Markers For Association Studies Research Articles

Effects of Somatotropic Axis Gene Polymorphisms on Milk Yields in Simmental Cattle

Due to the increasing world population, scientists aim to obtain high-yield products using new techniques and methods to meet needs in the fields of food, agriculture, and livestock. It is very important to selected the candidate genes and markers correctly, especially in the QTL and MAS techniques in livestock. Somatotropic axis genes affect yield traits, growth, reproduction, and milk production in cattle. In the study, we determined GH/AluI and IGFI/SnaBI gene polymorphisms using the PCR-RFLP technique in DNA samples obtained from 70 Simmental cattle. The allele frequencies of the genes were in the same proportion as 0.62 and 0.38, L and V for the GH gene and T and C for the IGFI gene. There was no significant relationship between the polymorphic genotypes of the genes we examined and lactation milk yields, 305-day milk yields, daily milk yields, and lactation periods of Simmental cattle. The probability of using bGH/AluI and IGFI/SnaBI genetic variations as markers in association studies with milk yield in cattle is extremely low.
 Keywords: Axis genes; RFLP; MAS; Simmental; milk yield

Genetic variability and genome‐wide marker association studies for starch traits contributing to low glycaemic index in pearl millet

AbstractPearl millet grains are naturally rich in high quality starch, dietary fibre, polyphenols and important micronutrients. Grains from a random subset of the global diversity panel (PMiGAP) comprising 166 pearl millet accessions were assessed for total starch (TS), rapidly digestible Starch (RDS), slowly digestible starch (SDS) and resistant starch (RS) content based on available glucose percentage after digestion at various time points. Highly significant genetic variations for SDS, RS and other starch traits were evident amongst the PMiGAP accessions leading to the identification of best accessions for use in the future pearl millet‐breeding programmes. To identify potential candidate genes associated with these starch traits, genome‐wide association studies (GWAS) were performed using 78K single‐nucleotide polymorphisms (SNPs) well distributed across the seven chromosomes of pearl millet. A total of 902 SNPs showed a strong association with various starch traits at ‐log p‐value range from 4.0–9.08. A total of 364 probable candidate genes were identified in the flanking regions of the significantly associated SNPs and high LD (linkage disequilibrium) region, which explains a correlation between nearby variants. Out of these, 19 probable candidate genes exhibited functional relationships with the starch biosynthesis pathway. Three starch synthase genes (Pgl_GLEAN_10026059 and Pgl_GLEAN_10027180) were found to be key probable candidate genes for SDS owing to their prior demonstrated involvement in amylose biosynthesis. Pgl_GLEAN_10018323, encoding β‐amylase and Pgl_GLEAN_10009197, encoding α‐amylase enzyme were identified as probable candidate genes for RDS content. The genetic variability being reported for SDS and RS in the germplasm panel, and the SNP markers associated with such variability, raises the possibility of developing pearl millet varieties with low glycaemic index using conventional and molecular breeding approaches.

Genetic association of LPL rs326 with BMI among the Kuwaiti population.

Lipoprotein lipase is a key enzyme in lipid metabolism with reported variants associated with obesity, hypertension, type 2 diabetes, and coronary heart disease. This study was performed to investigate the association between common lipoprotein lipase single nucleotide polymorphisms and metabolic disorders in a sample of Kuwaiti cohort (n = 494). Five lipoprotein lipase variants (rs1801177, rs295, rs326, ss2137497749, and ss2137497750) across the lipoprotein lipase gene were genotyped by real-time PCR employing the TaqMan allele discrimination assay. Genotype, allelic frequencies, and Hardy-Weinberg Equilibrium were determined for each variant in the cohort followed by multivariate and logistic regression analysis. A novel finding was observed for the G allele of single nucleotide polymorphism rs326 which was associated with increased BMI after adjusting for age and sex (β = 1.04; 95% confidence interval = 0.15-1.94; P = 0.02). Moreover, a significant difference in the distribution of the minor C allele of rs295 among coronary heart disease subjects compared with noncoronary heart disease, however, this significance was diminished after controlling for age, sex, and BMI. This study demonstrated that lipoprotein lipase rs326 may be indicative for the increased risk of obesity and possibly rs295 for coronary heart disease. The findings are also in agreement with other reports suggesting that intronic variants are important genetic markers in association studies. The findings warrant further studies in a large cohort to confirm and validate the results presented.

Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity.

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

Unravelling Differences in Candidate Genes for Drought Tolerance in Potato (Solanum tuberosum L.) by Use of New Functional Microsatellite Markers.

Potato is regarded as drought sensitive and most vulnerable to climate changes. Its cultivation in drought prone regions or under conditions of more frequent drought periods, especially in subtropical areas, requires intensive research to improve drought tolerance in order to guarantee high yields under limited water supplies. A candidate gene approach was used to develop functional simple sequence repeat (SSR) markers for association studies in potato with the aim to enhance breeding for drought tolerance. SSR primer combinations, mostly surrounding interrupted complex and compound repeats, were derived from 103 candidate genes for drought tolerance. Validation of the SSRs was performed in an association panel representing 34 mainly starch potato cultivars. Seventy-five out of 154 SSR primer combinations (49%) resulted in polymorphic, highly reproducible banding patterns with polymorphic information content (PIC) values between 0.11 and 0.90. Five SSR markers identified allelic differences between the potato cultivars that showed significant associations with drought sensitivity. In all cases, the group of drought-sensitive cultivars showed predominantly an additional allele, indicating that selection against these alleles by marker-assisted breeding might confer drought tolerance. Further studies of these differences in the candidate genes will elucidate their role for an improved performance of potatoes under water-limited conditions.

A Core Subset of the ex situ Collection of S. demissum at the US Potato Genebank

Useful genetic diversity found in wild potato germplasm is important for progress in potato breeding and science. An effective way to maximize its utilization is through characterization of ex situ collections. For example, marker-based core subsets from large collections are an effective strategy to accelerate evaluation, utilize germplasm, and enhance cost-effectiveness. This project used AFLP markers to create a core subset for the US Potato Genebank’s collection of S. demissum. This species from Mexico and Guatemala is known for excellent levels of late blight resistance and frost tolerance. A total of 149 accessions with diverse geographic origin were characterized with 1403 AFLP markers; these markers were effective on determining genetic associations among the accessions. For the core subset, the AFLP loci were considered as traits, with the presence of the marker as the required state to include in a core. The results of the analyses identified that 10 of the accessions of S. demissum captured 83% of all the markers detected in the whole collection. The inclusion of 28 additional accessions, which had between 1 to 5 unique markers, resulted in a core set of 38 accessions that captured 96% of all the marker diversity. We expect this can benefit the genebank and the potato community by opening opportunities for research, trait screenings, and marker association studies.

Variations in Interleukin-10 Gene Underlying Trypanotolerance in Nigerian Indigenous Cattle

This study looked into trypanotolerance as one of the interesting physiological traits of indigenous Nigerian cattle (Muturu) which has been well adapted to the tsetse infested zone of the middle belt and southern parts of Nigeria. Interleukin-10 gene amplification, sequencing and bioinformatics methods were applied to the genetic data of the Nigerian Muturu cattle to detect the genetic divergence that may be associated with trypanotolerance in the Muturu cattle as compared to the White Fulani cattle. Trypanosomosis in livestock and man is characterized by cellular changes and damages resulting in great loss in production and sometimes death. IL-10 has been implicated as a candidate gene in trypanotolerance in N’Dama. Thus, to uncover Muturu genetic signatures underlying trypanotolerance, this study compared variations in IL-10 gene of Muturu and White Fulani cattle. Variations in IL-10 gene (exon 1) were identified using DNA sequence polymorphism programme (DnaSP) version 5.10.01 to estimate haplotype frequencies, nucleotide diversity and sequence conservation. The results revealed twenty-four single nucleotide polymorphisms (SNPs) present in White Fulani while only one SNP was present in Muturu, showing that IL-10 gene was more conserved in the Muturu cattle. Eight haplotypes were present in exon 1 of IL-10 gene of White Fulani while that of Muturu was one. Three motifs were common to the two cattle breeds, while two others were found in White Fulani population alone. Prediction of secondary protein structure showed that the gene is a mixed folding protein in White Fulani while it is not in Muturu. The study concluded that the Muturu displayed clear genetic differences compared to White Fulani breed. SNPs (24) detected in White Fulani and one in Muturu could serve as useful marker for association studies with trypanotolerance while improvement of trypanotolerance in susceptible breeds can be achieved through gene manipulation using IL-10 gene.

