Molecular Biology

, Volume 52, Issue 2, pp 200–205 | Cite as

Identification of Fusion Transcripts in Leukеmic Cells by Whole-Transcriptome Sequencing

  • A. Yu. Ikonnikova
  • Yu. I. Ammour
  • A. V. Snezhkina
  • G. S. Krasnov
  • A. V. Kudryavtseva
  • T. V. Nasedkina
Genomics. Transcriptomics
  • 2 Downloads

Abstract

Genetic aberrations in leukemia often lead to the formation of expressed chimeric genes, which should be assessed for proper diagnosis and therapy. Modern methods of molecular diagnostic mainly allow to identify already known fusion genes. RNAseq is an efficient tool for identification of rare and novel chimeric transcripts. Here we present the results of the whole transcriptome analysis of bone marrow samples from five patients with acute myeloblastic leukemia and one, with myelodysplastic syndrome. The wholetranscriptome analysis was performed using Illumina/Solexa approach. We found rare or unknown chimeric transcripts including ETV6-MDS1, MN1-ETV6, OAZ1-PTMA, and MLLT10-GRIA4. Each of these transcripts was confirmed by RT-PCR and Sanger sequencing.

Keywords

massive parallel sequencing fusion genes whole-transcriptome analysis acute leukemia 

Abbreviations

AML

acute myeloid leukemia

CN-AML

cytogenetically normal AML

RT-PCR

reverse transcription-polymerase chain reaction

AF9 (MLLT3)

super elongation complex subunit gene

AF10 (MLLT10)

mixed lineage leukemia, translocated to, 10

AML1

gene of acute myeloid leukemia protein 1

AMPA4 (alpha 4)

glutamate ionotropic receptor AMPA type subunit 4 gene

ASXL1

additional sex combs like 1 transcriptional regulator

CBFA2T3

CBFA2/RUNX1 translocation partner 3 gene

CBFB

core-binding factor beta gene

CEBPA

CCAAT/enhancer-binding protein alpha gene

DHH (desert hedgehog)

gene of the signal protein of Hedgehog family

DNMT3A

DNA methyltransferase-3-alpha gene

ETO (eight twenty-one)

gene of translocation (8;21)

ETV6 (E-twentysix)

gene of specific variant 6 of E26 transformation family

EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit)

gene of histone-lysine-N-methyltransferase

FLT3

gene of fms related tyrosine kinase 3

GLIS2

GLIS family zinc finger 2 protein gene

GRIA4

glutamate ionotropic receptor AMPA-type subunit 4

RP1-170O19.22

gene of axonemal microtubule associated protein RP

GPR128

gene of the G protein-coupled receptor 128

HOXA10

homeobox A10 protein gene

IDH1

cytosolic isocitrate dehydrogenase (NADP(+)) 1 gene

IDH2

mitochondrial isocitrate dehydrogenase (NADP(+)) 2 gene

MDS1

myelodysplasia syndrome 1 gene

MLL

mixed lineage leukemia gene

MN1

gene of transcriptional regulator, meningioma proto-oncogene

MYH11

gene of myosin heavy chain 11

NGS

next-generation sequencing

NPM1

nucleophosmin gene

NUP98

nucleoporin 98

NUSAP1

nucleolar and spindle-associated protein 1 gene

OAZ1

ornithine decarboxylase antizyme 1 gene

PHF23

PHD finger protein 23 gene

PML

promyelocytic leukemia gene

PTMA

gene of prothymosin alpha

RARA1

gene of retinoic acid receptor alpha

RHEBL1

Ras homolog enriched in brain like 1 gene

SEPT6

gene of septin 6

TET2

tet-methylcytosine dioxygenase 2 gene

TFG

TRK-fused gene

WDR6

WD repeat domain 6

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Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • A. Yu. Ikonnikova
    • 1
  • Yu. I. Ammour
    • 2
  • A. V. Snezhkina
    • 1
  • G. S. Krasnov
    • 1
  • A. V. Kudryavtseva
    • 1
  • T. V. Nasedkina
    • 1
    • 2
  1. 1.Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
  2. 2.Federal Research and Clinical Center of Pediatric Hematology, Oncology, and ImmunologyMoscowRussia

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