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. Author manuscript; available in PMC: 2013 Mar 1.
Published in final edited form as: Prostate. 2011 Jul 11;72(4):410–426. doi: 10.1002/pros.21443

Chromosomes 4 and 8 Implicated in a Genome Wide SNP Linkage Scan of 762 Prostate Cancer Families Collected by the ICPCG

Lingyi Lu 1, Geraldine Cancel-Tassin 2, Antoine Valeri 2, Olivier Cussenot 2, Ethan M Lange 3,4, Kathleen A Cooney 3,5, James M Farnham 6, Nicola J Camp 6, Lisa A Cannon-Albright 6, Teuvo LJ Tammela 7, Johanna Schleutker 7, Josef Hoegel 8,9, Kathleen Herkommer 8,10,11, Christiane Maier 8,9, Walther Vogel 8,9, Fredrik Wiklund 12,13, Monica Emanuelsson 12,14, Henrik Grönberg 12,13, Kathleen E Wiley 15, Sarah D Isaacs 15, Patrick C Walsh 15, Brian T Helfand 16, Donghui Kan 16, William J Catalona 16, Janet L Stanford 17,18, Liesel M FitzGerald 17,18, Bo Johanneson 17,19, Kerry Deutsch 17,20, Laura McIntosh 17,18, Elaine A Ostrander 17,19, Stephen N Thibodeau 21, Shannon K McDonnell 21, Scott Hebbring 21, Daniel J Schaid 21, Alice S Whittemore 22,23,24, Ingrid Oakley-Girvan 22,24, Chih-Lin Hsieh 22,25, Isaac Powell 26,27, Joan E Bailey-Wilson 26,28, John D Carpten 26,29, Daniela Seminara 30, S Lilly Zheng 1, Jianfeng Xu 1, Graham G Giles 31,32, Gianluca Severi 31,32, John L Hopper 31,33, Dallas R English 31,33, William D Foulkes 31,34, Lovise Maehle 31,35, Pal Moller 31,35, Michael D Badzioch 31,36, Steve Edwards 31,37, Michelle Guy 31,37, Ros Eeles 31,37, Douglas Easton 31,38, William B Isaacs 18,*, the International Consortium for Prostate Cancer Genetics
PMCID: PMC3568777  NIHMSID: NIHMS301718  PMID: 21748754

Abstract

Background

In spite of intensive efforts, understanding of the genetic aspects of familial prostate cancer remains largely incomplete. In a previous microsatellite-based linkage scan of 1233 prostate cancer (PC) families, we identified suggestive evidence for linkage (i.e. LOD≥1.86) at 5q12, 15q11, 17q21, 22q12, and two loci on 8p, with additional regions implicated in subsets of families defined by age at diagnosis, disease aggressiveness, or number of affected members.

Methods

In an attempt to replicate these findings and increase linkage resolution, we used the Illumina 6000 SNP linkage panel to perform a genome-wide linkage scan of an independent set of 762 multiplex PC families, collected by 11 ICPCG groups.

Results

Of the regions identified previously, modest evidence of replication was observed only on the short arm of chromosome 8, where HLOD scores of 1.63 and 3.60 were observed in the complete set of families and families with young average age at diagnosis, respectively. The most significant linkage signals found in the complete set of families were observed across a broad, 37 cM interval on 4q13-25, with LOD scores ranging from 2.02 to 2.62, increasing to 4.50 in families with older average age at diagnosis. In families with multiple cases presenting with more aggressive disease, LOD scores over 3.0 were observed at 8q24 in the vicinity of previously identified common PC risk variants, as well as MYC, an important gene in PC biology.

Conclusions

These results will be useful in prioritizing future susceptibility gene discovery efforts in this common cancer.

Introduction

The recent discoveries of multiple SNPs across the genome as common, reproducible genetic risk factors for prostate cancer (PC) have been impressive. Over 30 common sequence variants have now been confirmed to be associated with PC risk, emphasizing the polygenic nature of inherited susceptibility for this disease (1). In spite of the substantial progress in this area, current estimates suggest that the identified loci do not explain the majority of the excess risk associated with PC family history (1), one of the most reproducible risk factors for PC (2,3).

