The clinical benefit of array-based comparative genomic
hybridization for detection of copy number variants in Czech
children with intellectual disability and developmental delay

J 2019

The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay

WAYHELOVÁ, Markéta, Jan SMETANA, Vladimíra VALLOVÁ, Eva HLADÍLKOVÁ, Hana FILKOVÁ et. al.

Basic information

Original name

The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay

Authors

WAYHELOVÁ, Markéta (203 Czech Republic, belonging to the institution), Jan SMETANA (203 Czech Republic, belonging to the institution), Vladimíra VALLOVÁ (703 Slovakia, belonging to the institution), Eva HLADÍLKOVÁ (203 Czech Republic), Hana FILKOVÁ (203 Czech Republic), Marta HANÁKOVÁ (203 Czech Republic), Marcela VILÉMOVÁ (203 Czech Republic), Petra NIKOLOVÁ (203 Czech Republic), Barbora GROMESOVÁ (203 Czech Republic), Renata GAILLYOVÁ (203 Czech Republic) and Petr KUGLÍK (203 Czech Republic, guarantor, belonging to the institution)

Edition

BMC MEDICAL GENOMICS, LONDON, BIOMED CENTRAL LTD, 2019, 1755-8794

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10603 Genetics and heredity

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.570

RIV identification code

RIV/00216224:14310/19:00110250

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1186/s12920-019-0559-7

UT WoS

000477034800001

Keywords in English

intellectual disability; developmental delay; microdeletion; microduplication; CNV; array CGH

Abstract

V originále

Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.

Links

MUNI/A/0958/2018, interní kód MU

Name: Podpora výzkumné činnosti studentů molekulární biologie a genetiky 7 (Acronym: MBG 7)

Investor: Masaryk University, Category A

Citovat

WAYHELOVÁ, Markéta, Jan SMETANA, Vladimíra VALLOVÁ, Eva HLADÍLKOVÁ, Hana FILKOVÁ, Marta HANÁKOVÁ, Marcela VILÉMOVÁ, Petra NIKOLOVÁ, Barbora GROMESOVÁ, Renata GAILLYOVÁ and Petr KUGLÍK. The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay. BMC MEDICAL GENOMICS. LONDON: BIOMED CENTRAL LTD, 2019, vol. 12, No 1, p. 111-121. ISSN 1755-8794. Available from: https://dx.doi.org/10.1186/s12920-019-0559-7.

@article{1546918,
   author = {Wayhelová, Markéta and Smetana, Jan and Vallová, Vladimíra and Hladílková, Eva and Filková, Hana and Hanáková, Marta and Vilémová, Marcela and Nikolová, Petra and Gromesová, Barbora and Gaillyová, Renata and Kuglík, Petr},
   article_location = {LONDON},
   article_number = {1},
   doi = {http://dx.doi.org/10.1186/s12920-019-0559-7},
   keywords = {intellectual disability; developmental delay; microdeletion; microduplication; CNV; array CGH},
   language = {eng},
   issn = {1755-8794},
   journal = {BMC MEDICAL GENOMICS},
   title = {The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay},
   url = {https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0559-7},
   volume = {12},
   year = {2019}
}

TY  - JOUR
ID  - 1546918
AU  - Wayhelová, Markéta - Smetana, Jan - Vallová, Vladimíra - Hladílková, Eva - Filková, Hana - Hanáková, Marta - Vilémová, Marcela - Nikolová, Petra - Gromesová, Barbora - Gaillyová, Renata - Kuglík, Petr
PY  - 2019
TI  - The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay
JF  - BMC MEDICAL GENOMICS
VL  - 12
IS  - 1
SP  - 111
EP  - 111
PB  - BIOMED CENTRAL LTD
SN  - 17558794
KW  - intellectual disability
KW  - developmental delay
KW  - microdeletion
KW  - microduplication
KW  - CNV
KW  - array CGH
UR  - https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0559-7
L2  - https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0559-7
N2  - Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.
ER  -

WAYHELOVÁ, Markéta, Jan SMETANA, Vladimíra VALLOVÁ, Eva HLADÍLKOVÁ, Hana FILKOVÁ, Marta HANÁKOVÁ, Marcela VILÉMOVÁ, Petra NIKOLOVÁ, Barbora GROMESOVÁ, Renata GAILLYOVÁ and Petr KUGLÍK. The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay. \textit{BMC MEDICAL GENOMICS}. LONDON: BIOMED CENTRAL LTD, 2019, vol.~12, No~1, p.~111-121. ISSN~1755-8794. Available from: https://dx.doi.org/10.1186/s12920-019-0559-7.

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