Gene for hereditary retinoblastoma assigned to human chromosome 13 by linkage to esterase D

Evaluation of three families with hereditary retinoblastoma demonstrates close linkage of the gene for this tumor with the genetic locus for esterase D. These results assign the gene for the hereditary form of retinoblastoma to band q14 on chromosome 13, the same region which is affected in the chromosome deletion form of this eye tumor, and therefore suggest a common underlying mechanism in the pathogenesis of these two forms of retinoblastoma.

A specific requirement for PDGF-C in palate formation and PDGFR-alpha signaling

PDGF-C is a member of the platelet-derived growth factor (PDGF) family, which signals through PDGF receptor (PDGFR) alphaalpha and alphabeta dimers. Here we show that Pdgfc(-/-) mice die in the perinatal period owing to feeding and respiratory difficulties associated with a complete cleft of the secondary palate. This phenotype was less severe than that of Pdgfra(-/-) embryos. Pdgfc(-/-) Pdgfa(-/-) embryos developed a cleft face, subepidermal blistering, deficiency of renal cortex mesenchyme, spina bifida and skeletal and vascular defects. Complete loss of function of both ligands, therefore, phenocopied the loss of PDGFR-alpha function, suggesting that both PDGF-A and PDGF-C signal through PDGFR-alpha to regulate the development of craniofacial structures, the neural tube and mesodermal organs. Our results also show that PDGF-C signaling is a new pathway in palatogenesis, different from, and independent of, those previously implicated.

Association mapping of disease loci, by use of a pooled DNA genomic screen

Genomic screening to map disease loci by association requires automation, pooling of DNA samples, and 3,000-6,000 highly polymorphic, evenly spaced microsatellite markers. Case-control samples can be used in an initial screen, followed by family-based data to confirm marker associations. Association mapping is relevant to genetic studies of complex diseases in which linkage analysis may be less effective and to cases in which multigenerational data are difficult to obtain, including rare or late-onset conditions and infectious diseases. The method can also be used effectively to follow up and confirm regions identified in linkage studies or to investigate candidate disease loci. Study designs can incorporate disease heterogeneity and interaction effects by appropriate subdivision of samples before screening. Here we report use of pooled DNA amplifications-the accurate determination of marker-disease associations for both case-control and nuclear family-based data-including application of correction methods for stutter artifact and preferential amplification. These issues, combined with a discussion of both statistical power and experimental design to define the necessary requirements for detecting of disease loci while virtually eliminating false positives, suggest the feasibility and efficiency of association mapping using pooled DNA screening.

A locus on chromosome 15q26 (IDDM3) produces susceptibility to insulin-dependent diabetes mellitus

To identify new loci predisposing to insulin-dependent diabetes mellitus (IDDM), we have investigated 250 families with more than one diabetic child. Affected sibling pair linkage analysis revealed strong evidence for an IDDM susceptibility locus near D15S107 on chromosome 15q26 (P = 0.0010) termed IDDM3. Families less predisposed through genes in the HLA region provided most of the evidence for linkage. In these families, discordant sibling pairs also showed linkage (P = 0.0052), and sibling pair disease concordance or discordance was strongly related to the proportion of genes the pair shared at D15S107 (P = 0.0003). Our study also revealed evidence for an IDDM locus on chromosome 11q13 (IDDM4) using affected siblings (P = 0.0043), but no evidence using discordant siblings.

Genetic linkage and association studies of Type I diabetes: challenges and rewards

Family and twin studies have shown clearly that Type I (insulin-dependent) diabetes mellitus has a genetic basis. However, only within the past decade has it been possible to systematically attempt to identify the genes that increase susceptibility to this disorder using linkage and association analysis of genetic markers distributed across the genome. More than 20 putative diabetes-predisposing genes have been localised in addition to HLA region susceptibility genes detected more than 25 years ago. Unfortunately, the effects of most diabetes-predisposing genes are weak, with the exception of HLA region susceptibility genes (which contribute about half of the genetic risk). The overall effects of diabetes-predisposing genes could be weak because the susceptibility gene occurs in only a small proportion of diabetic patients or the susceptibility gene (although it might be common) produces only a modest increase in risk, probably by acting in concert with other such genes to cause disease. The weak effects of these genes have made them difficult to locate, difficult to confirm in independent studies and difficult to isolate by genetic procedures. This paper summarizes the major challenges that have faced geneticists in mapping Type I diabetes genes, and reviews the progress achieved to date. The rewards of the genetic studies will be twofold: increased understanding of the causes of Type I diabetes, facilitating creation of preventative therapies, and enabling clinicians in the future to use genetic information to predict which children are predisposed to diabetes in order to target them for preventative therapies.

