Feasibility and performance of a novel probe panel to detect somatic DNA copy number alterations in clinical specimens for predicting prostate cancer progression.

BACKGROUND: To assess the feasibility of a novel DNA-based probe panel to detect copy number alterations (CNAs) in prostate tumor DNA and its performance for predicting clinical progression. METHODS: A probe panel was developed and optimized to measure CNAs in trace amounts of tumor DNA (2 ng) isolated from formalin-fixed paraffin-embedded tissues. Ten genes previously associated with aggressive disease were targeted. The panel's feasibility and performance were assessed in 175 prostate cancer (PCa) patients who underwent radical prostatectomy with a median 10-year follow-up, including 42 men who developed disease progression (either metastasis and/or PCa-specific death). Association with disease progression was tested using univariable and multivariable analyses. RESULTS: The probe panel detected CNAs in all 10 genes in tumor DNA isolated from either diagnostic biopsies or surgical specimens. A four-gene model (PTEN/MYC/BRCA2/CDKN1B) had the strongest association with disease progression; 64.3% of progressors and 22.5% of non-progressors had at least one CNA in these four genes, odds ratio (OR) (95% confidence interval) = 6.21 (2.77-13.87), P = 8.48E-06. The association with disease progression remained significant after adjusting for known clinicopathological variables. Among the seven progressors of the 65 patients with clinically low-risk disease, three (42.9%) had at least one CNA in these four genes. CONCLUSIONS: The probe panel can detect CNAs in trace amounts of tumor DNA from biopsies or surgical tissues at the time of diagnosis or surgery. CNAs independently predict metastatic/lethal cancer, particularly among men with clinically low-risk disease at diagnosis. If validated, this may improve current abilities to assess tumor aggressiveness.

Preimplantation genetic haplotyping for six Chinese pedigrees with thalassemia using a single nucleotide polymorphism microarray.

OBJECTIVE: The objective of this study is to demonstrate the accuracy and feasibility of using single nucleotide polymorphism (SNP) array-based preimplantation genetic haplotyping (PGH) in Chinese population, as the currently short tandem repeat method is labor-intensive and time-consuming. METHOD: Six pedigrees with thalassemia who underwent preimplantation genetic diagnosis in the First Affiliated Hospital of Sun Yat-sen University in China were included in this study. In vitro fertilization (IVF) cycles and embryo biopsies were performed in clinics. All embryos were diagnosed using both a polymerase chain reaction-based method with short tandem repeat and an SNP-based PGH (SNP microarray) method blindly. RESULTS: SNP-based PGH was successfully conducted for six pedigrees. Our result was concordant with the initial diagnosis based on the mutation detection (96.4%) and human leukocyte antigen matching (100%). All of the embryos detected to be suitable for IVF with PGH were also diagnosed as suitable using initial methods. CONCLUSION: This simple SNP-based PGH method offers simultaneous haplotyping and human leukocyte antigen matching, which facilitates the determination of optimal embryos for IVF with high accuracy. Further studies are needed to help improve this method into clinic utility. © 2017 John Wiley & Sons, Ltd.

Genetic markers associated with early cancer-specific mortality following prostatectomy.

BACKGROUND: This study sought to identify novel effectors and markers of localized but potentially life-threatening prostate cancer (PCa), by evaluating chromosomal copy number alterations (CNAs) in tumors from patients who underwent prostatectomy and correlating these with clinicopathologic features and outcome. METHODS: CNAs in tumor DNA samples from 125 patients in the discovery cohort who underwent prostatectomy were assayed with high-resolution Affymetrix 6.0 single-nucleotide polymorphism microarrays and then analyzed using the Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm. RESULTS: The assays revealed 20 significant regions of CNAs, 4 of them novel, and identified the target genes of 4 of the alterations. By univariate analysis, 7 CNAs were significantly associated with early PCa-specific mortality. These included gains of chromosomal regions that contain the genes MYC, ADAR, or TPD52 and losses of sequences that incorporate SERPINB5, USP10, PTEN, or TP53. On multivariate analysis, only the CNAs of PTEN (phosphatase and tensin homolog) and MYC (v-myc myelocytomatosis viral oncogene homolog) contributed additional prognostic information independent of that provided by pathologic stage, Gleason score, and initial prostate-specific antigen level. Patients whose tumors had alterations of both genes had a markedly elevated risk of PCa-specific mortality (odds ratio = 53; 95% CI = 6.92-405, P = 1 × 10(-4)). Analyses of 333 tumors from 3 additional distinct patient cohorts confirmed the relationship between CNAs of PTEN and MYC and lethal PCa. CONCLUSIONS: This study identified new CNAs and genes that likely contribute to the pathogenesis of localized PCa and suggests that patients whose tumors have acquired CNAs of PTEN, MYC, or both have an increased risk of early PCa-specific mortality.

