Clinically relevant copy-number variants in exome sequencing
data of patients with dystonia

J 2021

Clinically relevant copy-number variants in exome sequencing data of patients with dystonia

ZECH, M., S. BOESCH, M. SKORVANEK, J. NECPAL, J. SVANTNEROVA et. al.

Basic information

Original name

Clinically relevant copy-number variants in exome sequencing data of patients with dystonia

Authors

ZECH, M. (guarantor), S. BOESCH, M. SKORVANEK, J. NECPAL, J. SVANTNEROVA, M. WAGNER, Y. DINCER, A. SADR-NABAVI, T. SERRANOVA, Irena REKTOROVÁ (203 Czech Republic, belonging to the institution), P. HAVRANKOVA (203 Czech Republic), S. GANAI, A. MOSEJOVA, I. PRIHODOVA (203 Czech Republic), J. SARLAKOVA (203 Czech Republic), K. KULCSAROVA, O. ULMANOVA (203 Czech Republic), K. BECHYNE, M. OSTROZOVICOVA, V. HAN, J. R. VENTOSA, M. SHARIATI, A. SHOEIBI, S. WEBER, B. MOLLENHAUER, C. TRENKWALDER, R. BERUTTI, T. M. STROM, A. CEBALLOS-BAUMANN, V. MALL, B. HASLINGER, R. JECH (203 Czech Republic) and J. WINKELMANN

Edition

PARKINSONISM & RELATED DISORDERS, OXFORD, ELSEVIER SCI LTD, 2021, 1353-8020

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30210 Clinical neurology

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: 4.402

RIV identification code

RIV/00216224:14110/21:00121363

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1016/j.parkreldis.2021.02.013

UT WoS

000628766400001

Keywords in English

Copy-number variant; Dystonia; Read-depth analysis; Diagnostic yield

Abstract

V originále

Introduction: Next-generation sequencing is now used on a routine basis for molecular testing but studies on copy-number variant (CNV) detection from next-generation sequencing data are underrepresented. Utilizing an existing whole-exome sequencing (WES) dataset, we sought to investigate the contribution of rare CNVs to the genetic causality of dystonia. Methods: The CNV read-depth analysis tool ExomeDepth was applied to the exome sequences of 953 unrelated patients with dystonia (600 with isolated dystonia and 353 with combined dystonia; 33% with additional neurological involvement). We prioritized rare CNVs that affected known disease genes and/or were known to be associated with defined microdeletion/microduplication syndromes. Pathogenicity assessment of CNVs was based on recently published standards of the American College of Medical Genetics and Genomics and the Clinical Genome Resource. Results: We identified pathogenic or likely pathogenic CNVs in 14 of 953 patients (1.5%). Of the 14 different CNVs, 12 were deletions and 2 were duplications, ranging in predicted size from 124bp to 17 Mb. Within the deletion intervals, BRPF1, CHD8, DJ1, EFTUD2, FGF14, GCH1, PANK2, SGCE, UBE3A, VPS16, WARS2, and WDR45 were determined as the most clinically relevant genes. The duplications involved chromosomal regions 6q21-q22 and 15q11-q13. CNV analysis increased the diagnostic yield in the total cohort from 18.4% to 19.8%, as compared to the assessment of single-nucleotide variants and small insertions and deletions alone. Conclusions: WES-based CNV analysis in dystonia is feasible, increases the diagnostic yield, and should be combined with the assessment of single-nucleotide variants and small insertions and deletions.

Links

825575, interní kód MU

Name: European Joint Programme on Rare Diseases (Acronym: EJP RD)

Investor: European Union, Health, demographic change and wellbeing (Societal Challenges)

Citovat

ZECH, M., S. BOESCH, M. SKORVANEK, J. NECPAL, J. SVANTNEROVA, M. WAGNER, Y. DINCER, A. SADR-NABAVI, T. SERRANOVA, Irena REKTOROVÁ, P. HAVRANKOVA, S. GANAI, A. MOSEJOVA, I. PRIHODOVA, J. SARLAKOVA, K. KULCSAROVA, O. ULMANOVA, K. BECHYNE, M. OSTROZOVICOVA, V. HAN, J. R. VENTOSA, M. SHARIATI, A. SHOEIBI, S. WEBER, B. MOLLENHAUER, C. TRENKWALDER, R. BERUTTI, T. M. STROM, A. CEBALLOS-BAUMANN, V. MALL, B. HASLINGER, R. JECH and J. WINKELMANN. Clinically relevant copy-number variants in exome sequencing data of patients with dystonia. PARKINSONISM & RELATED DISORDERS. OXFORD: ELSEVIER SCI LTD, 2021, vol. 84, MAR 2021, p. 129-134. ISSN 1353-8020. Available from: https://dx.doi.org/10.1016/j.parkreldis.2021.02.013.