Single sperm typing demonstrates that reduced recombination is associated with the production of aneuploid 24,XY human sperm

To account for the increased proportion of paternal nondisjunction in 47,XXY males as compared to other trisomies, it has been suggested that the XY bivalent, with its reduced region of homology, is particularly susceptible to nondisjunction. Molecular studies of liveborn Klinefelter syndrome (47,XXY) individuals have reported an association between the absence of recombination in the pseudoautosomal region and nondisjunction of the XY bivalent. In this study we examined single sperm from a normal 46,XY male to determine if there is any alteration in the recombination frequency of aneuploid disomic 24,XY sperm compared to unisomic sperm (23,X or Y). Two DNA markers STS/STS pseudogene and DXYS15 were typed in sperm from a heterozygous man to determine if recombination had occurred in the pseudoautosomal region. Individual unisomic sperm (23,X or Y) were isolated using a FACStar(Plus) flow cytometer into PCR tubes. To identify disomic 24,XY sperm, 3-colour FISH analysis was performed with probes for chromosomes X,Y and 1. The 24,XY cells were identified using fluorescence microscopy, each disomic sperm was scraped off the slide using a glass needle attached to a micromanipulator and then put into a PCR tube. Hemi-nested PCR analysis of the two markers was performed to determine the frequency of recombination. A total of 329 unisomic sperm and 150 disomic sperm have been typed. The frequency of recombination between the two DNA markers was 38.3% for the unisomic sperm, similar to frequencies previously reported. The 24,XY disomic sperm had an estimated recombination frequency of 25.3%, however, a highly significant decrease compared to the unisomic 23,X or 23,Y sperm (chi(2) = 10.7, P = 0.001). This direct analysis of human sperm indicates that lack of recombination in the pseudoautosomal region is a significant cause of XY nondisjunction and thus Klinefelter syndrome.

Susceptibility to insulin-dependent diabetes mellitus maps to a locus (IDDM11) on human chromosome 14q24.3-q31

To locate genes predisposing to insulin-dependent diabetes mellitus (IDDM), an autoimmune disorder resulting from destruction of the insulin-producing pancreatic cells, we are testing linkage of IDDM susceptibility to polymorphic markers across the genome using families with two or more IDDM children. A new susceptibility locus (IDDM11) has been localized to chromosome 14q24.3-q31 by detection of significant linkage to microsatellite D14S67, using both maximum likelihood methods (LODmax = 4.0 at Theta = 0.20) and affected sib pair (ASP) methods (P = 1 x 10(-5)). This represents the strongest reported evidence for linkage to any IDDM locus outside the HLA region. The subset of families in which affected children did not show increased sharing of HLA genes (HLA sharing </= 50%) provided most of the support for D14S67 linkage (LODmax 4.6 at Theta = 0.12; ASP P < 5 x 10(-6)). There was significant linkage heterogeneity between the HLA-defined subsets of families (P = 0.009), suggesting that IDDM11 may be an important susceptibility locus in families lacking strong HLA region predisposition.

Absence of linkage of phonological coding dyslexia to chromosome 6p23-p21.3 in a large family data set

Previous studies have suggested that a locus predisposing to specific reading disability (dyslexia) resides on chromosome 6p23-p21.3. We investigated 79 families having at least two siblings affected with phonological coding dyslexia, the most common form of reading disability (617 people genotyped, 294 affected), and we tested for linkage with the genetic markers reported to be linked to dyslexia in those studies. No evidence for linkage was found by LOD score analysis or affected-sib-pair methods. However, using the affected-pedigree-member (APM) method, we detected significant evidence for linkage and/or association with some markers when we used published allele frequencies with weighting of rarer alleles. APM results were not significant when we used marker allele frequencies estimated from parents. Furthermore, results were not significant with the more robust SIMIBD method using either published or parental marker frequencies. Finally, family-based association analysis using the AFBAC program showed no evidence for association with any marker. We conclude that the APM method should be used only with extreme caution, because it appears to have generated false-positive results. In summary, using a large data set with high power to detect linkage, we were unable to find evidence for linkage or association between phonological coding dyslexia and chromosome 6p markers.

