichment by laser capture microdissection on protein and phosphoprotein drug target signaling activation measurements in human lung cancer: Implications for personalized medicine.Proteomics. Clinical applications · 2015Article
- Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer.Genome research · 2015Article
- Enrichment of single neurons and defined brain regions from human brain tissue samples for subsequent proteome analysis.Journal of neural transmission (Vienna, Austria : 1996) · 2015Article
- Article
- Upregulation of c-mip is closely related to podocyte dysfunction in membranous nephropathy.Kidney international · 2013Article
- Identification of evidence-based biospecimen quality-control tools: a report of the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group.The Journal of molecular diagnostics : JMD · 2013Review
- The PCR-Based Diagnosis of Central Nervous System Tuberculosis: Up to Date.Tuberculosis research and treatment · 2012Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLaser capture microdissection (LCM) can be applied to tissues where cells of interest are distinguishable from surrounding cell populations. Here, we have optimized LCM for fresh frozen normal breast tissue where large amounts of fat can cause problems during microdissection. Since the amount of DNA needed for genome wide analyses, such as single nucleotide polymorphism (SNP) arrays, is often greater than what can be obtained from the dissected tissue, we have compared three different whole genome amplification (WGA) kits for amplification of DNA from LCM material. In addition, the genome wide profiling methods commonly used today require extremely high DNA quality compared to PCR based techniques and DNA quality is thus critical for successful downstream analyses.
findingsWe found that by using FrameSlides without glass backing for LCM and treating the slides with acetone after staining, the problems caused by excessive fat could be significantly decreased. The amount of DNA obtained after extraction from LCM tissue was not sufficient for direct SNP array analysis in our material. However, the two WGA kits based on Phi29 polymerase technology (Repli-g® (Qiagen) and GenomiPhi (GE Healthcare)) gave relatively long amplification products, and amplified DNA from Repli-g® gave call rates in the subsequent SNP analysis close to those from non-amplified DNA. Furthermore, the quality of the input DNA for WGA was found to be essential for successful SNP array results and initial DNA fragmentation problems could be reduced by switching from a regular halogen lamp to a VIS-LED lamp during LCM.
conclusionsLCM must be optimized to work satisfactorily in difficult tissues. We describe a work flow for fresh frozen normal breast tissue where fat is inclined to cause problems if sample treatment is not adapted to this tissue. We also show that the Phi29-based Repli-g® WGA kit (Qiagen) is a feasible approach to amplify DNA of high quality prior to genome wide analyses such as SNP profiling.
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