Composite measure of linkage disequilibrium for testing interaction between unlinked loci

Widely used statistical interaction models essentially treated the interaction effect as a residual term and hence are likely to limit the power to detect interaction. Alternatively, interactions between two loci can be understood as irreducible dependencies between loci causing disease or viewed as the linkage disequilibrium (LD) between them. This motivated the development of LD-based statistics for the detection of interaction between two loci. Although LD-based statistics have demonstrated high power to detect interaction between two loci, in general, linkage phase information of marker loci for unrelated individuals is unknown. To overcome this limitation, we classify the interaction between two loci into intragametic interaction that characterizes interaction of two alleles from different loci on the same haplotype and intergametic interaction that characterizes the interaction of two alleles from different loci on different haplotypes. Then we show that intragametic and intergametic interaction will lead to the corresponding intragametic and intergametic LD. This stimulates the use of composite measure of LD for developing statistics to detect interaction between two unlinked loci. To study the validity of the composite LD-based statistic for testing interaction, we estimate its type 1 error rates by simulation. To evaluate the performance of the composite LD-based statistic for detection of interaction between two loci, we compare its power with logistic regression and apply it to two real examples. The preliminary results demonstrate that the composite LD-based statistic is a strong alternative to the logistic regressions and the intragametic LD-based statistic for the detection of interaction between two unlinked loci.     

人类白细胞抗原A和C座位基因重组二个家系分析

目的 探讨2个家系人类白细胞抗原(human leukocyte antigen,HLA)座位的重组情况.方法 采用聚合酶链反应-序列特异寡核苷酸探针技术检测2个家系成员HLA-A、-C、-B、-DRB1和-DQB1位点,应用测序分型方法进行HLA高分辨基因分型,然后通过家系遗传分析确定HLA基因重组相关位点,检测短串联重复序列位点确定其家系成员亲权关系.结果 2个家系HLA单倍型的重组发生在HLA-A和C位点之间,家系调查显示1例为父源、1例为母源HLA单倍型发生了交换后遗传给子代,短串联重复序列结果证实2个家系成员内具有高度的亲权关系.结论 发现了2个中国汉族人群HLA-A和C基因座位间的基因重组家系,为深入研究HLA的重组机制提供了基础.     

On extending the transmission/disequilibrium test (TDT)

The transmission/disequilibrium test (TDT), for evaluation of the null hypothesis of neither linkage nor association between a marker locus and disease, is extended to the more general situation of transmission of two multi-allele marker loci from parents to affected offspring. Transmission probabilities are derived for a generalized single locus disease model, where the disease locus is taken to lie between the two marker loci. There could be unlinked modifier loci for the disease. Examples of the extended TDT are given and it is shown how the contribution from each locus can be evaluated, both separately and jointly.     

Genetic control of resistance to subgroup A and subgroup C tumour viruses in Rhode Island Red fowl: evidence for linkage between the tumour virus a (tva) and tumour virus c (tvc) loci.

A study, using the Rhode Island Red (RIR) strain of fowl maintained at Houghton Poultry Research Station, was made to investigate the genetic control of cellular response to infection with viruses of subgroups A and C. Family matings within the RIR strain and test-crosses between the RIR parents and White Leghorn (WL) parents of known ararcrcr genotype were set up to ascertain linkage between the tumour virus a (tva) and tumour virus c (tvc) loci. The results confirmed that in this RIR strain, the two loci, tva and tvc, control the cellular response to viruses of subgroups A and C, respectively, as reported in other breeds of fowl (WL and New Hampshire). As in WL fowl, the two loci are linked. The linkage value of 0-22 in the male sex agreed well with that reported in the WL male sex, indicating that the two loci are located in the same sites in homologous chromosomes in the two breeds. However, in the RIR strain, no sex difference in crossing over between the two linked loci was found, contrary to that reported in WL fowl where the absence of crossing over between the two loci was observed in the heterogametic female sex.     

Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells

In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here, we demonstrate a new method to see endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps: First, we develop an anti-FLAG frankenbody that can bind FLAG-tagged proteins in diverse live-cell environments. The anti-FLAG frankenbody complements the anti-HA frankenbody, enabling two-color signal amplification from FLAG- and HA-tagged proteins. Second, we develop a pair of cell-permeable ZF probes that specifically bind two endogenous chromatin loci predicted to be involved in chromatin looping. By coupling our anti-FLAG and anti-HA frankenbodies with FLAG- and HA-tagged ZF probes, we simultaneously see the dynamics of the two loci in single living cells. This shows a close association between the two loci in the majority of cells, but the loci markedly separate from the triggered degradation of the cohesin subunit RAD21. Our ability to image two endogenous genomic loci simultaneously in single living cells provides a proof of principle that ZF probes coupled with frankenbodies are useful new tools for exploring genome dynamics in multiple colors.     

Multiple-genome comparison reveals new loci for Mycobacterium species identification

To identify loci useful for species identification and to enhance our understanding of the population structure and genetic variability of the genus Mycobacterium, we conducted a multiple-genome comparison of a total of 27 sequenced genomes in the suborder of Corynebacterineae (18 from the Mycobacterium genus, 7 from the Corynebacterium genus, 1 each from the Nocardia and Rhodococcus genera). Our study revealed 26 informative loci for species identification in Mycobacterium. The sequences from these loci were used in a phylogenetic analysis to infer the evolutionary relations of the 18 mycobacterial genomes. Among the loci that we identified, rpoBC, dnaK, and hsp65 were amplified from 29 ATCC reference strains and 17 clinical isolates and sequenced. The phylogenetic trees generated from these loci show similar topologies. The newly identified dnaK locus is more discriminatory and more robust than the widely used hsp65 locus. The length-variable rpoBC locus is the first intergenic locus between two protein-encoding genes being used for mycobacterial species identification. A multilocus sequence analysis system including the rpoBC, dnaK, and hsp65 loci is a robust tool for accurate identification of Mycobacterium species.     

The Aalpha6 locus: its relation to mating-type regulation of sexual development in Schizophyllum commune

We have isolated and examined the Aalpha6 mating-type locus of Schizophyllum commune as a first step toward resolving a functional difference between this locus and the Aalpha loci previously studied. Our analyses show Aalpha6 to be remarkably similar to the Aalpha loci of known structure. The locus is composed of two, divergently transcribed genes similar in size to known Z and Y genes of the Aalpha loci. We have termed the two genes, Z6 and Y6, on the basis of their demonstrated mating activities and encoded protein motifs. The Z6 gene encodes a homeodomain-related sequence, two acidic regions and a predicted coiled-coil motif. The Y6 gene encodes a homeodomain, predicted coiled-coil motif, two regions with homology to the Abeta locus gene V6, a basic region encoding a putative nuclear localization sequence and a serine-rich region. The Z6 and Y6 proteins share these features with the other known Z and Y proteins, respectively. One of the two amino acid sequences with homology to the AbetaV6 protein has not previously been reported.     

SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children

Mild mental impairment (MMI) represents the low extreme of the quantitative trait of general intelligence and is highly heritable. Quantitative trait loci (QTLs) conferring susceptibility to MMI, as for most complex traits, are likely to be of small effect size. Using a novel approach we call SNP-MaP (SNP Microarrays and Pooling), we have identified four loci associated with MMI. These four loci have been replicated in two SNP-MaP studies and verified by individual genotyping. The two SNP-MaP studies conducted were a case versus control comparison (n = 515 and n = 1028, respectively) and a low versus high general intelligence extremes group comparison (n = 503 and n = 505, respectively). Each of the four groups consisted of five independent 'subpools', with each subpool assayed on a separate microarray. Twelve loci showing the largest significant differences in both SNP-MaP studies were individually genotyped on 6154 children. Of the four loci positively associated with MMI, the minor allele of each conferred the greater risk for MMI. Two of the loci are close to known genes and may be in linkage disequilibrium with them. One of the loci is between the candidate genes KLF7 and CREB1, but given possible long-range effects on expression and the unknown importance of untranslated elements such as micro-RNAs, all four loci deserve attention as candidates. Although each SNP accounts for a small amount of variance, their effects are additive and they can be combined in a 'SNP set' that can be used as a genetic risk index for MMI in behavioral genomic analyses.     

