Genome Linkage Scan Research Articles

Whole Genome Linkage Scan Identifies a Novel Locus on 3q28 for TG/HDL-C Ratio Change Over Time

TG/HDL-C ratio (THR) represents a single inherited surrogate predictor of hyperinsulinemia or insulin resistance that is associated with premature aging processes, risk of diabetes and increased mortality. To identify genetic loci for THR change over time (ΔTHR), we conducted a whole genome linkage scan among subjects of European ancestry who had complete data from two exams collected about seven years apart from the Long Life Family Study (LLFS, n=3091), a study with familial clustering of exceptional longevity in the US and Denmark. Subjects with diabetes or using medications for dyslipidemia were excluded from this analysis. ΔTHR was derived using growth curve modeling, and adjusted for age, sex, PCs, familial membership, and then log-transformed to approximate normality. Our linkage scan was built on haplotype-based IBD estimation with 0.5 cM average spacing. Heritability of ΔTHR was moderate (46%), and evidence for significant linkage (LOD>3) was identified on 3q28 (LOD=4.1). This locus harbors ADIPOQ among several other promising candidate genes. Interestingly, several studies previously reported suggestive evidence of linkage at this locus for relevant traits including adiponectin, dementia, AD and SBP. This linkage signal was not explained by significant GWAS SNPs for LPL or those under the peak (LOD attenuated to 3.7). In conclusion, we found a novel genetic locus on 3q28 for ΔTHR in subjects without diabetes selected for exceptional survival and healthy aging. Further query of sequence elements including rare functional and regulatory variants at this locus is underway which may reveal novel insights on insulin resistance mechanisms for aging.

Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F2 intercross between Landrace and Korean native pigs.

ObjectiveThis study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F2 intercross between Landrace and Korean native pigs.MethodsEighteen FA composition traits were measured in more than 960 F2 progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes.ResultsWe detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value 3.6×10−39) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance.ConclusionOur findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.

A Major Locus for Quantitatively Measured Shank Skin Color Traits in Korean Native Chicken

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [L*], redness [a*], and yellowness [b*]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects b* value (logarithm of odds [LOD] = 47.5, p = 1.60×10−49) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences a* value (LOD = 14.2, p = 6.14×10−16). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and a* (PMGA = 1.69×10−28; PQTDT = 2.40×10−25). The strongest associations were between BCDO2 g.9367 A>C and b* (PMGA = 3.56×10−66; PQTDT = 1.68×10−65). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

Genome scan linkage analysis identifies quantitative trait loci affecting serum clinical-chemical traits in Korean native chicken.

Alterations in robustness- and health-related traits lead to physiological changes, such as changes in the serum clinical chemical parameters in individuals. Therefore, clinical-chemical traits can be used as biomarkers to examine the health status of chickens. The aim of the present study was to detect the quantitative trait loci (QTLs) influencing eight clinical-chemical traits (glucose, total protein, creatinine, high-density lipoprotein cholesterol, total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and α-amylase) in an F1 nuclear families comprising 83 F0 founders and 585 F1 progeny of Korean native chickens. Genotypic data on 135 DNA markers representing 26 autosomes have been generated for this resource pedigree. The total length of the map was 2729.4cM. We used a multipoint variance component linkage approach to identify QTLs for the traits. A significant QTL affecting serum α-amylase levels was identified on chicken chromosome (GGA) 7 [logarithm of odds (LOD)=3.02, P value=1.92×10(-4)]. Additionally, we detected several suggestive linkage signals for the levels of total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and creatinine on GGA 4, 12, 13, and 15. In this study, serum α-amylase levels related significant QTL was mapped on GGA7 and cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and creatinine traits related suggestive QTLs were detected on GGA4, 12, 13 and 15, respectively. Further verification and fine mapping of these identified QTLs can provide valuable information for understanding the variations of clinical chemical trait in chickens.

A Genetic Variant in the CD53 Gene Is Associated with Clinical Outcomes after Unrelated Bone Marrow Transplantation

Background: CD53, a member of the tetraspanin family of proteins, broadly expressed in hematopoietic cells, is implicated in leukocyte activation and cell survival responses to stress conditions. In a recent genome linkage scan, the single nucleotide variation, rs6679497 (C>G), in the intron of the CD53 gene was identified as an important regulator of TNF release from innate immune cells in response to inflammatory stimuli. (Bos SD: Eur J Hum Genet. 2010). Tumor necrosis factor alpha (TNF-ƒ¿) which is released pretransplant due to irradiation and cytotoxic preconditioning regimens, has been implicated in transplant complications.Methods: To assess the impact of rs6679497 variation of the CD53 gene, on transplant outcomes, we evaluated 322 of patients with hematologic malignancies transplanted through the Japan Marrow Donor Program. The functional relevance of the rs6679497 variation was investigated in a whole blood culture system using samples from healthy individuals. To investigate the effect of rs6679497 on mRNA transcription activity we performed allele-specific quantitative RT-PCR with a TaqMan probe of rs6679497 using cDNA from in vitro activated leukocytes from healthy donors with heterozygous genotypes.Results: There was a significantly lower overall survival in the recipients with the GG genotype in the univariate analysis (29% vs. 53% at 5-y; P=0.01) and multivariate analysis (relative risk=1.97; 95% confidence interval, 1.22-3.18; P=0.01, Figure 1). The donors s6679497 genotypes did not significant influence the transplant outcomes. In the allele-specific quantitative PCR, the mean ratio (G allele transcripts vs. C allele transcripts) was 1.5 which is higher than that of DNA amplicons, suggesting that the G allele has higher transcriptional activity than the C allele. Using the TF-SEARCH online tool, which predict putative transcription factor binding sites, the genomic region containing the G allele of s6679497 was found to create a novel consensus sequence corresponding to the putative binding element of GATA-1. In vitro stimulated leucocytes from healthy individuals possessing the G allele secreted higher levels of TNF-ƒ¿ than those without the G allele. Consistent with these results, flow cytometry studies revealed that monocytes from donors possessing the G allele express higher levels of CD53 on their surface (p=0.02) which may account for their higher TNF-ƒ¿ secretion. These findings substantiate the functional relevance of the rs6679497 variation, and indicate that the increased TNF-ƒ¿ secretion by individuals with the G allele likely account for their worse OS. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines.

BackgroundFor decades, genetic improvement based on measuring growth and body composition traits has been successfully applied in the production of meat-type chickens. However, this conventional approach is hindered by antagonistic genetic correlations between some traits and the high cost of measuring body composition traits. Marker-assisted selection should overcome these problems by selecting loci that have effects on either one trait only or on more than one trait but with a favorable genetic correlation. In the present study, identification of such loci was done by genotyping an F2 intercross between fat and lean lines divergently selected for abdominal fatness genotyped with a medium-density genetic map (120 microsatellites and 1302 single nucleotide polymorphisms). Genome scan linkage analyses were performed for growth (body weight at 1, 3, 5, and 7 weeks, and shank length and diameter at 9 weeks), body composition at 9 weeks (abdominal fat weight and percentage, breast muscle weight and percentage, and thigh weight and percentage), and for several physiological measurements at 7 weeks in the fasting state, i.e. body temperature and plasma levels of IGF-I, NEFA and glucose. Interval mapping analyses were performed with the QTLMap software, including single-trait analyses with single and multiple QTL on the same chromosome.ResultsSixty-seven QTL were detected, most of which had never been described before. Of these 67 QTL, 47 were detected by single-QTL analyses and 20 by multiple-QTL analyses, which underlines the importance of using different statistical models. Close analysis of the genes located in the defined intervals identified several relevant functional candidates, such as ACACA for abdominal fatness, GHSR and GAS1 for breast muscle weight, DCRX and ASPSCR1 for plasma glucose content, and ChEBP for shank diameter.ConclusionsThe medium-density genetic map enabled us to genotype new regions of the chicken genome (including micro-chromosomes) that influenced the traits investigated. With this marker density, confidence intervals were sufficiently small (14 cM on average) to search for candidate genes. Altogether, this new information provides a valuable starting point for the identification of causative genes responsible for important QTL controlling growth, body composition and metabolic traits in the broiler chicken.

Evidence for novel genetic loci associated with metabolic traits in Yup'ik people.

To identify genomic regions associated with fasting plasma lipid profiles, insulin, glucose, and glycosylated hemoglobin in a Yup'ik study population, and to evaluate whether the observed associations between genetic factors and metabolic traits were modified by dietary intake of marine derived omega-3 polyunsaturated acids (n-3 PUFA). A genome-wide linkage scan was conducted among 982 participants of the Center for Alaska Native Health Research study. n-3 PUFA intake was estimated using the nitrogen stable isotope ratio (δ(15) N) of erythrocytes. All genotyped SNPs located within genomic regions with LOD scores > 2 were subsequently tested for individual SNP associations with metabolic traits using linear models that account for familial correlation as well as age, sex, community group, and n-3 PUFA intake. Separate linear models were fit to evaluate interactions between the genotype of interest and n-3 PUFA intake. We identified several chromosomal regions linked to serum apolipoprotein A2, high density lipoprotein-, low density lipoprotein-, and total cholesterol, insulin, and glycosylated hemoglobin. Genetic variants found to be associated with total cholesterol mapped to a region containing previously validated lipid loci on chromosome 19, and additional novel peaks of biological interest were identified at 11q12.2-11q13.2. We did not observe any significant interactions between n-3 PUFA intake, genotypes, and metabolic traits. We have completed a whole genome linkage scan for metabolic traits in Native Alaskans, confirming previously identified loci, and offering preliminary evidence of novel loci implicated in chronic disease pathogenesis in this population.

A Novel Stratification Method in Linkage Studies to Address Inter- and Intra-Family Heterogeneity in Autism

Most genome linkage scans for autism spectrum disorders (ASDs) have failed to be replicated. Recently, a new ASD phenotypic sub-classification method was developed which employed cluster analyses of severity scores from the Autism Diagnostic Interview-Revised (ADI-R). Here, we performed linkage analysis for each of the four identified ADI-R stratified subgroups. Additional stratification was also applied to reduce intra-family heterogeneity and to investigate the impact of gender. For the purpose of replication, two independent sets of single nucleotide polymorphism markers for 392 families were used in our study. This deep subject stratification protocol resulted in 16 distinct group-specific datasets for linkage analysis. No locus reached significance for the combined non-stratified cohort. However, study-wide significant (P = 0.02) linkage scores were reached for chromosomes 22q11 (LOD = 4.43) and 13q21 (LOD = 4.37) for two subsets representing the most severely language impaired individuals with ASD. Notably, 13q21 has been previously linked to autism with language impairment, and 22q11 has been separately associated with either autism or language disorders. Linkage analysis on chromosome 5p15 for a combination of two stratified female-containing subgroups demonstrated suggestive linkage (LOD = 3.5), which replicates previous linkage result for female-containing pedigrees. A trend was also found for the association of previously reported 5p14-p15 SNPs in the same female-containing cohort. This study demonstrates a novel and effective method to address the heterogeneity in genetic studies of ASD. Moreover, the linkage results for the stratified subgroups provide evidence at the gene scan level for both inter- and intra-family heterogeneity as well as for gender-specific loci.

Failure of lower motor neuron radial outgrowth precedes retrograde degeneration in a feline model of spinal muscular atrophy

Feline spinal muscular atrophy (SMA) is a fully penetrant, autosomal recessive lower motor neuron disease in domestic cats that clinically resembles human SMA Type III. A whole genome linkage scan identified a ∼140-kb deletion that abrogates expression of LIX1, a novel SMA candidate gene of unknown function. To characterize the progression of feline SMA, we assessed pathological changes in muscle and spinal cord from 3 days of age to beyond onset of clinical signs. Electromyographic (EMG) analysis indicating denervation occurred between 10 and 12 weeks, with the first neurological signs occurring at the same time. Compound motor action potential (CMAP) amplitudes were significantly reduced in the soleus and extensor carpi radialis muscles at 8-11 weeks. Quadriceps femoris muscle fibers from affected cats appeared smaller at 10 weeks; by 12 weeks atrophic fibers were more prevalent than in age-matched controls. In affected cats, significant loss of L5 ventral root axons was observed at 12 weeks. By 21 weeks of age, affected cats had 40% fewer L5 motor axons than normal. There was no significant difference in total L5 soma number, even at 21 weeks; thus degeneration begins distal to the cell body and proceeds retrogradely. Morphometric analysis of L5 ventral roots and horns revealed that 4 weeks prior to axon loss, motor axons in affected cats failed to undergo radial enlargement, suggesting a role for the putative disease gene LIX1 in radial growth of axons.

