Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-based array-comparative genomic hybridization in human myeloma cell line

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61988987%3A17110%2F16%3AA1701LEA" target="_blank" >RIV/61988987:17110/16:A1701LEA - isvavai.cz</a>

Alternative codes found

RIV/00843989:_____/16:E0105588

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-based array-comparative genomic hybridization in human myeloma cell line

Original language description

Whole genome amplification (WGA) is an approach designed to overcome small amounts of DNA for genome-wide genetic tests used in many clinical applications. Various strategies of WGA have been developed; however, none of them can guarantee the absence of amplification bias. In this study, a total of four multiple displacement amplification (MDA)-based and two PCR-based WGA kits were compared in their effect on segmental copy-number (CN) changes and copy-number neutral loss of heterozygosity (cnnLOH) detection by three microarray platforms: CGH/4x44K (Agilent), CGH+SNP/4x180K (Agilent) and CGH+SNP/4x180K (OGT). Genomic imbalances-rich myeloma cell line U266 was used as material. The main outcomes are as follows: 1) MDA-based WGAs showed higher tendency to generate false positive imbalances in contrast to PCR-based WGAs with higher risk of false negativity; 2) the specific risk of false positivity and/or negativity increased with decreasing CN segments size; 3) single-cell WGAs showed significantly worse effect on results in comparison to WGAs with nanogram level of DNA as input; 4) PCR-based WGAs were incompatible with cnnLOH analysis based on SNP in restriction digestion sites and also showed higher risk of cnnLOH false negativity when combined with analysis based on simple hybridization. In conclusion, the results of this study help to choose WGA according to individual user requirements and options. Moreover, we have shown a strategy to verify and validate segmental CN changes detection by DNA array protocol including any WGA for any purpose to attain the highest efficiency without an unnecessary WGA bias.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

FD - Oncology and haematology

OECD FORD branch

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Project

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Continuities

V - Vyzkumna aktivita podporovana z jinych verejnych zdroju

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY

ISSN

1936-2625

e-ISSN

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Volume of the periodical

9

Issue of the periodical within the volume

7

Country of publishing house

US - UNITED STATES

Number of pages

5

Pages from-to

65-69

UT code for WoS article

000381729200036

EID of the result in the Scopus database

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