Abstract 1494: Interethnic germline variants in mitochondrial DNA polymerase (POLG1) induce mitochondrial dysfunction and confer tumorigenic properties

Abstract Purpose: Germline variants contribute to large fraction of the diversity observed among different ethnic groups and could give better insights in genetic predisposition and susceptibility from one population to another for certain disease including cancer. Decreased mitochondrial OXPHOS is one of the most common phenotypes of cancer cells. Mitochondrial DNA (mtDNA) depletion impairs OXPHOS and adaptive metabolic responses. In this context, DNA polymerase γ (POLG1) is known to function in human mitochondria and performs critical function of mtDNA replication and repair. POLG1 is the most frequent target of gene mutation and is involved in variety of mitochondrial diseases. POLG1 protein consists of exonuclease, linker and polymerase domain, each with distinct functions. Mutations in exonuclease domain leads to erroneous proofreading and is responsible for increased mutations in mtDNA whereas mutations in polymerase domain leads to erroneous replication and hence depletion in mtDNA. Germline variants in these domains of POLG1 may serve as important signature markers in association studies of individuals in a population study. Through our present study, we identified germline variants, examined copy number variation, expression and regulation of POLG1 gene in human cancers. We provide evidence that altered POLG1 expression as well as germline variations in POLG1 gene contribute to tumorigenesis. Methods: A comprehensive race based bioinformatics analysis of POLG1 gene in European-American and African-American was conducted and several unique germline mutations were discovered. To analyze functional contribution of these unique germline mutations in tumor progression, these unique prevalent mutations in the evolutionary conserved regions of exonuclease and polymerase domains we generated by site directed mutagenesis and functional and tumorigenic analysis was performed. Results: We observed marked differences in copy number variation of POLG1 through cBioPortal and Cosmic databases and validated the analysis in primary tumors and cancer cell lines. Our results also indicate that mtDNA copy number in cancer cell is governed by regulation of POLG1 methylation and demethylation status, suggestive of epigenetic regulation of POLG1. We identified a mitochondrial disease causing missense variation in polymerase domain of POLG1 at amino acid 1143 (E1143G) to be 25 times more prevalent in European-Americans when compared to African-Americans population. Expression of this germline variant (E1143G) increased glucose consumption, decreased ATP production and increased matrigel invasion. Discussion/ Conclusion: We demonstrate that POLG1 is epigenetically regulated and its unique germline variants contribute to disruption of mitochondrial function. Thus contributes to differences in increased predisposition to cancer in inter-ethnic population. Note: This abstract was not presented at the meeting. Citation Format: Prachi Bajpai, Bhupendra Singh, Kjerstin M. Owens, Vinodh Srinivasasainagendra, Hemant K. Tiwari, Keshav K. Singh. Interethnic germline variants in mitochondrial DNA polymerase (POLG1) induce mitochondrial dysfunction and confer tumorigenic properties [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1494. doi:10.1158/1538-7445.AM2017-1494

Genetic mapping of fiber color genes on two brown cotton cultivars in Xinjiang.

In the present study, genetic linkage analysis was carried out to map the fiber color loci Lc1 and Lc2 on two brown cotton cultivars with SSR and EST-SSR markers in the reference map by F2 segregation populations. The Lc1 locus carried by Xincaimian6 (Gossypium hirsutum L.) was flanked by the marker NAU2862 and NAU1043 on the long arm of Chromosome 07, with genetic distance 7.8 cM and 3.8 cM, respectively. The Lc2 carried by Xincaimian 5 (Gossypium hirsutum L.) was flanked by the marker NAU5433 and NAU2968 on the short arm of Chromosome 06, with genetic distance 4.4 cM and 7.4 cM respectively. Moreover, the marker NAU3735 and marker NAU5434 co-segregated with the Lc1 and the Lc2 locus, respectively. The results of marker association studies with these two loci provides the basic information for the final isolation of these important genes in colored cotton, and these linkage markers also could facilitate application of marker assisted selection in the future.

