Searching for transposable elements in hematological malignancies

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F19%3A00072426" target="_blank" >RIV/65269705:_____/19:00072426 - isvavai.cz</a>

Výsledek na webu

<a href="http://phdretreat.ceitec.cz/joint-retreat-2019/" target="_blank" >http://phdretreat.ceitec.cz/joint-retreat-2019/</a>

DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Searching for transposable elements in hematological malignancies

Popis výsledku v původním jazyce

Transposable elements, or transposons, are DNA units present in eukaryotic organisms in a broad diversity of their structures. They have played an important role in evolution of many genomes. In the human genome, the vast majority of transposons is represented by retroelements (REs) that can integrate new copies through RNA-mediated mechanisms. The long interspersed nucleic elements (LINE-1 or L1) utilize a &quot;copy-and-paste&quot; mechanism to retrotranspose copies into new genomic loci. Active L1 retrotransposons also drive retrotransposition of other mobile DNAs, namely, Alu, short interspersed elements (SINEs), and SVA transposons. Recent findings imply that genomic instability of cancer is associated with transposon reactivation. The main goal of our research is to explore RE activity in different types of hematological malignancies. To identify tumor-specific RE insertions, we adopted a protocol based on high-throughput sequencing of amplicons containing a part of AluYa5, Alu-Ya8 or L1-HS insertions, and their adjacent genomic regions. By using unique molecular identifiers, we aim to estimate the percentage of cancer cells bearing each particular insertion. We performed a pilot experiment on 42 tumornormal sample pairs from patients with chronic lymphocytic leukemia, acute lymphoblastic leukemia, and myelodysplastic syndrome. The libraries were sequenced on Illumina NextSeq and obtained sequences are currently subjected to an in-house bioinformatics pipeline for identification of somatic RE insertions.

Název v anglickém jazyce

Searching for transposable elements in hematological malignancies

Popis výsledku anglicky

Transposable elements, or transposons, are DNA units present in eukaryotic organisms in a broad diversity of their structures. They have played an important role in evolution of many genomes. In the human genome, the vast majority of transposons is represented by retroelements (REs) that can integrate new copies through RNA-mediated mechanisms. The long interspersed nucleic elements (LINE-1 or L1) utilize a &quot;copy-and-paste&quot; mechanism to retrotranspose copies into new genomic loci. Active L1 retrotransposons also drive retrotransposition of other mobile DNAs, namely, Alu, short interspersed elements (SINEs), and SVA transposons. Recent findings imply that genomic instability of cancer is associated with transposon reactivation. The main goal of our research is to explore RE activity in different types of hematological malignancies. To identify tumor-specific RE insertions, we adopted a protocol based on high-throughput sequencing of amplicons containing a part of AluYa5, Alu-Ya8 or L1-HS insertions, and their adjacent genomic regions. By using unique molecular identifiers, we aim to estimate the percentage of cancer cells bearing each particular insertion. We performed a pilot experiment on 42 tumornormal sample pairs from patients with chronic lymphocytic leukemia, acute lymphoblastic leukemia, and myelodysplastic syndrome. The libraries were sequenced on Illumina NextSeq and obtained sequences are currently subjected to an in-house bioinformatics pipeline for identification of somatic RE insertions.

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

30205 - Hematology

Projekt

<a href="/cs/project/GA19-11299S" target="_blank" >GA19-11299S: Úloha transpozibilních elementů u hematologických malignit</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů