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1.  Germline BRCA mutation does not prevent response to taxane-based therapy for the treatment of castration-resistant prostate cancer 
BJU international  2011;109(5):713-719.
Objective
To investigate the relationship between BRCA mutation status and response to taxane-based chemotherapy, since BRCA mutation carriers with prostate cancer appear to have worse survival than non-carriers and docetaxel improves survival in patients with castration-resistant prostate cancer.
Patients and Methods
We determined BRCA mutation prevalence in 158 Ashkenazi Jewish (AJ) men with castration-resistant prostate cancer. Clinical data were collected as part of an institutional prostate cancer research database and through additional medical record review.
Clinical records and DNA samples were linked through a unique identifier, anonymizing the samples before genetic testing for the AJ BRCA1/2 founder mutations.
Response to taxane-based therapy was defined by the prostate-specific antigen nadir within 12 weeks of therapy.
Results
In all, 88 men received taxane-based treatment, seven of whom were BRCA carriers (three BRCA1, four BRCA2; 8%). Initial response to taxane was available for all seven BRCA carriers and for 69 non-carriers.
Overall, 71% (54/76) of patients responded to treatment, with no significant difference between carriers (57%) and non-carriers (72%) (absolute difference 15%; 95% confidence interval −23% to 53%; P = 0.4).
Among patients with an initial response, the median change in prostate-specific antigen was similar for BRCA carriers (−63%, interquartile range −71% to −57%) and non-carriers (−60%, interquartile range −78% to −35%) (P = 0.6).
At last follow-up, all seven BRCA carriers and 49 non-carriers had died from prostate cancer. One BRCA2 carrier treated with docetaxel plus platinum survived 37 months.
Conclusion
In this small, hypothesis-generating study approximately half of BRCA carriers had a prostate-specific antigen response to taxane-based chemotherapy, suggesting that it is an active therapy in these individuals.
doi:10.1111/j.1464-410X.2011.10292.x
PMCID: PMC3971723  PMID: 21756279
castration-resistant prostate cancer; BRCA1; BRCA2; taxane; docetaxel; response
2.  Association of a HOXB13 Variant with Breast Cancer 
The New England journal of medicine  2012;367(5):480-481.
doi:10.1056/NEJMc1205138
PMCID: PMC3926433  PMID: 22853031
3.  Genome-wide analysis of the role of copy-number variation in pancreatic cancer risk 
Although family history is a risk factor for pancreatic adenocarcinoma, much of the genetic etiology of this disease remains unknown. While genome-wide association studies have identified some common single nucleotide polymorphisms (SNPs) associated with pancreatic cancer risk, these SNPs do not explain all the heritability of this disease. We hypothesized that copy number variation (CNVs) in the genome may play a role in genetic predisposition to pancreatic adenocarcinoma. Here, we report a genome-wide analysis of CNVs in a small hospital-based, European ancestry cohort of pancreatic cancer cases and controls. Germline CNV discovery was performed using the Illumina Human CNV370 platform in 223 pancreatic cancer cases (both sporadic and familial) and 169 controls. Following stringent quality control, we asked if global CNV burden was a risk factor for pancreatic cancer. Finally, we performed in silico CNV genotyping and association testing to discover novel CNV risk loci. When we examined the global CNV burden, we found no strong evidence that CNV burden plays a role in pancreatic cancer risk either overall or specifically in individuals with a family history of the disease. Similarly, we saw no significant evidence that any particular CNV is associated with pancreatic cancer risk. Taken together, these data suggest that CNVs do not contribute substantially to the genetic etiology of pancreatic cancer, though the results are tempered by small sample size and large experimental variability inherent in array-based CNV studies.
doi:10.3389/fgene.2014.00029
PMCID: PMC3923159  PMID: 24592275
pancreatic cancer; copy number variation; cancer risk; SNP microarrays; CNVs
4.  Evaluation of chromosome 6p22 as a breast cancer risk modifier locus in a follow-up study of BRCA2 mutation carriers 
Several common germline variants identified through genome-wide association studies of breast cancer risk in the general population have recently been shown to be associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. When combined, these variants can identify marked differences in the absolute risk of developing breast cancer for mutation carriers, suggesting that additional modifier loci may further enhance individual risk assessment for BRCA1 and BRCA2 mutation carriers. Recently, a common variant on 6p22 (rs9393597) was found to be associated with increased breast cancer risk for BRCA2 mutation carriers [Hazard ratio (HR)=1.55, 95% CI 1.25–1.92, p=6.0×10−5]. This observation was based on data from GWAS studies in which, despite statistical correction for multiple comparisons, the possibility of false discovery remains a concern. Here we report on an analysis of this variant in an additional 6,165 BRCA1 and 3,900 BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). In this replication analysis, rs9393597 was not associated with breast cancer risk for BRCA2 mutation carriers [HR=1.09, 95% CI 0.96–1.24, p=0.18]. No association with ovarian cancer risk for BRCA1 or BRCA2 mutation carriers or with breast cancer risk for BRCA1 mutation carriers was observed. This follow-up study suggests that, contrary to our initial report, this variant is not associated with breast cancer risk among individuals with germline BRCA2 mutations.
doi:10.1007/s10549-012-2255-6
PMCID: PMC3482828  PMID: 23011509
BRCA1; BRCA2; genetic modifier; association study
5.  A Recessive Founder Mutation in Regulator of Telomere Elongation Helicase 1, RTEL1, Underlies Severe Immunodeficiency and Features of Hoyeraal Hreidarsson Syndrome 
PLoS Genetics  2013;9(8):e1003695.
