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A combined segregation, linkage, and association analysis using the program COMBIN was performed on the simulated pedigree data prepared for the Second Genetic Analysis Workshop. The model used in COMBIN is described and the presented results illustrate its effectiveness in the analysis of such data. Linkage analysis was performed and maps for each linkage group are presented.
The Ly-6 locus is now regarded as a gene complex consisting of at least five closely linked loci (Ly-6A-Ly-6E) whose polymorphic products are identified by monoclonal antibodies and distinguished by different tissue distributions. Ly-6 has been assigned by other investigators to chromosome (Chr) 9 (linked to Thy-1) or to Chr 2. We report that the Ly-6 gene complex, together with the Xp-14 and Gdc-1 loci, is situated on Chr 15 linked to Gpt-1. These new linkage data are derived from four sources: (1) three separate crosses that failed to demonstrate linkage of Ly-6 to either Thy-1 on Chr 9 or to any of five genes present on Chr 2; (2) the NXSM recombinant inbred strains, which suggested the linkage of Ly-6 and Xp-14 to Gpt-1 on Chr 15; (3) several Gpt-1 and Gdc-1 congenic strains that confirmed the assignment of Ly-6 and Xp-14 to Chr 15; and (4) backcrosses that further confirmed the linkage of Ly-6, Gpt-1, Gdc-1, and Xp-14, the probable gene order being Gpt-1/Ly-6-Xp-14-Gdc-1.
Sry-related HMG-box genes are key regulators of several developmental processes. Sox9 encodes a transcription factor required for cartilage formation and testis determination in mammals. In zebrafish (Danio rerio) and stickleback (Gasterosteus aculeatus) two co-orthologs of Sox9 are present. To date, only one Sox9 had been identified in medaka (Oryzias latipes). We have now isolated the second Sox9 gene. Sequence analysis, phylogenetic data, linkage mapping as well as expression pattern all together suggest that the medaka Sox9a and Sox9b are co-orthologs. During embryogenesis, the expression pattern of Sox9a and Sox9b are distinct but overlap considerably in craniofacial cartilage elements. Comparing the zebrafish Sox9a and Sox9b expression patterns with medaka Sox9a and Sox9b expression domains revealed that some are identical but others are clearly different. We conclude that Sox9 regulatory subfunctions were not partitioned before divergence of the teleosts and evolved to lineage-specific expression domains.
We demonstrate a reliable method for mapping conventional loci and obtaining meiotic linkage data for the ciliated protozoan Tetrahymena thermophila. By coupling nullisomic deletion mapping with meiotic linkage mapping, loci known to be located on a particular chromosome or chromosome arm can be tested for recombination. This approach has been used to map three isozyme loci, EstA (Esterase A), EstB (Esterase B), and AcpA (Acid Phosphatase A), with respect to the ChxA locus (cycloheximide resistance) and 11 RAPDs (randomly amplified polymorphic DNAs). To assign isozyme loci to chromosomes, clones of inbred strains C3 or C2 were crossed to inbred strain B nullisomics. EstA, EstB and AcpA were mapped to chromosomes 1R, 3L and 3R, respectively. To test EstA and AcpA for linkage to known RAPD loci on their respective chromosomes, a panel of Round II (genomic exclusion) segregants from a B/C3 heterozygote was used. Using the MAPMAKER program, EstA was assigned to the ChxA linkage group on chromosome 1R, and a detailed map was constructed that includes 10 RAPDs. AcpA (on 3R), while unlinked to all the RAPDs assigned to chromosome 3 by nullisomic mapping, does show linkage to a RAPD not yet assignable to chromosomes by nullisomic mapping.
Linkage data for familial incontinentia pigmenti (IP2) and 17 X chromosomal markers are reported. The linkage previously found between IP2 and the F8C locus is confirmed (Z max = 11.85 at theta = 0.028). Linkage is established with distal markers DXS1108 (Z max = 10.06 at theta = 0.00) and DXYS154 (Z = 9.07 at theta = 0.019). Multipoint analysis supports the distal localization of the IP2 gene with respect to the F8C locus.
By using the genetic linkage data between the facioscapulohumeral muscular dystrophy (FSHD) gene and 57 markers on various autosomes, we have constructed an exclusion map for this disorder. The maximum likelihood location of the FSHD gene and the percentage of the excluded areas on each chromosome are presented here. This exclusion map shows that more than 80% of the genome has been excluded as a likely location of any locus responsible for FSHD in the majority of families. Chromosomes 3, 5, 10, 11, 15, and 19 remain largely unexcluded. Concentration on the highlighted areas of the genome should facilitate the identification of the site of the FSHD gene.
Pembrey et al. (1985) proposed a hypothesis regarding the nature of the fragile X [fra(X)] mutation. Recently they analyzed DNA linkage data (Winter and Pembrey 1986) that we and others have published on fra(X) pedigrees, found significant linkage heterogeneity, and modified their hypothesis to explain the observations. We would like to point out that their modified hypothesis is not supported by the data available.
