Genome-Wide Association Scan Identifies Candidate Polymorphisms Associated with Differential Response to Anti-TNF Treatment in Rheumatoid Arthritis

Liu, Chunyu; Batliwalla, Franak; Li, Wentian; Lee, Annette; Roubenoff, Ronenn; Beckman, Evan; Khalili, Houman; Damle, Aarti; Kern, Marlena; Furie, Richard; Dupuis, Josée; Plenge, Robert M.; Coenen, Marieke J. H.; Behrens, Timothy W.; Carulli, John P.; Gregersen, Peter K.

doi:10.2119/2008-00056.Liu

Molecular Medicine

Table 2 Sixteen SNPs with smallest P values with permutation exact P values ≤ 0.1

From: Genome-Wide Association Scan Identifies Candidate Polymorphisms Associated with Differential Response to Anti-TNF Treatment in Rheumatoid Arthritis

SNP	Pvalue^a of RelDAS*28	Permut. P value (RelDAS28)	Polymorphism	Allele associated with non-response (allele frequency)	Chr	Physical position	Known genes	Location^c	P value^b non-responders versus good responders (Adjusted)^d	Odds ratio (OR) being non-responder (95% CI)^b
rs983332	0.000005	0.008	A/C	A (0.21)	1	87844401	LMO4	F3U	0.00007 (0.00009)	10.2 (2.6,59.2)
rs928655	0.00003	0.07	A/G	A (0.77)	1	89561595	GBP6	I	0.0009 (0.0004)	5.5 (1.8, 20.2)
rs13393173	0.000004	0.02	A/G	A (0.12)	2	169214598	LASS6	I	0.004 (0.02)	6.8 (1.7,40.3)
rs437943	0.000004	0.1	A/G	G (0.33)	4	35194664	CENTD1	F3U	0.0007 (0.002)	4.6 (1.8,12.3)
rs10945919	0.0000003	0.004	A/G	G (0.32)	6	164157088	QKI	F3U	0.0007 (0.0008)	4.6 (1.8,12.3)
rs854555	0.000002	0.03	A/C	A (0.34)	7	94575042	PON1	I	0.0006 (0.001)	4.6 (1.8,12.3)
rs854548	0.000003	0.06	A/G	A (0.27)	7	94570471	PON1	F3U	0.00004 (0.0003)	8.5 (2.6, 36.5)
rs854547	0.000006	0.1	A/G	A (0.63)	7	94568507	PON1	F3U	0.003 (0.004)	3.6 (1.5,9.3)
rs7046653	0.0000005	0.01	A/G	A (0.26)	9	27480967	IFNK	F5U	0.0004 (0.002)	4.9 (1.8,14.0)
rs868856	0.0000005	0.01	C/T	T (0.26)	9	27479251	MOBKL2B	I	0.0005 (0.002)	4.9 (1.8,14.0)
rs774359	0.0000006	0.01	C/T	C (0.22)	9	27551049	C9orf72	3UTR	0.0005 (0.005)	5.4 (1.9,17.3)
rs2814707	0.000002	0.04	A/G	A (0.22)	9	27526397	MOBKL2B	F5U	0.0006 (0.007)	5.2 (1.8,16.7)
rs3849942	0.000005	0.07	A/G	A (0.21)	9	27533281	C9orf72	F3U	0.001 (0.01)	5.0 (1.7,15.8)
rs6028945	0.0000002	0.003	G/T	T (0.12)	20	38254219	MAFB	F3U	0.0004 (0.006)	11.2 (2.3, 108.1)
rs6138150	0.000003	0.05	C/T	T (0.84)	20	23795009	CST5	F3U	0.0002 (0.002)	11.1 (2.5, 103.3)
rs6071980	0.000003	0.05	C/T	C (0.13)	20	38301990	MAFB	F3U	0.0009 (0.01)	7.6 (1.9,44.6)

^aThese P values were obtained using the continuous relDAS28 as a dependent variable.
^bThese P values or Odds Ratios (95% CI) were obtained from Fisher exact test of 2 × 2 tables of allele frequencies in non-responders versus good responders.
^cF3U: flanking 3′-UTR; F5U: flanking 5′-UTR; I: intron; C: coding; 3UTR: 3′-UTR.
^dChi-square P values after adjusting for population substructure in EIGENSTRAT.

Back to article page

ISSN: 1528-3658

Contact us

Submission enquiries: Access here and click Contact Us
General enquiries: info@biomedcentral.com