Dyskeratosis congenita (DC) is a heterogeneous inherited bone marrow failure and cancer predisposition syndrome in which germline mutations in telomere biology genes account for approximately one-half of known families. Hoyeraal Hreidarsson syndrome (HH) is a clinically severe variant of DC in which patients also have cerebellar hypoplasia and may present with severe immunodeficiency and enteropathy. We discovered a germline autosomal recessive mutation in RTEL1, a helicase with critical telomeric functions, in two unrelated families of Ashkenazi Jewish (AJ) ancestry. The affected individuals in these families are homozygous for the same mutation, R1264H, which affects three isoforms of RTEL1. Each parent was a heterozygous carrier of one mutant allele. Patient-derived cell lines revealed evidence of telomere dysfunction, including significantly decreased telomere length, telomere length heterogeneity, and the presence of extra-chromosomal circular telomeric DNA. In addition, RTEL1 mutant cells exhibited enhanced sensitivity to the interstrand cross-linking agent mitomycin C. The molecular data and the patterns of inheritance are consistent with a hypomorphic mutation in RTEL1 as the underlying basis of the clinical and cellular phenotypes. This study further implicates RTEL1 in the etiology of DC/HH and immunodeficiency, and identifies the first known homozygous autosomal recessive disease-associated mutation in RTEL1.
Author Summary
Patients with dyskeratosis congenita (DC), a rare inherited disease, are at very high risk of developing cancer and bone marrow failure. The clinical features of DC include nail abnormalities, skin discoloration, and white spots in the mouth. Patients with Hoyeraal-Hreidarsson syndrome (HH) have symptoms of DC plus cerebellar hypoplasia, immunodeficiency, and poor prenatal growth. DC and HH are caused by defects in telomere biology; improperly maintained telomeres are thought to be a major contributor to carcinogenesis. In half the cases of DC, the causative mutation is unknown. By studying families affected by DC for whom a causative mutation has not yet been identified, we have discovered a homozygous germline mutation in RTEL1, a telomere maintenance gene that, if mutated, can result in HH. The mutations result in the inability of the RTEL1 protein to function properly at the telomere, and underscore its important role in telomere biology.
doi:10.1371/journal.pgen.1003695
PMCID: PMC3757051  PMID: 24009516
6.  Susceptibility Loci Associated with Prostate Cancer Progression and Mortality 
Purpose
Prostate cancer is a heterogenous disease with a variable natural history that is not accurately predicted by currently used prognostic tools.
Experimental Design
We genotyped 798 prostate cancer cases of Ashkenazi Jewish ancestry treated for localized prostate cancer between June 1988 and December 2007. Blood samples were prospectively collected and de-identified before being genotyped and matched to clinical data. The survival analysis was adjusted for Gleason score and PSA. We investigated associations between 29 single nucleotide polymorphisms (SNPs) and biochemical recurrence, castration-resistant metastasis, and prostate cancer-specific survival. Subsequently, we performed an independent analysis using a high resolution panel of 13 SNPs.
Results
On univariate analysis, 2 SNPs were associated (p<0.05) with biochemical recurrence; 3 SNPs were associated with clinical metastases; and 1 SNP was associated with prostate cancer-specific mortality. Applying a Bonferroni correction (p<0.0017), one association with biochemical recurrence (p=0.0007) was significant. Three SNPs showed associations on multivariable analysis, although not after correcting for multiple testing. The secondary analysis identified an additional association with prostate cancer-specific mortality in KLK3 (p<0.0005 by both univariate and multivariable analysis).
Conclusions
We identified associations between prostate cancer susceptibility SNPs and clinical endpoints. The rs61752561 in KLK3 and rs2735839 in the KLK2-KLK3 intergenic region associated strongly with prostate cancer-specific survival, and rs10486567 in 7JAZF1 gene associated with biochemical recurrence. A larger study will be required to independently validate these findings and determine the role of these SNPs in prognostic models.
doi:10.1158/1078-0432.CCR-10-0028
PMCID: PMC3732009  PMID: 20460480
Single nucleotide polymorphisms; Prostate cancer; Prognosis
7.  Improved survival for BRCA2-associated serous ovarian cancer compared to both BRCA-negative and BRCA1-associated serous ovarian cancer 
Cancer  2011;118(15):3703-3709.
BACKGROUND
Multiple observational studies have suggested that BRCA-associated ovarian cancers have improved survival compared to BRCA-negative ovarian cancers. Most of these studies, however, have combined BRCA1 and BRCA2 patients or evaluated only BRCA1 patients. We sought to examine if BRCA1− and BRCA2-associated ovarian cancers were associated with different outcomes.