Evidence for a susceptibility locus on chromosome 6q influencing phonological coding dyslexia

A linkage study of 96 dyslexia families containing at least two affected siblings (totaling 877 individuals) has found evidence for a dyslexia susceptibility gene on chromosome 6q11.2-q12 (assigned the name DYX4). Using a qualitative phonological coding dyslexia (PCD) phenotype (affected, unaffected, or uncertain diagnoses), two-point parametric analyses found highly suggestive evidence for linkage between PCD and markers D6S254, D6S965, D6S280, and D6S251 (LOD(max) scores = 2.4 to 2.8) across an 11 cM region. Multipoint parametric analysis supported linkage of PCD to this region (peak HLOD = 1.6), as did multipoint nonparametric linkage analysis (P = 0.012). Quantitative trait linkage analyses of four reading measures (phonological awareness, phonological coding, spelling, and rapid automatized naming speed) also provided evidence for a dyslexia susceptibility locus on chromosome 6q. Using a variance-component approach, analysis of phonological coding and spelling measures resulted in peak LOD scores at D6S965 of 2.1 and 3.3, respectively, under 2 degrees of freedom. Furthermore, multipoint nonparametric quantitative trait sibpair analyses suggested linkage between the 6q region and phonological awareness, phonological coding, and spelling (P = 0.018, 0.017, 0.0005, respectively, for unweighted sibpairs < 18 years of age). Although conventional significance thresholds were not reached in the linkage analyses, the chromosome 6q11.2-q12 region clearly warrants investigation in other dyslexia family samples to attempt replication and confirmation of a dyslexia susceptibility gene in this region.

Close genetic linkage between diabetes mellitus and kidd blood group

27 polymorphic genetic markers were analysed for possible linkage with insulin-dependent diabetes mellitus (IDDM). The data set contained 71 families with at least one affected member each. Under three different genetic models for IDDM, evidence was found for linkage between the disease and two distinct sets of marker loci: three markers on chromosome 6 (HLA, properdin factor B, and glyoxalase-1), and the Kidd blood group locus. The families apparently do not fall into two groups, one exhibiting linkage to the HLA complex and the other to the Kidd locus. Thus, two distinct disease-susceptibility loci may be involved in the inheritance of IDDM.

Immunoglobulin allotyping (Gm, Km) of GAW5 families

The following Gm and Km immunoglobulin allotypes were determined on the Genetic Analysis Workshop 5 insulin-dependent diabetes mellitus (GAW5 IDDM) families: G1m (1,2,3,17), G2m (23), G3m (5,10,11,13,14,21,28) and Km (1,3). Since the allotype G2m (23) has been rarely studied, due to paucity of typing reagents, it was of interest to compare the frequency of the halotype encoding this allotype in parents of North American GAW5 IDDM families with the frequency found in a previous investigation of healthy North Americans. Results indicated very similar frequencies of Gm haplotypes in the two groups.

Dense-map genome scan for dyslexia supports loci at 4q13, 16p12, 17q22; suggests novel locus at 7q36

Analysis of genetic linkage to dyslexia was performed using 133,165 array-based SNPs genotyped in 718 persons from 101 dyslexia-affected families. Results showed five linkage peaks with lod scores >2.3 (4q13.1, 7q36.1-q36.2, 7q36.3, 16p12.1, and 17q22). Of these five regions, three have been previously implicated in dyslexia (4q13.1, 16p12.1, and 17q22), three have been implicated in attention-deficit hyperactivity disorder (ADHD, which highly co-occurs with dyslexia; 4q13.1, 7q36.3, 16p12.1) and four have been implicated in autism (a condition characterized by language deficits; 7q36.1-q36.2, 7q36.3, 16p12.1, and 17q22). These results highlight the reproducibility of dyslexia linkage signals, even without formally significant lod scores, and suggest dyslexia predisposing genes with relatively major effects and locus heterogeneity. The largest lod score (2.80) occurred at 17q22 within the MSI2 gene, involved in neuronal stem cell lineage proliferation. Interestingly, the 4q13.1 linkage peak (lod 2.34) occurred immediately upstream of the LPHN3 gene, recently reported both linked and associated with ADHD. Separate analyses of larger pedigrees revealed lods >2.3 at 1-3 regions per family; one family showed strong linkage (lod 2.9) to a known dyslexia locus (18p11) not detected in our overall data, demonstrating the value of analyzing single large pedigrees. Association analysis identified no SNPs with genome-wide significance, although a borderline significant SNP (P = 6 × 10(-7)) occurred at 5q35.1 near FGF18, involved in laminar positioning of cortical neurons during development. We conclude that dyslexia genes with relatively major effects exist, are detectable by linkage analysis despite genetic heterogeneity, and show substantial overlapping predisposition with ADHD and autism.