English

Protein and fat percent as content of milk are high-priority criteria for financial aims and selection of programs in dairy cattle. In order to incorporate information on marker- quantitative trait locus (QTL) associations, QTL detection and parameter estimation should also be performed. Microsatellite markers are most valuable markers in association studies between different loci with the production traits. With the aim of analysis markers previously identified by other researchers in QTLs of milk fat and protein percent traits in Iranian Holstein dairy cattle sample population, we use ten microsatellite markers on chromosomes 1, 6, 7 and 20. All microsatellite markers were genotype in 156 dairy cattle which have at least one year data of milk fat and protein record using 6 to 8% polyacrylamide gel electrophoreses determined with silver nitrate staining. We find 7, 5 and 8 out of 10 markers showing significant effect on milk fat percent in 1 to 120, 120 to 240 and 240 to 360 milking days, respectively. Our results show 6, 8 and 9 out of 10 markers have significant effect on protein percent in 1 to 120, 120 to 240 and 240 to 360 milking days respectively.   Key words: Fat percent, Iranian Holstein cattle, microsatellites, milking days, protein percent, quantitative trait locus (QTL).

Analysis of the 227 bp short interspersed nuclear element (SINE) insertion of the promoter of the myostatin (MSTN) gene in different horse breeds.

The myostatin (MSTN) gene encodes a protein known to be a negative regulator of muscle mass in mammalian species. Different polymorphisms of the horse (Equus caballus) MSTN gene have been identified, including single nucleotide polymorphisms and a short interspersed nuclear element (SINE) insertion of 227 bp within the promoter of the gene. The SINE insertion has been associated with performance traits in Thoroughbred racehorses and it was proposed as a predictor of optimum racing distance. The aims of this study were to perform in silico analysis to identify putative gains or abrogation of transcription-factor binding sites (TFBSs) generated by the SINE allele of the promoter and to analyse the frequency of the SINE insertion in horses used for racing (gallop and trot) and other purposes. The SINE insertion was genotyped in 227 horses from 10 breeds belonging to different morphological types (brachimorphic, mesomorphic, meso-dolichomorphic and dolichomorphic). The presence of the insertion was confirmed in the Quarter Horse (SINE allele frequency of 0.81) and in the Thoroughbred (0.51), whereas the SINE allele did not segregate in any of the other analysed breeds. As the SINE MSTN gene polymorphism may be population or breed specific, it is not a useful marker for association studies in all breeds.

Characterization and association of the Pit-1 gene in the Indian buffalo

Pituitary-specific transcription factor (Pit-1) is responsible for pituitary development and hormone expression in mammals. In present study, a comparison of buffalo Pit-1 gene sequences with Bos taurus revealed no nucleotide changes however, 7 single nucleotide polymorphisms (SNPs), one of which was non-synonymous were found within Indian buffalo breeds (Bubalus bubalis). SNP c.160 T>A alters the encoded amino acid from methionine to lysine. Association of all SNPs with milk production traits was assessed in Mehsana buffalo populations and the results demonstrated that SNP c.160 T>A was significantly associated with the milk fat percentage (P=0.0358). Sequence analysis showed that the buffalo Pit-1 protein shares high homology with cattle (Bos taurus) (100%), goat (99%), sheep (99%), human (96%) and pig (98%). Polymorphisms detected in buffalo Pit-1 gene are expected to have functional significance and might be useful as genetic markers in association studies for milk fat and milk yield in buffalo.

Characterization of gene polymorphisms related to immune system physiology in Mangalarga horses

The objectives of this study were to standardize a PCR-RFLP genotyping method for the AY_731081:g.1900T>C SNP of the equine CD14 gene, and to characterize this SNP and two other polymorphisms (AY_005808: c.1530A>G of the TLR4 gene and AX_463789: g.133T>C of the Cε gene) in Mangalarga horses, in order to contribute to future studies investigating the association between DNA markers and traits related to immune system physiology in this breed. A total of 151 Mangalarga horses of both sexes and variable ages, representative of the population of São Paulo State, were used. PCR-RFLP was found to be adequate for genotyping of the AY_731081: g.1900T>C SNP of the equine CD14 gene. However, this polymorphism is probably not present in Mangalarga horses, thus impairing association studies using this marker in the breed. The population genetic parameters obtained for the TLR4 AY_005808:c.1530A>G and Cε AX_463789:g.133T>C polymorphisms suggest the use of these markers in association studies with immune system-related traits in Mangalarga horses.

