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|Title:||Relationship between the germline polymorphisms and somatic mutations in the JAK2 locus in Chinese patients with myeloproliferative neoplasms||Authors:||Koh, Su Pin||Advisors:||Yung, Benjamin (HTI)
Yip, Shea-ping (HTI)
Bone marrow -- Tumors
Disease susceptibility -- Genetic aspects
|Issue Date:||2015||Publisher:||The Hong Kong Polytechnic University||Abstract:||Myeloproliferative neoplasms (MPNs) manifest as a group of haematological malignancies characterised by a somatic mutation (JAK2 V617F) that causes the bone marrow to produce too many blood cells. This mutation is found in polycythaemia vera (~95%), essential thrombocythaemia and primary myelofibrosis (both ~50%) and is considered as a major genetic factor contributing to the development of these MPNs. Within my study period, there is no genetic association study of MPN in the Hong Kong population. In this study, I aimed at investigating the relationship between germline JAK2 polymorphisms and MPNs in Hong Kong Chinese to find causal variants that contribute to MPNs. In part I of this thesis, 19 tag single nucleotide polymorphisms (SNPs) within the JAK2 locus were analysed in 172 MPN patients and 470 healthy controls. Three of these 19 SNPs defined the reported JAK2 46/1 haplotype: rs10974944, rs12343867 and rs12340895. Allele and haplotype frequencies were compared between the patients and controls by logistic regression with adjustment for sex and age. Permutation test was used to correct for multiple comparisons. With significant findings from the 19 SNPs, I then examined 76 additional SNPs across the 148.7-kb region of JAK2 via imputation with the SNP data from the 1000 Genomes Project. This is the first MPN study that employed SNP imputation in the data analysis. In single-marker analysis, 15 SNPs showed association with JAK2 V617F-positive MPNs (n=128). Exhaustive variable-sized sliding-window haplotype analysis identified 184 haplotypes showing significant differences (P<0.05) in frequencies between patients and controls even after multiple-testing correction. However, single-marker alleles exhibited the strongest association with V617F-positive MPNs and among all MPNs. In local Hong Kong Chinese, the strongest signal came from rs12342421: asymptotic P=3.76×10⁻¹⁵, empirical P=2.00×10⁻⁵ for 50,000 permutations, OR=3.55 for the minor allele C, and 95% CI, 2.59-4.87. This SNP was also found by conditional logistic regression to contribute an independent effect in significant haplotype windows, and its role was not changed even with the imputation of additional 76 SNPs. In silico analysis suggested that several transcription factors might bind to rs12342421. Further functional validation is necessary to prove its involvement in the pathogenesis of MPNs.
Part II of this study is the first meta-analysis assessing the relationship between JAK2 polymorphism and the risk of MPNs, within my study period. Significant association was observed between JAK2 risk alleles and MPNs particularly the V617F-positive cohort, and to a lesser extent the V617F-negative MPNs but the exact mechanism of how the JAK2 polymorphisms affect MPNs was not explored and thus is still unknown. Further research looking for the true causal variants between JAK2 polymorphisms and MPNs is demanded. Large sample clinical studies should be carried out to verify more risk factors in order to make early detection and prevention at the gene level possible. However, sample recruitment was beyond the control of the study. International collaboration may increase the power to study and detect rare variants if any. Based on the results generated from part I and II of this study, we hypothesised that there are JAK2 disease-causing variants that may remain untyped in the current genotyping approach. Based on our association results from case-control study, Lo-usZoom software identified two recombination hotspots covering a region of 330kb (including 142kb of JAK2). Therefore, finer scale deep sequencing analysis was performed to explore the undiscovered variants which may be the real causal variants. The 330kb of JAK2 gene and the coding exons (all isoforms) of eight MPN-associated genes including 50bp upstream and downstream of the regions were targeted by a custom SeqCap EZ Choice Library from Roche NimbleGen. In total, 121 regions were targeted comprising 401.324 kb of target sequence. Samples from 48 MPN patients and 48 sex- and age-matched controls were sequenced on the Illumina's MiSeq benchtop sequencer. QC filters were applied to remove poor sequencing reads using Illumina internal platforms and GATK. A total of 532 variants were found. NGS and genotyping together with imputation (part I & II of this project) detected strong signal from intronic SNPs within the recombination hotspots. Consistent results from these studies further strengthen our hypothesis that rs12342421 (S8) and other strongly associated polymorphisms, are in strong LD with some untyped causal variants that are predisposing to MPN. Further functional validation is necessary to prove the involvement of such variants in the pathogenesis of MPN. In the long run, future studies on larger sample cohort may give further insight on the pathogenesis of V617F-positive and -negative MPNs.
|Description:||xxii, 313 pages : color illustrations
PolyU Library Call No.: [THS] LG51 .H577P HTI 2015 Koh
|URI:||http://hdl.handle.net/10397/71565||Rights:||All rights reserved.|
|Appears in Collections:||Thesis|
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