Chromosomal Regions Of Interest Research Articles

One-step cloning and targeted duplication of Pantoea ananatis chromosomal fragments

In this study, we describe a novel method for one-step cloning and targeted duplication of P. ananatis chromosomal fragments. According to this method, the chromosomal region of interest is subcloned in vivo via λ Red recombination into the short synthetic non-replicable DNA fragment containing the excisable antibiotic-resistance marker gene and φ80 att-P site. The resulting circular non-replicating DNA molecule was immediately inserted into an alternative chromosomal locus due to φ80-integrase activity. To this end, the specially designed helper plasmid pONI, which can provide both the λ Red recombineering and φ80-integrase-mediated insertion, was constructed. In the described method, PCR amplification of the cloning fragment is unnecessary, making it convenient for manipulation of long-length DNA. Additionally, the possibility of spontaneous mutations occurring is completely precluded. This method was effectively used for the targeted chromosomal integration of additional copies of individual genes and operons up to 16 kb in size.

Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.).

A large-effect QTL was fine mapped, which revealed 79 gene models, with 10 promising candidate genes, along with a novel inversion. In commercial maize breeding, doubled haploid (DH) technology is arguably the most efficient resource for rapidly developing novel, completely homozygous lines. However, the DH strategy, using in vivo haploid induction, currently requires the use of mutagenic agents which can be not only hazardous, but laborious. This study focuses on an alternative approach to develop DH lines-spontaneous haploid genome duplication (SHGD) via naturally restored haploid male fertility (HMF). Inbred lines A427 and Wf9, the former with high HMF and the latter with low HMF, were selected to fine-map a large-effect QTL associated with SHGD-qshgd1. SHGD alleles were derived from A427, with novel haploid recombinant groups having varying levels of the A427 chromosomal region recovered. The chromosomal region of interest is composed of 45 megabases (Mb) of genetic information on chromosome 5. Significant differences between haploid recombinant groups for HMF were identified, signaling the possibility of mapping the QTL more closely. Due to suppression of recombination from the proximity of the centromere, and a newly discovered inversion region, the associated QTL was only confined to a 25 Mb region, within which only a single recombinant was observed among ca. 9,000 BC1 individuals. Nevertheless, 79 gene models were identified within this 25 Mb region. Additionally, 10 promising candidate genes, based on RNA-seq data, are described for future evaluation, while the narrowed down genome region is accessible for straightforward introgression into elite germplasm by BC methods.

Whole-Mount RNA, Single-Molecule RNA (smRNA), and DNA Fluorescence In Situ Hybridization (FISH) in Mammalian Embryos.

Fluorescence in situ hybridization (FISH) provides a valuable tool for studying the spatial localization of and expression level of genes and cell function in diverse biological contexts. In this chapter, we describe a protocol for the simultaneous detection of RNA (including single-molecule (sm)RNA) and DNA in mammalian embryos using FISH. RNA FISH is a technique that enables the detection and visualization of specific RNA molecules within cells. With advancements in technology, the sensitivity and specificity of RNA FISH has been improved to allow the detection of individual mRNA molecules. Both RNA and smRNA are detected using a set of fluorescent-labeled probes, which are complementary to a specific nucleotide sequence corresponding to the gene of interest. These probes hybridize to the target RNA molecules, enabling the simultaneous detection of multiple RNAs within the same cell or tissue. DNA FISH is performed using probes directed at the DNA sequence to detect the genome region of interest. In this chapter, we provide a protocol to process mammalian embryos for FISH with probe examples specifically for studying X-Chromosome activity. By utilizing other probe designs, this protocol can be adapted for the visualization and quantification of other genes and chromosomal regions of interest.

Utilization of a Targeted Next Generation Sequencing Assay to Identify Copy Number Alterations in Chronic Lymphocytic Leukemia and Monoclonal B-Cell Lymphocytosis

Utilization of a Targeted Next Generation Sequencing Assay to Identify Copy Number Alterations in Chronic Lymphocytic Leukemia and Monoclonal B-Cell Lymphocytosis

Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.

