Common variation at 3p22.1 and 7p15.3 influences multiple myeloma risk

Abstract

To identify risk variants for multiple myeloma (MM), we conducted a genome-wide association study totaling of 1,675 MM cases and 5,903 controls. We identified risk loci for MM at 3p22.1 (rs1052501, ULK4; odds ratio [OR]=1.32; P=7.47x10^-9) and 7p15.3 (rs4487645, OR=1.38; P=3.33x10^-15). In addition, we observed a promising association at 2p23.3 (rs6746082, OR=1.29; P=1.22x10^-7). Our study reports previously unidentified genomic regions associated with MM risk that may lead to new etiological insights.

Multiple myeloma (MM) is a malignancy of plasma cells primarily located within the bone marrow¹. In the US ~16,000 individuals are diagnosed each year with MM and ~11,000 die of the disease². Monoclonal gammopathy of undetermined significance (MGUS; a pre-malignant clone of plasma cells producing a monoclonal paraprotein) is present in ~2% of individuals older than 50 years, and the risk of progressing to multiple myeloma is 1% each year³. The increased risk of MM in the relatives of MGUS cases is consistent with MGUS being a marker of genetic susceptibility⁴. To date no lifestyle or environmental exposures have been consistently linked to an increased risk of MM or MGUS. Predicated on the hypothesis that part of the 2- to 4-fold elevated risk of MM in relatives of individuals with MM⁵ is a consequence of the co-inheritance of multiple low-risk variants, we conducted two genome-wide association studies (GWAS).

The two GWAS were conducted in the UK and Germany (UK-GWAS and German-GWAS). Genotyping of both case series was conducted using Illumina Omni Express BeadChips. Cases for the UK-GWAS comprised 1,371 patients ascertained through the UK Medical Research Council (MRC) Myeloma-IX trial⁶. Genotype frequencies were compared with publicly accessible genotype data generated by the UK Wellcome Trust Case-Control Consortium 2 (WTCCC2) study of 2,699 individuals from the 1958 British Birth Cohort (58C)⁷ and 2,501 individuals from the UK Blood Service collections (UKBS), that had been genotyped using Illumina Human1.2M-Duo Custom_v1 Array BeadChips (Supplementary Methods). The German-GWAS was based on genotyping 384 MM cases ascertained through Heidelberg University Clinic. Genotype frequencies were compared with publicly accessible genotype data generated by the Heinz-Nixdorf Recall (HNR) study of 704 individuals⁸ from the German population that had been genotyped using Illumina HumaOmni-Quad BeadChips (Supplementary Methods).

Genotype data from the two GWAS were filtered on the basis of pre-specified quality-control measures (Supplementary Methods). Individual SNPs were excluded from further analysis if they showed deviation from the Hardy–Weinberg equilibrium with a P<1.0x10^-6 in controls, an individual SNP genotype yield <95%, or a minor allele frequency <1%. This filtering resulted in the use of 422,839 autosomal SNPs, common to both case-control series. A total of 80 case samples were removed during quality control steps for reasons including a failure to genotype, unknown duplicates and closely related individuals or non-CEU ancestry (Supplementary Figure 1; Supplementary Figure 2).

Prior to undertaking the meta-analysis of the two GWAS, we searched for potential errors and biases in the datasets. Quantile-quantile plots of genome-wide chi-square values showed there was minimal inflation of the test statistics rendering substantial cryptic population substructure or differential genotype calling between cases and controls unlikely in either GWAS (genomic control inflation factor⁹, λ_gc=1.033 and 1.059 in UK and German GWAS respectively; Supplementary Figure 3). For completeness principal components analysis was performed using the Eigenstrat¹⁰ software to determine the effects of population substructure on our findings (λ_corrected=1.010 and 1.005 in UK and German GWAS respectively; Supplementary Figure 3).