Association of prostate cancer risk with SNPs in regions containing androgen receptor binding sites captured by ChIP-On-chip analyses.

BACKGROUND: Genome-wide association studies (GWAS) have identified approximately three dozen single nucleotide polymorphisms (SNPs) consistently associated with prostate cancer (PCa) risk. Despite the reproducibility of these associations, the molecular mechanism for most of these SNPs has not been well elaborated as most lie within non-coding regions of the genome. Androgens play a key role in prostate carcinogenesis. Recently, using ChIP-on-chip technology, 22,447 androgen receptor (AR) binding sites have been mapped throughout the genome, greatly expanding the genomic regions potentially involved in androgen-mediated activity. METHODOLOGY/PRINCIPAL FINDINGS: To test the hypothesis that sequence variants in AR binding sites are associated with PCa risk, we performed a systematic evaluation among two existing PCa GWAS cohorts; the Johns Hopkins Hospital and the Cancer Genetic Markers of Susceptibility (CGEMS) study population. We demonstrate that regions containing AR binding sites are significantly enriched for PCa risk-associated SNPs, that is, more than expected by chance alone. In addition, compared with the entire genome, these newly observed risk-associated SNPs in these regions are significantly more likely to overlap with established PCa risk-associated SNPs from previous GWAS. These results are consistent with our previous finding from a bioinformatics analysis that one-third of the 33 known PCa risk-associated SNPs discovered by GWAS are located in regions of the genome containing AR binding sites. CONCLUSIONS/SIGNIFICANCE: The results to date provide novel statistical evidence suggesting an androgen-mediated mechanism by which some PCa associated SNPs act to influence PCa risk. However, these results are hypothesis generating and ultimately warrant testing through in-depth molecular analyses.

Genome-wide copy-number variation analysis identifies common genetic variants at 20p13 associated with aggressiveness of prostate cancer.

The genetic determinants for aggressiveness of prostate cancer (PCa) are poorly understood. Copy-number variations (CNVs) are one of the major sources for genetic diversity and critically modulate cellular biology and human diseases. We hypothesized that CNVs may be associated with PCa aggressiveness. To test this hypothesis, we conducted a genome-wide common CNVs analysis in 448 aggressive and 500 nonaggressive PCa cases recruited from Johns Hopkins Hospital (JHH1) using Affymetrix 6.0 arrays. Suggestive associations were further confirmed using single-nucleotide polymorphisms (SNPs) that tagged the CNVs of interest in an additional 2895 aggressive and 3094 nonaggressive cases, including those from the remaining case subjects of the JHH study (JHH2), the NCI Cancer Genetic Markers of Susceptibility (CGEMS) Study, and the CAncer of the Prostate in Sweden (CAPS) Study. We found that CNP2454, a 32.3 kb deletion polymorphism at 20p13, was significantly associated with aggressiveness of PCa in JHH1 [odds ratio (OR) = 1.30, 95% confidence interval (CI): 1.01-1.68; P = 0.045]. The best-tagging SNP for CNP2454, rs2209313, was used to confirm this finding in both JHH1 (P = 0.045) and all confirmation study populations combined (P = 1.77 × 10(-3)). Pooled analysis using all 3353 aggressive and 3584 nonaggressive cases showed the T allele of rs2209313 was significantly associated with an increased risk of aggressive PCa (OR = 1.17, 95% CI: 1.07-1.27; P = 2.75 × 10(-4)). Our results indicate that genetic variations at 20p13 may be responsible for the progression of PCa.

Distinct Genomic Alterations in Prostate Tumors Derived from African American Men.

