A Discordant-Sibship Test for Disequilibrium and Linkage: No Need for Parental Data

The sibship disequilibrium test (SDT) is designed to detect both linkage in the presence of association and association in the presence of linkage (linkage disequilibrium). The test does not require parental data but requires discordant sibships with at least one affected and one unaffected sibling. The SDT has many desirable properties: it uses all the siblings in the sibship; it remains valid if there are misclassifications of the affectation status; it does not detect spurious associations due to population stratification; asymptotically it has a chi2 distribution under the null hypothesis; and exact P values can be easily computed for a biallelic marker. We show how to extend the SDT to markers with multiple alleles and how to combine families with parents and data from discordant sibships. We discuss the power of the test by presenting sample-size calculations involving a complex disease model, and we present formulas for the asymptotic relative efficiency (which is approximately the ratio of sample sizes) between SDT and the transmission/disequilibrium test (TDT) for special family structures. For sib pairs, we compare the SDT to a test proposed both by Curtis and, independently, by Spielman and Ewens. We show that, for discordant sib pairs, the SDT has good power for testing linkage disequilibrium relative both to Curtis''s tests and to the TDT using trios comprising an affected sib and its parents. With additional sibs, we show that the SDT can be more powerful than the TDT for testing linkage disequilibrium, especially for disease prevalence >.3.     

Lack of association and linkage between HLA and familial polyposis coli

Summary We investigated possible association of and linkage between HLA and familial polyposis coli (FPC). In 182 individuals from 66 pedigrees of FPC and 108 individuals from a normal population, HLA-A,-B, and-C antigens were determined. When the frequencies of HLA antigens in 66 unrelated patients and in normal controls were compared, no association of FPC with HLA was observed. For the linkage analysis, HLA haplotypes of 17 affected sib pairs were investigated by the affected sib pair method. The number of pairs which shared two, one, and no haplotypes identical by descent was not significantly different from the number expected with random occurrence (P>0.95). Finally, seven families were analyzed using Morton's sequential test. A maximum lod score of-0.056 at a recombination fraction of 0.4, and a lod of-3.089 at a recombination fraction of 0.05 were obtained. Therefore, there is neither an association of nor linkage between FPC and HLA.     

Association of the GABRD gene and childhood‐onset mood disorders

The chromosome 1p36 region was previously indicated as a locus for susceptibility to recurrent major depressive disorder based on a linkage study in a sample of 497 sib pairs. We investigated the gamma‐aminobutyric acid A (GABA_A) δ receptor subunit gene, GABRD, as a susceptibility gene to childhood‐onset mood disorders (COMD) because of substantial evidence implicating GABAergic dysfunction in mood disorders and the position of this gene near the 1p36 linkage region. Using a sample consisting of 645 Hungarian families with a child/adolescent proband diagnosed with a mood disorder with the onset of the first episode before age 15, we found some evidence for the association of two polymorphisms located within the gene, rs2376805 and rs2376803, as well as significant evidence for biased transmission of the haplotypes of these two markers (global χ² test for haplotypes = 12.746, 3 df, P = 0.0052). Furthermore, significant evidence of association was only observed in male subjects (n = 438) when the results were analyzed by sex (χ² = 9.000 1 df, P = 0.003 for rs2376805). This was in contrast with the previous linkage findings, as LOD scores exceeding 3 were only in female–female pairs in that study. These findings point to the GABRD gene as a susceptibility gene for COMD; however, this gene may not explain the previous linkage finding.     