Using data on all cases and controls from both series, we derived joint odds ratios (ORs) and confidence intervals (CIs) under a fixed effects model for each SNP, and associated P-values¹¹. In the combined analysis 19 SNPs, which annotate three genomic regions, showed evidence for an association with MM at P_combined<5.0x10^-7 with evidence of an association at P<0.05 in both datasets (Supplementary Table 1). We successfully genotyped the most highly associated SNPs mapping to the three regions in 169 MM cases ascertained through the UK MRC Myeloma-VII trial (Supplementary Methods). For controls we made use of Illumina Hap550K BeadChip genotype data generated on 927 healthy individuals from the UK as part of a study of colorectal cancer we had previously conducted¹².

In a combined analysis the rs1052501 association at 3p22.1 and the rs4636103 association at 7p15.3 attained genome-wide significance (P-values 7.47x10^-9 and 3.33x10^-15 respectively; Table 1)

Table 1. Summary results for the rs4487645 (7p15.3), rs1052501 (3p22.1) and rs6746082 (2p23.3) SNPs associated with multiple myeloma risk.

	RAFa	Case genotypes			RAFa	Control genotypes			ORb	95% CIc	P-value	Padjustedd
rs4487645 (7p15.3)		CC	AC	AA		CC	AC	AA
UK-GWAS	0.71	669	548	103	0.65	2216	2333	646	1.34	1.22-1.47	1.07x10-9	3.23x10-9
German-GWAS	0.76	206	126	22	0.67	320	300	83	1.55	1.26-1.90	2.66x10-5	6.40x10-5
UK replication	0.73	92	64	13	0.65	383	421	113	1.50	1.16-1.95	0.002	-
Combined									1.38	1.28-1.50	3.33x10-15	2.62x10-14
											Phet=0.36, I2=1%
rs1052501 (3p22.1)		GG	AG	AA		GG	AG	AA
UK-GWAS	0.20	54	422	845	0.16	137	1391	3668	1.31	1.18-1.46	8.65x10-7	6.04x10-7
German-GWAS	0.19	10	118	226	0.16	17	185	502	1.32	1.04-1.68	0.021	0.085
UK replication	0.21	9	52	108	0.16	25	248	643	1.34	1.00-1.79	0.049	-
Combined									1.32	1.20-1.45	7.47x10-9	1.81x10-8
											Phet=0.99, I2=0%
rs6746082 (2p23.3)		AA	AC	CC		AA	AC	CC
UK-GWAS	0.82	889	392	40	0.79	3202	1758	238	1.26	1.13-1.41	4.17x10-5	3.79x10-5
German-GWAS	0.84	247	97	10	0.77	415	258	31	1.50	1.18-1.90	8.21x10-4	3.63x10-3
UK replication	0.82	115	47	7	0.79	574	294	49	1.22	0.91-1.64	0.177	-
Combined									1.29	1.17-1.42	1.22X10-7	4.02x10-7
											Phet=,0.39 I2=0%

^aRisk allele frequency (RAF).

^bOdds ratio.

^c95% Confidence Interval.

^dEigenstrat adjusted P-values.

rs1052501 localizes to exon 17 of the serine/threonine-protein kinase unc-51-like kinase 4 (ULK4) gene (41,900,402bps) within a 516kb region of linkage disequilibrium (LD) on 3p22.1 (Figure 1). The G to A substitution at rs1052501 results in an alanine to threonine change at amino acid 542 which is predicted to be tolerated / benign by the in silico algorithms SIFT and Polyphen respectively. The Atg1/ULK complex is a key regulator of mTOR-mediated autophagy¹³ but have thus far not been directly implicated in MM pathogenesis. However, autophagy genes are increasingly being considered as tumor suppressors¹⁴ and intriguingly mTOR regulation represents an important therapeutic target in myelomatous plasma cells¹⁵. In addition to ULK4 the region of extensive LD encompasses the 5’ part of TRAK1 (trafficking protein, kinesin binding 1; MIM 608112) which has a crucial role in regulating the endocytic trafficking of GABA(A) receptors.

Figure 1. Regional plots of association results and recombination rates for the 2p23.3, 3p22.1 and 7p15.3 susceptibility loci.