Attempts to map PC susceptibility genes by linkage analysis of individual family collections have yielded few reproducible leads despite numerous genome-wide scans, most likely due to genetic and disease heterogeneity (46). In an effort to address this question more effectively, we previously carried out a large linkage study that included 1233 PC families collected by members of the International Consortium for Prostate Cancer Genetics (ICPCG) (7). This study provided strong evidence that one or a few major genes cannot account for the majority of disease in PC families. At the same time, a number of loci demonstrated suggestive linkage signals, consistent with a complex genetic etiology for this disease. To extend these studies using a higher resolution marker set, and to assess which of these linkage signals might warrant additional investigation, in this report we describe a second combined linkage analysis with 6000 SNPs to interrogate an independent set of 762 families collected by the ICPCG.

RESULTS

Study Population - 762 Prostate Cancer Families

Table 1 summarizes the characteristics of the 762 PC families from the 11 ICPCG groups participating in this analysis. Fifty-three percent of families had a mean age at diagnosis of <65 years, and 21% had four or more affected family members. Most of the families (65%) were collected in Europe or Australia, with the remainder collected in the U.S. The current analysis was restricted to Caucasian families; analysis of linkage results from African American pedigrees collected by members of the ICPCG will be described in a separate report.

Table 1.

Characteristics of 762 ICPCG Families

Mean Age at Diagnosis Number of Affected Members Families with
Aggressive PCa
TOTAL
ICPCG MEMBER <65 ≥65 2 3 4 ≥5 Families Affected
Individuals
Non-Affected
Individuals
ACTANE 108 71 89 72 13 5 150 179 380 83
Univ TAMPERE 24 33 16 32 6 3 42 57 144 159
CeRePP 87 87 110 49 11 4 63 174 385 73
FHCRC 3 10 12 1 0 0 3 13 27 0
JHU 19 5 2 10 5 7 10 24 78 24
MAYO Clinic 6 5 2 6 2 1 0 11 29 10
Univ MICHIGAN 88 43 55 58 12 6 0 131 344 0
Northwestern Univ 12 2 11 3 0 0 0 14 29 6
Univ UMEA 11 24 7 19 7 2 4 35 88 25
Univ ULM 34 16 17 28 5 0 17 50 114 21
Univ UTAH 13 61 0 0 55 19 59 74 143 268
TOTAL 405 357 321 278 116 47 348 762 1761 699

SNP Scan Linkage Results

Shown in Figure 1 and Table 2 are the linkage results for the entire set of 762 families using dominant (dom), recessive (rec), and nonparametric (KCLOD or asm) linkage models. The strongest evidence of linkage in the complete set of families is located in a broad region with multiple peaks on the proximal and mid-q arm of chromosome 4. A maximum HLOD=2.62 was observed under a recessive model at 4q22 at 97 cM, along with several other peaks over 1.86 between 74 cM and 115 cM, 4q13-25. An examination of LOD scores by individual family collection indicates that six of the seven largest family collections had scores over 0.9 in the 12 cM interval between 83 cM and 102 cM on this chromosome, using either a recessive or asm model (Table 3).

Figure 1.

Figure 1

Figure 1

Figure 1

a. Plot of LOD scores for all families by chromosome.

b. Chromosomes with LOD scores > 1.86 in all families.

c. Chromosomes with LOD Scores > 1.5 in all families.

Table 2.