Childhood apraxia of speech (CAS) is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the genetic etiology of CAS in two large multigenerational families with familial CAS. Complementary genomic methods included Markov chain Monte Carlo linkage analysis, copy-number analysis, identity-by-descent sharing, and exome sequencing with variant filtering. No overlaps in regions with positive evidence of linkage between the two families were found. In one family, linkage analysis detected two chromosomal regions of interest, 5p15.1-p14.1, and 17p13.1-q11.1, inherited separately from the two founders. Single-point linkage analysis of selected variants identified CDH18 as a primary gene of interest and additionally, MYO10, NIPBL, GLP2R, NCOR1, FLCN, SMCR8, NEK8, and ANKRD12, possibly with additive effects. Linkage analysis in the second family detected five regions with LOD scores approaching the highest values possible in the family. A gene of interest was C4orf21 (ZGRF1) on 4q25-q28.2. Evidence for previously described causal copy-number variations and validated or suspected genes was not found. Results are consistent with a heterogeneous CAS etiology, as is expected in many neurogenic disorders. Future studies will investigate genome variants in these and other families with CAS.

Prenatal diagnosis of proximal partial trisomy 1q confirmed by comparative genomic hybridization array: Molecular cytogenetic analysis, fetal pathology and review of the literature

Partial trisomy of the long arm of chromosome 1 (1q) is an exceptionally rare chromosomal abnormality and most of the prenatally diagnosed cases are associated with either complete (q11-qter) or large (q21-qter) duplications with pre- or perinatal demise of all reported cases. The most common sonographic findings associated with this karyotype abnormality include ventriculomegaly, increased nuchal translucency or nuchal fold, renal and cardiac abnormalities, craniofacial dysmorphism, and limb deformities. However, there is a wide spectrum of clinical manifestations due to the great variability in the extent of the duplication size and the possible contribution of additional genetic rearrangements in the final phenotype. We report on a female fetus with sole partial trisomy 1q presenting with multiple structural malformations in the second trimester scan. Standard karyotyping demonstrated a large duplication on the proximal end of chromosome 1 [46,XX,dup(1)(pter→q31::q31→q12::q31→qter)] and further application of comparative genomic hybridization array confirmed the diagnosis and offered a precise characterization of the genetic defect. A fetus with nonmosaic partial trisomy 1q that was prenatally diagnosed upon multiple abnormal ultrasound findings is presented. A detailed review of the currently available literature on the prenatal diagnostic approach of partial trisomy 1q in terms of fetal sonographic assessment and molecular cytogenetic investigation is also provided. The use of novel molecular techniques such comparative genomic hybridization array could shed further light on the correlation between the genes identified in the chromosomal region of interest and the resultant phenotype.

Linkage of Type 2 Diabetes on Chromosome 9p24 in Mexican Americans: Additional Evidence from the Veterans Administration Genetic Epidemiology Study (VAGES)

Objective: Type 2 diabetes (T2DM) is a complex metabolic disease and is more prevalent in certain ethnic groups such as the Mexican Americans. The goal of our study was to perform a genome-wide linkage (GWL) analysis to localize T2DM susceptibility loci in Mexican Americans. Methods: We used the phenotypic and genotypic data from 1,122 Mexican-American individuals (307 families) who participated in the Veterans Administration Genetic Epidemiology Study (VAGES). GWL analysis was performed using the variance components approach. Data from 2 additional Mexican-American family studies, the San Antonio Family Heart Study (SAFHS) and the San Antonio Family Diabetes/Gallbladder Study (SAFDGS), were combined with the VAGES data to test for improved linkage evidence. Results: After adjusting for covariate effects, T2DM was found to be under significant genetic influences (h² = 0.62, p = 2.7 × 10^-6). The strongest evidence for linkage of T2DM occurred between markers D9S1871 and D9S2169 on chromosome 9p24.2-p24.1 (LOD = 1.8). Given that we previously reported suggestive evidence for linkage of T2DM at this region also in SAFDGS, we found the significant and increased linkage evidence (LOD = 4.3, empirical p = 1.0 × 10^-5, genome-wide p = 1.6 × 10^-3) for T2DM at the same chromosomal region, when we performed a GWL analysis of the VAGES data combined with the SAFHS and SAFDGS data. Conclusion: Significant T2DM linkage evidence was found on chromosome 9p24 in Mexican Americans. Importantly, the chromosomal region of interest in this study overlaps with several recent genome-wide association studies involving T2DM-related traits. Given its overlap with such findings and our own initial T2DM association findings in the 9p24 chromosomal region, high throughput sequencing of the linked chromosomal region could identify the potential causal T2DM genes.