Novel Variant of Thyroglobulin Promoter Triggers Thyroid Autoimmunity through an Epigenetic Interferon α-modulated Mechanism

Autoimmune thyroid diseases (AITD) arise from complex interactions between genetic, epigenetic, and environmental factors. Whole genome linkage scans and association studies have established thyroglobulin (TG) as a major AITD susceptibility gene. However, the causative TG variants and the pathogenic mechanisms are unknown. Here, we describe a genetic/epigenetic mechanism by which a newly identified TG promoter single-nucleotide polymorphism (SNP) variant predisposes to AITD. Sequencing analyses followed by case control and family-based association studies identified an SNP (-1623A→G) that was associated with AITD in the Caucasian population (p = 0.006). We show that the nucleotide substitution introduced by SNP (-1623A/G) modified a binding site for interferon regulatory factor-1 (IRF-1), a major interferon-induced transcription factor. Using chromatin immunoprecipitation, we demonstrated that IRF-1 binds to the 5' TG promoter motif, and the transcription factor binding correlates with active chromatin structure and is marked by enrichment of mono-methylated Lys-4 residue of histone H3, a signature of active transcriptional enhancers. Using reporter mutations and siRNA approaches, we demonstrate that the disease-associated allele (G) conferred increased TG promoter activity through IRF-1 binding. Finally, treatment of thyroid cells with interferon α, a known trigger of AITD, increased TG promoter activity only when it interacted with the disease-associated variant through IRF-1 binding. These results reveal a new mechanism of interaction between environmental (IFNα) and genetic (TG) factors to trigger AITD.

Familial Dyslexia in a Large Swedish Family: A Whole Genome Linkage Scan

There is a compelling body of evidence that developmental dyslexia runs in families and seems to be highly inheritable. Several investigations during the last two decades have shown possible locations of genes that might be involved in dyslexia, including regions of chromosomes 1, 2, 3, 6, 11, 13, 15 and 18. In addition, six candidate genes (KIAA0319, DYX1C1, DCDC2, ROBO1, MRPL19 and C2ORF3) seem to be related to dyslexia. The present study carried out a whole genome scan in a six-generation pedigree. In addition to literacy skills the assessment included cognitive skills and records concerning the history of reading and writing ability. Thirty-five percent were regarded as dyslexic in the family. A linkage analysis using both a quantitative and a qualitative approach has been performed. No evidence was obtained to support the hypothesis that the transmission of dyslexia in this pedigree is due to a highly penetrant major gene, and previous linkage findings were not replicated; however, power in this small study was not adequate to confirm linkage of genes with small to moderate effects. The results were discussed in relation to diagnostic procedures and sample characteristics.

Linkage disequilibrium mapping of the chromosome 6q21–22.31 bipolar I disorder susceptibility locus

We previously reported genome-wide significant evidence for linkage between chromosome 6q and bipolar I disorder (BPI) by performing a meta-analysis of original genotype data from 11 genome scan linkage studies. We now present follow-up linkage disequilibrium mapping of the linked region utilizing 3,047 single nucleotide polymorphism (SNP) markers in a case-control sample (N = 530 cases, 534 controls) and family-based sample (N = 256 nuclear families, 1,301 individuals). The strongest single SNP result (rs6938431, P = 6.72 x 10(-5)) was observed in the case-control sample, near the solute carrier family 22, member 16 gene (SLC22A16). In a replication study, we genotyped 151 SNPs in an independent sample (N = 622 cases, 1,181 controls) and observed further evidence of association between variants at SLC22A16 and BPI. Although consistent evidence of association with any single variant was not seen across samples, SNP-wise and gene-based test results in the three samples provided convergent evidence for association with SLC22A16, a carnitine transporter, implicating this gene as a novel candidate for BPI risk. Further studies in larger samples are warranted to clarify which, if any, genes in the 6q region confer risk for bipolar disorder.

