Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia, BMC Medical Genetics (2017)

Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia

Seong Gu Heo[1], Youngil Koh[2], Jong Kwang Kim[3], Jongsun Jung[4], Hyung-Lae Kim[5], Sung-Soo Yoon[6] and Ji Wan Park[7]

[1]Department of Medical Genetics, College of Medicine, Hallym University / Wide River Institute of Immunology, Seoul National University, [2]Department of Internal Medicine, Seoul National University Hospital, [3]Omics Core Lab., National Cancer Center / The Catholic University, [4]Syntekabio Inc. , [5]Department of Biochemistry, School of Medicine, Ewha Womans University, [6]Department of Internal Medicine, Seoul National University Hospital, [7]Department of Medical Genetics, College of Medicine, Hallym University / http://orcid.org/0000-0003-0840-1696

Abstract

Background:

Acute myeloid leukemia (AML) is a biologically and clinically heterogeneous cancer of the bone marrow that is characterized by the rapid growth of abnormal myeloid cells.

Methods:

We performed a mutational analysis to identify AML somatic mutations using the whole-exome sequencing data of 36 tumor-normal sample pairs from Korean patients with de novo AML. We explored the functional impact of the genes identified in the mutational analyses through an integrated Gene Ontology (GO) and pathway analysis.

Results:

A total of 11 genes, including NEFH (p = 6.27 × 10−13 and q = 1.18 × 10−8) and TMPRSS13 (p = 1.40 × 10−10 and q = 1.32 × 10−6), also demonstrated q values less than 0.1 in 36 Korean AML patients. Five out of the 11 novel genes have previously been reported to be associated with other cancers. Two gene mutations, CEBPA (p = 5.22 ×10−5) and ATXN3 (p = 9.75 × 10−4), showed statistical significance exclusively in the M2 and M3 subtypes of the French-American-British classifications, respectively. A total of 501 genes harbored 478 missense, 22 nonsense, 93 frameshift indels, and/or three stop codon deletions and these gene mutations significantly enriched GO terms for signal transduction (GO:0007165, p = 1.77 × 10−3), plasma membrane (GO:0005886, p = 3.07 × 10−4), and scaffold protein binding (GO:0097110, p = 8.65 × 10−4). The mitogen-activated protein kinase (hsa04010, 7.67 × 10−4 ) was the most enriched Kyoto Encyclopedia of Genes and Genomes pathway.

Conclusions:

Morphological AML subtypes may in part reflect subtype specific patterns of genomic alterations. Following validation, future studies to evaluate the usefulness of these genes in genetic testing for the early diagnosis and prognostic prediction of AML patients would be worthwhile.

Keywords:

Acute myeloid leukemia, Gene ontology, Pathway analysis, Somatic mutation, Subtype-specific mutation, Whole-exome sequencing

🔗 Open Link

http://bmcmedgenet.biomedcentral.com/articles/10.1186/s12881-017-0382-y