LOD Score Summary - All Families (n = 762)a

Chr pos (cM) LODb model region SNP pos (bp)
2 77 1.60 rec 2p16.1 rs1961245 54947346
2 108 1.66 rec 2p11.2 rs11395 86219368
2 131 1.85 asm 2q14.2 rs280192 121453918
2 216 1.66 asm 2q35 rs750365 218099958
4 77 2.02 rec 4q13.1 rs1489572 63718358
4 93 2.26 asm 4q21.23 rs1383972 86603603
4 98 2.62 rec 4q22.1 rs729685 90654547
4 102 2.58 rec 4q22.2 rs183993 95349298
4 114 2.58 rec 4q25 rs1879053 111616647
8 59 1.63 dom 8p11.21 rs868586 40824258
8 142 1.63 asm 8q24.22 rs1062064 133081648
11 7 1.53 dom 11p15.4 rs2231963 4581846
12 114 1.62 asm 12q23.2 rs1544921 100635554
16 81 1.50 rec 16q21 rs1027277 61242497
18 43 1.93 rec 18q11.2 rs948384 18260958
a

All scores >1.5

b

HLOD scores listed for dom and rec models

Table 3.

LOD Scores on Chromosome 4

group LODa pos (cM) model # families
ACTANE 1.20 98 asm 179
Univ Tampere 1.36 83 rec 57
CeRePP 1.54 83 rec 174
Univ Umea 1.71 102 rec 35
Univ Ulm 0.94 102 rec 50
Univ Utah 1.00 93 rec 74
MAYO Clinic 0.36 83 rec 11
FHCRC 0.00 83–102 rec 13
JHU 0.33 83 rec 24
Univ Michigan 0.00 83–102 rec 131
NW Univ 0.09 102 asm 14
a

HLOD scores listed for rec model

One other region, 18q11, reached the threshold for suggestive evidence of linkage: rec HLOD=1.93 at 43cM. Including results from all three linkage models, LOD scores over 1.5 were observed at 8p11 (59 cM), 8q24 (142 cM), 11p15 (7 cM), 12q23 (114 cM), 16q21 (81 cM), and multiple positions on both arms of chromosome 2 (2p16, 77 cM; 2p11, 108 cM; 2q14, 131 cM; and 2q35, 216 cM) (Table 2).

Linkage Signals in Subsets of Families

To explore variables that might impact the linkage results, we analyzed subsets of families characterized by young or old average age at diagnosis (≤65, vs 65 or older), five or more affected individuals, or multiple members affected with more aggressive disease. For the 405 families with young age of diagnosis, the most significant evidence for linkage was observed on 8p11 at 59 cM (dom HLOD=3.60 vs 1.63 at this same position in all families). Two other regions showing suggestive linkage in this family subset were observed, at 3p24 (asm LOD=2.05 at 35 cM), and 1q44 (asm LOD =1.95 at 269 cM) (Figure 2, Table 4).

Figure 2.

Figure 2

Figure 2

a. Plot of LOD Scores for families with average age at diagnosis under 65.

b. Chromosomes with LOD scores ≥ 1.86 in families with young age at diagnosis (<65).

Table 4.

LOD Score Summary - Subsets of Familes

Chr pos (cM) LODa model region SNP pos (bp)
Families with early age atdiagnosis (<65, n=410)
1 269 1.95 asm 1q44 rs1148917 243595288
3 35 2.05 asm 3p24.3 rs826423 15316855
8 59 3.60 dom 8p11.21 rs868586 40824258
Families with older age at diagnosis (≥65, n=353)
4 95 4.50 rec 4q22.1 rs729685 90654547
12 113 3.14 dom 12q23.2 rs1544921 100635554
13 15 2.23 rec 13q12.13 rs977655 25202569
18 43 1.91 rec 18q11.2 rs948384 18260958
Families with more aggressive disease (n=348)
1 255 2.11 dom 1q43 rs528011 236344348
2 218 2.24 asm 2q35 rs746233 220209631
4 149 1.94 dom 4q32.1 rs716428 156864474
8 126 3.17 rec 8q24.13 rs2833 124055830
8 132 3.17 dom 8q24.21 rs7814955 127491272
8 139 3.09 asm 8q24.21 rs766811 130073850
12 146 2.23 dom 12q24.31 rs2197777 124356099
Families with five or more affected (n=47)
13 128 2.46 asm 13q34 rs1885688 112942237
15 40 2.00 rec 15q14 rs276855 37318605
16 48 2.00 rec 16p12.1 rs991911 24198554
a