Opportunities and limitations of genetic analysis of hypertensive rat strains

Genetic influences contribute upto 30–50% to blood pressure variability in human essential hypertension [1]. Intense efforts have been dedicated to unraveling the role of genes in this disease, following two parallel and interacting tracks. Studies on human populations have mostly focused on the candidate gene linkage approach, associating single nucleotide polymorphic (SNP) markers with the hypertensive phenotype. In spite of some promising observations [2], most attempts to replicate association studies have not been encouraging [3]. There are calls for application of stricter quality criteria for genetic studies, including better definition of phenotype characteristics, increased attention to environmental factors, sharing and combining data resources and more emphasis on whole genome-linkage scans in the context of collaborative multidisciplinary approaches [4–17]. Recently, however, there has been impressive progress in designing studies, understanding the mechanisms of disease and genotyping technology [17]. The second parallel track is the development and study of rodent experimental models of disease. Genetically hypertensive rat strains have been developed over the past 60 years. The models were obtained from initial random rat populations by brother—sister mating selecting for a high blood pressure phenotype. The better characterized genetically hypertensive strains are the spontaneously hypertensive rat (SHR) [18], stroke-prone SHR (SPSHR) [19], Dahl saltsensitive [20], Milan hypertensive (MHS) [21], New Zealand genetically hypertensive [22], Sabra hypertensive (SBH) [23] and the Lyon hypertensive rats [24]. Comparisons are generally made with inbred normotensive strains derived from the original rat population and sharing most of the genetic background with the corresponding hypertensive strain. The most common normotensive strains are the Dahl salt-resistant, Wistar—Kyoto (WKY), Milan normotensive (MNS), genetically normotensive, Sabra normotensive (SBN) and Lyon normotensive and Lyon low blood pressure rats [18–24]. Physiological and pharmacological approaches to the study of these models have enhanced our understanding of many systems for blood pressure control. During the 1990s, technological advances allowed the use of quantitative trait locus (QTL) mapping to identify chromosomal regions with possible genetic variants affecting blood pressure. Many candidate genes for a role in human hypertension were identified as a consequence of findings in rodent animal models [25–30].

HTR3B is associated with alcoholism with antisocial behavior and alpha EEG power—an intermediate phenotype for alcoholism and co-morbid behaviors

Alcohol use disorders (AUD) with co-morbid antisocial personality disorder (ASPD) have been associated with serotonin (5-HT) dysfunction. 5-HT3 receptors are potentiated by ethanol and appear to modulate reward. 5-HT3 receptor antagonists may be useful in the treatment of early-onset alcoholics with co-morbid ASPD. Low-voltage alpha electroencephalogram (EEG) power, a highly heritable trait, has been associated with both AUD and ASPD. A recent whole genome linkage scan in one of our samples, Plains American Indians (PI), has shown a suggestive linkage peak for alpha power at the 5-HT3R locus. We tested whether genetic variation within the HTR3A and HTR3B genes influences vulnerability to AUD with comorbid ASPD (AUD + ASPD) and moderates alpha power. Our study included three samples: 284 criminal alcoholic Finnish Caucasians and 234 controls; two independent community-ascertained samples with resting EEG recordings: a predominantly Caucasian sample of 191 individuals (Bethesda) and 306 PI. In the Finns, an intronic HTR3B SNP rs3782025 was associated with AUD + ASPD ( P = .004). In the Bethesda sample, the same allele predicted lower alpha power ( P = 7.37e −5). Associations between alpha power and two other HTR3B SNPs were also observed among PI ( P = .03). One haplotype in the haplotype block at the 3′ region of the gene that included rs3782025 was associated with AUD + ASPD in the Finns ( P = .02) and with reduced alpha power in the Bethesda population ( P = .00009). Another haplotype in this block was associated with alpha power among PI ( P = .03). No associations were found for HTR3A. Genetic variation within HTR3B may influence vulnerability to develop AUD with comorbid ASPD. 5-HT3R might contribute to the imbalance between excitation and inhibition that characterize the brain of alcoholics.