We aim to understand, from acquired genetic alterations in tumors, why African American (AA) men are more likely to develop aggressive prostate cancer. By analyzing somatic mutations in 39 genes using deeper next-generation sequencing with an average depth of 2,522 reads for tumor DNA and genome-wide DNA copy-number alterations (CNA) in prostate cancer in a total of 171 AA/black men and comparing with those in 860 European American (EA)/white men, we here present several novel findings. First, >35% of AA men harbor damaging mutations in APC, ATM, BRCA2, KDM6A, KMT2C, KMT2D, MED12, ZFHX3, and ZMYM3, each with >1% of mutated copies. Second, among genes with >10% of mutated copies in tumor cells, ZMYM3 is the most frequently mutated gene in AA prostate cancer. In a patient's tumor with >96% frameshift mutations of ZMYM3, we find allelic imbalances in 10 chromosomes, including losses of five and gains of another four chromosomes, suggesting its role in maintaining genomic integrity. Third, when compared to prostate cancer in EA/white men, a higher frequency of CNAs of MYC, THADA, NEIL3, LRP1B, BUB1B, MAP3K7, BNIP3L and RB1, and a lower frequency of deletions of RYBP, TP53, and TMPRSS2-ERG are observed in AA/black men. Finally, for the above genes with higher frequency of CNAs in AA than in EA, deletion of MAP3K7, BNIP3L, NEIL3 or RB1, or gain of MYC significantly associates with both higher Gleason grade and advanced pathologic stage in AA/black men. Deletion of THADA associates with advanced pathologic stage only. IMPLICATIONS: A higher frequency of damaging mutation in ZMYM3 causing genomic instability along with higher frequency of altered genomic regions including deletions of MAP3K7, BNIP3L, RB1, and NEIL3, and gain of MYC appear to be distinct somatically acquired genetic alterations that may contribute to more aggressive prostate cancer in AA/black men.

HOXA9, PCDH17, POU4F2, and ONECUT2 as a Urinary Biomarker Combination for the Detection of Bladder Cancer in Chinese Patients with Hematuria.

BACKGROUND: DNA methylation biomarkers for bladder cancer (BCa) have not been evaluated extensively in the Chinese population. OBJECTIVE: To develop and validate a urinary biomarker combination of methylation assays in a group of Chinese patients with hematuria. DESIGN, SETTING, AND PARTICIPANTS: A total of 192 urine samples were collected and evaluated from patients with microscopic or gross hematuria, including 97 BCa patients and 95 controls with benign diseases. A two-stage study was conducted: the first stage being assay construction and the second stage being assay validation. Eighty-one urine samples were analyzed for the hypermethylation of eight selected genes in stage 1 and then a four-gene panel was constructed. An additional 111 urine samples were analyzed using the four-gene panel (including HOXA9, PCDH17, POU4F2, and ONECUT2) for independent validation. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The positive predictive value (PPV) and negative predictive value (NPV) were calculated for the combination methylation assay. Uni- and multivariate binary logistic regression analyses (backward elimination, conditional) were performed to calculate the association between BCa and each predictor variable. RESULTS AND LIMITATIONS: The combination assay of HOXA9, PCDH17, POU4F2, and ONECUT2 was selected based on the results of multivariate logistic regression analysis in stage 1. Using a strategy of three-level risk stratification, the assay yielded a consistent PPV of 100%. With an estimated BCa prevalence of 10% in a general hematuria population, the assay would result in an overall NPV of 98%. This combined methylation biomarker would yield an overall area under the receiver operating characteristic curve of 0.871 (with a sensitivity of 90.5% and a specificity of 73.2%) if using the prediction model from multivariate regression analysis. In addition, over half of BCa cases would be predicted accurately and ∼60% of unnecessary cystoscopies could be spared. This study had several limitations. First, the sample size was relatively small. Second, it was performed in a case-control population rather than in a natural hematuria cohort. CONCLUSIONS: A combination methylation assay of HOXA9, PCDH17, POU4F2, and ONECUT2 resulted in high PPV and NPV in Chinese patients with hematuria. With accurate risk prediction, the urinary biomarker combination could spare a sizeable proportion of low-risk patients from extensive and invasive examination. PATIENT SUMMARY: In the present study, we looked at the predictive performance of a urinary biomarker combination of HOXA9, PCDH17, POU4F2, and ONECUT2. We found that this urinary biomarker combination may help discriminate bladder cancer from other benign diseases in patients with hematuria, resulting in a reduction of unnecessary invasive examination in patients at low risk.