HLOD scores listed for dom and rec models

In families with an average age at diagnosis of 65 or greater (n=357), LOD scores over 1.86 are seen in a broad region spanning the centromere of chromosome 4 (51cM-122cM), which overlaps with the strongest region of linkage observed in the complete set of families. The peak for this subset analysis was at 95cM, 4q22, with a rec HLOD =4.50. Other positions with LOD scores over 1.86 in this subset of families were observed on chromosomes 12, 13 and 18 (dom HLOD = 3.14, rec HLOD = 2.23 and 1.91 at 113 cM, 15 cM and 43 cM, respectively) (Figure 3, Table 4).

Figure 3.

Figure 3

Figure 3

a. Plot of LOD Scores for families with average age at diagnosis ≥ 65.

b. Chromosomes with LOD scores ≥ 1.86 in families with average age at diagnosis ≥65.

The strongest linkage signals in families with more aggressive disease were seen on chromosome 8 where LOD scores reached over 3.0 across a 14 cM interval at 8q24 (126–140 cM, high score 3.17 at 132 cM, dom model). Four other regions were of interest in this group: 1q43 (dom HLOD = 2.11 at 255 cM), 2q35 (asm LOD = 2.24 at 218 cM), and 4q32 (dom HLOD = 1.94 at 149 cM), 12q24 (dom HLOD = 2.23 at 146 cM) (Figure 4, Table 4).

Figure 4.

Figure 4

Figure 4

a. Plot of LOD Scores for families with more aggressive disease.

b. Chromosomes with LOD scores ≥1.86 in families with more aggressive disease.

In families with 5 or more affected individuals, suggestive evidence of linkage was observed at three regions: 13q34 (asm LOD = 2.46, 128 cM), 15q14 (40 cM, dom HLOD = 2.0), and 16p12.1 (rec HLOD = 2.0, 48 cM) (Figure 5, Table 4). On chromosome 21, an HLOD of 1.78 was observed at 45cM, in the vicinity of the ERG and TMPRSS2 genes, in this family subset (Figure 5c).

Figure 5.

Figure 5

Figure 5

a. Plot of LOD Scores for families with 5 or more affected members.

b. Chromosomes with LOD scores ≥ 1.86 in families with 5 or more affected members.

c. Chromosome 21 in families with 5 or more affected members. The position of ERG and TMPRSS2, two genes known to undergo common genomic rearrangement leading to gene fusion and activation of ERG (41), is noted.

Comparison of Two Linkage Scans in ICPCG Families

To search for reproducible linkage signals, we compared the results of this SNP linkage scan (designated here SNP scan) with our previous scan of 1,233 families using microsatellite markers (MS scan) (7). Of the six regions of suggestive linkage found in the MS scan, none were supported by LOD scores reaching the threshold for suggestive linkage, i.e. ≥1.86, in the SNP scan. However, more modest evidence of replication was observed on the proximal short arm of chromosome 8. In the SNP scan, an HLOD of 1.63 was observed at 8p11 (59 cM) under a dominant model. In the MS scan, two signals were observed on 8p, one at 60 cM (1.94) and one at 46 cM (1.97), under recessive and dominant models respectively. For the remaining four regions of suggestive linkage found in our first scan, at 5q12, 15q11, 17q21 and 22q12, little or no evidence for linkage was seen in the SNP scan (LOD scores <0.4).

Similarly, for all regions reaching LOD scores of 1.5 or greater in the complete set of families analyzed in the SNP scan, including the multiple loci on chromosomes 2 and 4, 8p11, 11p15, 12q23, 16q21, and 18q11, the highest score observed in the MS scan was 0.53 at 133 cM on chromosome 2.