(a-c) Association results of both genotyped (triangles) and imputed (circles) SNPs in the GWAS samples and recombination rates within the loci: (a) 2p23.3, (b) 3p22.1, (b) 7p15.3. For each plot, −log₁₀ P values (y axis) of the SNPs are shown according to their chromosomal positions (x axis). The top genotyped SNP in each combined analysis is a large triangle and is labeled by its rsID. The color intensity of each symbol reflects the extent of LD with the top genotyped SNP: white (r²=0) through to dark red (r²=1.0). Genetic recombination rates (cM/Mb), estimated using HapMap CEU samples, are shown with a light blue line. Physical positions are based on NCBI build 36 of the human genome. Also shown are the relative positions of genes and transcripts mapping to each region of association. Genes have been redrawn to show the relative positions; therefore, maps are not to physical scale.

rs4487645 maps to intron 80 of the DNAH11 (dynein, axonemal, heavy chain 11 MIM 603339) gene at 7p15.3 (21,904,765bps; Figure 1). DNAH11 encodes a dynein heavy chain microtubule-dependent motor ATPase, which is involved in respiratory cilia movement; germline DNAH11 mutations causing Kartagener Syndrome (situs inversus totalis and primary ciliary dyskinesia). The 88kb region of LD annotated by rs4487645 also encompasses the 3’ part of the CDCA7L (cell division cycle associated 7-like; MIM 609685) gene (Figure 1). Deregulation of MYC typifies plasma cell neoplasms^16,17. CDCA7L therefore represents an attractive candidate for the functional basis of the rs4487645 association since CDCA7L is a MYC-interacting protein, acts as a binding partner of p75 and potentiates MYC-transformational activity^18,19.

In addition to the 3p22.1 and 7p15.3 loci the rs6746082 association at 2p23.3 was promising but did not attain genome-wide significance (P=1.22x10^-7). rs6746082 localizes to intron 12 of DTNB (25,512,748 bps; Figure 1) within a 256kb region of LD on 2p23.3. DTNB (MIM 602415) encodes dystrobrevin beta, a component of the dystrophin-associated protein complex which is abundantly expressed in brain and other tissues but not in muscle. Alternatively spliced transcript variants encoding different DTNB isoforms exist but none have thus far been implicated in the biology of MM.

Elucidation of the basis of the 2p23.3, 3p22.1, and 7p15.3 associations will require fine–mapping and functional analyses, however to explore the region further we imputed unobserved genotypes in UK and German GWA cases and controls using HapMap Phase III and 1000genomes data (Supplementary Methods). This analysis did not provide for substantive evidence of a stronger association at each of the three loci to that provided by rs4487645, rs1052501, or rs6746082 (Supplementary Methods, Figure 1; Supplementary Table 2). To examine if any directly typed or imputed SNPs annotate a putative transcription factor binding/enhancer element, we conducted a bioinformatic search of the region of association using Transfac Matrix Database²⁰, and PReMod²¹ software. These analyses did not provide evidence that rs4487645, rs1052501, or rs6746082, or closely correlated SNP maps with a known or predicted transcription regulatory region (Supplementary Table 2).

To explore whether the rs4487645, rs1052501, rs6746082 associations reflects cis-acting regulatory effects on DNAH11 or CDCA7L, ULK4 or TRAK1, and DTNB respectively, we studied mRNA expression in the plasma cells of 191 MM patients using Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, USA)²² and 90 EBV–lymphoblastoid cell lines using Sentrix Human-6 Expression BeadChips (Illumina, San Diego, USA)^23,24. There was no consistent statistically significant relationship between rs4487645, rs1052501, rs6746082 and expression after adjustment for multiple testing (Supplementary Figure 4). This does not preclude the possibility of subtle effects of genotype with a cumulative long-term impact since we could only detect >5% difference in expression by genotype with 80% power and levels of RNA at a single time point may not adequately capture the impact of differential expression in tumor development.