AT LEAST FOUR MHC CLASS I GENES ARE TRANSCRIBED IN THE HORSE: PHYLOGENETIC ANALYSIS SUGGESTS AN UNUSUAL EVOLUTIONARY HISTORY FOR THE MHC IN THIS SPECIES

Nineteen horse MHC class I specificities have been serologically identified previously at a single locus (ELA-A), and two other specificities appear to be coded at other loci. Biochemical studies indicate that there are at least two expressed loci. In order to establish the number of transcribed horse MHC class I genes, we made a cDNA library from a heterozygous animal (ELA-A3/A7), and screened for positive clones using a bovine class I probe. More than 200 class I clones were isolated in this way, and so far seven unique full length sequences have been identified. All of the sequences are predicted to code for surface expressed, functional molecules. The number of different sequences identified demonstrate that at least four genes are transcribed, although variations in transmembrane length (which is generally conserved in class I loci) suggest that five genes could be represented. Evolutionary analysis of these sequences (and two additional sequences known to represent different horse class I loci) reveals no firm relationships, such that the division between the different loci cannot be discerned. These results suggest an unusual evolutionary history for the horse MHC, the precise nature of which may be revealed only following further cross-species comparisons.     

The co-inheritance of type 1 diabetes and multiple sclerosis in Sardinia cannot be explained by genotype variation in the HLA region alone

Type 1 diabetes (T1D) and multiple sclerosis (MS) are two autoimmune diseases which exhibit a considerably higher incidence in Sardinia compared with the surrounding southern European populations. Surprisingly, a 5-fold increased prevalence of T1D has also been observed in Sardinian MS patients. Susceptibility to both disorders is associated with common variants of the HLA-DRB1 and -DQB1 loci. In this study, we determined the relative contribution of genotype variation of these loci to the co-occurrence of the two disorders in Sardinia. We genotyped 1052 T1D patients and 1049 MS patients (31 of whom also had T1D) together with 1917 ethnically matched controls. On the basis of the absolute risks for T1D of the HLA-DRB1-DQB1 genotypes, we established that these loci would only contribute to a 2-fold increase in T1D prevalence in MS patients. From this evidence, we conclude that shared disease associations due to the HLA-DRB1-DQB1 loci provide only a partial explanation for the observed increased prevalence of T1D in Sardinian MS patients. The data suggest that variation at other non-HLA class II loci, and/or unknown environmental factors contribute significantly to the co-occurrence of these two traits.     

Somatic mutations at CA-repeat loci.

We found somatic mutations, detected as novel PCR bands, at three separate polymorphic CA-repeat loci. At one of these loci, analyzed in a three-generation pedigree, a new band generated from the same paternal allele was observed in four of six offspring. The other two children inherited the alternative paternal allele unchanged. Somatic mutations at two additional loci were identified upon subsequent comparison of banding patterns among 25 cancers and their corresponding normal tissues at 15 CA-repeat loci. Since somatic mutations of CA-repeats seem to be quite frequent, individuals who are mosaic for CA-repeat alleles at a particular locus probably are not unusual. Hence, the possibility of somatic mutation generating new length alleles at CA-repeat loci should be considered when one compares DNA samples, whether in forensic and paternity testing, loss of heterozygosity studies, or linkage analyses.     