Linkage data on phosphoglycolate phosphatase (PGP) E.C. 3.1.3.18 and 26 other human genetic markers are presented. One hundred and one families from the southwestern area of Germany were tested. Close linkage between PGP and the following markers could be ruled out: ABO, acP, ADA, GPT, PGM1, GLO, HLA, and PGM3. There is some evidence for possible linkage with MNSs, Rh, Gm and EsD. Family segregation data confirm the hypothesis formerly established by Barker and Hopkinson: three common alleles PG1, PGP2 and PGP3 at an autosomal locus PGP.
We analysed the clinical picture of 101 sibs (43 sib pairs, 5 triplets) with autosomal recessive proximal spinal muscular atrophy (SMA). Linkage data of 20 sibships, which were available for analysis, were in agreement with chromosome 5q linkage. The patients were classified according to the motor development into SMA I (never sat), SMA II (sitting without support), and SMA III (walking without aids). Three sibs with adult onset (> 30 years = SMA IV) were discussed as a separate entity. Age-of-onset of the 101 patients showed a wide spectrum (prenatal to 47 years). Among sib pairs with SMA I and SMA II the ages-of-onset appeared to be very similar except of one atypically discordant sib pair. With regard to SMA III, 3 out of 13 sibships (23%) showed a marked variation in age-of-onset ranging from 5-15 years within a family. Concerning acquired motor development (ability to sit and walk), 7 sibships (15%) belonged to different SMA types. Ages of death in 29 sib pairs in whom at least one sib had died before the age of 20 years were strikingly discordant. Neither the degree of disability nor the respiratory deficits are reliable predictors of life expectancy. Although a predominance of males can be observed, no significant effect of gender has been established in familial cases. The existence of multiple allelism seems to be the most suitable explanation for the high interfamilial variability considering the clinical concordance in most affected sib pairs.
Linkage data for familial incontinentia pigmenti (IP2) and nine X chromosomal markers are reported. Previously found linkage between IP2 and the DXS52 locus is confirmed with the maximum lod score of 6.19 at a recombination fraction of 0.03. Linkage is also established with loci DXS134, DXS15 and DXS33. Multipoint analysis allows us to localize the IP2 locus outside a block of seven linked markers of the Xq28 region.
Linkage data on human factor H (HF) and 22 other human genetic markers are presented. Close linkage at theta less than 0.10 can be ruled out for a series of marker systems (Rh, PGM1, ACP1, Jk, Tf, Gc, MNSs, ME2, HLA, GLO1, ORM, Gt, PI, Hp, GPT). Strong evidence for linkage was obtained for peptidase A (PEPA) with lods greater than 3.0 at theta = 0.10 in males and at theta = 0.20 for the sexes combined. From this result the HF locus can be provisionally assigned to chromosome 18.
Linkage heterogeneity frequently occurs for complex genetic diseases, and statistical methods must account for it to avoid severe loss in power to discover susceptibility genes. A common method to allow for only a fraction of linked pedigrees is to fit a mixture likelihood and then to test for linkage homogeneity, given linkage (admixture test), or to test for linkage while allowing for heterogeneity, using the heterogeneity LOD (HLOD) score. Furthermore, features of the families, such as mean age at diagnosis, may help to discriminate families that demonstrate linkage from those that do not. Pedigree features are often used to create homogeneous subsets, and LOD or HLOD scores are then computed within the subsets. However, this practice introduces several problems, including reduced power (which results from multiple testing and small sample sizes within subsets) and difficulty in interpretation of results. To address some of these limitations, we present a regression-based extension of the mixture likelihood for which pedigree features are used as covariates that determine the probability that a family is the linked type. Some advantages of this approach are that multiple covariates can be used (including quantitative covariates), covariates can be adjusted for each other, and interactions among covariates can be assessed. This new regression method is applied to linkage data for familial prostate cancer and provides new insights into the understanding of prostate cancer linkage heterogeneity.
Evidence of the existence of major prostate cancer (PC)-susceptibility genes has been provided by multiple segregation analyses. Although genomewide screens have been performed in over a dozen independent studies, few chromosomal regions have been consistently identified as regions of interest. One of the major difficulties is genetic heterogeneity, possibly due to multiple, incompletely penetrant PC-susceptibility genes. In this study, we explored two approaches to overcome this difficulty, in an analysis of a large number of families with PC in the International Consortium for Prostate Cancer Genetics (ICPCG). One approach was to combine linkage data from a total of 1,233 families to increase the statistical power for detecting linkage. Using parametric (dominant and recessive) and nonparametric analyses, we identified five regions with "suggestive" linkage (LOD score >1.86): 5q12, 8p21, 15q11, 17q21, and 22q12. The second approach was to focus on subsets of families that are more likely to segregate highly penetrant mutations, including families with large numbers of affected individuals or early age at diagnosis. Stronger evidence of linkage in several regions was identified, including a "significant" linkage at 22q12, with a LOD score of 3.57, and five suggestive linkages (1q25, 8q13, 13q14, 16p13, and 17q21) in 269 families with at least five affected members. In addition, four additional suggestive linkages (3p24, 5q35, 11q22, and Xq12) were found in 606 families with mean age at diagnosis of < or = 65 years. Although it is difficult to determine the true statistical significance of these findings, a conservative interpretation of these results would be that if major PC-susceptibility genes do exist, they are most likely located in the regions generating suggestive or significant linkage signals in this large study.