Multiple myeloma is characterized by male predominance. We assessed the relationship between sex, age at diagnosis and rs4487645, rs1052501, rs6746082 by case-only analysis using data from all series (Supplementary Table 3). The association with MM was not related to age or sex (Supplementary Table 3). Several subtypes of MM are recognized which have unique clinico-pathological phenotypes²⁵. Hierarchically MM can be divided into hyperdiploid and non-hyperdiploid subtypes^26,27. The latter is primarily composed of cases harboring IGH translocations (t(11;14)(q13;q32), t(4;14)(p16;q32) and t(14;16)(q32;q23), and is typified by more aggressive disease. Trisomies and a more indolent form of the disease characterize hyperdiploid MM^25,28. Case-only analysis provided no evidence for a subtype specific association after adjustment for multiple testing, consistent with the risk variant having a generic effect on MM (Supplementary Table 3).

The risks of MM associated with rs4487645, rs1052501 and rs6746082 are modest, collectively accounting for only ~4% of the familial risk of MM. However, the carrier frequency of risk alleles are high in the European population therefore the loci make a significant contribution to the development of MM in terms of population attributable fraction, underlying ~37% of cases. It will be intriguing to explore how our findings translate to non-European populations, which have a lower prevalence of MGUS and MM²⁹. As the frequencies of rs4487645, rs1052501 and rs6746082 genotypes in the CHB/JPT and YRI populations are significantly different to the CEU population it is possible that 2p23.3, 3p22.1 and 7p15.3 variation in part underscores differences in disease incidence.

Our findings provide evidence that common genetic variation influences MM risk. Furthermore, these findings in conjunction with recent observations from Hodgkin’s lymphoma³⁰ and chronic lymphocytic leukemia³¹ GWAS raise the possibility that genetic determined dysregulation of MYC may be a common mechanism of predisposition to hematological malignancies of B-cell lineage. Given the modest size of our study and as evidenced by an over-representation of association signals after exclusion of SNPs mapping to regions of LD at the 2p23.3, 3p22.1 and 7p15.3 associations (Supplementary Figure 3), it is likely that further risk variants for MM will be identified through additional studies.

Methods

Subjects

Genome-wide association study

UK-GWAS: The UK study was based on MM cases (ICD-10 C90.0; 819 male; mean age at diagnosis 64.1 years, SD 10.3) ascertained through the UK Medical Research Council (MRC) Myeloma-IX trial⁶. All cases were UK residents. For controls, we used publicly accessible data generated by the Wellcome Trust Case Control Consortium from the 1958 Birth Cohort (58C; also known as the National Child Development Study)⁷ and UK Blood Service (UKBS). Genotyping of both sets of controls was conducted using Illumina Human 1.2M-Duo Custon_v1 Array chips. SNP calling was performed using Illuminus Software. Full details of genotyping, SNP calling and QC have been previously reported (www.wtccc.org.uk). Concordant with previous findings comparison of the two control series showed little evidence for systematic bias (inflation factor λ=1.019; Supplementary Figure 1)³⁰.

German-GWAS: The German study was based on 384 MM patients (ICD-10 C90.0; 229 male; mean age at diagnosis 54.5 years, SD 8.0) ascertained through Heidelberg University Centre. For controls, we used publicly accessible genotype data on 704 healthy individuals, with no past history of malignancy enrolled into the Heinz Nixdorf Recall (HNR) study⁸.

Replication

For replication we genotyped 169 additional cases of MM (93 male) collected through the UK Medical Research Council (MRC) Myeloma-VII trial. For controls we made use of previously generated data from a UK GWAS of colorectal cancer (420 males, 507 females, aged 18-69 years)¹².

Ethics

Collection of blood samples and clinico-pathological information from subjects was undertaken with informed consent and relevant ethical review board approval in accordance with the tenets of the Declaration of Helsinki.

Karotyping

Conventional cytogenetic studies of MM cells were conducted using standard karotyping methodologies and standard criteria to define a clone were applied. Where possible meta-phase FISH was used to confirm iFISH abnormalities were present in the same cells as the abnormalities detected by conventional cytogenetics. iFISH and ploidy classification of UK samples was conducted using the methodology described by Chiecchio et al³². iFISH and ploidy classification of German samples was performed as previously described^33,34.