The importance of molecular cytogenetic analysis prior to using cell lines in research: The case of the KG-1a leukemia cell line

KG-1 and its less differentiated subline KG-1a are leukemia cell lines used in research in a number of laboratories. The karyotypes of the two lines were initially identical. In the following years, further analysis revealed that the cell lines had acquired additional karyotypical abnormalities and differed in the presence of certain typical chromosomal rearrangements. To obtain cytogenetic authentication prior to the use of the two cell lines, we analyzed their karyotype by combining DAPI- and CMA-chromosome bandings and a fluorescence in situ hybridization (FISH)-based approach by using BAC clones useful for the identification of chromosome regions of interest. Sequences of the MYC, PLZF, RARA and BCR genes, that are known to play a critical role in leukemogenesis, and certain BAC clones mapped to five known common fragile sites (CFS) were used for the FISH analysis. A telomeric probe (TTAGGG)n and a set of BAC clones were used to characterize the marker chromosome der(1) that was observed in the cell line KG-1a. The existence of notable differences between the karyotype of the KG-1a cell line previously described, and that described in this study, demonstrate that the use of established cancer cell lines should be preceded by cytogenetic and/or molecular characterization.

SORCS1 and APOE polymorphisms interact to confer risk for late-onset Alzheimer's disease in a Northern Han Chinese population

Sortilin-related VPS domain containing receptor 1 (SORCS1), is located on chromosome 10q23.3, a chromosomal region of interest in Alzheimer's disease (AD) defined by many genome-wide and chromosome10-specific studies. Recently, three intronic variants (rs12571141, rs17277986 and rs6584777) within SORCS1 were reported to be associated with AD in Caucasian. In order to assess the involvement of the SORCS1 polymorphisms in the progression of late-onset AD (LOAD), we conducted an independent replication study in 1198 unrelated Northern Han Chinese subjects comprising 598 LOAD patients and 600 healthy controls matched for gender and age. The results revealed no significant differences in the distributions of genotype or allele between LOAD and control groups in the total sample. However, when these data were stratified by the Apolipoprotein E (APOE) ε4 status, we observed significant differences in the genotypes and allele frequencies (rs12571141: P=0.001, rs17277986: P=0.005, rs6584777: P=0.023) in APOE ε4 allele carriers. Moreover, the association was further demonstrated in logistic regression analysis (rs12571141: P=0.002, OR=0.424; rs17277986: P=0.004, OR=0.447; rs6584777: P=0.019, OR=0.523) and haplotype analysis (GCC: P=0.002, ATT: P=0.002, ACC: P=0.025) in this subset. Our data suggested that SORCS1 was in interaction with APOE in the development of LOAD in a Northern Han Chinese population.

Four new Finnish families with LGMD1D; refinement of the clinical phenotype and the linked 7q36 locus

The objective is to refine the clinical and morphological phenotype and the chromosomal region of interest, in the recently reported 7q36 linked autosomal dominant limb-girdle muscular dystrophy (LGMD1 D/E), by describing four new informative Finnish families. Examinations of the patients included serum CK, neurophysiological studies, cardiac and respiratory function examinations, muscle biopsies and muscle imaging. DNA samples were analyzed by genotyping. Patients in all families had very similar phenotypes with onset of muscle weakness in the pelvic girdle muscles between the fourth and sixth decade, later involvement of the shoulder girdle, and marked walking difficulties in the eighth decade. Muscle biopsies showed myopathic and/or dystrophic features. Genotyping confirmed linkage to the same locus at chromosome 7q36 in all families by one identically segregating haplotype. The linked region was narrowed down from <6.3 to <3.4 Mb. Sequencing of the genes in the area is ongoing, aiming to identify the genetic defect.