Identification of genomic regions contributing to etoposide-induced cytotoxicity

Etoposide is routinely used in combination-based chemotherapy for testicular cancer and small-cell lung cancer; however, myelosuppression, therapy-related leukemia and neurotoxicity limit its utility. To determine the genetic contribution to cellular sensitivity to etoposide, we evaluated cell growth inhibition in Centre d' Etude du Polymorphisme Humain lymphoblastoid cell lines from 24 multi-generational pedigrees (321 samples) following treatment with 0.02-2.5 microM etoposide for 72 h. Heritability analysis showed that genetic variation contributes significantly to the cytotoxic phenotypes (h (2) = 0.17-0.25, P = 4.9 x 10(-5)-7.3 x 10(-3)). Whole genome linkage scans uncovered 8 regions with peak LOD scores ranging from 1.57 to 2.55, with the most significant signals being found on chromosome 5 (LOD = 2.55) and chromosome 6 (LOD = 2.52). Linkage-directed association was performed on a subset of HapMap samples within the pedigrees to find 22 SNPs significantly associated with etoposide cytotoxicity at one or more treatment concentrations. UVRAG, a DNA repair gene, SEMA5A, SLC7A6 and PRMT7 are implicated from these unbiased studies. Our findings suggest that susceptibility to etoposide-induced cytotoxicity is heritable and using an integrated genomics approach we identified both genomic regions and SNPs associated with the cytotoxic phenotypes.

Common Genetic Origins for EEG, Alcoholism and Anxiety: The Role of CRH-BP

The resting EEG is a dynamic index of cortical activation, cognitive function and consciousness and is therefore an intermediate phenotype for many behaviors in which arousal is implicated such as anxiety and alcoholism. We performed a dense whole genome linkage scan using 3878 unlinked SNPs in a large pedigree derived from a population isolate sample of 328 Plains American Indians. Alpha (8–13 Hz), theta (4–8 Hz) and beta (13–30 Hz) EEG power was heritable (0.58–0.27) and stable over a 2 year period (r = 0.82–0.53). Genetic correlations between frequency bands were high (0.75). Linkage peaks for EEG power in all three frequency bands converged on chromosome 5q13-14 with genome-wide significant LOD scores of 3.5 (empirical p<0.0001) for alpha and beta power. A logical candidate gene, corticotropin releasing hormone-binding protein (CRH-BP), was located at the apex of these convergent linkage peaks. CRH-BP was significantly associated with alpha power in the Plains Indians and also in a replication sample of 188 Caucasians. Moreover, the same SNPs and haplotypes, located within the CRH-BP haplotype block, were also associated with anxiety disorders in the Plains Indians and alcohol use disorders in the Caucasians. CRH-BP modulates CRH which influences cortical and hippocampal EEG activity and is the primary mediator of the neuroendocrine stress response. Our results suggest a likely role for CRH-BP in stress-related alcoholism and highlight the use of the resting EEG as an intermediate phenotype for arousal-related behaviors such as anxiety and addiction.

Comparison of whole genome linkage scans in premenopausal and postmenopausal women: no bone-loss-specific QTLs were implicated

This study was conducted to investigate if there exist bone-loss-specific quantitative trait loci (QTLs) for females. Genome-wide linkage scans were conducted in total, premenopausal, and postmenopausal women, respectively. No QTLs exclusively were found in postmenopausal women, suggesting that no bone-loss-specific QTL was implicated independent of BMD in our sample. Bone mineral density (BMD) in elderly women is determined jointly by peak bone mass achieved before menopause and by subsequent bone loss upon and after menopause. Peak bone mass is under strong genetic control, but whether bone loss has genetic determination independent of peak BMD is unknown. To investigate if there exist bone-loss-specific quantitative trait loci (QTLs) for females, we conducted genome-wide linkage scans in 2,582 Caucasian females from 451 pedigrees including 1,486 premenopausal and 1,096 postmenopausal women. Linkage analyses were performed in the total sample and premenopausal and postmenopausal women subgroups, respectively, and the results were compared. No linkage evidence was found exclusively in postmenopausal women. Linkage signals identified are largely consistent in the total, premenopausal, and postmenopausal samples. For example, for spine BMD, for the total sample, a significant linkage was obtained on 15q13 (LOD = 3.67), and LOD scores of 1.52 and 2.49 were achieved on 15q13 in premenopausal and postmenopausal women, respectively. We did not find any QTLs exclusively in postmenopausal women; hence, no specific QTL for bone loss was implicated independent of BMD in our female sample.