Integration of somatic deletion analysis of prostate cancers and germline linkage analysis of prostate cancer families reveals two small consensus regions for prostate cancer genes at 8p.

The evidence for tumor suppressor genes at 8p is well supported by many somatic deletion studies and genetic linkage studies. However, it remains a challenge to pinpoint the tumor suppressor genes at 8p primarily because the implicated regions are broad. In this study, we attempted to narrow down the implicated regions by incorporating evidence from both somatic and germline studies. Using high-resolution Affymetrix arrays, we identified two small common deleted regions among 55 prostate tumors at 8p23.1 (9.8-11.5 Mb) and 8p21.3 (20.6-23.7 Mb). Interestingly, our fine mapping linkage analysis at 8p among 206 hereditary prostate cancer families also provided evidence for linkage at these two regions at 8p23.1 (5.8-11.2 Mb) and at 8p21.3 (19.6-23.9 Mb). More importantly, by combining the results from the somatic deletion analysis and genetic linkage analysis, we were able to further narrow the regions to approximately 1.4 Mb at 8p23.1 and approximately 3.1 Mb at 8p21.3. These smaller consensus regions may facilitate a more effective search for prostate cancer genes at 8p.

Identification of Cancer-Specific Methylation of Gene Combination for the Diagnosis of Bladder Cancer.

Here we conducted an evidence-based study in developing and validating a urinary biomarker combination of gene methylation assays in patients with hematuria. A number of 99 urine samples were obtained and detected from Chinese patients with hematuria. The Cancer Genome Atlas cohort with methylation (HM450) beta-values and clinical data of 412 bladder cancer and 21 matching normal tissue was included as a validation series. A risk score formula was then developed and calculated by the targeted genes, weighted by their estimated regression coefficients from the multivariable binary logistic regression analyses, and evaluated by receiver operating characteristic (ROC) curves analysis. The combination assay of HOXA9, ONECUT2, PCDH17, PENK, TWIST1, VIM and ZNF154 was singled out according to the results of multivariate logistic regression analysis. The higher probability of DNA methylation of all the selected 7 genes was found in bladder cancer group than the control group. Remarkable higher DNA methylation beta-values of all the selected 7 genes were also displayed in bladder cancer tissues compared with their matching normal bladder tissues. And the AUC value of our risk score model were 0.894 and 0.851 in respective cohort, revealing highlighted predictive value of our risk score model on bladder cancer diagnosis. In conclusions, a urinary combined methylation assay of HOXA9, ONECUT2, PCDH17, PENK, TWIST1, VIM and ZNF154 displayed accurate prediction of bladder cancer in hematuria patients, which provided the guidance for the patients at early stage tumor and during the follow-up after operation. Of course, prospective study based on a hematuria cohort with a large sample size should be conducted to validate these findings in the future.

Deletion of a small consensus region at 6q15, including the MAP3K7 gene, is significantly associated with high-grade prostate cancers.

PURPOSE: Chromosome 6q14-21 is commonly deleted in prostate cancers, occurring in approximately 22% of all tumors and approximately 40% of metastatic tumors. However, candidate prostate tumor suppressor genes in this region have not been identified, in part due to the large and broad nature of the deleted region implicated in previous studies. EXPERIMENTAL DESIGN: We first used high-resolution Affymetrix single nucleotide polymorphism arrays to examine DNA from malignant and matched nonmalignant cells from 55 prostate cancer patients. We identified a small consensus region on 6q14-21 and evaluated the deletion status within the region among additional 40 tumors and normal pairs using quantitative PCR and fluorescence in situ hybridization. We finally tested the association between the deletion and Gleason score using the Fisher's exact test. RESULTS: Tumors with small, interstitial deletions at 6q14-21 defined an 817-kb consensus region that is affected in 20 of 21 tumors. The MAP3K7 gene is one of five genes located in this region. In total, MAP3K7 was deleted in 32% of 95 tumors. Importantly, deletion of MAP3K7 was highly associated with higher-grade disease, occurring in 61% of tumors with Gleason score >or=8 compared with only 22% of tumors with Gleason score

Antibody repertoire development in swine.