Comparison of Two Linkage Scans in Subsets of Families

In families with an young age at diagnosis, dom HLOD scores ≥ 1.86 were observed on 3p in both scans, although the peak locations differed by over 20cM (35 cM in SNP scan and 57 cM in MS scan). When comparing regions of linkage in the scans of families with five or more affected members, peaks over 1.86 were observed within 15cM of each other on 16p12 (at 34cM in MS scan and 49cM in SNP scan) (asm LOD 2.04 and 2.14 respectively).

Of the three regions reaching suggestive linkage (6p22, 11q14, and 20q11) in our previous MS scan of families with aggressive disease, one region, 11q14 provided some evidence of an overlapping signal in the SNP scan with a rec HLOD score of 0.8 at 100 cM. Also in this group of families, coinciding linkage signals occurred at 8q24, where dom HLOD scores of 1.17 and 3.05 were observed in the same positions (137 cM) in the MS and SNP scans, respectively.

Discussion

In this report, we describe a genome-wide linkage study of 762 families collected by members of the ICPCG. This is the second largest collection of PC families analyzed to date to assess linkage across the genome. A primary rationale behind this study was to determine whether linkage signals observed in an earlier microsatellite linkage scan of 1,233 families could be replicated, as a means to identify loci warranting further study.

Of the six regions of suggestive linkage observed in the previous MS scan of 1,233 PC families (7), one region, 8p11, attained a LOD score over 1.5 in the present SNP scan. In addition, overlapping linkage signals in the two scans provided some evidence of replication in defined subsets of families analyzed. Both families with young age at diagnosis and families with five or more affected individuals had moderate linkage signals at 3p24 and 16p12, respectively, in both scans. In addition, the subset of families with clinically aggressive disease showed linkage to 8q24 in both scans. Thus, while overall replication of previous linkage peaks was quite limited, several loci, particularly on chromosome 8, showed consistent linkage signals in two large, jndependent collections of prostate cancer families.

Chromosome 8 has long been suggested to harbor both prostate tumor suppressor gene(s) and oncogene(s) due to the frequent copy number alterations (deletions of 8p and gains of 8q, respectively) occurring somatically in specimens of prostate tumor tissue (810, reviewed in 11, 12). At the germline level, linkage at 8p has been observed in PC family collections from Japan, Sweden, Germany and the US (1317), although in the majority of these studies the signals observed were more telomeric than the one observed here. In addition, a large case-control study conducted by PRACTICAL found two SNPs at 8p21, near NKX3.1, to be associated with PC risk (18).

The 8q24 locus been extensively analyzed by GWAS, with five or more regions reproducibly shown to be associated with PC risk (1921). Historically, the region was first identified through a fine-mapping study of a linkage peak observed in a genome-wide scan of Icelandic PC families (22). Linkage to this region was also reported by Camp et al (23) in extended PC families from Utah. It will be of interest to determine whether any of the susceptibility loci identified in the original study and the association studies since, contribute to the linkage signals observed here. A gene of particular interest for PC, MYC, lies in the region of linkage observed in this study in families with more aggressive disease. Previous studies have demonstrated the common up-regulation of this gene early in human prostate carcinogenesis (24, 25), amplification of the gene in advanced PC (26, 27), and the ability of prostate specific expression of this gene to induce PC in animal models (28, 29). Such studies, together with recent work demonstrating interactions between risk loci and MYC regulatory elements have led to the hypothesis that the 8q24 risk alleles that have been identified to date modify PCa risk mechanistically by altering MYC regulation and expression (3034).

In the complete family collection, the strongest linkage signals in this study were observed on the proximal and mid q arm of chromosome 4. One important aspect of this signal is the contributions provided by the multiple different family collections. Interestingly, six of the seven largest family collections (ranging from 35 to 174 families) had LOD scores over 0.9 in the 12 cM interval between 93 cM and 105 cM on this chromosome, whereas the four smaller collections (n < 25 families) contributed little evidence to this signal. Curiously, the six positive family collections include all five groups originating from Europe/Australia, suggesting a possible geographical association to the chromosome 4 linkage, although limited sample size of the US family sets, or chance occurrence are also possible explanations for this observation. It is of interest that recent GWAS findings have led to the identification and confirmation of several SNPs on 4q22 and 4q24, in introns of PDLIM5, and upstream of TET2, respectively, as being associated with PC risk (18). Whether or not common risk alleles at these or nearby loci play a role in the linkage signal observed in the larger family collections studied here is a question for further investigation.