Dissection of complex adult traits in a mouse synthetic population

Finding the causative genetic variations that underlie complex adult traits is a significant experimental challenge. The unbiased search strategy of genome-wide association (GWAS) has been used extensively in recent human population studies. These efforts, however, typically find only a minor fraction of the genetic loci that are predicted to affect variation. As an experimental model for the analysis of adult polygenic traits, we measured a mouse population for multiple phenotypes and conducted a genome-wide search for effector loci. Complex adult phenotypes, related to body size and bone structure, were measured as component phenotypes, and each subphenotype was associated with a genomic spectrum of candidate effector loci. The strategy successfully detected several loci for the phenotypes, at genome-wide significance, using a single, modest-sized population (N = 505). The effector loci each explain 2%-10% of the measured trait variation and, taken together, the loci can account for over 25% of a trait's total population variation. A replicate population (N = 378) was used to confirm initially observed loci for one trait (femur length), and, when the two groups were merged, the combined population demonstrated increased power to detect loci. In contrast to human population studies, our mouse genome-wide searches find loci that individually explain a larger fraction of the observed variation. Also, the additive effects of our detected mouse loci more closely match the predicted genetic component of variation. The genetic loci discovered are logical candidates for components of the genetic networks having evolutionary conservation with human biology.     

Phylogeny and recombination history of gallid herpesvirus 2 (Marek's disease virus) genomes

Phylogenetic analyses based on concatenated amino acid sequences from orthologous loci from eight genomes of alpha herpesviruses infecting birds provided strong support for the following hypotheses: (1) gallid HV3 is a sister taxon to gallid HV2 but gallid HV1 is not closely related to the other two chicken herpesviruses; (2) meleagrid HV1 is closer to both gallid HV2 and gallid HV3 than is gallid HV1; (3) within gallid HV2, the virulent GA genome forms an outgroup to both the avirulent CVI988 genome and the highly virulent Md5 and Md11 genomes. Analysis of the pattern of synonymous nucleotide substitution between orthologous genes shared by four complete genomes of gallid HV2 showed strong evidence of past events of homologous recombination that homogenized certain loci between genomes. Eight of these loci represented cases of loci homogenized between the CVI988, on the one hand, and the Md5 and Md11 genomes, on the other hand. Two others represented loci where the GA genome was homogenized with those of Md5 and Md11. The two loci (UL49.5 and RLORF12) that were homogenized among the virulent genomes GA, Md5, and Md11 are candidates for contributing to viral virulence.     

Characterization of endogenous viral loci in five lines of white Leghorn chickens

Five lines of chickens have been examined for the presence of DNA sequences related to the endogenous avian retrovirus. Five new loci have been identified, based upon analysis with the restriction endonucleases SacI and BamHI. One locus has been associated with the production of infectious endogenous virus. Restriction endonuclease mapping suggested a limited similarity between the flanking cellular sequences of two of these loci, ev-17 and ev-18, and several endogenous loci, including ev-1, already characterized. The data suggested that these two loci might have been generated by chromosomal duplication. Hybridization analysis with a probe containing the cellular sequences that flank ev-1, however, revealed that these flanking sequences shared no detectable homology with the cellular sequences that surround ev-17, ev-18, or nine other endogenous loci that were examined. These results are consistent with the hypothesis that several of the endogenous viral loci resulted either from independent infections of the germ line or from virus transpositions.     

Organization and structure of wild rabbit kappa2 genes: implications for regulation of kappa expression

In domestic populations, the rabbit kappa light chains are known to be encoded by two loci which are unequally expressed. The kappa1 chains account for the majority of total serum kappa chains, and display an unusual complex polymorphism. In order to study the evolution and the putative correlations between the expression, the organization and the structure of the kappa genes, we analysed the kappa loci in wild rabbit populations. The kappa genes of b95, b97 and b98 allotypes are organized in two loci similar to that of domestic rabbits. The structure of the constant region of the kappa2 locus was determined from a wild rabbit which expresses b95 allotype kappa1 chains. The Ckappa2bas2 of b95 displays a single silent mutation when compared to Ckappa2bas2 associated with b4 and one amino acid change relative to Ckappa2bas1 chain. Therefore, in contrast to the kappa1 locus, the constant regions of the kappa2 locus display strong conservation during evolution. A model based on conformation of the kappa chains is discussed to explain the evolution and expression of the two kappa loci.     