Essential arterial hypertension and polymorphism of angiotensinogen M235T gene

Several candidate genes, chosen from the renin‐ angiotensin system, were examined for their association with essential hypertension. The genes of the renin‐ angiotensin system (RAS) are good candidates for such an approach because this system is well known to be involved in the control of blood pressure. One of these candidate genes is the gene encoding for angiotensinogen (the most important gene of the RAS associated with essential hypertension in the most population, is the gene for angiotensin‐converting enzyme‐ ACE). One DNA polymorphism within exon 2‐ with threonine instead of methionine at position 235 (M235T) was found to be significantly associated with hypertension. The objective of this study is the analysis of M235T polymorphism in angiotensinogen gene in Romanian patients with essential hypertension as well as controls. We examined 38 patients with essential hypertension and 21 normotensive patients. In order to identify the M235T angioteninogen variant, we used the following methods: DNA extraction, PCR amplification and enzymatic digestion of the PCR product using Tth IIII restriction endonuclease enzyme. In the study groups, the M235T variant (Met?Thr in aminoacid position 235) was found more frequently in hypertensive patients (81,57%), than in control subjects (66,66%). We identified 52,63% M235T heterozygotes in the hypertensive group compared with 47,61% in the control group, and 28,94% T235T homozygotes in the hypertensive group compared with 19,04% in the control group. The results of our study suggest an association of the M235T polymorphism in the gene encoding angiotensinogen with essential hypertension     

Angiotensin I-converting enzyme (ACE): estimation of DNA haplotypes in unrelated individuals using denaturing gradient gel blots

The angiotensin I-converting enzyme (ACE) gene (17q23) is a candidate gene for essential hypertension and related diseases, but investigation of its role in human pathology is hampered by a lack of identified polymorphisms. Currently, a 287-bp insertion/deletion (I/D) RFLP in intron 16 represents the only one known. Additional polymorphisms for the ACE gene would make most families informative for linkage studies and would allow haplotypes to be assigned in association studies. To increase the information provided by the ACE gene, we used a sensitive screening technique, denaturing gradient gel electrophoresis (DGGE) blots, to identify polymorphisms and combined this with gene counting to identify haplotypes. Five independent polymorphisms, restriction fragment melting polymorphisms (RFMPs), were identified by four probes (encompassing half of the ACE cDNA) in digests produced by three restriction enzymes (DdeI, RsaI, and AluI). One RFMP has three alleles while the others have two alleles. In a sample of 67 unrelated control subjects, minor allele frequencies ranged from 0.12 to 0.49. A significant level of linkage disequilibrium was found for all pairs of markers. The four most informative RFMPs, taken in combination, define 24 potential haplotypes. Based on gene counting, 11 of the 24 are rare or nonexistent in this population, and the estimated heterozygosity of the remaining 13 haplotypes approaches 80%. Under these conditions for the ACE locus, phase-unknown genotypes could be assigned to haplotype pairs in unrelated subjects with reasonable certainty. Thus, using DGGE blot technique for identifying numerous DNA polymorphisms in a candidate locus, in combination with gene counting, one can often identify DNA haplotypes for both related and unrelated study subjects at a candidate locus. These markers in the ACE gene should be useful for clinical and epidemiologic studies of the role of ACE in human disease.     

Family and population studies on the human pepsinogen A multigene family

Summary Human pepsinogen A (PGA) displays highly polymorphic isozymogen patterns after polyacrylamide gel electrophoresis and activity staining. The patterns differ with respect to the presence and the relative intensity of the individual fractions. Family studies strongly suggest that these isozymogen patterns are encoded by allelic haplotypes, encompassing different numbers and types of PGA genes. In this paper, we confirm the essential features of this multigene model. We establish the relationship between the haplotypes and the corresponding isozymogen patterns by determination of the PGA polymorphism at both the DNA and the protein level in 117 Dutch individuals, 60 of whom were unrelated. The combination of HindIII and EcoRI restriction fragment length polymorphisms (RFLPs) has enabled us to define different haplotypes, which are shown to segregate within families. Most genes are characterized by their specific EcoRI fragments. The HindIII RFLP is in strong linkage disequilibrium with PGA genes showing strong expression of the relevant isozymogen. Although a general picture of the relationship between genotypes and phenotypes is emerging, there are exceptions, suggesting that rare haplotypes evolve by unique crossover events.     