METHODS
A single-institution retrospective analysis of patients seen between January 1, 1996 and February 1st, 2011 for a new diagnosis of histologically confirmed Stage III or IV serous ovarian, fallopian tube, or primary peritoneal cancer and who underwent BRCA mutation testing on one of two IRB approved follow-up studies. Patients tested for BRCA mutations beyond 24 months of diagnosis were excluded from analysis to minimize selection bias from including patients referred for genetic testing because of long survival.
RESULTS
Data from 190 patients (143 BRCA−, 30 BRCA1+, 17 BRCA2+) were analyzed. During the study period, 73 deaths were observed (60 BRCA−, 10 BRCA1+, 3 BRCA2+). Median follow-up time for the remaining 117 survivors was 2.5 years. At 3 years, 69.4%, 90·7%, and 100% of BRCA−, BRCA1+, and BRCA2+ patients were alive, respectively. On univariate analysis, age, BRCA2, debulking status, and type of first-line therapy (intravenous or intraperitoneal) were significant predictors of overall survival (OS). On multivariate analysis, BRCA2 status (HR .20; 95% CI, .06–.65; P=.007) but not BRCA1 status (HR .70; 95% CI, .36–1.38; P=.31) predicted for improved OS compared to BRCA-patients. When carriers of BRCA2 mutations were directly compared to carriers of BRCA1 mutations, BRCA2 mutation status appeared to confer an improved OS (HR .29; 95% CI, 0.08–1.05; P=.060), although this finding did not reach significance.
CONCLUSION
Our data suggest that BRCA2 status confers an overall survival advantage compared to both BRCA− and BRCA1 status in high-grade serous ovarian cancer. This finding may have important implications for clinic trial design.
doi:10.1002/cncr.26655
PMCID: PMC3625663  PMID: 22139894
Ovarian cancer; BRCA1; BRCA2; PARP inhibitors
8.  Germline BRCA mutations denote a clinicopathologic subset of prostate cancer 
Purpose
Increased prostate cancer risk has been reported for BRCA mutation carriers but BRCA-associated clinicopathologic features have not been clearly defined.
Experimental Design
We determined BRCA mutation prevalence in 832 Ashkenazi Jewish (AJ) men diagnosed with localized prostate cancer between 1988 and 2007 and 454 AJ controls, and compared clinical outcome measures among 26 BRCA mutation carriers and 806 non-carriers. Kruskal-Wallis tests were used to compare age of diagnosis and Gleason Score (GS), and logistic regression models to determine associations between carrier status, prostate cancer risk, and GS. Hazard ratios for clinical endpoints were estimated using Cox proportional hazards models.
Results
BRCA2 mutations were associated with a threefold risk of prostate cancer (OR [95% CI]=3.18 [1.52-6.66]; p = 0.002), and presented with more poorly differentiated (GS ≥ 7) tumors(85% vs. 57%, p= 0.0002) compared with non-BRCA associated PC. BRCA1 mutations conferred no increased risk. After 7,254 person-years of follow-up, and adjusting for clinical stage, PSA, GS, and treatment, BRCA2 and BRCA1 mutation carriers had a higher risk of recurrence (HR [95% CI] = 2.41[1.23, 4.75] and 4.32 [1.31, 13.62], respectively) and prostate cancer -specific death (HR [95% CI] = 5.48 [2.03, 14.79] and 5.16 [1.09,24.53], respectively) than non-carriers.
Conclusions
BRCA2 mutation-carriers had an increased risk of prostate cancer and a higher histological grade, and BRCA1 or BRCA2 mutations were associated with a more aggressive clinical course. These results may have impact on tailoring clinical management of this subset of hereditary prostate cancer.
doi:10.1158/1078-0432.CCR-09-2871
PMCID: PMC3713614  PMID: 20215531
BRCA1; BRCA2; prostate cancer; clinicopathologic associations
9.  Assessment of SLX4 Mutations in Hereditary Breast Cancers 
PLoS ONE  2013;8(6):e66961.
Background
SLX4 encodes a DNA repair protein that regulates three structure-specific endonucleases and is necessary for resistance to DNA crosslinking agents, topoisomerase I and poly (ADP-ribose) polymerase (PARP) inhibitors. Recent studies have reported mutations in SLX4 in a new subtype of Fanconi anemia (FA), FA-P. Monoallelic defects in several FA genes are known to confer susceptibility to breast and ovarian cancers.