Swine belong to the Order Artiodactyla and like mice and humans, express IgM, IgD, IgG, IgE and IgA antibodies but a larger number of IgG subclasses. Like rabbits and chickens, expressed V(H) genes belong to the ancestral V(H)3 family and only 5 comprise >80% of the pre-immune repertoire. Since they use primarily two D(H) segments and have a single J(H) like chickens, junctional diversity plays a relatively greater role in repertoire formation than in humans and mice. Proportional light chain usage surprisingly resembles that in humans and is therefore distinctly different from the predominant kappa chain usage (>90%) of lab rodents and predominant lambda chain usage in other ungulates (>90%). The pre-immune V(kappa) repertoire also appears restricted since >95% of V(kappa)J(kappa) rearrangements use only a few members of the IGKV2 family and only J(kappa)2. Two V(lambda) families (IGLV3 and IGLV8) are used in forming the pre-immune repertoire. Antibodies that do not utilize light chains as in camelids, or the lengthy CDR3 regions seen in cattle that use V(H)4 family genes, have not been reported in swine. B cell lymphogenesis first occurs in the yolk sac but early VDJ rearrangements differ from mice and humans in that nearly 100% are in-frame and N-region additions are already present. Swine possess ileal Peyers patches like sheep which may be important for antigen-independent B cell repertoire diversification. The presence of pro B-like cells in interlobular areas of thymus and mature B cells in the thymic medulla that have switched to especially IgA in early gestation, is so far unique among mammals. The offspring of swine are believed to receive no passive immunity in utero and are precosial. Thus, they are a useful model for studies on fetal-neonatal immunological development. The model has already shown that: (a) colonization of the gut is required for responsiveness to TD and TI-2 antigens, (b) responsiveness due to colonization depends on bacterial PAMPs and (c) some viral pathogens can interfere with the establishment of immune homeostasis in neonates. Studies on swine reinforce concerns that caution be used when paradigms arising from studies in one mammal are extrapolated to other mammals, even when similarities are predicted by taxonomy and phylogeny. Swine exemplify a situation in which evolutionary diversification of the immune system is not characteristic of an entire order or even of other related systems in the same species.

Characterization of porcine CD19 and anti-CD19 monoclonal antibodies.

CD19 is an important pan B cell marker and co-stimulatory protein in humans and mice. Efforts to further characterize B cell ontogeny in swine have been hampered by the lack of monoclonal antibodies (mAb) to valuable surface markers like Vpre-B, CD19, CD34 and CD43. We report here on the complete nucleotide and deduced amino acid sequence of porcine CD19, the cross-reactivity of anti-human CD19 monoclonals and efforts to prepare anti-porcine CD19 mAb to bacterially-expressed products. Porcine CD19 is highly homologous to those in the few other species studied, i.e. human, mouse and guinea pig, but only in certain domains. Among the 14 CD19 exons, homology approaches 90% to human CD19 in exons 6, 9, 11 and 12 and is approximately 80% with other species in this region. The highly homologous C-terminal cytoplasmic region contains nine tyrosines including the YEND/E motif that binds the SH2 domain of Fyn. Two different porcine CD19 isoforms that differ in their 3' UTRs were identified just as in human CD19. Thus, the signaling properties of CD19 may be similar to those in humans. On the other hand, only 60% sequence similarity was seen in exons 1-5 that encode the N-terminal extracellullar region that is involved in ligand binding and is the target of CD19-specific mAb. This probably explains why only 1 of the 17 anti-human CD19 mAb tested recognized swine B cells. Furthermore, when the extracellular domains of CD19 were expressed in E. coli, mAbs to the bacterially-expressed product did not recognize CD19 on porcine B cells suggesting that carbohydrate-dependent conformation may determine antigenicity.

Antibody repertoire development in fetal and neonatal piglets. XII. Three IGLV genes comprise 70% of the pre-immune repertoire and there is little junctional diversity.