Pseudoautosomal Linkage of Hodgkin Disease

Heritable factors appear to account for much of the risk for Hodgkin disease (HD). There is evidence for an HLA-linked gene, but other predisposing loci remain unaccounted for. The observation of a family coinheriting both HD and Leri-Weill dyschondrosteosis (LWD) suggests that a gene conferring risk for HD resides adjacent to the LWD locus. The gene responsible for LWD, SHOX, localizes to the short-arm pseudoautosomal region (PAR) of the X and Y chromosomes. A unique segregation pattern for PAR-linked genes has been predicted-that affected sibs will tend to be same sex. An excess of sex-concordant affected sib pairs with HD has been noted but has been attributed to an environmental etiology. These two observations-sex concordance in sib pairs with HD and cosegregation of HD and LWD-impelled a test of the hypothesis that there is a PAR-localized gene for HD. By first scoring recombinations dissociating sex from phenotype in individuals from pedigrees with LWD, we determined a male maximum recombination frequency (thetamax) of.405. This places SHOX near the short-arm telomeres of the sex chromosome and supports the prediction that PAR recombination is obligatory for spermatogenesis. By inferring recombinations between HD and sexual phenotype in sib pairs, we predict, for the postulated HD gene, a male thetamax as high as .254, which places it in proximity to SHOX. Morton's nonparametric affected-sib-pair "beta" model was used in the evaluation of linkage between HD and phenotypic sex and gave a LOD score of 2.41. Using this approach, we reevaluated evidence for HLA linkage in HD in haplotyped sib pairs and found a LOD score of 2.00. The resulting beta values indicate that the putative PAR- and HLA-linked loci account for 29% and 40%, respectively, of the heritability of HD in an American population.     

High‐density linkage maps fail to detect any genetic component to sex determination in a Rana temporaria family

Sex chromosome differentiation in Rana temporaria varies strikingly among populations or families: whereas some males display well‐differentiated Y haplotypes at microsatellite markers on linkage group 2 (LG₂), others are genetically undistinguishable from females. We analysed with RADseq markers one family from a Swiss lowland population with no differentiated sex chromosomes, and where sibship analyses had failed to detect any association between the phenotypic sex of progeny and parental haplotypes. Offspring were reared in a common tank in outdoor conditions and sexed at the froglet stage. We could map a total of 2177 SNPs (1123 in the mother, 1054 in the father), recovering in both adults 13 linkage groups (= chromosome pairs) that were strongly syntenic to Xenopus tropicalis despite > 200 My divergence. Sexes differed strikingly in the localization of crossovers, which were uniformly distributed in the female but limited to chromosome ends in the male. None of the 2177 markers showed significant association with offspring sex. Considering the very high power of our analysis, we conclude that sex determination was not genetic in this family; which factors determined sex remain to be investigated.     

Significant depletion of NPY in the innervation of the rat mesenteric,renal arteries and kidneys in experimentally (aorta coarctation) induced hypertension

Summary The distribution and concentrations of neuropeptide Y (NPY) in kidneys, renal arteries, heart, aorta, mesenteric artery and adrenal glands from aorta-ligated hypertensive rats were studied by immunocytochemistry and radioimmunoassay. Immunocytochemistry showed that in the hypertensive animals NPY-immunoreactive fibres were decreased in both kidney and renal artery, above and below the ligation, and in mesenteric arteries. The depletion of NPY-containing nerves in the kidney was more pronounced around the juxtaglomerular apparatus than in other areas of the organ. By radioimmunoassay, the concentrations of NPY immunoreactivity were significantly lower in the hypertensive animals when compared with the controls, (kidney: hypertensive 1.0±0.1; controls 2.0±0.2 pmol/g, mean±SEM; p<0.05 renal artery: hypertensive 5.0±0.8; controls 12.1±2.0; p<0.05 and mesenteric artery: hypertensive 8.6±1.9; 17.6±3.0; p<0.01). While there were no statistically significant changes in the levels of NPY immunoreactivity in the other areas studied, there was a general trend for the level to fall in the renal artery below the ligation (hypertensive 10.6±1.5; control 15.3±2.4; p>0.05). It is of interest that changes were observed in the vasoconstrictor peptide NPY in this commonly used model of hypertension.     

Nitric oxide and superoxide dismutase modulate endothelial progenitor cell function in type 2 diabetes mellitus

Background

The renin-angiotensin aldosterone system (RAAS) plays an important role in regulating the blood pressure and the genetic polymorphisms of RAAS genes has been extensively studied in relation to the cardiovascular diseases in various populations with conflicting results. The aim of this study was to determine the association of five genetic polymorphisms (A6G and A20C of angiotensinogen (AGT), MboI of renin, Gly460Trp of aldosterone synthase and Lys173Arg of adducin) of RAAS genes in Malaysian essential hypertensive and type 2 diabetic subjects.