Methods and Results
To determine if SLX4 is involved in breast cancer susceptibility, we sequenced the entire SLX4 coding region in 738 (270 Jewish and 468 non-Jewish) breast cancer patients with 2 or more family members affected by breast cancer and no known BRCA1 or BRCA2 mutations. We found a novel nonsense (c.2469G>A, p.W823*) mutation in one patient. In addition, we also found 51 missense variants [13 novel, 23 rare (MAF<0.1%), and 15 common (MAF>1%)], of which 22 (5 novel and 17 rare) were predicted to be damaging by Polyphen2 (score = 0.65–1). We performed functional complementation studies using p.W823* and 5 SLX4 variants (4 novel and 1 rare) cDNAs in a human SLX4-null fibroblast cell line, RA3331. While wild type SLX4 and all the other variants fully rescued the sensitivity to mitomycin C (MMC), campthothecin (CPT), and PARP inhibitor (Olaparib) the p.W823* SLX4 mutant failed to do so.
Conclusion
Loss-of-function mutations in SLX4 may contribute to the development of breast cancer in very rare cases.
doi:10.1371/journal.pone.0066961
PMCID: PMC3694110  PMID: 23840564
10.  A germline JAK2 SNP is associated with predisposition to the development of JAK2V617F-positive myeloproliferative neoplasms 
Nature genetics  2009;41(4):455-459.
Polycythemia vera, essential thrombocythemia and primary myelofibrosis are myeloproliferative neoplasms (MPN) characterized by multilineage clonal hematopoiesis1–5. Given that the identical somatic activating mutation in the JAK2 tyrosine kinase gene (JAK2V617F) is observed in most individuals with polycythemia vera, essential thrombocythemia and primary myelofibrosis6–10, there likely are additional genetic events that contribute to the pathogenesis of these phenotypically distinct disorders. Moreover, family members of individuals with MPN are at higher risk for the development of MPN, consistent with the existence of MPN predisposition loci11. We hypothesized that germline variation contributes to MPN predisposition and phenotypic pleiotropy. Genome-wide analysis identified an allele in the JAK2 locus (rs10974944) that predisposes to the development of JAK2V617F-positive MPN, as well as three previously unknown MPN modifier loci. We found that JAK2V617F is preferentially acquired in cis with the predisposition allele. These data suggest that germline variation is an important contributor to MPN phenotype and predisposition.
doi:10.1038/ng.342
PMCID: PMC3676425  PMID: 19287384
11.  The KL-VS sequence variant of Klotho and cancer risk in BRCA1 and BRCA2 mutation carriers 
Breast Cancer Research and Treatment  2012;132(3):1119-1126.
Klotho (KL) is a putative tumor suppressor gene in breast and pancreatic cancers located at chromosome 13q12. A functional sequence variant of Klotho (KL-VS) was previously reported to modify breast cancer risk in Jewish BRCA1 mutation carriers. The effect of this variant on breast and ovarian cancer risks in non-Jewish BRCA1/BRCA2 mutation carriers has not been reported. The KL-VS variant was genotyped in women of European ancestry carrying a BRCA mutation: 5,741 BRCA1 mutation carriers (2,997 with breast cancer, 705 with ovarian cancer, and 2,039 cancer free women) and 3,339 BRCA2 mutation carriers (1,846 with breast cancer, 207 with ovarian cancer, and 1,286 cancer free women) from 16 centers. Genotyping was accomplished using TaqMan® allelic discrimination or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Data were analyzed within a retrospective cohort approach, stratified by country of origin and Ashkenazi Jewish origin. The per-allele hazard ratio (HR) for breast cancer was 1.02 (95% CI 0.93–1.12, P = 0.66) for BRCA1 mutation carriers and 0.92 (95% CI 0.82–1.04, P = 0.17) for BRCA2 mutation carriers. Results remained unaltered when analysis excluded prevalent breast cancer cases. Similarly, the per-allele HR for ovarian cancer was 1.01 (95% CI 0.84–1.20, P = 0.95) for BRCA1 mutation carriers and 0.9 (95% CI 0.66–1.22, P = 0.45) for BRCA2 mutation carriers. The risk did not change when carriers of the 6174delT mutation were excluded. There was a lack of association of the KL-VS Klotho variant with either breast or ovarian cancer risk in BRCA1 and BRCA2 mutation carriers.
doi:10.1007/s10549-011-1938-8
PMCID: PMC3352679  PMID: 22212556
Breast cancer; Ovarian cancer-Klotho; BRCA; Modifier gene
12.  Genetics, Genomics and Cancer Risk Assessment: State of the art and future directions in the era of personalized medicine 
CA: a cancer journal for clinicians  2011;10.3322/caac.20128.
Scientific and technologic advances are revolutionizing our approach to genetic cancer risk assessment, cancer screening and prevention, and targeted therapy, fulfilling the promise of personalized medicine. In this monograph we review the evolution of scientific discovery in cancer genetics and genomics, and describe current approaches, benefits and barriers to the translation of this information to the practice of preventive medicine. Summaries of known hereditary cancer syndromes and highly penetrant genes are provided and contrasted with recently-discovered genomic variants associated with modest increases in cancer risk. We describe the scope of knowledge, tools, and expertise required for the translation of complex genetic and genomic test information into clinical practice. The challenges of genomic counseling include the need for genetics and genomics professional education and multidisciplinary team training, the need for evidence-based information regarding the clinical utility of testing for genomic variants, the potential dangers posed by premature marketing of first-generation genomic profiles, and the need for new clinical models to improve access to and responsible communication of complex disease-risk information. We conclude that given the experiences and lessons learned in the genetics era, the multidisciplinary model of genetic cancer risk assessment and management will serve as a solid foundation to support the integration of personalized genomic information into the practice of cancer medicine.
doi:10.3322/caac.20128
PMCID: PMC3346864  PMID: 21858794
Genomics; genetic cancer risk assessment; genetic counseling; prevention; genetics; hereditary cancer
13.  Susceptibility Loci Associated with Specific and Shared Subtypes of Lymphoid Malignancies 
PLoS Genetics  2013;9(1):e1003220.