Stanford et al (35) recently reported a SNP based linkage scan in which several linkage signals were reported that coincide with results from this study. Specifically, coincident peaks were observed at 15q13-14 and 2q14-21 in this study and the one reported here, although the signals were observed in different subsets of PC families. Evidence of linkage to the long arm of chromosome 8 (8q22) was observed in the complete set of 289 Caucasian families.

One of the aims of this study was to replicate findings from our earlier MS scan (7); however few loci were observed in both studies. While this is disappointing, it is not surprising given the known genetic heterogeneity of PC. Indeed, a limitation of our study is the potentially heterogeneous genetic and environmental influences arising from a collection of families from multiple locations across the U.S., Europe, and Australia. Over half of the families (65%) studied in this scan were collected in Europe or Australia, while the majority of families (79%) studied in our previous MS scan were collected in the U.S. Differences in intensity of PC screening in Europe versus the U.S. may lead to substantial differences in the distribution of disease stage at diagnosis (e.g., lower stage due to widespread PSA testing in the U.S.). While we have attempted to address some of these differences by examining specific subsets of PC families stratified by age at diagnosis and clinical and pathologic variables of the disease, this may not be sufficient to account for the heterogeneity that may be introduced by the differences in clinical practices between the continents.

It should be noted that with respect to comparability with our previous MS scan, while in general the family characteristics were quite similar, the families in this scan had on average fewer members affected with PC (~2.3 per family compared to~3.5 in the MS scan). This fact could have implications with respect to the linkage evidence on 8q24. Smaller numbers of affected individuals within families could reflect a greater presence of sporadic disease. While little is known about the role of 8q24 susceptibility variants in familial PC, there is unequivocal evidence that these risk alleles are associated with sporadic PC even though the relative risks associated with these risk alleles are small to modest. It is interesting to note that the Icelandic families in which the 8q24 locus was originally identified through linkage analysis were of similar average size to the families in this study (22).

The strengths of this study are its large size and increased genetic information and resolution due to the use of dense SNP panels for genotyping. While the wide area of family ascertainment may generate heterogeneity, the large number of families afforded by this approach increases power and possibly results in the identification of more robust genetic signals. Finally, the large number of families increases our ability to examine potentially more homogeneous subsets of families while still maintaining reasonable levels of power.

In summary, in an examination of results from a high resolution SNP scan of 762 families and a previous MS scan of 1233 independent PC families, no locus emerges as an unequivocally strong candidate. However, our results suggest that a broad region on proximal 4q, and multiple regions on chromosome 8 are possible candidate regions harboring PC susceptibility loci. In light of evidence from this and previous studies, further analysis of these regions appears warranted.

Methods

Ascertainment of Families

The ICPCG study populations have been previously described in detail (36). Each group within the ICPCG recruited PC families and eleven ICPCG groups contributed to this combined genome-wide screen: ACTANE (Anglo/Canadian/Texan/Australian/Norwegian/European Union Biomed), Centre de Recherche sur les Pathologies Prostatiques, (CeRePP) in France, Johns Hopkins University (JHU), Mayo Clinic, University of Michigan, Northwestern University, PROGRESS (Prostate Cancer Genetic Research Study, Fred Hutchinson Cancer Research Center), University of Tampere in Finland, University of Ulm in Germany, Karolinska Insititute in Sweden, and University of Utah. There were 762 PC pedigrees in this combined analysis. The research protocols and informed consent procedures were approved by each group’s institutional review board.