Methods

RAAS gene polymorphisms were determined using mutagenically separated PCR and PCR-RFLP method in a total of 270 subjects consisting of 70 hypertensive subjects without type 2 diabetes mellitus (T2DM), 60 T2DM, 65 hypertensive subjects with T2DM and 75 control subjects.

Results

There was significant difference found in age, body mass index, systolic/diastolic blood pressure, fasting plasma glucose and high density lipoprotein cholesterol levels between the hypertensive subjects with or without T2DM and control subjects. No statistically significant differences between groups were found in the allele frequency and genotype distribution for A20C variant of AGT gene, MboI of renin, Gly460Trp of aldosterone and Lys173Arg of adducin (p > 0.05). However, the results for A6G of AGT gene revealed significant differences in allele and genotype frequencies in essential hypertension with or without T2DM (p < 0.001).

Conclusion

Among the five polymorphisms of RAAS genes only A6G variant of AGT gene was significantly associated in Malaysian essential hypertensive and type 2 diabetic subjects. Therefore, A6G polymorphism of the AGT gene could be a potential genetic marker for increased susceptibility to essential hypertension with or without T2DMin Malaysian subjects.     

Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.)

Five single nucleotide polymorphism (SNP) sites corresponding to substitutions in the protein sequence of the β-amylase gene Bmy1 at amino acid (AA) positions 115, 165, 233, 347 and 430 were genotyped in 493 cultivated barley accessions by Pyrosequencing and a CAPS assay. A total of 6 different haplotypes for the Bmy1 gene were discovered of which 4 haplotypes were identified as previously described alleles Bmy1-Sd1, Bmy1-Sd2L, Bmy1-Sd2H and Bmy1-Sd3, while 2 haplotypes were new. A broad spectrum of haplotypes was found in spring barleys, while the winter barleys were dominated by the newly described haplotype Bmy1-Sd4. Individual haplotype frequencies varied between the geographic regions.Three pairs of SNP loci within the gene showed highly significant (P<0.0001) elevated values of linkage disequilibrium (LD) with r ² > 0.6. In the European and Asian subpopulations different loci were in linkage disequilibrium due to the differences in haplotype frequency distributions. By applying LD data to select haplotype tagging SNPs, three SNP sites corresponding to AA positions 115, 233 and 347 were identified that allowed to discriminate 4 haplotypes and to capture 91.6% of the available diversity by distinguishing 452 out of 493 accessions. In a subset of 2-rowed German spring barley varieties 4 SNPs and 2 haplotypes had a significant association with the malting quality parameter final attenuation limit which is related to the total amylolytic enzymatic activity.     

Common variation in KLKB1 and essential hypertension risk: tagging-SNP haplotype analysis in a case-control study

The human plasma kallikrein gene (KLKB1) encodes plasma kallikrein, a serine protease that catalyzes the release of kinins and other vasoactive peptides and may be involved in the pathogenesis of hypertension. In this study, we performed a haplotype-based study to assess the effect of common genetic variation in the KLKB1 gene on the risk of essential hypertension. Eight common single nucleotide polymorphisms (SNPs) were selected from the HapMap database and used to determine the pattern of linkage disequilibrium (LD) and haplotype structure within the KLKB1 gene. Four tag SNPs were then identified with over 85% power to predict both common haplotypes and remaining common SNPs, and genotyped in 1,317 cases with essential hypertension and 1,269 healthy controls. Single SNP analyses indicated that SNPs rs2304595 and rs4253325 were significantly associated with hypertension, adjusted for covariates. Compared with the most common Hap2 CAGC, Hap1 AGAC and Hap3 CGAC, which carry the susceptible rs2304595 G allele and rs4253325 A allele, were found to significantly increase the risk of essential hypertension with adjusted odds ratios equal to 1.37 and 1.17, respectively (P < 0.0001 and 0.028). A strongly significant interaction with gene-drinking was also observed. Among drinkers, the adjusted OR for Hap1 relative to Hap2 was increased to 2.50 (95% CI, 2.40 to 2.61; P < 0.0001). This was the first study to perform association analysis of the KLKB1 gene with essential hypertension. Our findings suggested that common genetic variation in the KLKB1 gene might contribute to the risk of hypertension in the northern Han Chinese population. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Conflict of interests: None.     