Genotyping

DNA was extracted from EDTA-venous blood samples using Qiagen (Crawley, UK) Flexigene or QIAamp methodologies and quantified using PicoGreen (Invitrogen, Carlsbad, USA). Genotyping of cases in the GWAS was conducted using Illumina OmniExpress BeadChips according to the manufacturer's protocols (Illumina, San Diego, USA). To ensure quality of genotyping, duplicates were included on each sample plate (showing a concordance >99.99%). DNA samples with GenCall scores <0.25 at any locus were considered “no calls”. In each sample series a SNP was deemed to have failed if <95% of DNA samples generated a genotype at the locus. Cluster plots were manually inspected for all SNPs considered for replication.

Evaluating and editing cluster positions

Intensity data from arrays were imported into Illumina's BeadStudio clustering and calling software application. For the small subset of loci that were not clustered properly by the automated algorithm, the data were reviewed to identify loci that needed to be removed, manually edited or left unchanged. Clustered SNPs were evaluated using the metrics listed in the SNP Table of the BeadStudio software. These metrics are based on all samples for each locus and thus provide overall performance information for each locus. To identify loci potentially needing to be edited or removed, each quality metric column in the SNP table was sequentially sorted. Metrics used for identifying poorly or incorrectly clustered data included intensity, cluster separation, position of each cluster (AA, AB, BB), Hardy-Weinberg equilibrium, call frequency and variation of cluster width. The reproducibility of control samples on each plate, as well as replicates were also used to identify missclustered loci. Although not all cluster plots were assessed, ~10% of the lowest-performing loci were examined. Of these 10%, ~20% were edited or annotated (to indicate loci with nearby polymorphisms or hemizygous deletions) and ~2% were excluded. Review of data was conducted by a second individual to determine if any metrics were missed or if further editing was required. Overall, this process provides for substantially increased genotyping accuracy.

Validation of Illumina SNP genotypes

To confirm genotyping accuracy for rs4487645, rs1052501, rs6746082 SNPs we confirmed genotypes by ABI 3730xl Sanger sequencing in >184 randomly selected samples from each of the UK case, 58C and HNR control series (concordance >99.5%); PCR primers available on request.

Replication genotyping

Replication of rs4487645, rs1052501, rs6746082 associations were performed by ABI 3730xl Sanger sequencing of all MRC Myeloma-VII trial samples.

Statistical and bioinformatic analysis

We applied pre-determined quality control metrics to the GWAS data. We restricted analyses to samples for whom >95% of SNPs were successfully genotyped, thus eliminating 28 cases. We computed identity-by-state (IBS) probabilities for all pairs (cases and controls) to search for duplicates and closely related individuals amongst samples (defined as IBS ≥0.80, thereby excluding first-degree relatives). For all identical pairs the sample having the highest call rate was retained, eliminating 17 MM cases. To identify individuals who might have non-Western European ancestry, we merged our case and control data with phase II HapMap samples (60 western European [CEU], 60 Nigerian [YRI], 90 Japanese [JPT] and 90 Han Chinese [CHB]). For each pair of individuals we calculated genome-wide IBS distances on markers shared between HapMap and our SNP panel, and used these as dissimilarity measures upon which to perform principal component analysis. The first two principal components for each individual were plotted and any individual not present in the main CEU cluster was excluded from analyses. We removed 35 cases with non-CEU ancestry and one 58C control which had previously been identified as being diagnosed with Hodgkin Lymphoma (HL)³⁰. In each sample series we filtered out SNPs having a minor allele frequency [MAF] <1%, and a call rate <95%. We also excluded SNPs showing departure from Hardy-Weinberg equilibrium (HWE) at P<10^-6 in controls. For replication and validation analysis call rates were >95% per 384-well plate for each SNP; cluster plots were visually examined by two researchers.