Autosomal dominant retinitis pigmentosa (adRP) is known to result from mutations in two different retinal genes--rhodopsin and peripherin--while a third locus has been implicated by linkage data. However, families have been reported in which all three known loci have been excluded. We report linkage of adRP in one such family to two microsatellite markers on chromosome 7p. D7S435 has previously been localized to 7p13-15.1; D7S460, previously only localized to chromosome 7, maps to within 2 cM of D7S435 with a lod score of 12.15. Two point linkage analysis between these markers and adRP gave lod scores of 5.65 (theta = 0) and 4.19 (theta = 0.046) for D7S460 and D7S435, respectively. Multipoint analysis gave a maximum lod score of 8.22. These data strongly suggest a new adRP locus on chromosome 7p.
D1S2 was one of the first restriction fragment length polymorphisms (RFLPs) assigned to chromosome 1, but its regional location was unknown. In this paper we present data that place this RFLP into both the genetic map and the physical-cytogenetic map. Linkage data maps D1S2 7 cM from PGM1, which is localized to the middle of the short arm at 1p22.1. Southern blot analysis of DNA samples from somatic cell hybrids containing parts of chromosome 1 maps D1S2 proximal to 1p32 and distal to PGM1.
Multivariate linkage analysis using several correlated traits may provide greater statistical power to detect susceptibility genes in loci whose effects are too small to be detected in univariate analysis. In this analysis, we apply a new approach and perform a linkage analysis of several electrophysiological phenotypes of the Collaborative Study on the Genetics of Alcoholism data of the Genetic Analysis Workshop 14. Our approach is based on a variance-component model to map candidate genes using repeated or longitudinal measurements. It can take into account covariate effects and time-dependent genetic effects in general pedigree data. We compare our results with the ones obtained by SOLAR using single measurement data. Our multivariate linkage analysis found linkage evidence on two regions on chromosome 4: around marker GABRB1 at 51.4 cM and marker FABP2 at 116.8 cM (unadjusted p-value = 0.00006).
The combined use of the arbitrarily primed polymerase chain reaction [AP-PCR, also known as random amplification of polymorphic DNA (RAPD)] and isozyme mapping resulted in the production of 87 potential marker loci, enabling an overall expansion within the genetic map of the fish genus Xiphophorus. Use of DNA sequencing-style acrylamide gels and carefully controlled conditions of amplification and silver staining allowed exceptional resolution and reproducibility of AP-PCR/RAPD generated markers. Linkage analysis of AP-PCR/RAPD and isozyme markers resulted in the addition of 16 new markers to Xiphophorus linkage groups (LGs) I, II, III, V, IX, X, XII, and XIV. Addition of 5 AP-PCR/RAPD markers to linkage group U6 containing the Tailspot pigment pattern locus (P) and designation of eight new unassigned linkage groups with 22 markers was also accomplished. Genetic linkage data allowed inference of the existence of a novel pigment pattern modifier locus. Expansion of the Xiphophorus gene map by linkage analysis of AP-PCR/RAPD markers in conjunction with isozyme polymorphisms should lead to the rapid saturation of genetic linkage groups such as LG V, which will probably be instrumental to cloning the Diff tumor suppressor gene locus.
Balanced reciprocal translocations associated with genetic disorders have facilitated the identification of a variety of genes for early-onset monogenic disorders, but only rarely the genes associated with common and complex disorders. To assess the potential of chromosomal breakpoints associated with common/ complex disorders, we investigated the full spectrum of diseases in 731 carriers of balanced reciprocal translocations without known early-onset disorders in a nation-wide questionnaire-based re-examination. In 42 families, one of the breakpoints at the cytogenetic level concurred with known linkage data and/or the translocation co-segregated with the reported phenotype, for example, we found a significant linkage (lod score=2.1) of dyslexia and a co-segregating translocation with a breakpoint in a previously confirmed locus for dyslexia. Furthermore, we identified 441 instances of at least two unrelated carriers with concordant breakpoints and traits. If applied to other populations, re-examination of translocation carriers may identify additional genotype-phenotype associations, some of which may be novel and others that may coincide with and provide additional support of data presented here.