The genetics of lymphoma susceptibility reflect the marked heterogeneity of diseases that comprise this broad phenotype. However, multiple subtypes of lymphoma are observed in some families, suggesting shared pathways of genetic predisposition to these pathologically distinct entities. Using a two-stage GWAS, we tested 530,583 SNPs in 944 cases of lymphoma, including 282 familial cases, and 4,044 public shared controls, followed by genotyping of 50 SNPs in 1,245 cases and 2,596 controls. A novel region on 11q12.1 showed association with combined lymphoma (LYM) subtypes. SNPs in this region included rs12289961 near LPXN, (PLYM = 3.89×10−8, OR = 1.29) and rs948562 (PLYM = 5.85×10−7, OR = 1.29). A SNP in a novel non-HLA region on 6p23 (rs707824, PNHL = 5.72×10−7) was suggestive of an association conferring susceptibility to lymphoma. Four SNPs, all in a previously reported HLA region, 6p21.32, showed genome-wide significant associations with follicular lymphoma. The most significant association with follicular lymphoma was for rs4530903 (PFL = 2.69×10−12, OR = 1.93). Three novel SNPs near the HLA locus, rs9268853, rs2647046, and rs2621416, demonstrated additional variation contributing toward genetic susceptibility to FL associated with this region. Genes implicated by GWAS were also found to be cis-eQTLs in lymphoblastoid cell lines; candidate genes in these regions have been implicated in hematopoiesis and immune function. These results, showing novel susceptibility regions and allelic heterogeneity, point to the existence of pathways of susceptibility to both shared as well as specific subtypes of lymphoid malignancy.
Author Summary
B-cell lymphomas comprise several diseases representing aberrant proliferations of immune cells at various stages of maturation. It might be expected that dissimilar subtypes of lymphoma will have different etiologic and pathogenic mechanisms, reflecting the distinct histologic and clinical characteristics of these diseases. This study aims to define both shared as well as specific genetic risk factors for lymphoma. Utilizing a genome-wide approach, we discovered novel locations in the genome associated with risk for lymphoid malignancies. Common variants in these regions, on chromosome 11q12.1 and 6p23, were each associated with a modest modification of risk for lymphoma. These regions harbor several genes of biological importance in lymphoid maturation and function. We also further characterized the HLA region at 6p21.32, previously associated with lymphoma risk and thought to be important in immune function. Some of the associated SNP markers were specific for one common subtype of lymphoma, e.g. follicular lymphoma. However, others were associated with combined subsets of disease, suggesting that there are both shared and subtype-specific associations between common genetic variants and human lymphoid cancer. Secondary analyses showed that the two novel regions harbor candidates that are biologically relevant and that regulate cell development and hematopoiesis.
doi:10.1371/journal.pgen.1003220
PMCID: PMC3547842  PMID: 23349640
14.  Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G p.I2285V variant 
Human mutation  2009;30(11):1543-1550.
Variants of Unknown Significance (VUS) in BRCA1 and BRCA2 are common, and present significant challenges for genetic counseling. We observed that BRCA2: c.6853A>G (p.I2285V) (Brest cancer Information Core [BIC] name: 7081A>G; http://nhgri.nih.gov/bic/) co-occurs in trans with the founder mutation c.5946delT (p.S1982RfsX22) (BIC name: 6174delT), supporting the published classification of p.I2285V as a neutral variant. However, we also noted that when compared with wild-type BRCA2, p.I2285V resulted in increased exclusion of exon 12. Functional assay using allelic complementation in Brca2-null mouse embryonic stem cells revealed that p.I2285V, an allele with exon 12 deleted and wild-type BRCA2 were all phenotypically indistinguishable, as measured by sensitivity to DNA-damaging agents, effect on irradiation-induced Rad51 foci formation, homologous recombination and overall genomic integrity. An allele frequency study showed the p.I2285V variant was identified in 15/722 (2.1%) Ashkenazi Jewish cases and 10/475 (2.1%) ethnically-matched controls, odds ratio: 0.99 (95% confidence interval: 0.44–2.21), P = 0.97. Thus the p.I2285V variant is not associated with an increased risk for breast cancer. Taken together, our clinical and functional studies strongly suggest that exon 12 is functionally redundant and therefore missense variants in this exon are likely to be neutral. Such comprehensive functional studies will be important adjuncts to genetic studies of variants.
doi:10.1002/humu.21101
PMCID: PMC3501199  PMID: 19795481
BRCA2; unclassified variants; co-occurrence; exon splicing enhancer; exon skipping; in-frame deletion; neutral variant; Embryonic Stem (ES) cells
16.  Including Additional Controls from Public Databases Improves the Power of a Genome-Wide Association Study 
Human Heredity  2011;72(1):21-34.