Main analyses were undertaken using R (v2.6), Stata v.10 (State College, Texas, US) and PLINK (v1.06)³⁵ software. The association between each SNP and risk of MM was assessed by the Cochran-Armitage trend test. The adequacy of the case-control matching and possibility of differential genotyping of cases and controls were formally evaluated using quantile-quantile (Q-Q) plots of test statistics. The inflation factor λ was based on the 90% least significant SNPs⁹. We undertook adjustment for possible population substructure using Eigenstrat software. Odds ratios (ORs) and associated 95% confidence intervals (CIs) were calculated by unconditional logistic regression. Meta-analysis was conducted using standard methods¹¹. Cochran’s Q statistic to test for heterogeneity¹¹ and the I² statistic to quantify the proportion of the total variation due to heterogeneity were calculated³⁶.I² values ≥75% are considered characteristic of large heterogeneity^36,37. To conduct a pooled analysis incorporating Eigenstrat adjusted P-values from the GWAS we used the weighted Z-method implemented in the program METAL³⁸. Associations by sex, age and clinic-pathological phenotypes were examined by logistic regression in case-only analyses.

The familial relative risk of MM attributable to any locus is given by the formula³⁹:

$${\lambda }^{*}=\frac{p{\left(p{r}_2+q{r}_1\right)}^2+q{\left(p{r}_1+q\right)}^2}{{\left(p^2{r}_2+2pq{r}_1+q^2\right)}^2}$$

where p is the population frequency of the minor allele, q=1-p, and r₁ and r₂ are the relative risks (approximated by the odds ratios) for heterozygotes and the rarer homozygotes, relative to the more common homozygotes. From λ* it is possible to quantify the impact the locus makes to the overall familial risk of MM seen in first-degree relatives. Assuming a multiplicative interaction between risk alleles the proportion of the overall familial risk attributable to the locus is given by log(λ*)/log(λ₀), where λ₀, the overall familial risk of MM is assumed on the basis of epidemiological studies to be 2.45⁵.

The population attributable fraction was estimated from 1 - Π_i1 - x_i, where x_i = p.(OR_pa-1)/(p.(OR_pa-1)+1), p is the frequency of the risk allele in the population and OR_pa is the per allele ORs.

Prediction of the untyped SNPs was carried out using IMPUTEv2, based on HapMap Phase III haplotypes release 2 (HapMap Data Release 27/phase III Feb 2009 on NCBI B36 assembly, dbSNP26) and 1000genomes. Imputed data were analysed using SNPTEST v2 to account for uncertainties in SNP prediction. LD metrics between HapMap SNPs were based on Data Release 27/phase III (Feb 2009) on NCBI B36 assembly, dbSNP26, viewed using Haploview software (v4.2) and plotted using SNAP. LD blocks were defined on the basis of HapMap recombination rate (cM/Mb) as defined using the Oxford recombination hotspots⁴⁰ and on the basis of distribution of confidence intervals defined by Gabriel et al⁴¹. To annotate potential regulatory sequences within disease loci we implemented in silico searches using Transfac Matrix Database v7.29²⁰, and PReMod10²¹ software. We used the in silico algorithms SIFT and PolyPhen to predict the impact of amino acid substitutions.

Relationship between SNP genotype and mRNA expression

To examine for a relationship between SNP genotype and expression levels of CDCA7L, DNAH11, ULK4, TRAK1 and DTNB in MM, we made use of Affymetrix Human Genome U133 Plus 2.0 array data we previously generated on the plasma cells from 192 MM patients from the MRC Myeloma IX trial²². To examine for a relationship between SNP genotype and expression levels in lymphocytes we made use of publicly available expression data generated from analysis of 90 Caucasian derived Epstein-Barr virus–transformed lymphoblastoid cell lines using Sentrix Human-6 Expression BeadChips (Illumina, San Diego, USA)^23,24. Online recovery of data was performed using WGAViewer Version 1.25 Software. Differences in the distribution of levels of mRNA expression between SNP genotypes were compared using a Wilcoxon-type test for trend⁴². Power of assays to establish a relationship between genotype and expression we made using STATA software assuming allele-based test of difference in normalized logRNA expression (imposing a Bonferroni corrected P-value of 0.005 to address multiple testing).

Supplementary Material

Note: Supplementary information is available on the Nature Genetics website