Systematic analysis of splicing defects in selected primary
immunodeficiencies-related genes

J 2017

Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes

GRODECKÁ, Lucie; Pavla HUJOVÁ; Michal KRAMÁREK; Tereza KRSJAKOVA; Tatiana KOVÁČOVÁ et al.

Základní údaje

Originální název

Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes

Autoři

GRODECKÁ, Lucie; Pavla HUJOVÁ; Michal KRAMÁREK; Tereza KRSJAKOVA; Tatiana KOVÁČOVÁ ; Katarína VONDRÁŠKOVÁ; Barbora RAVCUKOVA; Kristýna HRNČÍŘOVÁ; Přemysl SOUČEK a Tomáš FREIBERGER

Vydání

Clinical Immunology, San Diego, Elsevier Inc. 2017, 1521-6616

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30102 Immunology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.557

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/17:00095654

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

Splicing prediction; Splicing-affecting variants; Cryptic splice sites; Primary immunodeficiencies

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 2. 2018 16:31, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Both variants affecting splice sites and those in splicing regulatory elements (SREs) can impair pre-mRNA splicing, eventually leading to severe diseases. Despite the availability of many prediction tools, prognosis of splicing affection is not trivial, especially when SREs are involved. Here, we present data on 92 in silico-/55 minigene-analysed variants detected in genes responsible for the primary immunodeficiencies development (namely BTIC, CD4OLG, IL2RG, SERPINGI, STAT3, and WAS). Of 20 splicing-affecting variants, 16 affected splice site while 4 disrupted potential SRE. The presence or absence of splicing defects was confirmed in 30 of 32 blood-derived patients' RNAs. Testing prediction tools performance, splice site disruptions and creations were reliably predicted in contrast to SRE-affecting variants for which just ESRseq, Delta HZ(EI)-scores and EX-SKIP predictions showed promising results. Next, we found an interesting pattern in cryptic splice site predictions. These results might help PID-diagnosticians and geneticists cope with potential splicing-affecting variants. (C) 2017 Elsevier Inc. All rights reserved.

Návaznosti

MUNI/A/1183/2015, interní kód MU

Název: Patogeneze a léčba humorální imunodeficiencí

Investor: Masarykova univerzita, Patogeneze a léčba humorální imunodeficiencí, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

NV16-34414A, projekt VaV

Název: Určení genových oblastí náchylných ke vzniku mutací ovlivňujících sestřih mRNA

Citovat

GRODECKÁ, Lucie; Pavla HUJOVÁ; Michal KRAMÁREK; Tereza KRSJAKOVA; Tatiana KOVÁČOVÁ; Katarína VONDRÁŠKOVÁ; Barbora RAVCUKOVA; Kristýna HRNČÍŘOVÁ; Přemysl SOUČEK a Tomáš FREIBERGER. Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes. Clinical Immunology. San Diego: Elsevier Inc., 2017, roč. 180, July, s. 33-44. ISSN 1521-6616. Dostupné z: https://doi.org/10.1016/j.clim.2017.03.010.

@article{1387540,
   author = {Grodecká, Lucie and Hujová, Pavla and Kramárek, Michal and Krsjakova, Tereza and Kováčová, Tatiana and Vondrášková, Katarína and Ravcukova, Barbora and Hrnčířová, Kristýna and Souček, Přemysl and Freiberger, Tomáš},
   article_location = {San Diego},
   article_number = {July},
   doi = {https://doi.org/10.1016/j.clim.2017.03.010},
   keywords = {Splicing prediction; Splicing-affecting variants; Cryptic splice sites; Primary immunodeficiencies},
   language = {eng},
   issn = {1521-6616},
   journal = {Clinical Immunology},
   title = {Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes},
   url = {http://www.sciencedirect.com/science/article/pii/S1521661616305083?via%3Dihub},
   volume = {180},
   year = {2017}
}

TY  - JOUR
ID  - 1387540
AU  - Grodecká, Lucie - Hujová, Pavla - Kramárek, Michal - Krsjakova, Tereza - Kováčová, Tatiana - Vondrášková, Katarína - Ravcukova, Barbora - Hrnčířová, Kristýna - Souček, Přemysl - Freiberger, Tomáš
PY  - 2017
TI  - Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes
JF  - Clinical Immunology
VL  - 180
IS  - July
SP  - 33-44
EP  - 33-44
PB  - Elsevier Inc.
SN  - 15216616
KW  - Splicing prediction
KW  - Splicing-affecting variants
KW  - Cryptic splice sites
KW  - Primary immunodeficiencies
UR  - http://www.sciencedirect.com/science/article/pii/S1521661616305083?via%3Dihub
L2  - http://www.sciencedirect.com/science/article/pii/S1521661616305083?via%3Dihub
N2  - Both variants affecting splice sites and those in splicing regulatory elements (SREs) can impair pre-mRNA splicing, eventually leading to severe diseases. Despite the availability of many prediction tools, prognosis of splicing affection is not trivial, especially when SREs are involved. Here, we present data on 92 in silico-/55 minigene-analysed variants detected in genes responsible for the primary immunodeficiencies development (namely BTIC, CD4OLG, IL2RG, SERPINGI, STAT3, and WAS). Of 20 splicing-affecting variants, 16 affected splice site while 4 disrupted potential SRE. The presence or absence of splicing defects was confirmed in 30 of 32 blood-derived patients' RNAs. Testing prediction tools performance, splice site disruptions and creations were reliably predicted in contrast to SRE-affecting variants for which just ESRseq, Delta HZ(EI)-scores and EX-SKIP predictions showed promising results. Next, we found an interesting pattern in cryptic splice site predictions. These results might help PID-diagnosticians and geneticists cope with potential splicing-affecting variants. (C) 2017 Elsevier Inc. All rights reserved.
ER  -

GRODECKÁ, Lucie; Pavla HUJOVÁ; Michal KRAMÁREK; Tereza KRSJAKOVA; Tatiana KOVÁČOVÁ; Katarína VONDRÁŠKOVÁ; Barbora RAVCUKOVA; Kristýna HRNČÍŘOVÁ; Přemysl SOUČEK a Tomáš FREIBERGER. Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes. \textit{Clinical Immunology}. San Diego: Elsevier Inc., 2017, roč.~180, July, s.~33-44. ISSN~1521-6616. Dostupné z: https://doi.org/10.1016/j.clim.2017.03.010.

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