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

J 2016

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

MIKULÁŠOVÁ, Aneta, Jan SMETANA, Markéta WAYHELOVÁ, Helena JANYŠKOVÁ, Samuel Adeyinka OKUBOTE et. al.

Basic information

Original name

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

Authors

MIKULÁŠOVÁ, Aneta (203 Czech Republic, belonging to the institution), Jan SMETANA (203 Czech Republic, belonging to the institution), Markéta WAYHELOVÁ (203 Czech Republic, belonging to the institution), Helena JANYŠKOVÁ (203 Czech Republic, belonging to the institution), Samuel Adeyinka OKUBOTE (566 Nigeria, belonging to the institution), Roman HÁJEK (203 Czech Republic) and Petr KUGLÍK (203 Czech Republic, guarantor, belonging to the institution)

Edition

International Journal of Clinical and Experimental Pathology, 2016, 1936-2625

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 1.706

RIV identification code

RIV/00216224:14310/16:00088952

Organization unit

Faculty of Science

UT WoS

000381729200036

Keywords in English

whole genome amplification; array-comparative genomic hybridization; copy-number changes

Abstract

V originále

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 4 multiple displacement amplification (MDA)-based and 2 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 3 microarray platforms: CGH/4×44 K (Agilent), CGH+SNP/4×180 K (Agilent) and CGH+SNP/4×180 K (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.

Links

NT13492, research and development project

Name: Úloha genetických abnormalit ve vývoji a progresi prekancerózy monoklonální gamapatie nejasného významu

Citovat

MIKULÁŠOVÁ, Aneta, Jan SMETANA, Markéta WAYHELOVÁ, Helena JANYŠKOVÁ, Samuel Adeyinka OKUBOTE, Roman HÁJEK and Petr KUGLÍK. Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-array based comparative genomic hybridization in human myeloma cell line. International Journal of Clinical and Experimental Pathology. 2016, vol. 9, No 7, p. 6965-6980. ISSN 1936-2625.

@article{1374408,
   author = {Mikulášová, Aneta and Smetana, Jan and Wayhelová, Markéta and Janyšková, Helena and Okubote, Samuel Adeyinka and Hájek, Roman and Kuglík, Petr},
   article_number = {7},
   keywords = {whole genome amplification; array-comparative genomic hybridization; copy-number changes},
   language = {eng},
   issn = {1936-2625},
   journal = {International Journal of Clinical and Experimental Pathology},
   title = {Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-array based comparative genomic hybridization in human myeloma cell line},
   volume = {9},
   year = {2016}
}

TY  - JOUR
ID  - 1374408
AU  - Mikulášová, Aneta - Smetana, Jan - Wayhelová, Markéta - Janyšková, Helena - Okubote, Samuel Adeyinka - Hájek, Roman - Kuglík, Petr
PY  - 2016
TI  - Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-array based comparative genomic hybridization in human myeloma cell line
JF  - International Journal of Clinical and Experimental Pathology
VL  - 9
IS  - 7
SP  - 6965
EP  - 6965
SN  - 19362625
KW  - whole genome amplification
KW  - array-comparative genomic hybridization
KW  - copy-number changes
N2  - 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 4 multiple displacement amplification (MDA)-based and 2 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 3 microarray platforms: CGH/4×44 K (Agilent), CGH+SNP/4×180 K (Agilent) and CGH+SNP/4×180 K (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.
ER  -

MIKULÁŠOVÁ, Aneta, Jan SMETANA, Markéta WAYHELOVÁ, Helena JANYŠKOVÁ, Samuel Adeyinka OKUBOTE, Roman HÁJEK and Petr KUGLÍK. Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-array based comparative genomic hybridization in human myeloma cell line. \textit{International Journal of Clinical and Experimental Pathology}. 2016, vol.~9, No~7, p.~6965-6980. ISSN~1936-2625.

Detailed Information on Publication Record