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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00843989:_____/16:E0105588

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

FD - Onkologie a hematologie

OECD FORD obor

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Projekt

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Návaznosti

V - Vyzkumna aktivita podporovana z jinych verejnych zdroju

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY

ISSN

1936-2625

e-ISSN

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Svazek periodika

9

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

5

Strana od-do

65-69

Kód UT WoS článku

000381729200036

EID výsledku v databázi Scopus

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