Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2 View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-12

AUTHORS

Tú Nguyen-Dumont, Zhi L Teo, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Nelly Sabbaghian, Marc Tischkowitz, William D Foulkes, Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer (kConFab), Graham G Giles, John L Hopper, Australian Breast Cancer Family Registry, Melissa C Southey, Daniel J Park

ABSTRACT

BACKGROUND: Massively parallel sequencing (MPS) has revolutionised biomedical research and offers enormous capacity for clinical application. We previously reported Hi-Plex, a streamlined highly-multiplexed PCR-MPS approach, allowing a given library to be sequenced with both the Ion Torrent and TruSeq chemistries. Comparable sequencing efficiency was achieved using material derived from lymphoblastoid cell lines and formalin-fixed paraffin-embedded tumour. METHODS: Here, we report high-throughput application of Hi-Plex by performing blinded mutation screening of the coding regions of the breast cancer susceptibility gene PALB2 on a set of 95 blood-derived DNA samples that had previously been screened using Sanger sequencing and high-resolution melting curve analysis (n = 90), or genotyped by Taqman probe-based assays (n = 5). Hi-Plex libraries were prepared simultaneously using relatively inexpensive, readily available reagents in a simple half-day protocol followed by MPS on a single MiSeq run. RESULTS: We observed that 99.93% of amplicons were represented at ≥10X coverage. All 56 previously identified variant calls were detected and no false positive calls were assigned. Four additional variant calls were made and confirmed upon re-analysis of previous data or subsequent Sanger sequencing. CONCLUSIONS: These results support Hi-Plex as a powerful approach for rapid, cost-effective and accurate high-throughput mutation screening. They further demonstrate that Hi-Plex methods are suitable for and can meet the demands of high-throughput genetic testing in research and clinical settings. More... »

PAGES

48

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Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1755-8794-6-48

DOI

http://dx.doi.org/10.1186/1755-8794-6-48

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1020069105

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24206657


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