Progress in clinical genetics of prostate cancer

Prostate cancer is among the leading causes of morbidity and mortality from cancer in men. Epidemiologic data suggest that dominant susceptibility genes may be responsible for 5%-10% of all of the cases and 30-40% of early onset cases. Familial clustering of prostate cancer is observed in 10-20% of men with prostate cancer. Scandinavian study of twins suggests that the heritability of prostate cancer may be as high as 42%. The genetic basis of prostate cancer is complex and appears to involve multiple susceptibility genes. Three candidate susceptibility genes have been positionally cloned—HPC1, HPC2/ELAC2, and MSR1—but a clear role for any of these genes in hereditary prostate cancer has not been established. There is evidence that mutations in BRCA1 or BRCA2 predispose to prostate cancer, but the contribution of these two genes to prostate cancer etiology is relatively small. It has been reported that mutations in NBS1 and CHEK2 may confer moderate increase in the risk of prostate cancer. We found that germline mutations in BRCA1, CHEK2, NBS1 confer increased prostate cancer risk in Polish men. Numerous common low-risk polymorphisms associated with prostate cancer have been reported, many located in genes involved in the DNA damage repair and cell cycle control pathways (i.e. CDKN1B, BRCA2, ATM, XRCC1, XRCC2, ERCC2), however most of these associations have not been replicated. In the past two years, the results of several genome-wide searches for prostate cancer susceptibility loci have been reported. Several chromosomal regions of interest have been identified, including loci on chromosomes 2, 3, 6, 7, 8, 10, 11, 17, 19 and X. It is believed that identification of genetic markers for prostate cancer will improve prevention, diagnosis and management with prostate cancer.

Implication of IL-33 gene polymorphism in Chinese patients with Alzheimer's disease

Interleukin-33 (IL-33), a newly described member of the IL-1 family, is located on chromosome 9p24, a chromosomal region of interest in Alzheimer's disease (AD) defined by many genome-wide studies. Three intronic rs1157505, rs11792633, and rs7044343 single nucleotide polymorphisms (SNPs) within IL-33 have recently been reported to be associated with risk of AD in Caucasian populations. In order to assess the involvement of the IL-33 polymorphisms in the risk of developing late onset AD (LOAD), we analyzed the genotype and allele distributions of these 3 polymorphisms in 704 Han Chinese subjects. The minor alleles of the rs11792633 polymorphism within IL-33 was significantly associated with a reduced risk of LOAD (odds ratio [OR] = 0.73, p = 0.005). Furthermore, rs11792633 polymorphism was still strongly associated with LOAD (dominant model: OR = 0.67, p = 0.015; recessive model: OR 0.57, p = 0.021; additive model: OR = 0.71, p = 0.004) after adjusting for age, gender, and the apolipoprotein E (APOE) ε4 status. Our results support the evidence that genetic variants of IL-33 affect susceptibility to LOAD in Han Chinese.

Analysis of SNPs and Haplotypes in Vitamin D Pathway Genes and Renal Cancer Risk

In the kidney vitamin D is converted to its active form. Since vitamin D exerts its activity through binding to the nuclear vitamin D receptor (VDR), most genetic studies have primarily focused on variation within this gene. Therefore, analysis of genetic variation in VDR and other vitamin D pathway genes may provide insight into the role of vitamin D in renal cell carcinoma (RCC) etiology. RCC cases (N = 777) and controls (N = 1,035) were genotyped to investigate the relationship between RCC risk and variation in eight target genes. Minimum-p-value permutation (Min-P) tests were used to identify genes associated with risk. A three single nucleotide polymorphism (SNP) sliding window was used to identify chromosomal regions with a False Discovery Rate of <10%, where subsequently, haplotype relative risks were computed in Haplostats. Min-P values showed that VDR (p-value = 0.02) and retinoid-X-receptor-alpha (RXRA) (p-value = 0.10) were associated with RCC risk. Within VDR, three haplotypes across two chromosomal regions of interest were identified. The first region, located within intron 2, contained two haplotypes that increased RCC risk by approximately 25%. The second region included a haplotype (rs2239179, rs12717991) across intron 4 that increased risk among participants with the TC (OR = 1.31, 95% CI = 1.09–1.57) haplotype compared to participants with the common haplotype, TT. Across RXRA, one haplotype located 3′ of the coding sequence (rs748964, rs3118523), increased RCC risk 35% among individuals with the variant haplotype compared to those with the most common haplotype. This study comprehensively evaluated genetic variation across eight vitamin D pathway genes in relation to RCC risk. We found increased risk associated with VDR and RXRA. Replication studies are warranted to confirm these findings.