Interaction of HLA and immunoglobulin antigens in type 1 (insulin-dependent) diabetes

We analyzed 88 unrelated subjects with Type 1 (insulin-dependent) diabetes and 64 sibling controls (maximum one per diabetic) for associations between immunoglobulin allotype antigens (GM and KM) and Type 1 diabetes. None were found. However, we did find interactions between GM, HLA-DR, and Type 1 diabetes (significant or of borderline significance after considering the effect of multiple tests): possession of Glm(2) appeared to increase susceptibility to diabetes in individuals who had HLA-DR3 but not HLA-DR4, while possession of G3m(5) appeared to increase susceptibility in individuals who had HLA-DR4 but not HLA-DR3. These results suggest that genetic predisposition to Type 1 diabetes is partially determined by alleles at the GM locus (or a locus in linkage disequilibrium with GM) interacting with alleles at the HLA-DR locus (or a locus in linkage disequilibrium with HLA-DR).

Linkage analysis of neurofibromatosis (von Recklinghausen disease)

Linkage analysis of 28 genetic markers was undertaken in 108 subjects from 11 families with well-documented, classic, peripheral neurofibromatosis. Fifty-four persons were affected in one four-generation family, seven three-generation families, and three two-generation families. Lod scores were calculated using the standard LIPED programme for 49 combinations of theta male and theta female from 0.01 to 0.50. Lod scores excluded close linkage with 16 markers, including most tested on chromosome 1 and HLA on chromosome 6, and were inconclusive for 12 markers, including the secretor locus, closely linked to myotonic dystrophy. Analysis of five informative families resulted in a lod score of +2.2 for close linkage with GC on chromosome 4. However, the lod score for GC in the one additional informative family was negative, so that the final interpolated maximum was Z = 0.89 for theta male = 0.03, theta female = 0.28. Further studies are needed to evaluate this suggestion of linkage and possible genetic heterogeneity.

Genes predisposing to IDDM in multiplex families

Analysis of HLA haplotypes occurring in more than one, only one, or no diabetics in GAW5 multiplex insulin-dependent diabetes mellitus (IDDM) families suggested: 1) DR3, DR4, DRw6, and DRw8 are positively associated, and DR2 is negatively associated, with IDDM; 2) DR4 haplotypes are more diabetogenic than DR3 haplotypes; some DR3 haplotypes lacking B8/B18 are more diabetogenic than those carrying B8/B18; DR3 haplotypes with DR beta TaqI bands [2,5,10/11] are more diabetogenic than those without; DR4 haplotypes that carry DQw3.2 are more diabetogenic than those that do not; some DR2 haplotypes are diabetogenic rather than protective. Analysis of DR3 and DR4 transmission from DR3/X and DR4wX (X not equal to 3,4) healthy parents suggested: 3) no distortion of transmission to healthy children and 4) mothers transmit DR4 (and perhaps DR3) less often than fathers to diabetic children. Analysis of INS, GM, and HLA haplotype sharing in affected sib pairs suggested: 5) random segregation of INS haplotypes and 6) a tendency to increased sharing of GM haplotypes in affected sib pairs who were HLA-identical and DR3/4, compared with pairs who were not.

Association of AXIN2 with non-syndromic oral clefts in multiple populations

We have previously shown the association of AXIN2 with oral clefts in a US population. Here, we expanded our study to explore the association of 11 AXIN2 markers in 682 cleft families from multiple populations. Alleles for each AXIN2 marker were tested for transmission distortion with clefts by means of the Family-based Association Test. We observed an association with SNP rs7224837 and all clefts in the combined populations (p = 0.001), and with SNP rs3923086 and cleft lip and palate in Asian populations (p = 0.004). We confirmed our association findings in an additional 528 cleft families from the United States (p < 0.009). We tested for gene-gene interaction between AXIN2 and additional cleft susceptibility loci. We assessed and detected Axin2 mRNA and protein expression during murine palatogenesis. In addition, we also observed co-localization of Axin2 with Irf6 proteins, particularly in the epithelium. Our results continue to support a role for AXIN2 in the etiology of human clefting. Additional studies should be performed to improve our understanding of the biological mechanisms linking AXIN2 to oral clefts.

Localization of a gene for incomplete X-linked congenital stationary night blindness to the interval between DXS6849 and DXS8023 in Xp11.23

Congenital stationary night blindness (CSNB) is a nonprogressive retinal disorder characterized by night blindness, nystagmus, myopia, a variable decrease in visual acuity, an abnormal electroretinographic response, and a disturbance in dark adaptation. Two forms of X-linked CSNB have been defined, complete CSNB in which rod function is extinguished, and incomplete CSNB in which rod function is reduced but not extinguished, as seen by electroretinography and dark adaptometry. In studying a large family of Mennonite ancestry, we have confirmed linkage between the locus (CSNB2) for incomplete CSNB and genetic markers in the Xp11 region. In particular, lod scores of 12.25 and 15.26 at zero recombination were observed between CSNB2 and the markers DXS573 and DXS255. Detailed analysis of critical recombinant chromosomes in this extended family have refined the minimal region for the CSNB2 locus to the interval between DXS6849 and DXS8023 in Xp11.23.

