ARResT/AssignSubsets: a novel application for robust
subclassification of chronic lymphocytic leukemia based on B
cell receptor IG stereotypy

J 2015

ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy

BYSTRÝ, Vojtěch; Andreas AGATHANGELIDIS; Vasileios BIKOS; Lesley Ann SUTTON; Panagiotis BALIAKAS et al.

Základní údaje

Originální název

ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy

Autoři

BYSTRÝ, Vojtěch; Andreas AGATHANGELIDIS; Vasileios BIKOS; Lesley Ann SUTTON; Panagiotis BALIAKAS; Anastasia HADZIDIMITRIOU; Kostas STAMATOPOULOS a Nikos DARZENTAS

Vydání

Bioinformatics, Oxford, Oxford University Press, 2015, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.766

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/15:00086128

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

PATHOGENETIC IMPLICATIONS; IMMUNOGLOBULIN; GENES

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 4. 2016 14:46, Mgr. Eva Špillingová

Anotace

V originále

Motivation: An ever-increasing body of evidence supports the importance of B cell receptor immunoglobulin (BcR IG) sequence restriction, alias stereotypy, in chronic lymphocytic leukemia (CLL). This phenomenon accounts for similar to 30% of studied cases, one in eight of which belong to major subsets, and extends beyond restricted sequence patterns to shared biologic and clinical characteristics and, generally, outcome. Thus, the robust assignment of new cases to major CLL subsets is a critical, and yet unmet, requirement. Results: We introduce a novel application, ARResT/AssignSubsets, which enables the robust assignment of BcR IG sequences from CLL patients to major stereotyped subsets. ARResT/AssignSubsets uniquely combines expert immunogenetic sequence annotation from IMGT/V-QUEST with curation to safeguard quality, statistical modeling of sequence features from more than 7500 CLL patients, and results from multiple perspectives to allow for both objective and subjective assessment. We validated our approach on the learning set, and evaluated its real-world applicability on a new representative dataset comprising 459 sequences from a single institution.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

7E13008, projekt VaV

Název: Next Generation Sequencing Platform for Targeted Personalized Therapy of Leukemia (Akronym: NGS-PTL)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Next Generation Sequencing Platform for Targeted Personalized Therapy of Leukemia

Citovat

BYSTRÝ, Vojtěch; Andreas AGATHANGELIDIS; Vasileios BIKOS; Lesley Ann SUTTON; Panagiotis BALIAKAS; Anastasia HADZIDIMITRIOU; Kostas STAMATOPOULOS a Nikos DARZENTAS. ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. Bioinformatics. Oxford: Oxford University Press, 2015, roč. 31, č. 23, s. 3844-3846. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btv456.

@article{1331637,
   author = {Bystrý, Vojtěch and Agathangelidis, Andreas and Bikos, Vasileios and Sutton, Lesley Ann and Baliakas, Panagiotis and Hadzidimitriou, Anastasia and Stamatopoulos, Kostas and Darzentas, Nikos},
   article_location = {Oxford},
   article_number = {23},
   doi = {https://doi.org/10.1093/bioinformatics/btv456},
   keywords = {PATHOGENETIC IMPLICATIONS; IMMUNOGLOBULIN; GENES},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy},
   url = {http://bioinformatics.oxfordjournals.org/content/31/23/3844},
   volume = {31},
   year = {2015}
}

TY  - JOUR
ID  - 1331637
AU  - Bystrý, Vojtěch - Agathangelidis, Andreas - Bikos, Vasileios - Sutton, Lesley Ann - Baliakas, Panagiotis - Hadzidimitriou, Anastasia - Stamatopoulos, Kostas - Darzentas, Nikos
PY  - 2015
TI  - ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy
JF  - Bioinformatics
VL  - 31
IS  - 23
SP  - 3844-3846
EP  - 3844-3846
PB  - Oxford University Press
SN  - 13674803
KW  - PATHOGENETIC IMPLICATIONS
KW  - IMMUNOGLOBULIN
KW  - GENES
UR  - http://bioinformatics.oxfordjournals.org/content/31/23/3844
L2  - http://bioinformatics.oxfordjournals.org/content/31/23/3844
N2  - Motivation: An ever-increasing body of evidence supports the importance of B cell receptor immunoglobulin (BcR IG) sequence restriction, alias stereotypy, in chronic lymphocytic leukemia (CLL). This phenomenon accounts for similar to 30% of studied cases, one in eight of which belong to major subsets, and extends beyond restricted sequence patterns to shared biologic and clinical characteristics and, generally, outcome. Thus, the robust assignment of new cases to major CLL subsets is a critical, and yet unmet, requirement. Results: We introduce a novel application, ARResT/AssignSubsets, which enables the robust assignment of BcR IG sequences from CLL patients to major stereotyped subsets. ARResT/AssignSubsets uniquely combines expert immunogenetic sequence annotation from IMGT/V-QUEST with curation to safeguard quality, statistical modeling of sequence features from more than 7500 CLL patients, and results from multiple perspectives to allow for both objective and subjective assessment. We validated our approach on the learning set, and evaluated its real-world applicability on a new representative dataset comprising 459 sequences from a single institution.
ER  -

BYSTRÝ, Vojtěch; Andreas AGATHANGELIDIS; Vasileios BIKOS; Lesley Ann SUTTON; Panagiotis BALIAKAS; Anastasia HADZIDIMITRIOU; Kostas STAMATOPOULOS a Nikos DARZENTAS. ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. \textit{Bioinformatics}. Oxford: Oxford University Press, 2015, roč.~31, č.~23, s.~3844-3846. ISSN~1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btv456.

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