We characterized 239 lambda rearrangements from fetal and germfree (GF) piglets to: (1) determine if transcripts recovered from the earliest sites of B cell lymphogenesis were unique (2) determine what proportion of the genome is used to form the pre-immune repertoire (3) estimate the degree of somatic hypermutation and junctional diversity during ontogeny and (4) test whether piglets maintained germfree in isolators (GF piglets) have a more diversified repertoire than fetal piglets. We show that all expressed lambda genes belong to the IGLV3 and IGLV8 families and only IGLJ2 and IGLJ3 were expressed and used equally throughout fetal and neonatal life. Only genes of the IGLV8 family were used in yolk sac and fetal liver and in these tissues, IGLV8-10 comprised >50%. However, the IGLV8 genes recovered at these early sites of B cell lymphogenesis were recovered at all stages of development. Thus, no unique lambda rearrangement was recovered at the first sites of B cell development. The frequency of somatic hypermutation (SHM) in fetal piglets was ~5.9 per Kb equivalent, mutation were concentrated in CDR regions and did not increase in GF piglets. The average CDR3 length was 30 nt ± 2.7 and did not change in GF piglets. Similar to the heavy chain pre-immune repertoire in this species, three IGLV genes account for ~70% of the repertoire. Unlike the heavy chain repertoire, junctional diversity was very limited.

Evaluation of PPP2R2A as a prostate cancer susceptibility gene: a comprehensive germline and somatic study.

PPP2R2A, mapped to 8p21.2, codes for the α isoform of the regulatory B55 subfamily of protein phosphatase 2 (PP2A). PP2A is one of the four major serine/threonine phosphatases and is implicated in the negative control of cell growth and division. Because of its known functions and location within a chromosomal region where evidence for linkage and somatic loss of heterozygosity was found, we hypothesized that either somatic copy number changes or germline sequence variants in PPP2R2A may increase prostate cancer (PCa) risk. We examined PPP2R2A deletion status in 141 PCa samples using Affymetrix SNP arrays. It was found that PPP2R2A was commonly (67.1%) deleted in tumor samples, including a homozygous deletion in three tumors (2.1%). We performed a mutation screen for PPP2R2A in 96 probands of hereditary prostate cancer families. No high risk mutations were identified. In addition, we re-analyzed 10 SNPs of PPP2R2A in sporadic PCa cases and controls. No significant differences in the allele and genotype frequencies were observed among either PCa cases and controls or PCa aggressive and non-aggressive cases. Taken together, these results suggest that a somatic deletion rather than germline sequence variants of PPP2R2A may play a more important role in PCa susceptibility.

Compilation of a comprehensive gene panel for systematic assessment of genes that govern an individual's drug responses.

AIMS: Polymorphisms of genes involved in the pharmacokinetic and pharmacodynamic processes underlie the divergent drug responses among individuals. Despite some successes in identifying these polymorphisms, the candidate gene approach suffers from insufficient gene coverage whereas the genome-wide association approach is limited by less than ideal coverage of SNPs in some important genes. To expand the potential of the candidate approach, we aim to delineate a comprehensive network of drug-response genes for in-depth genetic studies. MATERIALS & METHODS: Pharmacologically important genes were extracted from various sources including literatures and web resources. These genes, along with their homologs and regulatory miRNAs, were organized based on their pharmacological functions and weighted by literature evidence and confidence levels. Their coverage was evaluated by analyzing three commercial SNP chips commonly used for genome-wide association studies: Affymetrix SNP array 6.0, Illumina HumanHap1M and Illumina Omni. RESULTS: A panel of drug-response genes was constructed, which contains 923 pharmacokinetic genes, 703 pharmacodynamic genes and 720 miRNAs. There are only 16.7% of these genes whose all known SNPs can be directly or indirectly (r(2) > 0.8) captured by the SNP chips with coverage of more than 80%. This is possibly because these SNPs chips have notably poor performance over rare SNPs and miRNA genes. CONCLUSION: We have compiled a panel of candidate genes that may be pharmacologically important. Using this knowledgebase, we are able to systematically evaluate genes and their variants that govern an individual's response to a given pharmaceutical therapy. This approach can serve as a necessary complement to genome-wide associations.

Association of a germ-line copy number variation at 2p24.3 and risk for aggressive prostate cancer.