An Analysis of Growth, Differentiation and Apoptosis Genes with Risk of Renal Cancer

We conducted a case-control study of renal cancer (987 cases and 1298 controls) in Central and Eastern Europe and analyzed genomic DNA for 319 tagging single-nucleotide polymorphisms (SNPs) in 21 genes involved in cellular growth, differentiation and apoptosis using an Illumina Oligo Pool All (OPA). A haplotype-based method (sliding window analysis of consecutive SNPs) was used to identify chromosome regions of interest that remained significant at a false discovery rate of 10%. Subsequently, risk estimates were generated for regions with a high level of signal and individual SNPs by unconditional logistic regression adjusting for age, gender and study center. Three regions containing genes associated with renal cancer were identified: caspase 1/5/4/12(CASP 1/5/4/12), epidermal growth factor receptor (EGFR), and insulin-like growth factor binding protein-3 (IGFBP3). We observed that individuals with CASP1/5/4/12 haplotype (spanning area upstream of CASP1 through exon 2 of CASP5) GGGCTCAGT were at higher risk of renal cancer compared to individuals with the most common haplotype (OR:1.40, 95% CI:1.10–1.78, p-value = 0.007). Analysis of EGFR revealed three strong signals within intron 1, particularly a region centered around rs759158 with a global p = 0.006 (GGG: OR:1.26, 95% CI:1.04–1.53 and ATG: OR:1.55, 95% CI:1.14–2.11). A region in IGFBP3 was also associated with increased risk (global p = 0.04). In addition, the number of statistically significant (p-value<0.05) SNP associations observed within these three genes was higher than would be expected by chance on a gene level. To our knowledge, this is the first study to evaluate these genes in relation to renal cancer and there is need to replicate and extend our findings. The specific regions associated with risk may have particular relevance for gene function and/or carcinogenesis. In conclusion, our evaluation has identified common genetic variants in CASP1, CASP5, EGFR, and IGFBP3 that could be associated with renal cancer risk.

Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease

The only recognized genetic determinant of the common forms of Alzheimer's disease (AD) is the epsilon 4 allele of the apolipoprotein E gene (APOE). To identify new candidate genes, we recently performed transcriptomic analysis of 2741 genes in chromosomal regions of interest using brain tissue of AD cases and controls. From 82 differentially expressed genes, 1156 polymorphisms were genotyped in two independent discovery subsamples (n=945). Seventeen genes exhibited at least one polymorphism associated with AD risk, and following correction for multiple testing, we retained the interleukin (IL)-33 gene. We first confirmed that the IL-33 expression was decreased in the brain of AD cases compared with that of controls. Further genetic analysis led us to select three polymorphisms within this gene, which we analyzed in three independent case-control studies. These polymorphisms and a resulting protective haplotype were systematically associated with AD risk in non-APOE epsilon 4 carriers. Using a large prospective study, these associations were also detected when analyzing the prevalent and incident AD cases together or the incident AD cases alone. These polymorphisms were also associated with less cerebral amyloid angiopathy (CAA) in the brain of non-APOE epsilon 4 AD cases. Immunohistochemistry experiments finally indicated that the IL-33 expression was consistently restricted to vascular capillaries in the brain. Moreover, IL-33 overexpression in cellular models led to a specific decrease in secretion of the A beta(40) peptides, the main CAA component. In conclusion, our data suggest that genetic variants in IL-33 gene may be associated with a decrease in AD risk potentially in modulating CAA formation.