Definition of Affection Status and Classification of Pedigrees

Affected individuals were defined as men diagnosed with PC that had been confirmed by either medical records or death certificates. Self- or relative-reported affected men without either medical records or death certificate confirmation were considered as having unknown affection status. All men without a diagnosis of PC were coded as having unknown affection status, regardless of whether they had undergone screening for PC. Hence, all analyses were based on the sharing of marker genotypes among affected individuals, with no consideration of the phenotype for the remaining subjects. Family members not considered affected nonetheless contributed genotype information, when available, to increase the linkage information content among the affected men. Although such an approach may result in some loss of power, it provided a uniform approach across all participating groups, particularly important because screening of unaffected men varied across groups.

For subset analyses, pedigrees were stratified according to the following criteria: 1) average age at diagnosis within families, contrasting <65 years to 65+ years; 2) families with aggressive disease based on criteria previously described (37). Briefly, families meeting these criteria had three or more affected individuals with PC with at least one of the following clinicopathologic characteristics: Gleason score 7 or higher, TNM stage of T3 or T4, pretreatment serum PSA ≥20 ng/mL, or death from PC before age 65. In these families, other cases not meeting any of the criteria for aggressive disease were classified as having unknown disease status; 3) families having 5 or more affected individuals..

Genotyping

Genome-wide SNP linkage scan genotyping was performed at the Center for Inherited Disease Research using Illumina's HumanLinkage-12 Genotyping BeadChip (http://www.cidr.jhmi.edu/human_snp.html). These chips assay 6,090 SNP markers, with an average intermarker distance of 0.58 cM across the genome and an average marker heterozygosity of 0.43 in Caucasians.

Statistical Analysis: Linkage-Analysis Methods

The computer programs Pedcheck (http://watson.hgen.pitt.edu/register/docs/pedcheck.html) and PREST (http://galton.uchicago.edu/~mcpeek/software/prest/) were used for checking whether the genotypes of individuals within a pedigree are consistent with their specified relationships. Based on these analyses, 58 individuals were removed from further analysis.

Both parametric and non-parametric linkage analyses were performed using Merlin software (38). The parametric LOD scores were computed using either a dominant or a recessive model, as described in elsewhere (5). LOD scores allowing for linkage heterogeneity among families (HLOD) were estimated using HOMOG (39). Non-parametric LOD scores were calculated using the Kong and Cox exponential allele sharing model score (herein referred to as asm) (40). Marker allele frequencies for each SNP were estimated by counting alleles across all genotyped subjects, ignoring genetic relationships. Multipoint linkage statistics were calculated at 0.5 cM intervals across the genome.

We used the r-square option (≥ 0.1) of Merlin to remove SNPs that were in linkage disequilibrium (LD). This is necessary to reduce the positive bias of strong marker LD among flanking SNPs on linkage results, and to reduce the memory and time requirements for large pedigrees. To further fit pedigree data into the memory limits of Merlin software, trimming of family members was conducted. Un-genotyped subjects or subjects with missing phenotypes were trimmed. Trimming was performed on each pedigree to obtain a maximum bit size of 24.

To facilitate comparison of the results of this SNP scan with our previous scan using microsatellite (MS) markers, we aligned the results of these two linkage scans based on physical map positions (Build 35) of both the microsatellite markers and SNP markers.

