JAK2 haplotype is a major risk factor for the development of myeloproliferative neoplasms

Abstract

Chronic myeloproliferative neoplasms (MPNs) are a group of related conditions characterized by the overproduction of cells from one or more myeloid lineages. More than 95% of cases of polycythemia vera, and roughly half of essential thrombocythemia and primary myelofibrosis acquire a unique somatic 1849G>T JAK2 mutation (encoding V617F) that is believed to be a critical driver of excess proliferation. We report here that JAK2(V617F)-associated disease is strongly associated with a specific constitutional JAK2 haplotype, designated 46/1, in all three disease entities compared to healthy controls (polycythemia vera, n = 192, P = 2.9 x 10(-16); essential thrombocythemia, n = 78, P = 8.2 x 10(-9) and myelofibrosis, n = 41, P = 8.0 x 10(-5)). Furthermore, JAK2(V617F) specifically arises on the 46/1 allele in most cases. The 46/1 JAK2 haplotype thus predisposes to the development of JAK2(V617F)-associated MPNs (OR = 3.7; 95% CI = 3.1-4.3) and provides a model whereby a constitutional genetic factor is associated with an increased risk of acquiring a specific somatic mutation.

Figure 1

Allele distortions due to aUPD enable direct reading of JAK2 haplotypes. (a) The JAK2^V617F mutation (indicated by an asterisk) and flanking SNPs are reduced to homozygosity in a proportion of cells following mitotic recombination. (b) SNPs and JAK2^V617F were quantified by pyrosequencing. In many cases that harbored a homozygous JAK2^V617F clone, it was possible to directly read the haplotype on which the mutation arose by the finding that one allele at each SNP predominated (allelic ratio ≥0.6, for example, cases E659, E2433 and E2513). In cases with a homozygous clone and %V617F <90%, it was usually possible to read the residual haplotype (that is, the haplotype of the chromosome that had not acquired JAK2^V617F) by the finding of allelic ratios between 0.1–0.4 (for example, cases E2433 and E2513). Where the homozygous clone was small or nonexistent (most cases with %V617F <60%), neither the JAK2^V617F nor wild-type haplotype could be read (for example, case E1186).

Figure 2

SNPs, haplotypes and LD around JAK2. (a) The nine most common JAK2 haplotypes in the UK population. The 14 SNPs in bold were analyzed by the WTCCC in 1,500 blood donors from which the frequencies were determined; asterisks indicate SNPs that tag 46/1, which are highlighted in gray. rs78644782, rs10124001 and rs10758669 are immediately upstream of JAK2; all other SNPs are within JAK2 introns. (b) LD in the JAK2 region (HapMap data release 23a/phase II March 2008).

Figure 3

Familial polycythemia vera pedigree. The two affected individuals (UPNs 534 and 533) are shown as black circles. The genotype for rs12340895 is shown (G = 46/1 allele; C = non-46/1 allele), as is the %V617F in affected cases. Allele-specific PCR for UPN 534 showed that JAK2^V617F arose on the 46/1 allele. All other individuals had normal blood counts and were negative for JAK2^V617F, PRV1 overexpression and endogenous erythroid colony growth.

Figure 4

Association between JAK2 haplotype and numbers of hemopoietic colonies. CFU-GM and BFU-E colony growth per 4 × 10⁵ peripheral blood mononuclear cells from 56 healthy controls that were 46/1 nullizygous (C/C at rs12340895, n = 30) or had at least one 46/1 allele (G/C, n = 21; or G/G, n = 5). Box plots illustrate the 95% range (vertical lines), median (horizontal lines) and interquartile range (boxes). Colony numbers were compared by the Mann-Whitney U test.