Global Tests for Linkage

To test for global linkage along a genome or in a chromosomal region, the maximum over the marker locations of mean alleles shared identical by descent of affected relative pairs, Z(max), can be used. Feingold et al. (1993) derived a Gaussian approximation to the distribution of the Z(max). As an alternative we propose to sum over the observed marker locations along the chromosomal region of interest. Two test statistics can be derived. (1) The likelihood ratio statistic (LR) and (2) the corresponding score statistic. The score statistic appears to be the average mean IBD over all available marker locations. The null distribution of the LR and score tests are asymptotically a 50: 50 mixture of chi-square distributions of null and one degree of freedom and a normal distribution, respectively.We compared empirically the type I error and power of these two new test statistics and Z(max) along a chromosome and in a candidate region. Two models were considered, namely (1) one disease locus and (2) two disease loci. The new test statistics appeared to have reasonable type I error. Along the chromosome, for both models we concluded that for very small effect sizes, the score test has slightly more power than the other test statistics. For large effect sizes, the likelihood ratio statistic was comparable to and sometimes performed better than Z(max) and both test statistics performed much better than the score test. For candidate regions of about 30 cM, all test statistics were comparable when only one disease-locus existed and the score and likelihood ratio statistics had somewhat better power than Z(max) when two disease loci existed.

Abstract PR-6: Variation in VDR pathway genes and renal cancer risk

Abstract PR-6 The conversion of vitamin D to its main biologically active form, 1,25-dihydroxy vitamin D, occurs in the kidney. Since the most biologically active form of vitamin D exerts its activity through binding to the intracellular vitamin D receptor (VDR), most studies of genetic susceptibility have primarily focused on variation within the VDR gene. But, the concert of genes that interact with VDR are vast; therefore, an analysis of genetic variation in VDR and other genes in its pathway may provide insight into the role of vitamin D in renal cell carcinoma (RCC) etiology. In this case-control study, we investigated the relationship between RCC risk and 139 single nucleotide polymorphisms (SNPs) in 8 target genes (VDR, RXRA, RXRB, CYP24A1, GC, STAT1, THRAP4 and TRAP5) of the expanded vitamin D pathway from subjects residing in Central and Eastern Europe. 1,097 RCC cases and 1,476 controls were recruited for this study where genomic DNA was analyzed using an Illumina Oligo Pool-All (OPA) assay. First, the minimum-p-value permutation (Min-P) test was used to identify genes that were associated with RCC risk and that remained significant at a cut off level of 10%. Next, a haplotype-based sliding window analysis of three consecutive SNPs was used to identify chromosome regions of interest that remained significant at a False Discovery Rate (FDR) of 10%. For these regions, haplotype relative risks were computed using the HaploStats package in R. Significant Min-P values were observed for two genes, which were selected for in-depth analysis: VDR (P-value: 0.024) and RXRA (P-value: 0.100). Two chromosomal regions of interest within the VDR gene were identified using the haplotype-based sliding window technique. The first region identified two haplotypes within intron 2, centered around rs4760648, that significantly increased RCC risk (haplotype 1: OR= 1.25; 95% CI= 1.04-1.50 and hapotype 2: OR= 1.26; 95% CI= 1.02-1.54) when compared to patients with the most common referent haplotype. The second signal identified a haplotype (rs886441 and rs12717991) located within intron 4 of the VDR gene that was associated with increased risk among participants with the TG (OR= 1.29; 95%CI= 1.08-1.54) haplotype compared to participants with most common referent haplotype, CA. The global p-values in R for these haplotypes were 0.025 and 0.028, respectively. Across the RXRA gene, a single haplotype located downstream, 3’ of the coding sequence, centered around rs3118523 was shown to increase RCC risk (OR= 1.41; 95% CI= 1.10-1.82) among individuals with the variant haplotype compared to those with the most common haplotype. This is the first study to our knowledge to comprehensively evaluate genetic variation in VDR and other pathway genes in relation to RCC risk. While replication and fine mapping studies will be required to confirm these findings, this study suggests that genes in the vitamin D pathway may modify RCC risk. Citation Information: Cancer Prev Res 2008;1(7 Suppl):PR-6.