Though genome-wide association studies (GWAS) have identified numerous susceptibility loci for common diseases, their use is limited due to the expense of genotyping large cohorts of individuals. One potential solution is to use ‘additional controls’, or genotype data from control individuals deposited in public repositories. While this approach has been used by several groups, the genetically heterogeneous nature of the population of the United States makes this approach potentially problematic. We empirically investigated the utility of this approach in a US-based GWAS. In a small GWAS of pancreatic cancer in New York, we observed clear population structure differences relative to controls from the database of Genotypes and Phenotypes (dbGaP). When we conduct the GWAS using these additional controls, we find large inflation of the test statistic that is properly corrected by using eigenvectors from principal components analysis as covariates. To deal with errors introduced due to different sources, we propose simultaneously genotyping a small number of controls along with cases and then comparing this group to the additional controls. We show that removing SNPs that show differences between these control groups reduces false-positive findings. Thus, through an empirical approach, this report provides practical guidance for using additional controls from publicly available datasets.
doi:10.1159/000330149
PMCID: PMC3171281  PMID: 21849791
Genome-wide association studies; Additional controls; dbGaP; Population stratification; Pancreatic cancer
17.  Polymorphisms of ADIPOQ and ADIPOR1 and prostate cancer risk 
Objective
Studies have linked prostate cancer risk with insulin resistance and obesity. Circulating levels of adiponectin, a protein involved in insulin resistance and obesity, have been associated with prostate cancer risk. We studied the association of prostate cancer risk with haplotype tagging single nucleotide polymorphisms (SNPs) of the adiponectin (ADIPOQ) and adiponectin receptor 1 (ADIPOR1) chosen based on their functional relevance or association with other types of cancer.
Materials-Methods
DNA samples from 465 cases and 441 healthy volunteers from New York City were genotyped for ADIPOQ rs266729, rs822395, rs822396, rs1501299 and rs2241766 SNPs and ADIPOR1 rs12733285, rs1342387, rs7539542, rs2232853 and rs10920531 SNPs. We performed both single and multiple SNP analyses.
Results
We found that rs12733285, rs7539452, rs266729, rs822395, rs822396 and rs1501299 were significantly associated with prostate cancer risk. Haplotype analysis confirmed these results and identified five ADIPOQ 4-SNP haplotypes and one ADIPOR1 2-SNP haplotype tightly associated with prostate cancer risk. Importantly two ADIPOQ SNPs, rs266729 and rs1501299 have been previously associated with colon and breast cancer risk, respectively, in the same direction as in this study.
Conclusions
These findings suggest that variants of the adiponectin pathway may be associated with susceptibility to various forms of common cancers and warrant validation studies.
doi:10.1016/j.metabol.2011.01.005
PMCID: PMC3134585  PMID: 21397927
18.  Germline mutations in BAP1 predispose to melanocytic tumors 
Nature Genetics  2011;43(10):1018-1021.
Common acquired melanocytic nevi are benign neoplasms that are composed of small uniform melanocytes and typically present as flat or slightly elevated, pigmented lesions on the skin. We describe two families with a new autosomal dominant syndrome characterized by multiple skin-colored, elevated melanocytic tumors. In contrast to common acquired nevi, the melanocytic neoplasms in affected family members ranged histopathologically from epithelioid nevi to atypical melanocytic proliferations that showed overlapping features with melanoma. Some affected patients developed uveal or cutaneous melanomas. Segregating with this phenotype, we found inactivating germline mutations of the BAP1 gene. The majority of melanocytic neoplasms lost the remaining wild-type allele of BAP1 by various somatic alterations. In addition, we found BAP1 mutations in a subset of sporadic melanocytic neoplasms showing histologic similarities to the familial tumors. These findings suggest that loss of BAP1 is associated with a clinically and morphologically distinct type of melanocytic neoplasm.
doi:10.1038/ng.910
PMCID: PMC3328403  PMID: 21874003
19.  Risk-Reducing Salpingo-Oophorectomy for the Prevention of BRCA1- and BRCA2-Associated Breast and Gynecologic Cancer: A Multicenter, Prospective Study 
Journal of Clinical Oncology  2008;26(8):1331-1337.
Purpose
Risk-reducing salpingo-oophorectomy (RRSO) has been widely adopted as a key component of breast and gynecologic cancer risk-reduction for women with BRCA1 and BRCA2 mutations. Despite 17% to 39% of all BRCA mutation carriers having a mutation in BRCA2, no prospective study to date has evaluated the efficacy of RRSO for the prevention of breast and BRCA-associated gynecologic (ovarian, fallopian tube or primary peritoneal) cancer when BRCA2 mutation carriers are analyzed separately from BRCA1 mutation carriers.