Acknowledgements

We would like to express our gratitude to the many families who participated in the studies involved in the International Consortium for Prostate Cancer Genetics (ICPCG). The ICPCG, including the consortium’s Data Coordinating Center (DCC), is made possible by a grant from the National Institutes of Health U01 CA89600 (to W.B.I.). Additional support to participating groups, or members within groups, is as follows: ACTANE Group: This study, and recruitment of U.K. families, was supported by Cancer Research U.K (CR-UK) grant no C5047/A3354. Additional support was provided by The Prostate Cancer Research Foundation, The Times Christmas Appeal and the Institute of Cancer Research. We thank S. Seal and A. Hall for kindly storing and logging the samples that were provided. D.F.E is a Principal Research Fellow of CR-UK. Funding in Australia was obtained from The Cancer Council Victoria, The National Health and Medical Research Council (grants 940934, 251533, 209057, 126402, 396407), Tattersall’s and The Whitten Foundation. We would like to acknowledge the work of the study coordinator M. Staples and the Research Team B. McCudden, J. Connal, R. Thorowgood, C. Costa, M. Kevan, and S. Palmer, and to J. Karpowicz for DNA extractions. The Texas study of familial prostate cancer was initiated by the Department of Epidemiology, M.D. Anderson Cancer Center. M.B. was supported by an NCI Post-doctoral Fellowship in Cancer Prevention (R25). BC/CA/HI Group: USPHS CA67044. CeRePP: Association pour la Recherche sur le Cancer, grant number 5441. FHCRC Group: USPHS CA80122 (to J.L.S.)and USPHS CA78836 (to E.A.O), with additional support from the Fred Hutchinson Cancer Research Center. E.A.O and B.J. acknowledge the Intramural Program of the National Human Genome Research Institute. JHU Group:.USPHS CA58236 (to W.B.I.) Mayo Clinic Group: USPHS CA72818. Michigan Group: USPHS CA079596. Northwestern Group: The Urological Research Foundation. University of Tampere Group: The Competitive Research Funding of the Pirkanmaa Hospital District, Reino Lahtikari Foundation, Finnish Cancer Organisations, Sigrid Juselius Foundation, and Academy of Finland grant 211123. University of Ulm Group: Deutsche Krebshilfe, grant number 70-3111-V03. Karolinska Institute Group Swedish Cancer Society and a Spear grant from the Umeå University Hospital, Umeå, Sweden. University of Utah Group: Data collection was supported by USPHS CA90752 (to L.A.C.-A.) and by the Utah Cancer Registry, which is funded by Contract #N01-PC-35141 from the National Cancer Institute's Surveillance, Epidemiology, and End Results Program with additional support from the Utah State Department of Heath and the University of Utah. G.B.C. was supported by National Library of Medicine training grant NLM T15 LM07124. N.J.C. was supported in part by USPHS CA98364 (to N.J.C.). L.C.A. acknowledges support from the Huntsman Cancer Foundation. DCC: The study is partially supported by USPHS CA106523 (to J.X.), USPHS CA95052 (to J.X.), and Department of Defense grant PC051264 (to J.X.).

Other investigators who contributed to this work: ACTANE Group: UK, Sutton: S. Bullock, Q. Hope, S. Bryant, S. Mulholland, S. Jugurnauth, N. Garcia, L. O'Brien, B. Gehr-Swain, A. Hall, R. Wilkinson, A. Ardern-Jones, D. Dearnaley, The UKGPCS Collaborators, British Association of Urological Surgeons' Section of Oncology. UK, Cambridge: Chris Evans, M. Dawn Teare, (Cancer Research UK Genetic Epidemiology Unit, Strangeways Research Labs, Cambridge). Australia: Melissa Southey (The Cancer Council of Victoria and The University of Melbourne, Carlton, Australia). Canada: Nancy Hamel, Steven Narod, Jaques Simard. (Department of Medical Genetics, McGill University, Montreal, Quebec; Oncology and Molecular Endocrinology Research Center, CHUL Research Center; Laval University, Quebec City, and Women's College Hospital Research Institute, University of Toronto). Texas: Chris Amos (MD Anderson Cancer Centre, Houston, TX and Division of Medical Genetics, University of Washington Medical Centre, Seattle, WA). Norway, Oslo: Ketil Heimdal, Lovise Mahle, Pal Moller+ (Unit of Medical Genetics, Norwegian Radium Hospital, Oslo). Norway, Ullevaal: Nicolai Wessel, Tone Andersen (Dept of Oncology, Ullevaal University Hospital, Oslo). EU Biomed: Tim Bishop, The EU Biomed Prostate Cancer Linkage Consortium (Cancer Research UKGenetic Epidemiology Laboratory, St James’ University Hospital, Leeds, UK).

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