Genome-wide association study of copy number variation identified gremlin1 as a candidate gene for lean body mass

Lean body mass (LBM) is a heritable trait predicting a series of health problems, such as osteoporotic fracture and sarcopenia. We aim to identify sequence variants associated with LBM by a genome-wide association study (GWAS) of copy number variants (CNVs). We genotyped genome-wide CNVs of 1627 individuals of the Chinese population with Affymetrix SNP6.0 genotyping platform, which comprised of 9 40 000 copy number probes. We then performed a GWAS of CNVs with lean mass at seven sites: left and right arms, left and right legs, total of limb, trunk and whole body. We identified a CNV that is associated with LBM variation at the genome-wide significance level (CNV2073, Bonferroni corrected P-value 0.002 at right arm). CNV2073 locates at chromosome 15q13.3, which has been implicated as a candidate region for LBM by our previous linkage studies. The nearest gene, gremlin1, has a key role in the regulation of skeletal muscle formation and repair. Our results suggest that the gremlin1 gene is a potentially important gene for LBM variation. Our findings also show the utility and efficacy of CNV as genetic markers in association studies.

Hopelessness, a potential endophenotpye for suicidal behavior, is influenced by TPH2 gene variants

Hopelessness is one of the strongest risk factors for suicidal behavior but relevant genetic studies are poorly available. Tryptophan hydroxylase (TPH) is widely considered to be a good candidate for genetic association studies on depression and suicide, however, investigations on these complex, multifactorial phenotypes have resulted in conflicting data. We hypothesized that hopelessness could be a mediating phenotype between TPH2 gene, depression and suicidal behavior. Depressive phenotype and suicidal risk were investigated of 760 individuals from general population by Zung Self Rating Depression Scale (ZDS), Beck's Hopelessness Scale (BHS) and a detailed background questionnaire. All participants' DNA samples were genotyped for 7 tag SNPs in TPH2 gene. Generalized linear models were performed for single marker association studies and p-values were corrected by Bonferroni criteria. In haplotype analyses score tests were used and permutated p-values were computed. Four SNPs of TPH2 gene showed association with hopelessness but only rs6582078 had a significant effect on the BHS scores after Bonferroni's correction; GG individuals had significantly higher BHS scores, while GT and TT had intermediate and lower BHS scores respectively (p=0.0047). Compared with other genotypes, homozygous GG individuals also had almost three times greater estimated suicidal risk, as did carriers of the AA genotype of rs6582078 (OR=2.87; p=0.005) and also of rs1352250 (OR=2.86; p=0.006). A risk and a protective haplotype of TPH2 gene were also identified in association with hopelessness. ZDS scores have not shown any association with TPH2 gene. We found that hopelessness, with its allied increased suicidal risk was strongly associated with TPH2 gene variants in multiple tests. These findings suggest that TPH2 gene confers risk for suicidal behavior while hopelessness can be a potential endophenotype for suicidal vulnerability.

Biomarkers of cardiac fibrosis: New insights

Cardiac fibrosis is an important determinant of clinical outcomes in patients with cardiomyopathies and other forms of heart failure. Intensive research in the past few years has identified new mechanisms of fibrosis that have caused a paradigm shift in our understanding of this process. An important new mechanism involves the reactivation of the embryologic process of cardiac morphogenesis called endothelial-mesenchymal transition as a source of fibroblasts during pathology. New and high resolution imaging techniques, serum biomarker discovery and genetic risk marker association studies are beginning to identify fibrosis early in the course of disease. Incorporating biologic predictors of fibrosis along with clinical and/or imaging predictors is likely to improve our ability to perform early risk stratification in patients with heart failure and identify patients at risk for poor outcomes that may benefit from closer monitoring and earlier interventions. Drug discovery research will enable the development of new drugs targeted to these pathways of fibrosis. The application of more personalized approaches to monitoring and therapy has the potential to significantly improve outcomes in cardiomyopathy patients.