Patients and Methods
A total of 1,079 women 30 years of age and older with ovaries in situ and a deleterious BRCA1 or BRCA2 mutation were enrolled onto prospective follow-up studies at one of 11 centers from November 1, 1994 to December 1, 2004. Women self-selected RRSO or observation. Follow-up information through November 30, 2005, was collected by questionnaire and medical record review. The effect of RRSO on time to diagnosis of breast or BRCA-associated gynecologic cancer was analyzed using a Cox proportional-hazards model.
Results
During 3-year follow-up, RRSO was associated with an 85% reduction in BRCA1-associated gynecologic cancer risk (hazard ratio [HR] = 0.15; 95% CI, 0.04 to 0.56) and a 72% reduction in BRCA2-associated breast cancer risk (HR = 0.28; 95% CI, 0.08 to 0.92). While protection against BRCA1-associated breast cancer (HR = 0.61; 95% CI, 0.30 to 1.22) and BRCA2-associated gynecologic cancer (HR = 0.00; 95% CI, not estimable) was suggested, neither effect reached statistical significance.
Conclusion
The protection conferred by RRSO against breast and gynecologic cancers may differ between carriers of BRCA1 and BRCA2 mutations. Further studies evaluating the efficacy of risk-reduction strategies in BRCA mutation carriers should stratify by the specific gene mutated.
doi:10.1200/JCO.2007.13.9626
PMCID: PMC3306809  PMID: 18268356
20.  Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry 
Human Genetics  2012;131(7):1173-1185.
Genetic variation on the Y chromosome has not been convincingly implicated in prostate cancer risk. To comprehensively analyze the role of inherited Y chromosome variation in prostate cancer risk in individuals of European ancestry, we genotyped 34 binary Y chromosome markers in 3,995 prostate cancer cases and 3,815 control subjects drawn from four studies. In this set, we identified nominally significant association between a rare haplogroup, E1b1b1c, and prostate cancer in stage I (P = 0.012, OR = 0.51; 95% confidence interval 0.30–0.87). Population substructure of E1b1b1c carriers suggested Ashkenazi Jewish ancestry, prompting a replication phase in individuals of both European and Ashkenazi Jewish ancestry. The association was not significant for prostate cancer overall in studies of either Ashkenazi Jewish (1,686 cases and 1,597 control subjects) or European (686 cases and 734 control subjects) ancestry (Pmeta = 0.078), but a meta-analysis of stage I and II studies revealed a nominally significant association with prostate cancer risk (Pmeta = 0.010, OR = 0.77; 95% confidence interval 0.62–0.94). Comparing haplogroup frequencies between studies, we noted strong similarities between those conducted in the US and France, in which the majority of men carried R1 haplogroups, resembling Northwestern European populations. On the other hand, Finns had a remarkably different haplogroup distribution with a preponderance of N1c and I1 haplogroups. In summary, our results suggest that inherited Y chromosome variation plays a limited role in prostate cancer etiology in European populations but warrant follow-up in additional large and well characterized studies of multiple ethnic backgrounds.
Electronic supplementary material
The online version of this article (doi:10.1007/s00439-012-1139-5) contains supplementary material, which is available to authorized users.
doi:10.1007/s00439-012-1139-5
PMCID: PMC3374121  PMID: 22271044
21.  Variants at 6q21 implicate PRDM1 in the etiology of therapy-induced second malignancies after Hodgkin lymphoma 
Nature medicine  2011;17(8):941-943.
Survivors of pediatric Hodgkin lymphoma (HL) are at significant risk for radiation therapy (RT)-induced second malignant neoplasms (SMNs). We identified two variants at chromosome 6q21 associated with SMNs in HL survivors treated with RT as children but not as adults. The variants comprise a risk locus associated with decreased basal PRDM1 expression and impaired induction of PRDM1 by radiation exposure. These data suggest a novel gene-exposure interaction that may implicate PRDM1 in the etiology of RT-induced SMNs.
doi:10.1038/nm.2407
PMCID: PMC3229923  PMID: 21785431
22.  Genome-Wide Association Studies of Cancer 
Journal of Clinical Oncology  2010;28(27):4255-4267.
Knowledge of the inherited risk for cancer is an important component of preventive oncology. In addition to well-established syndromes of cancer predisposition, much remains to be discovered about the genetic variation underlying susceptibility to common malignancies. Increased knowledge about the human genome and advances in genotyping technology have made possible genome-wide association studies (GWAS) of human diseases. These studies have identified many important regions of genetic variation associated with an increased risk for human traits and diseases including cancer. Understanding the principles, major findings, and limitations of GWAS is becoming increasingly important for oncologists as dissemination of genomic risk tests directly to consumers is already occurring through commercial companies. GWAS have contributed to our understanding of the genetic basis of cancer and will shed light on biologic pathways and possible new strategies for targeted prevention. To date, however, the clinical utility of GWAS-derived risk markers remains limited.
doi:10.1200/JCO.2009.25.7816
PMCID: PMC2953976  PMID: 20585100
23.  Personalized medicine: new genomics, old lessons 
Human Genetics  2011;130(1):3-14.