Confirmation of chromosome 7q11 locus for predisposition to intracranial aneurysm

A significant linkage of intracranial aneurysm (IA) has recently been reported to chromosomal region 7q11 (MLS=3.22) in a genomic search of 85 Japanese nuclear families with at least two affected siblings (104 sib pairs). This region contains the elastin gene (ELN, OMIM 130160), which is a functional candidate gene for IA. We have replicated this finding through linkage analyses in 13 extended pedigrees from Utah, comprising 39 IA cases. We genotyped three markers flanking ELN and performed two-point and multipoint parametric analyses, employing simple dominant and recessive models. Analyses utilizing a recessive affecteds-only model yielded significant confirmation of linkage to the region (best evidence, multipoint TLOD=2.34, at D7S2421, corrected P=0.001). This study is the first to confirm the linkage of the 7q11 locus for IA.     

The Angiotensin Infusion Test and Peripheral Venous Renin Activity

Forty hypertensive patients were studied to examine the assumption that the angiotensin pressor dose reflects endogenous renin activity. Peripheral renin activity was assayed by the method of Boucher et al.⁴ Sensitivity to the infusion of synthetic angiotensin II was determined as suggested by Kaplan and Silah.¹Sixteen patients with essential hypertension with normal renal angiography required 3.8 ng. angiotensin/kg./min. to raise the diastolic pressure 20 mm. Hg. All but one were sensitive to angiotensin infusion of less than 5 ng./kg./min. Renin activity was normal in all except in one sensitive subject. Angiotensin infusion response and mean renin activity in 13 patients with essential hypertension with abnormal renal angiography were similar to that of the first group. The pressor dose in 11 renovascular hypertensives was 9.8 ng./kg./min. All but three had elevated plasma renin activity.Our results suggest that: (1) the angiotensin infusion test is suitable for differentiating patients with true renovascular hypertension from those with essential hypertension with or without associated renal artery disease; (2) the angiotensin pressor dose correlates with the level of peripheral venous renin activity (p < 0.01).     

Tests of sib diversification theories of outcrossing in Impatiens capensis: Effects of inbreeding and neighbour relatedness on production and infestation

Several models of the evolution of genetic systems posit very strong frequency-dependent selection acting on small spatial scales; in such circumstances a genetically diverse sibship outperforms a genetically uniform sibship, and genes for mixis may spread in a population. Such selection regimes may derive from resource limitation and/or parasite transmission. We describe a greenhouse experiment designed to test these ideas, using the annual herb Impatiens capensis. Plants were potted in pairs; the genetic variance within pots was manipulated by using progeny from either inbred or outcrossed parents and by using either full sibs or unrelated individuals. Treatment combinations designed to increase genetic diversity resulted in greater phenotypic variance in both morphology and production, though not in the density of spider mites or whiteflies. Despite evidence of resource limitation, there was no effect of genetic diversity on productivity, nor was there an effect on infestation. These results fail to support either the sib competition or the sib contagion theory of outcrossing.     

The affected sib-set method: revision based on the mixed model using a conditional probability approach]

