Shaikh Abdul Rehman Khalil, Ujjan Ikram, Irfan Muhammad, Naz Arshi, Shamsi Tahir, Khan Muhammad Tariq Masood, Shakeel Muhammad
Department of Pathology, Liaquat University of Medical & Health Sciences Jamshoro, Hyderabad, Sindh, Pakistan.
Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine & Drug Research, University of Karachi, Karachi, Sindh, Pakistan.
PeerJ. 2021 Feb 9;9:e10678. doi: 10.7717/peerj.10678. eCollection 2021.
The tet oncogene family member 2 () gene has been reported to be involved in DNA methylation and epigenetic regulation in acute myeloid leukemia (AML). Various studies have proven functional role of mutations in AML. We herein studied the frequency and genotype-phenotype correlation of gene in AML patients in Sindh, Pakistan.
The current study was carried out at Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan, in collaboration with National Institute of Blood Disease & Bone Marrow Transplant, Karachi, Pakistan, during the period from June 2019 to June 2020. A total of 130 patients diagnosed with AML were screened for mutations. Whole exome sequencing of 14 individuals was carried out to find the genetic variants in gene. The pathogenicity of the variants was predicted by SIFT, PolyPhen2, Mutation Taster and CADD Phred scores. The allele frequency of the variants was compared with global population using 1000 genomes project and Exome Aggregation Consortium (ExAC). Furthermore, exon 3 and exon 5 of the gene were sequenced by using Sanger sequencing. The findings were correlated with subtypes of AML and corresponding karyotypes.
Through the exome sequencing, 17 genetic variants (13 SNPs and four indels) were identified in 14 individuals. Of these, four variants that is, one frameshift deletion, one frameshift insertion and two nonsense variants were novel and not present in dbSNP151 database. Three novel variants were found in exon 3 including two frameshift variants that is, p.T395fs and G494fs, predicted as deleterious by CADD Phred scores, and one stop-gain variant (p.G898X) predicted as deleterious by Mutation Taster and CADD Phred scores. One novel non sense variant (p.Q1191X) was found in the exon 5 predicted as deleterious by SIFT, Mutation Taster and CADD Phred scores. Sanger sequencing analysis revealed one novel deletion at g105233851: del.TAGATAGA, and one novel SNP g;105233861 T>G identified in the gene. Majority of the exon 3 mutations were seen in the patients diagnosed with AML with maturation, and had a normal karyotype.
mutations were identified in around 16% of the total patients of our study indicating other mechanisms being involved in pathophysiology of AML in this cohort. The mutations provide a prognostic value in determining AML classification.
据报道，tet癌基因家族成员2（）基因参与急性髓系白血病（AML）的DNA甲基化和表观遗传调控。多项研究证实了AML中突变的功能作用。我们在此研究了巴基斯坦信德省AML患者基因的频率及基因型 - 表型相关性。
本研究于2019年6月至2020年6月期间，在巴基斯坦詹姆肖罗的利亚卡特医学与健康科学大学与巴基斯坦卡拉奇的国家血液疾病与骨髓移植研究所合作开展。共对130例确诊为AML的患者进行了突变筛查。对14名个体进行全外显子组测序以发现基因中的遗传变异。通过SIFT、PolyPhen2、Mutation Taster和CADD Phred评分预测变异的致病性。使用千人基因组计划和外显子组聚合联盟（ExAC）将变异的等位基因频率与全球人群进行比较。此外，使用桑格测序法对基因的外显子3和外显子5进行测序。研究结果与AML亚型及相应核型相关。
通过外显子组测序，在14名个体中鉴定出17个遗传变异（13个单核苷酸多态性和4个插入缺失）。其中，4个变异，即1个移码缺失、1个移码插入和2个无义变异是新发现的，不存在于dbSNP151数据库中。在外显子3中发现了3个新变异，包括2个移码变异，即p.T395fs和G494fs，CADD Phred评分预测为有害，以及1个终止密码子获得变异（p.G898X），Mutation Taster和CADD Phred评分预测为有害。在外显子5中发现1个新的无义变异（p.Q1191X），SIFT、Mutation Taster和CADD Phred评分预测为有害。桑格测序分析在基因中发现1个新的缺失g105233851: del.TAGATAGA和1个新的单核苷酸多态性g;105233861 T>G。外显子3的突变大多见于诊断为成熟型AML且核型正常的患者。
在我们研究的所有患者中，约16%发现了突变，表明该队列中AML的病理生理学还涉及其他机制。突变在确定AML分类方面具有预后价值。