Personalized medicine uses traditional, as well as emerging concepts of the genetic and environmental basis of disease to individualize prevention, diagnosis and treatment. Personalized genomics plays a vital, but not exclusive role in this evolving model of personalized medicine. The distinctions between genetic and genomic medicine are more quantitative than qualitative. Personalized genomics builds on principles established by the integration of genetics into medical practice. Principles shared by genetic and genomic aspects of medicine, include the use of variants as markers for diagnosis, prognosis, prevention, as well as targets for treatment, the use of clinically validated variants that may not be functionally characterized, the segregation of these variants in non-Mendelian as well as Mendelian patterns, the role of gene–environment interactions, the dependence on evidence for clinical utility, the critical translational role of behavioral science, and common ethical considerations. During the current period of transition from investigation to practice, consumers should be protected from harms of premature translation of research findings, while encouraging the innovative and cost-effective application of those genomic discoveries that improve personalized medical care.
doi:10.1007/s00439-011-1028-3
PMCID: PMC3128266  PMID: 21706342
24.  Blood biomarker levels to aid discovery of cancer-related single nucleotide polymorphisms: kallikreins and prostate cancer 
Polymorphisms associated with prostate cancer include those in three genes encoding major secretory products of the prostate: KLK2 (encoding kallikrein-related peptidase 2; hK2), KLK3 (encoding prostate-specific antigen; PSA), and MSMB (encoding beta-microseminoprotein). PSA and hK2, members of the kallikrein family, are elevated in serum of men with prostate cancer. In a comprehensive analysis which included sequencing of all coding, flanking, and 2kb of putative promoter regions of all 15 kallikrein (KLK) genes spanning ≈280 Kb on chromosome 19q, we identified novel SNPs and genotyped 104 SNPs in 1419 cancer cases and 736 controls in CAPS1, with independent replication in 1267 cases and 901 controls in CAPS2. This verified prior associations of SNPs in KLK2 and in MSMB (but not in KLK3) with prostate cancer. Twelve SNPs in KLK2 and KLK3 were associated with levels of PSA forms or hK2 in plasma of control subjects. Based on our comprehensive approach, this is likely to represent all common KLK variants associated with these phenotypes. A T allele at rs198977 in KLK2 associated with increased cancer risk and a striking decrease of hK2 levels in blood. We also found a strong interaction between rs198977 genotype and hK2 levels in blood in predicting cancer risk. Based on this strong association, we developed a model for predicting prostate cancer risk from standard biomarkers, rs198977 genotype, and rs198977 x hK2 interaction; this model had greater accuracy than did biomarkers alone (AUC 0.874 vs 0.866), providing proof in principle to clinical application for our findings.
doi:10.1158/1940-6207.CAPR-09-0206
PMCID: PMC2865570  PMID: 20424135
prostate cancer; prostate-specific antigen; human kallikrein-related peptidase 2; genetic variation; case-control study
25.  Identification and characterization of novel SNPs in CHEK2 in Ashkenazi Jewish men with prostate cancer 
Cancer letters  2008;270(1):173-180.
Checkpoint kinase 2 (CHEK2) is a protein involved in arresting cell cycle in response to DNA damage. To investigate whether it plays an important role in the development of prostate cancer (PRCA) in the Ashkenazi Jewish (AJ) population, we sequenced CHEK2 in 75 AJ individuals with prostate, breast, or no cancer (n = 25 each). We identified seven coding SNPs (five are novel) that changed the amino acid sequence, resulting in R3W, E394F, Y424H, S428F, D438Y, P509S, and P509L. We determined the frequency of each variant in 76 AJ families collected by members of the International Consortium for Prostate Cancer Genetics (ICPCG) where ≥ 2 men were affected by PRCA. Only one variant, Y424H in exon 11, was identified in more than two families. Exon 11 was then screened in nine additional AJ ICPCG families (a total of 85 families). The Y424H variant occurred in nine affected cases from four different families; however it did not completely segregate with the disease. We performed bioinformatics analysis, which showed that Y424H is a non-conservative missense substitution that falls at a position that is invariant in vertebrate CHEK2 orthologs. Both SIFT and Align-GVGD predict that Y424H is a loss of function mutation, however the frequency of Y424H was not significantly different between unselected AJ cases from Montreal/Memorial Sloan Kettering Cancer Centre (MSKCC) and AJ controls from Israel/MSKCC (OR 1.18, 95%CI: 0.34–4.61, p=.99). Moreover, functional assays using S. Cerevisae revealed that the Y424H substitution did not alter function of CHEK2 protein. Although we cannot rule out a subtle influence of the CHEK2 variants on PRCA risk, these results suggest that germline CHEK2 mutations have a minor role in PRCA susceptibility in AJ men.
doi:10.1016/j.canlet.2008.05.006
PMCID: PMC2969172  PMID: 18571837
checkpoint kinase 2; prostate cancer; single-nucleotide polymorphism; Ashkenazi Jewish; budding yeast

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