Abstract A89: Association of genes involved in lipid metabolism-peroxidation and risk of renal cancer in the Central European Renal Cancer Case-Control Study

Abstract A89 Recent descriptive studies have reported increases in kidney cancer incidence since the 1970s in the United States and globally. Lipid peroxidation has been suggested as a unifying mechanistic pathway by which several known risk factors including obesity, hypertension, and chemicals directly damage cells of the proximal renal tubules and induce renal carcinogenesis. This study investigated the association between renal cell cancer (RCC) risk and variation in genes that modify the effects of lipid peroxidation, inflammation, and oxidative stress. We conducted a case-control study of RCC (987 cases and 1298 controls) from Central and Eastern Europe and analyzed genomic DNA for 635 single nucleotide polymorphisms (SNPs) thirty-eight candidate genes using an Illumina Oligo Pool-All (OPA). First, the minimum p-value permutation test (MINP) was used to identify genes that remained significant with an FDR&amp;lt;5%. Subsequently, a haplotype-based sliding window analysis of three consecutive SNPs was used to identify chromosome regions of interest that remained significant at a FDR&amp;lt;5%. Six genes were selected for in-depth analysis after multiple testing correction of the single marker associations: APOE, GPX4, NOS2A and PTGS2. The overall gene-level p-values for these genes were 0.017, 0.020, 0.055 and 0.069 using the MINP test, respectively. The minimum FDR-adjusted p-values in a sliding window haplotype analysis were 0.0005, 0.0007, 0.0002 and 1.09x10-5, respectively. For these regions, age-, sex- and center-adjusted haplotype relative risks were computed using the HaploStats package in R. After adjustment, a strong signal centered around the promoter region of APOE gene (rs405509) remained significantly associated with decreased risk of RCC compared to persons homozygous for the referent haplotype (OR=0.73 95% CI:0.59-0.91); global p=0.001). A second haplotype window spanning from IVS7+11 to IVS12-52 of the NOS2A gene that was significantly associated with increased risk (OR=1.36 (95% CI:1.05-1.78); p-global p-0.006). Additional haplotype windows spanning the trans-membrane and tyrosine kinase domains of INSR (rs28601) and intron 2 of LEPR (rs970467) genes also were investigated further (FDR-adjusted p &amp;lt;0.05). After adjustment in Haplostats, two additional high risk haplotypes were identified that were significantly associated with risk. To our knowledge this is the first and largest study of RCC conducted to evaluate these genes in relation to RCC. Although replication and fine mapping studies will be required to confirm these findings, this study supports the hypothesis variation in genes influencing lipid metabolism/peroxidation may increase susceptibility to sporadic kidney cancer. Citation Information: Cancer Prev Res 2008;1(7 Suppl):A89.

Genetics of sarcoidosis

Increased familial occurrences as well as different disease modes in different ethnic groups suggest a genetic influence in sarcoidosis. Also, genetic analyses have revealed a number of chromosomal regions and specific genes associated with sarcoidosis. This review brings up some recent discoveries on the genetic contribution to sarcoidosis. As a more detailed clinical classification of patients is performed, stronger genetic associations between distinct clinical phenotypes and specific gene variants have been revealed. The strong association between human leucocyte antigen DRB10301/DQB10201 and good prognosis in patients with Löfgren's syndrome is one such recent example. Linkage studies have revealed certain chromosomal regions of interest and furthermore pointed out specific genes of interest, for example, a variant of the butyrophilin-like 2 gene. Sarcoidosis is a complex disease which is influenced by a multitude of genes and environmental factors. The strongest genetic associations are found within the human leucocyte antigen region, in which several specific human leucocyte antigen alleles clearly associate with disease risk and phenotype, but additional genes in the same region may turn out to be important as well. Future studies on large, clinically well defined patient cohorts will help to elucidate the genetic impact on sarcoidosis.

Genes and cigarette smoking

Attempts to further our understanding of the determinants of cigarette smoking, tobacco addiction and related behaviours have included the dissection of genetic influences on these phenotypes. This review summarizes the current state of evidence from both twin and adoption studies and molecular genetic studies. We also review future research horizons and the direction which studies of this kind are likely to take in the near future. There is consistent evidence from twin and adoption studies that genetic factors play a role in the aetiology of cigarette smoking. Nevertheless, despite a large number of candidate gene studies, and a smaller number of linkage studies, few reported associations and chromosomal regions of interest have proved to replicate reliably. This is due most probably to the small effects of individual loci on complex behaviours such as smoking. Future research is likely to include the study of gene x environment interactions (including gene x treatment interactions, which offer the prospect of genetically tailored smoking cessation treatment) and the use of more sophisticated smoking-related phenotypes, such as longitudinal smoking trajectories, and intermediate phenotypes which use technologies such as neuroimaging and other laboratory and biobehavioural measures.