The contribution of genes outside the major histocompatibility complex to susceptibility to ankylosing spondylitis

Recent data have presented several new nonmajor histocompatibility complex genes in predisposition to ankylosing spondylitis, which will be summarized here. A retrospective meta-analysis of three previous whole genome linkage scans confirmed a strong linkage at chromosome 16q and moderate linkage at sites on chromosomes 3, 10, and 19q, and a meta-analysis of studies of the interleukin-1 (IL-1) region genes in ankylosing spondylitis suggested the susceptibility to be conferred by the IL-1A gene. More recently, the use of genotyping chips, derived from the International Hapmap resource, which provides an extensive genomic coverage of large disease cohorts, have made it possible to conduct successful genome-wide association studies. One such study has led to the identification and validation of two new genes, IL23R and ARTS1, in ankylosing spondylitis pathogenesis. A tremendous amount of progress has been made with respect to understanding the genetic basis of ankylosing spondylitis. The recent identification of two new genes, ARTS1 and IL23R, and confirmation of IL-1A association further substantiate that ankylosing spondylitis is determined to a large extent by genes outside the major histocompatibility complex.

Linkage to Chromosome 1p36 for Attention-Deficit/Hyperactivity Disorder Traits in School and Home Settings

Limited success has been achieved through previous attention-deficit/hyperactivity disorder (ADHD) linkage scans, which were all designed to map genes underlying the dichotomous phenotype. The International Multi-centre ADHD Genetics (IMAGE) project performed a whole genome linkage scan specifically designed to map ADHD quantitative trait loci (QTL). A set of 1094 single selected Caucasian ADHD nuclear families was genotyped on a highly accurate and informative single nucleotide polymorphism (SNP) panel. Two quantitative traits measuring the children's symptoms in home and school settings were collected and standardized according to a population sample of 8000 children to reflect the developmental nature and gender prevalence difference of ADHD. Univariate linkage test was performed on both traits and their mean score. A significant common linkage locus was found at chromosome 1p36 with a locus-specific heritability of 5.1% and a genomewide empirical p < .04. Setting-specific suggestive linkage signals were also found: logarithm of odds (LOD) = 2.2 at 9p23 for home trait and LOD = 2.6 at 11q21 for school trait. These results indicate that given large samples with proper phenotypic measures, searching for ADHD genes with a QTL strategy is an important alternative to using the clinical diagnosis. The fact that our linkage region 1p36 overlaps with the dyslexia QTL DYX8 further suggests it is potentially a pleiotropic locus for ADHD and dyslexia.

Genomewide Linkage Scan for Combined Obesity Phenotypes using Principal Component Analysis

Traditional whole genome linkage scans for obesity were usually performed for a number of correlated obesity related phenotypes separately without considering their correlations. The purpose of this study was to identify quantitative trait loci (QTLs) underlying variations in multiple correlated obesity phenotypes. We performed principal component analysis (PCA) for four highly correlated obesity phenotypes (body mass index [BMI], fat mass, percentage of fat mass [PFM], and lean mass) in a sample of 427 pedigrees (comprising 3,273 individuals) and generated two independent principal components (PC1 and PC2). A whole genome linkage scan (WGS) was then conducted for PC1 and PC2. For PC1, the strongest linkage signal was identified on chromosome 20p12 (LOD = 2.67). For PC2, two suggestive linkages were found on 5q35 (LOD = 2.03) and 7p22 (LOD = 2.18). This study provided evidence supporting several previously identified linkage regions for obesity (e.g., 1p36, 6p23 and 7q34). In addition, our approach by linear combination of highly correlated obesity phenotypes identified several novel QTLs which were not found in genome linkage scans for individual phenotypes.