Whole-Genome Copy Number Alteration Profiling

The presence of CNA was investigated with a whole-genome low-coverage NGS approach by using the Ampli1™ LowPass Kit for the Ion Torrent (Menarini Silicon Biosystems) workflow described by Ferrarini et al. [37 (link)]. The size selection of the pooled libraries was performed using E-Gel™ SizeSelect™ II Agarose Gels, 2% (Invitrogen, Carlsbad, CA, USA) on E-Gel™ iBase™ and E-Gel™ Safe Imager™ (Invitrogen). The concentration and length of the pool were assessed using the Qubit™ 3.0 Fluorometer (Invitrogen) and Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany), respectively. The pooled libraries were loaded on an Ion 520™ Chip (Thermo Fisher Scientific, Waltham, MA, USA). Template preparation on Ion Chef and sequencing on the GeneStudio™ S5 System (Thermo Fisher Scientific) were performed, setting the run as described in the Ampli1 LowPass protocol.

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Rossi T., Gallerani G., Angeli D., Cocchi C., Bandini E., Fici P., Gaudio M., Martinelli G., Rocca A., Maltoni R, & Fabbri F. (2020). Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer. Cancers, 12(9), 2490.

Publication 2020

E-Gel™ iBase™ E-Gel™ Safe Imager™ Qubit™ 3.0 Fluorometer Bioanalyzer High Sensitivity DNA Kit Ion 520™ Chip GeneStudio™ S5 System

Agarose Chip Genome Sensitivity Silicon

Corresponding Organization : Istituti di Ricovero e Cura a Carattere Scientifico

Other organizations : Ospedale G.B. Morgagni - L.Pierantoni

Top 5 similar protocols

Variable analysis

independent variables

Whole-genome low-coverage NGS approach
Ampli1™ LowPass Kit for the Ion Torrent (Menarini Silicon Biosystems) workflow
Size selection of the pooled libraries using E-Gel™ SizeSelect™ II Agarose Gels, 2% (Invitrogen)
Concentration and length assessment of the pool using Qubit™ 3.0 Fluorometer (Invitrogen) and Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies)
Pooled libraries loaded on an Ion 520™ Chip (Thermo Fisher Scientific)
Template preparation on Ion Chef and sequencing on the GeneStudio™ S5 System (Thermo Fisher Scientific)

dependent variables

Presence of CNA

control variables

Ampli1 LowPass protocol

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