@article{1758063,
   author = {Zech, M. and Boesch, S. and Skorvanek, M. and Necpal, J. and Svantnerova, J. and Wagner, M. and Dincer, Y. and SadrandNabavi, A. and Serranova, T. and Rektorová, Irena and Havrankova, P. and Ganai, S. and Mosejova, A. and Prihodova, I. and Sarlakova, J. and Kulcsarova, K. and Ulmanova, O. and Bechyne, K. and Ostrozovicova, M. and Han, V. and Ventosa, J. R. and Shariati, M. and Shoeibi, A. and Weber, S. and Mollenhauer, B. and Trenkwalder, C. and Berutti, R. and Strom, T. M. and CeballosandBaumann, A. and Mall, V. and Haslinger, B. and Jech, R. and Winkelmann, J.},
   article_location = {OXFORD},
   article_number = {MAR 2021},
   doi = {http://dx.doi.org/10.1016/j.parkreldis.2021.02.013},
   keywords = {Copy-number variant; Dystonia; Read-depth analysis; Diagnostic yield},
   language = {eng},
   issn = {1353-8020},
   journal = {PARKINSONISM & RELATED DISORDERS},
   title = {Clinically relevant copy-number variants in exome sequencing data of patients with dystonia},
   url = {https://www.sciencedirect.com/science/article/pii/S1353802021000547?via%3Dihub},
   volume = {84},
   year = {2021}
}

TY  - JOUR
ID  - 1758063
AU  - Zech, M. - Boesch, S. - Skorvanek, M. - Necpal, J. - Svantnerova, J. - Wagner, M. - Dincer, Y. - Sadr-Nabavi, A. - Serranova, T. - Rektorová, Irena - Havrankova, P. - Ganai, S. - Mosejova, A. - Prihodova, I. - Sarlakova, J. - Kulcsarova, K. - Ulmanova, O. - Bechyne, K. - Ostrozovicova, M. - Han, V. - Ventosa, J. R. - Shariati, M. - Shoeibi, A. - Weber, S. - Mollenhauer, B. - Trenkwalder, C. - Berutti, R. - Strom, T. M. - Ceballos-Baumann, A. - Mall, V. - Haslinger, B. - Jech, R. - Winkelmann, J.
PY  - 2021
TI  - Clinically relevant copy-number variants in exome sequencing data of patients with dystonia
JF  - PARKINSONISM & RELATED DISORDERS
VL  - 84
IS  - MAR 2021
SP  - 129-134
EP  - 129-134
PB  - ELSEVIER SCI LTD
SN  - 13538020
KW  - Copy-number variant
KW  - Dystonia
KW  - Read-depth analysis
KW  - Diagnostic yield
UR  - https://www.sciencedirect.com/science/article/pii/S1353802021000547?via%3Dihub
N2  - Introduction: Next-generation sequencing is now used on a routine basis for molecular testing but studies on copy-number variant (CNV) detection from next-generation sequencing data are underrepresented. Utilizing an existing whole-exome sequencing (WES) dataset, we sought to investigate the contribution of rare CNVs to the genetic causality of dystonia. Methods: The CNV read-depth analysis tool ExomeDepth was applied to the exome sequences of 953 unrelated patients with dystonia (600 with isolated dystonia and 353 with combined dystonia; 33% with additional neurological involvement). We prioritized rare CNVs that affected known disease genes and/or were known to be associated with defined microdeletion/microduplication syndromes. Pathogenicity assessment of CNVs was based on recently published standards of the American College of Medical Genetics and Genomics and the Clinical Genome Resource. Results: We identified pathogenic or likely pathogenic CNVs in 14 of 953 patients (1.5%). Of the 14 different CNVs, 12 were deletions and 2 were duplications, ranging in predicted size from 124bp to 17 Mb. Within the deletion intervals, BRPF1, CHD8, DJ1, EFTUD2, FGF14, GCH1, PANK2, SGCE, UBE3A, VPS16, WARS2, and WDR45 were determined as the most clinically relevant genes. The duplications involved chromosomal regions 6q21-q22 and 15q11-q13. CNV analysis increased the diagnostic yield in the total cohort from 18.4% to 19.8%, as compared to the assessment of single-nucleotide variants and small insertions and deletions alone. Conclusions: WES-based CNV analysis in dystonia is feasible, increases the diagnostic yield, and should be combined with the assessment of single-nucleotide variants and small insertions and deletions.
ER  -

ZECH, M., S. BOESCH, M. SKORVANEK, J. NECPAL, J. SVANTNEROVA, M. WAGNER, Y. DINCER, A. SADR-NABAVI, T. SERRANOVA, Irena REKTOROVÁ, P. HAVRANKOVA, S. GANAI, A. MOSEJOVA, I. PRIHODOVA, J. SARLAKOVA, K. KULCSAROVA, O. ULMANOVA, K. BECHYNE, M. OSTROZOVICOVA, V. HAN, J. R. VENTOSA, M. SHARIATI, A. SHOEIBI, S. WEBER, B. MOLLENHAUER, C. TRENKWALDER, R. BERUTTI, T. M. STROM, A. CEBALLOS-BAUMANN, V. MALL, B. HASLINGER, R. JECH and J. WINKELMANN. Clinically relevant copy-number variants in exome sequencing data of patients with dystonia. \textit{PARKINSONISM \&{} RELATED DISORDERS}. OXFORD: ELSEVIER SCI LTD, 2021, vol.~84, MAR 2021, p.~129-134. ISSN~1353-8020. Available from: https://dx.doi.org/10.1016/j.parkreldis.2021.02.013.

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