Solving complex karyotypes in leukemia samples using long-read
sequencing.

a 2023

Solving complex karyotypes in leukemia samples using long-read sequencing.

STRÁNSKÁ, Kamila; Sabina ADAMOVÁ; Michaela BOHÚNOVÁ; Jan SVATOŇ; Karol PÁL et al.

Základní údaje

Originální název

Solving complex karyotypes in leukemia samples using long-read sequencing.

Autoři

Vydání

European Human Genetics Conference (ESHG), Glasgow, United Kingdom, 2023

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

30204 Oncology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/23:00132999

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

long-read sequencing; chronic lymphocytic leukemia

Štítky

NÚVR_CEITEC, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 22. 12. 2025 13:03, Mgr. Petra Trembecká, Ph.D.

Anotace

V originále

Highly complex karyotypes represent an adverse prognostic marker in leukemia samples. Their detailed study is substantive to identify specific genomic defects contributing to the deterioration of the disease course. Methods of classical and molecular cytogenomics are widely used in laboratory diagnostics to detect chromosomal aberrations, but their resolution is limited. We aim to employ Oxford Nanopore whole genome long-read sequencing to decipher cancer genome in difficult and ambiguous cases of chronic lymphocytic leukemia with complex karyotypes. Methods: Complex karyotype cases were identified and characterized using classical (IL-2/CpG-stimulated chromosomal banding) and molecular (24xCyte Multicolor FISH, CytoScan HD Array) cytogenomics. For long-read sequencing, high molecular weight DNA was isolated using chloroform-isopropanol extraction, fragmented using an injection needle, and short DNA fragments were eliminated (SRE XS Kit). The sequencing libraries were prepared using Ligation Sequencing Kit and sequenced on the MinION or PromethION sequencer. Sequences were aligned to the hg19 human genome reference, and structural variants were identified using the split read method, filtered, and annotated. Results/Conclusion: For each patient, we obtained sequencing data enabling 10× (MinION), or >20× (PromethION) average coverage of the genome. We performed a comprehensive comparison of long-read sequencing results with those of classical and molecular cytogenomics and assessed the benefits and shortcomings of long-read sequencing in deciphering the structure of genomic rearrangements in the tested chronic lymphocytic leukemia cases. Long-read sequencing provides more accurate characterization of breakpoints and majority of genome rearrangement events.

Návaznosti

LM2023067, projekt VaV

Název: Národní centrum lékařské genomiky

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, NCLG: Národní centrum lékařské genomiky

MUNI/A/1224/2022, interní kód MU

Název: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit X

Investor: Masarykova univerzita, Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit X

NU21-08-00237, projekt VaV

Název: Pokročilé sekvenační metody pro analýzu strukturních přestaveb nádorového genomu

Investor: Ministerstvo zdravotnictví ČR, Pokročilé sekvenační metody pro analýzu strukturních přestaveb nádorového genomu, Podprogram 1 - standardní

Citovat

STRÁNSKÁ, Kamila; Sabina ADAMOVÁ; Michaela BOHÚNOVÁ; Jan SVATOŇ; Karol PÁL; Eva ONDROUŠKOVÁ; Marie JAROŠOVÁ; Kristýna ZÁVACKÁ; Karolína ČERNOVSKÁ; Jakub Paweł PORC; Filip PARDY; Boris TICHÝ; Šárka POSPÍŠILOVÁ; Jana KOTAŠKOVÁ a Karla PLEVOVÁ. Solving complex karyotypes in leukemia samples using long-read sequencing. In European Human Genetics Conference (ESHG), Glasgow, United Kingdom. 2023.

@proceedings{2360071,
   author = {Stránská, Kamila and Adamová, Sabina and Bohúnová, Michaela and Svatoň, Jan and Pál, Karol and Ondroušková, Eva and Jarošová, Marie and Závacká, Kristýna and Černovská, Karolína and Porc, Jakub Paweł and Pardy, Filip and Tichý, Boris and Pospíšilová, Šárka and Kotašková, Jana and Plevová, Karla},
   booktitle = {European Human Genetics Conference (ESHG), Glasgow, United Kingdom},
   keywords = {long-read sequencing; chronic lymphocytic leukemia},
   language = {eng},
   title = {Solving complex karyotypes in leukemia samples using long-read sequencing.},
   url = {https://eshg2018.floq.live/event/eshg2023/search?objectClass=timeslot&objectId=645954e15d10763cee46ac06&type=detail},
   year = {2023}
}

TY  - CONF
ID  - 2360071
AU  - Stránská, Kamila - Adamová, Sabina - Bohúnová, Michaela - Svatoň, Jan - Pál, Karol - Ondroušková, Eva - Jarošová, Marie - Závacká, Kristýna - Černovská, Karolína - Porc, Jakub Paweł - Pardy, Filip - Tichý, Boris - Pospíšilová, Šárka - Kotašková, Jana - Plevová, Karla
PY  - 2023
TI  - Solving complex karyotypes in leukemia samples using long-read sequencing.
KW  - long-read sequencing
KW  - chronic lymphocytic leukemia
UR  - https://eshg2018.floq.live/event/eshg2023/search?objectClass=timeslot&objectId=645954e15d10763cee46ac06&type=detail
N2  - Highly complex karyotypes represent an adverse prognostic marker in leukemia samples. Their detailed study is substantive to identify specific genomic defects contributing to the deterioration of the disease course. Methods of classical and molecular cytogenomics are widely used in laboratory diagnostics to detect chromosomal aberrations, but their resolution is limited. We aim to employ Oxford Nanopore whole genome long-read sequencing to decipher cancer genome in difficult and ambiguous cases of chronic lymphocytic leukemia with complex karyotypes. Methods: Complex karyotype cases were identified and characterized using classical (IL-2/CpG-stimulated chromosomal banding) and molecular (24xCyte Multicolor FISH, CytoScan HD Array) cytogenomics. For long-read sequencing, high molecular weight DNA was isolated using chloroform-isopropanol extraction, fragmented using an injection needle, and short DNA fragments were eliminated (SRE XS Kit). The sequencing libraries were prepared using Ligation Sequencing Kit and sequenced on the MinION or PromethION sequencer. Sequences were aligned to the hg19 human genome reference, and structural variants were identified using the split read method, filtered, and annotated. Results/Conclusion: For each patient, we obtained sequencing data enabling 10× (MinION), or >20× (PromethION) average coverage of the genome. We performed a comprehensive comparison of long-read sequencing results with those of classical and molecular cytogenomics and assessed the benefits and shortcomings of long-read sequencing in deciphering the structure of genomic rearrangements in the tested chronic lymphocytic leukemia cases. Long-read sequencing provides more accurate characterization of breakpoints and majority of genome rearrangement events.
ER  -

STRÁNSKÁ, Kamila; Sabina ADAMOVÁ; Michaela BOHÚNOVÁ; Jan SVATOŇ; Karol PÁL; Eva ONDROUŠKOVÁ; Marie JAROŠOVÁ; Kristýna ZÁVACKÁ; Karolína ČERNOVSKÁ; Jakub Paweł PORC; Filip PARDY; Boris TICHÝ; Šárka POSPÍŠILOVÁ; Jana KOTAŠKOVÁ a Karla PLEVOVÁ. Solving complex karyotypes in leukemia samples using long-read sequencing. In \textit{European Human Genetics Conference (ESHG), Glasgow, United Kingdom}. 2023.

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