Using an Uncertainty-Coding Matrix in Bayesian Regression Models for Haplotype-Specific Risk Detection in Family Association Studies

Haplotype association studies based on family genotype data can provide more biological information than single marker association studies. Difficulties arise, however, in the inference of haplotype phase determination and in haplotype transmission/non-transmission status. Incorporation of the uncertainty associated with haplotype inference into regression models requires special care. This task can get even more complicated when the genetic region contains a large number of haplotypes. To avoid the curse of dimensionality, we employ a clustering algorithm based on the evolutionary relationship among haplotypes and retain for regression analysis only the ancestral core haplotypes identified by it. To integrate the three sources of variation, phase ambiguity, transmission status and ancestral uncertainty, we propose an uncertainty-coding matrix which combines these three types of variability simultaneously. Next we evaluate haplotype risk with the use of such a matrix in a Bayesian conditional logistic regression model. Simulation studies and one application, a schizophrenia multiplex family study, are presented and the results are compared with those from other family based analysis tools such as FBAT. Our proposed method (Bayesian regression using uncertainty-coding matrix, BRUCM) is shown to perform better and the implementation in R is freely available.

Novel single nucleotide polymorphism identification in interleukin-6 gene of Pakistani sheep

The present study aimed to identify single-nucleotide polymorphism (SNP) in coding and non-coding regions of interleukin-6 (IL-6) gene of Pakistani sheep. The IL-6 gene of 205 animals from nine sheep breeds were sequenced for screening of SNP. Characterizing the IL-6 gene revealed thirteen SNP sites within the intronic region of IL-6 gene. The novel SNPs found in the present study can serve as genetic marker for association studies with susceptibility/resistance to parasite infection in sheep. This is first report of SNP polymorphism of IL-6 gene of Pakistani sheep.

Alternate Statistical Tools and Limitations in Genetic Marker Association Studies in Single-Arm Drug Cancer Trials

In this issue of the Journal, Graziano et al 1 investigate the associations of a number of genotype and haplotype markers with clinical outcome in a sample of patients with metastatic colorectal cancer receiving salvage cetuximab plus irinotecan therapy. This Editorial will review of some of the statistical issues in the results and discussions.Genotypeandhaplotypesmarkerswillbecollectivelyreferredto as genetic markers. In genetic marker association studies, the first set of analyses commonly consists of the investigation of potential pairwise associations between each genetic marker and the clinical outcome of interest.Theseunivariateanalyses,astheyarecommonlyreferredtointhe medicalliterature,arethenfollowedbyaninvestigationoftheeffectof adjustingforotherpotentiallyimportantmolecular,clinical,ordemographic variables. These multivariate analyses are commonly carried out using log-linear parametric logistic models 2 for binary outcomes and log-linear semiparametric Cox proportional hazards models 3 for time-to-event outcomes subject to censoring. The employment of these models is attractive, as they provide a unified framework for statistical inference on the variables and point and interval estimation of the effects (odds ratios for binary outcomes and hazard ratios for time-to-event outcomes). The use of these methods is also attractive from a practical point of view, as they have been widely implemented in commercial software distributions that allow the user, from the novice to the expert, to generate massive amount of output through graphical user interfaces. As with any model, one needs to be concerned about robustness ofthefindingswithrespecttodeviationsfromthemodelassumptions. Considerable deviations may not only invalidate the inferences but mayalsorendertheinterpretationoftheresultsdifficult.Forexample,

Chapter 2 Genetics of the Framingham Heart Study Population

This chapter provides an introduction to the Framingham Heart Study and the genetic research related to cardiovascular diseases conducted in this unique population. It briefly describes the origins of the study, the risk factors that contribute to heart disease, and the approaches taken to discover the genetic basis of some of these risk factors. The genetic architecture of several biological risk factors has been explained using family studies, segregation analysis, heritability, and phenotypic and genetic correlations. Many quantitative trait loci underlying cardiovascular diseases have been discovered using different molecular markers. Additionally, initial results from genome-wide association studies using 116,000 markers and the prospects of using 550,000 markers for association studies are presented. Finally, the use of this unique sample to study genotype and environment interactions is described.