We searched for deletions in the germ-line genome among 498 aggressive prostate cancer cases and 494 controls from a population-based study in Sweden [CAncer of the Prostate in Sweden (CAPS)] using Affymetrix SNP arrays. By comparing allele intensities of approximately 500,000 SNP probes across the genome, a germ-line deletion at 2p24.3 was observed to be significantly more common in cases (12.63%) than in controls (8.28%); P = 0.028. To confirm the association, we genotyped this germ-line copy number variation (CNV) in additional subjects from CAPS and from Johns Hopkins Hospital (JHH). Overall, among 4,314 cases and 2,176 controls examined, the CNV was significantly associated with prostate cancer risk [odds ratio (OR), 1.25; 95% confidence interval (95% CI), 1.06-1.48; P = 0.009]. More importantly, the association was stronger for aggressive prostate cancer (OR, 1.31; 95% CI, 1.08-1.58; P = 0.006) than for nonaggressive prostate cancer (OR, 1.19; 95% CI, 0.98-1.45; P = 0.08). The biological effect of this germ-line CNV is unknown because no known gene resides in the deletion. Results from this study represent the first novel germ-line CNV that was identified from a genome-wide search and was significantly, but moderately, associated with prostate cancer risk. Additional confirmation of this association and functional studies are warranted.

Homozygous deletions and recurrent amplifications implicate new genes involved in prostate cancer.

Prostate cancer cell lines provide ideal in vitro systems for the identification and analysis of prostate tumor suppressors and oncogenes. A detailed characterization of the architecture of prostate cancer cell line genomes would facilitate the study of precise roles of various genes in prostate tumorigenesis in general. To contribute to such a characterization, we used the GeneChip 500K single nucleotide polymorphic (SNP) array for analysis of genotypes and relative DNA copy number changes across the genome of 11 cell lines derived from both normal and cancerous prostate tissues. For comparison purposes, we also examined the alterations observed in the cell lines in tumor/normal pairs of clinical samples from 72 patients. Along with genome-wide maps of DNA copy number changes and loss of heterozygosity for these cell lines, we report previously unreported homozygous deletions and recurrent amplifications in prostate cancers in this study. The homozygous deletions affected a number of biologically important genes, including PPP2R2A and BNIP3L identified in this study and CDKN2A/CDKN2B reported previously. Although most amplified genomic regions tended to be large, amplifications at 8q24.21 were of particular interest because the affected regions are relatively small, are found in multiple cell lines, are located near MYC, an oncogene strongly implicated in prostate tumorigenesis, and are known to harbor SNPs that are associated with inherited susceptibility for prostate cancer. The genomic alterations revealed in this study provide an important catalog of positional information relevant to efforts aimed at deciphering the molecular genetic basis of prostate cancer.

Evidence for two independent prostate cancer risk-associated loci in the HNF1B gene at 17q12.

We carried out a fine-mapping study in the HNF1B gene at 17q12 in two study populations and identified a second locus associated with prostate cancer risk, approximately 26 kb centromeric to the first known locus (rs4430796); these loci are separated by a recombination hot spot. We confirmed the association with a SNP in the second locus (rs11649743) in five additional populations, with P = 1.7 x 10(-9) for an allelic test of the seven studies combined. The association at each SNP remained significant after adjustment for the other SNP.

DNA copy number alterations in prostate cancers: a combined analysis of published CGH studies.

BACKGROUND: Identifying genomic regions that are commonly deleted or gained in neoplastic cells is an important approach to identify tumor suppressor genes and oncogenes. Studies in the last two decades have identified a number of common DNA copy number alterations in prostate cancer. However, because of various sample sizes, diverse tumor types and sources, as well as a variety of detection methods with various sensitivities and resolutions, it is difficult to summarize and fully interpret the overall results. METHODS: We performed a combined analysis of all published comparative genomic hybridization (CGH) studies of prostate cancer and estimated the frequency of alterations across the genome for all tumors, as well as in advanced and localized tumors separately. A total of 41 studies examining 872 cancers were included in this study. RESULTS: The frequency of deletions and gains were estimated in all tumors, as well as in advanced and localized tumors. Eight deleted and five gained regions were found in more than 10% of the prostate tumors. An additional six regions were commonly deleted and seven were commonly gained in advanced tumors. While 8p was the most common location of deletion, occurring in about a third of all tumors and about half of advanced tumors, 8q was the most commonly gained region, affecting about a quarter of all tumors and about half of all advanced tumors. CONCLUSIONS: The large number of tumors examined in this combined analysis provides better estimates of the frequency of specific alterations in the prostate cancer cell genome, and offers important clues for prioritizing efforts to identify tumor suppressor genes and oncogenes in these altered regions.