One of the implicit assumptions of the single locus model, having been used so far in the analysis of linkage between the genetic marker locus and the disease predisposition locus, is the requirement of independent--from the rest of genotype--action of genotypes of the disease predisposition locus considered. In this communication, it is emphasized that the lack of this requirement makes problematical the theoretical substantiation of the affected sib-pair method in the linkage analysis. To remove this obstacle, explicit pointing out of independence of the action of the single locus genotypes on the rest of the genotype is necessary in formulating of the single locus model which, with due regard for this assumption, represents a special, perhaps, unique case of the gene action characterized by incomplete differential penetrances of the genotypes under conditions, when the genes of the rest of genotype involved to the disease, are fixed. In this connection, the mixed model of inheritance with the "major gene", proposed by Morton and MacLean (1974), is considered, on the basis of which the theoretical expectations of the proportions of the affected sib pairs, sharing the x = 2, 1, 0 haplotypes, identical by descent (IBD) in phenotypic matings with the h = 2, 1, 0 affected parents are derived. Based on the combinatorial analysis of IBD relationships in sib pairs and of the distribution of sibships of any size s greater than or equal to 2 by the numbers L = 2, 3, 4 haplotypes, inherited by s siblings, the empirical assessment of data on sibships of any size with r greater than or equal to 2 affected siblings is considered, which makes it possible to reduce the data observed on distribution of the numbers L in sibships, to that of the IBD relationships in the affected sib pairs. It is also pointed out that conditional probability approach, proposed by the author earlier, allows at the same time to obtain the empirical estimates of the recurrence risks, conditional both on phenotypes of siblings (r affected; s-r normal siblings), and on the number of L haplotypes inherited by sibships.     

Linkage of type I diabetes to 15q26 (IDDM3) in the Danish population

Affected sib pair and linkage disequilibrium analysis, intrafamilial and case-control association studies were performed on 81 Danish multiplex insulin-dependent diabetes mellitus (IDDM) families (382 individuals) and 82 healthy Danish controls. The results confirm the linkage of D15S107 to IDDM in these Danish IDDM families (P = 0.010). When these data are combined with those of previous studies, an even stronger case for linkage can be made (P = 0.0005). Our analyses show that the D15S107*130 allele provides increased susceptibility (P = 0.02, relative risk = 3.55) and that the D15S107 locus contributes up to 16% of the familial clustering of IDDM. The analysis of affected sib pairs suggests that HLA and D15S107 may possibly act independently of each other. Taken together with our previous findings, our results suggest that three causes of susceptibilities can be discerned in the IDDM patient population: (1) a major susceptibility caused by the HLA-DRB1 alleles; (2) a minor susceptibility caused by the joint action of HLA and other non-HLA gene(s); and (3) a minor susceptibility caused by non-HLA gene(s). Received: 18 March 1996 / Revised: 17 May 1996     

Plasma norepinephrine concentrations: No differences among normal volunteers and low,high or normal renin hypertensive patients

Plasma norepinephrine concentrations were measured by a sensitive radioenzymatic method in 51 patients with essential hypertension and 26 age-matched normal volunteers under conditions of ad libitum sodium intake, after volume expansion by infusion of saline intravenously, and after volume contraction by administration of furosemide orally. The hypertensive patients were classified into low, normal and high renin groups both by renin-sodium indexing and by their renin response to furosemide and saline administration. Plasma norepinephrine concentrations were similar among normal volunteers and patients with low, normal or high renin hypertension while the people were either recumbent or after they stood for 5 min. These and other results do not support the hypothesis that abnormal activity of the sympathetic nervous system accounts for the low or high renin values seen in many hypertensive patients.     

Signals for Parent-Offspring Recognition: Strong Sib-Sib Call Similarity in Cliff Swallows but not Barn Swallows

We tested the prediction that the calls of sibling cliff swallow (Hirundo pyrrhonota) chicks are more similar than those of sibling barn swallow (Hirundo rustica) chicks. This prediction was derived from the hypothesis that the call of the colonial cliff swallow, but not the call of the noncolonial barn swallow, has been selected for signature function (i.e., for individual distinctiveness). In Study 1 we examined the calls of 22 cliff swallow sibling pairs and 23 barn swallow sibling pairs. The intraclass correlations for 4 of the 5 cliff swallow variables were significantly different from zero, and each of the 4 was approximately 0.5. Only one of the 4 barn swallow call variables was significantly different from zero. In a discriminant-function analysis of these data, cliff swallow chick calls were correctly identified as to sibship in 82 % of the cases, barn swallow chick calls in only 46 % of the cases. In Study 2 we cross-fostered eggs between cliff swallow nests to create foster sibships (all chicks in a nest were unrelated). We found no similarities among foster sib calls, and thus no evidence for call imitation of the calls of sibs or parents, suggesting that genetic differences are the main source of variance in cliff swallow chick calls.