{"doi":"10.1038/srep11711","title":"Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method","abstract":"<jats:title>Abstract</jats:title><jats:p>Current whole genome amplification (WGA) methods lead to amplification bias resulting in over- and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.</jats:p>","journal":"Scientific Reports","year":2015,"id":607887,"datarank":0.5926865577872142,"base_score":3.9512437185814275,"endowment":3.9512437185814275,"self_citation_contribution":0.5926865577872142,"citation_network_contribution":0.0,"self_endowment_contribution":0.5926865577872142,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":51,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1560987,"name":"Dieter De Coninck","orcid":null,"position":1,"is_corresponding":false},{"id":1560988,"name":"Christodoulos Christodoulou","orcid":null,"position":2,"is_corresponding":false},{"id":1560989,"name":"Tom Sante","orcid":null,"position":3,"is_corresponding":false},{"id":734233,"name":"Annelies Dheedene","orcid":null,"position":4,"is_corresponding":false},{"id":123449,"name":"Björn Heindryckx","orcid":null,"position":5,"is_corresponding":false},{"id":1560991,"name":"Etienne Van den Abbeel","orcid":null,"position":6,"is_corresponding":false},{"id":1560992,"name":"Petra De Sutter","orcid":null,"position":7,"is_corresponding":false},{"id":888145,"name":"Björn Menten","orcid":"0000-0001-8182-659X","position":8,"is_corresponding":false},{"id":88801,"name":"Dieter Deforce","orcid":"0000-0002-0635-661X","position":9,"is_corresponding":false},{"id":678527,"name":"Filip Van Nieuwerburgh","orcid":"0000-0001-8815-5485","position":10,"is_corresponding":false},{"id":1560986,"name":"Lieselot Deleye","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method","abstract":"Current whole genome amplification (WGA) methods lead to amplification bias resulting in over- and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.","is_dataset_classified":null,"base_score":3.9512437185814275,"endowment":3.9512437185814275,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"26122179","pmcid":"PMC4485032","openalex_id":"https://openalex.org/W2192980020","authors":[],"funders":[],"total_grants":0,"fwci":5.8509,"citation_percentile":0.96559424,"influential_citations":0,"citation_trend":[{"year":2015,"count":1},{"year":2016,"count":5},{"year":2017,"count":12},{"year":2018,"count":8},{"year":2019,"count":4},{"year":2020,"count":4},{"year":2021,"count":1},{"year":2022,"count":7},{"year":2023,"count":2},{"year":2024,"count":1},{"year":2025,"count":3},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.nature.com/articles/srep11711.pdf","host_type":"journal"},{"url":"https://www.nature.com/articles/srep11711.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1038/srep11711","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/26122179","host_type":"repository"},{"url":"http://hdl.handle.net/1854/LU-6868639","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4485032","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC4485032","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC4485032?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Genomic variations and chromosomal abnormalities","Genomics and Phylogenetic Studies","Chromosomal and Genetic Variations"],"mesh_terms":["Cell Line","Chromosomes, Human","Female","Humans","Gene Library","Genome, Human","Sequence Analysis, DNA","Gene Dosage","Nucleic Acid Amplification Techniques","Comparative Genomic Hybridization","DNA Copy Number Variations","Single-Cell Analysis","High-Throughput Nucleotide Sequencing"],"keywords":["False positive paradox","Genome","Multiple displacement amplification","Computational biology","Biology","DNA sequencing","DNA","Polymerase chain reaction","Molecular biology","Genetics","Gene","Computer science","DNA extraction"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-30T07:10:50.171870Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}