藏族群体Y染色体14个短串联重复序列基因座遗传多态性

目的调查藏族Y染色体上14个短串联重复序列基因座及单倍型的遗传多态性。方法应用AmpFISTRYfilerTM PCR Amplification kit进行复合PCR扩增,自动基因分析仪电泳检测126名藏族男性无关个体血样。结果在14个基因座中共检出121个等位基因,基因多样性分布在0.4104(DYS391)至0.9489(DYS385a,b)之间,除了DYS391以外,其余等位基因频率多样性均大于0.5。由14个基因座组成的Y染色体单倍型系统单倍型有105种,单倍型频率多样性0.9998。结论上述14个Y-短串联重复基因座在藏族群体中具有较好的多态性,单倍型具有很高的遗传多态性。     

Identification of new loci controlling collagen-induced arthritis in mouse using a partial advanced intercross and congenic strains

Collagen-induced arthritis (CIA) is a well studied mouse model of the human disease rheumatoid arthritis (RA). Both CIA and RA are complex diseases affected by multiple genes as well as environmental factors. Identifying the genes that determine susceptibility to arthritis would give invaluable clues to the largely unknown aetiology of RA. In this study, we dissected a known locus, Cia6 , as well as a genomic region on chromosome 14 with no previously known arthritis loci, using a partial advanced intercross and a collection of congenic strains. The chromosome 14 congenic fragment, containing the T-cell receptor alpha ( Tcra ) locus, was included based on the hypothesis that the Cia6 locus is caused by a polymorphism in the Tcr beta ( Tcrb ) locus and that the two loci interact. Splitting up the congenic fragments revealed multiple loci affecting arthritis traits as well as production of collagen-specific autoantibodies. In total seven new loci were identified of which four were in the previously unlinked chromosome 14 region. Both Tcr loci were within CIA loci making them candidate susceptibility genes. The results demonstrate the importance of breaking up genetic regions in smaller fragments to identify the underlying complex set of loci.     

The C8A and C8B loci are closely linked on chromosome 1

Close linkage was demonstrated between the loci governing the polymorphisms of complement component C8 α-γ ( C8A ) and β ( C8B ). Both C8 loci were linked to the chromosome 1 marker loci PGM1 and Rh . The distance between the two C8 loci and PGM1 appeared identical in males and females. A female/male ratio of 1.6 was observed between the two C8 loci and Rh . No evidence for linkage between the C8 loci and Fy was found. Preliminary results of this study were presented at the Eighth International Workshop on Human Gene Mapping, Helsinki, August 1985 (Rogde et al. 1985b).     

Fundamental theorem of natural selection in two loci

Expressions for the various genetic effects in a two locus system are given in terms of the genie and marginal gametic frequencies. The lines of argument leading to an exact expression for the change in mean fitness have been indicated. A set of general conditions is given under which the mean fitness is bound to increase every generation. Two multiplicative loci initially in linkage equilibrium are found to possess this increasing property in addition to two additive loci. The premises in which Fisher's fundamental theorem holds in a two locus system are explored and the results of a recent investigation by Ewens are examined.     

Polymorphism of Qa and Tla loci of the mouse

Congenic lines carrying H-2 haplotypes derived from wild mice were typed serologically with polyclonal and monoclonal antibodies specific for Tla, Qa-1, and Qa-2 antigens. The typing revealed the presence of a minimum of five Tla, four Qa-1 , and three Qa-2 alleles in the 32 lines. Two new Tla , two new Qa-1 , and one new Qa-2 alleles could be described. This polymorphism of Tla and Qa loci is lower than that detected at the K and D loci in the same lines. The serological typing for Qa-2 antigens correlates remarkably well with previously published results of typing with cytolytic T lymphocytes. This correlation supports the identity of loci detected by the two methods.