ArticleNucleic acids research2008
Impact of whole genome amplification on analysis of copy number variants.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed, 90 citations in OpenAlex.
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- Cancer evolution: Darwin and beyond.The EMBO journal · 2021Review
- Digital-WGS: Automated, highly efficient whole-genome sequencing of single cells by digital microfluidics.Science advances · 2020Article
- Article
- An Internal Control for Evaluating Bisulfite Conversion in the Analysis of Short Stature Homeobox 2 Methylation in Lung Cancer.Asian Pacific journal of cancer prevention : APJCP · 2019Article
- Prenatal DNA Sequencing: Clinical, Counseling, and Diagnostic Laboratory Considerations.Prenatal diagnosis · 2018Review
- The spectrum of somatic mutations in monoclonal gammopathy of undetermined significance indicates a less complex genomic landscape than that in multiple myeloma.Haematologica · 2017Article
- Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells.Oncotarget · 2017Article
- Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality.Molecular genetics and metabolism reports · 2017Article
- Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue.Genome medicine · 2016Article
- Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations.Molecular cancer research : MCR · 2016Article
- Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis.The Journal of molecular diagnostics : JMD · 2016Article
- Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma.Genes, chromosomes & cancer · 2016Article
- Calibrating genomic and allelic coverage bias in single-cell sequencing.Nature communications · 2015Article
- Characterization of cells from patient-derived fibrovascular membranes in proliferative diabetic retinopathy.Molecular vision · 2015Article
- Somatic mosaicism in the human genome.Genes · 2014Review
- Optimized whole-genome amplification strategy for extremely AT-biased template.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Current challenges in the bioinformatics of single cell genomics.Frontiers in oncology · 2014Review
- The applications of single-cell genomics.Human molecular genetics · 2013Review
- Are morphological criteria sufficient for the identification of circulating tumor cells in renal cancer?Journal of translational medicine · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale copy number variants (CNVs) have recently been recognized to play a role in human genome variation and disease. Approaches for analysis of CNVs in small samples such as microdissected tissues can be confounded by limited amounts of material. To facilitate analyses of such samples, whole genome amplification (WGA) techniques were developed. In this study, we explored the impact of Phi29 multiple-strand displacement amplification on detection of CNVs using oligonucleotide arrays. We extracted DNA from fresh frozen lymph node samples and used this for amplification and analysis on the Affymetrix Mapping 500k SNP array platform. We demonstrated that the WGA procedure introduces hundreds of potentially confounding CNV artifacts that can obscure detection of bona fide variants. Our analysis indicates that many artifacts are reproducible, and may correlate with proximity to chromosome ends and GC content. Pair-wise comparison of amplified products considerably reduced the number of apparent artifacts and partially restored the ability to detect real CNVs. Our results suggest WGA material may be appropriate for copy number analysis when amplified samples are compared to similarly amplified samples and that only the CNVs with the greatest significance values detected by such comparisons are likely to be representative of the unamplified samples.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.