Genetic association between germline JAK2polymorphisms and myeloproliferative neoplasms in Hong Kong Chinese population: a case–control study

Table 2 Exhaustive haplotype analyses for variable-sized sliding windows across 19 genotyped JAK2 SNPs for V617F -positive MPNs ^a

		SW with Omnibus Test P _emp < .05			Most Significant Omnibus Test
SNPs, No.	SWs, No.	SWs, No.	First SW	Last SW	SW	P _asym	P _emp
1	19	14 ^b	S1	S18	S8 ^d	3.76 × 10⁻¹⁵	2.00 × 10⁻⁵
2	18	17 ^c	S1…S2	S18…S19	S8…S9	2.13 × 10⁻¹⁴	2.00 × 10⁻⁵
3	17	17	S1…S3	S17…S19	S8…S10	6.33 × 10⁻¹⁴	2.00 × 10⁻⁵
4	16	16	S1…S4	S16…S19	S7…S10	8.25 × 10⁻¹³	2.00 × 10⁻⁵
5	15	15	S1…S5	S15…S19	S8…S12	4.45 × 10⁻¹²	2.00 × 10⁻⁵
6	14	14	S1…S6	S14…S19	S8…S13	2.75 × 10⁻¹²	2.00 × 10⁻⁵
7	13	13	S1…S7	S13…S19	S8…S14	2.21 × 10⁻¹²	2.00 × 10⁻⁵
8	12	12	S1…S8	S12…S19	S8…S15	9.00 × 10⁻¹²	2.00 × 10⁻⁵
9	11	11	S1…S9	S11…S19	S6…S14	2.38 × 10⁻¹¹	2.00 × 10⁻⁵
10	10	10	S1…S10	S10…S19	S6…S15	9.09 × 10⁻¹²	2.00 × 10⁻⁵
11	9	9	S1…S11	S9…S19	S6…S16	3.03 × 10⁻¹¹	2.00 × 10⁻⁵
12	8	8	S1…S12	S8…S19	S6…S17	6.69 × 10⁻¹¹	2.00 × 10⁻⁵
13	7	7	S1…S13	S7…S19	S6…S18	1.21 × 10⁻¹⁰	2.00 × 10⁻⁵
14	6	6	S1…S14	S6…S19	S6…S19	2.60 × 10⁻¹⁰	2.00 × 10⁻⁵
15	5	5	S1…S15	S5…S19	S4…S18	3.02 × 10⁻⁹	2.00 × 10⁻⁵
16	4	4	S1…S16	S4…S19	S4…S19	1.97 × 10⁻⁹	2.00 × 10⁻⁵
17	3	3	S1…S17	S3…S19	S3…S19	2.74 × 10⁻⁹	2.00 × 10⁻⁵
18	2	2	S1…S18	S2…S19	S2…S19	2.96 × 10⁻⁸	2.00 × 10⁻⁵
19	1	1	S1…S19	S1…S19	S1…S19	6.72 × 10⁻⁸	2.00 × 10⁻⁵

Abbreviations: SNP, single nucleotide polymorphism; SW, sliding window; P _asym, asymptotic P value; P _emp, empirical P value.
^aThe SW is shown as Sx…Sy, where Sx is the first SNP and Sy is the last SNP of the SW for JAK2 gene. Please refer to Table 1 for the identity of the SNP concerned. Each sliding window was tested by an omnibus test adjusted for sex and age (implemented in PLINK). Multiple comparisons were corrected by running 50,000 permutations to give the P _emp value. The smallest P _emp value generated after permutation is the same for all fixed-size SWs (2 × 10⁻⁵); note that the lowest P _emp value achievable with 50,000 permutations is 2 × 10⁻⁵. The most significant results for each fixed-size SW are shown in the three rightmost columns. Note that, among all the 190 SWs tested, S8 always appears in the most significant SW.
^bOf the nineteen SNPs tested, five (S5, S6, S11, S16, and S19) did not give P _emp < 0.05.
^c All the SWs gives P _emp < 0.05 except S5…S6.
^dOf all the 190 SWs tested, S8 (i.e. rs12342421) alone gives the most significant result for association with V617F-positive MPNs.

ISSN: 2730-6844