Transforming growth factor alpha: a modifying locus for nonsyndromic cleft lip with or without cleft palate?

Most (but not all) studies have found weak but significant association between restriction fragment length polymorphisms at the transforming growth factor alpha (TGFA) locus on chromosome 2p13 and nonsyndromic cleft lip with or without cleft palate (CL +/- P). However, all attempts to demonstrate genetic linkage between TGFA and CL +/- P in families have produced consistently negative lod scores which provide evidence against linkage. We typed a 3-allele single-strand conformation polymorphism at TGFA in 14 extended families with multiple CL +/- P members from West Bengal, India. No significant TGFA differences were observed between the entire sample of 34 affected people and a sample of 38 unaffected people unrelated to each other (p = 0.39). However, affected individuals with CL only showed significant differences from unaffected individuals (p = 0.008). More interestingly, the CL only and CL+P groups of individuals differed strongly from each other in their TGFA frequencies (p = 0.0002). Using an autosomal dominant model with reduced penetrance for the inheritance of a major CL +/- P locus (suggested by our prior segregation analyses), a non-significant maximum lod score of 0.13 at a recombination frequency of 20% was obtained. We suggest that the TGFA locus only modifies expression (severity) of the CL +/- P trait, which is controlled by a major (necessary) locus elsewhere; this could explain the difficulty in obtaining positive linkage results.

HLA-DR effects in a large German IDDM dataset

DR4 and DR3 are in strongest linkage disequilibrium with IDDM susceptibility genes, and DR1 demonstrates a lesser degree of positive disequilibrium. DR3/DR4 heterozygotes have the highest risk. The DR1 increase occurs almost exclusively in DR4/DR1 heterozygotes, suggesting that DR1 may be in disequilibrium with the same susceptibility gene as DR3. Homozygotes for DR4 and especially DR3 have a higher risk than heterozygotes of either with DRX. GLO-2 is increased in diabetic haplotypes carrying DR4, DR3 or DR1.

Linkage analysis of five pedigrees affected with typical autosomal dominant retinitis pigmentosa

Five pedigrees (including an expanded version of a previously reported pedigree) exhibited typical autosomal dominant retinitis pigmentosa were analysed for linkage of RP to 29 genetic markers. No significant lod scores resulted. The largest lod score is +1.51 and suggests linkage between RP and Rh blood group at an estimated recombination fraction of 20% in males and 40% in females. Further studies are needed to confirm or refute this suggested linkage.

Genetic linkage studies of transferrin, pseudocholinesterase, and chromosome 1 loci

Genetic linkage analysis of a pedigree with four different alleles for pseudocholinesterase (CHE1) gives a positive lod score of 0.37 at theta = 0.16 for linkage with transferrin (TF), a finding which supports previous reports of linkage between CHE1 and TF. Evaluation of linkage relations of CHE1 and TF using unreported families from our data bank fails to establish linkage with chromosome 1 loci (6-PGD, Rh, PGM1, AMY2 and FY). These results are consistent with recent studies which suggest that TF is on human chromosome 3.

Genetic risk factors in diabetic retinopathy

Diabetic retinopathy is the leading cause of blindness in adults aged 30 to 65 years. However, 20% of the diabetic population does not develop significant retinopathy. To examine the influence of immune-related genetic factors on the development of diabetic retinopathy, we studied immunoglobulin allotypes in 102 subjects aged 8 to 20 years, who had had Type 1 (insulin-dependent) diabetes mellitus for 4.5 to 11 years (mean 7.3 years). HLA had been previously typed on 59 of these subjects. Retinopathy was assessed by expert review of retinal photographs. Among the 44 patients who had evidence of retinopathy, 33(75%) were G2m(23+), while among the 58 patients without retinopathy but with similar duration of disease, only 28(48%) were G2m(23+) (p = 0.006). The HLA-DR types of patients with and without retinopathy were not significantly different. We conclude that there is significant evidence of an association between G2m(23) at the locus encoding IgG2 subclass heavy chains and susceptibility to the development of diabetic retinopathy early in the clinical course of the disease. Our findings provide important independent confirmation of a previous report of association between Gm allotypes and predisposition to diabetic retinopathy. We are unable to determine if the Gm effect on development of retinopathy is due to the G2m(23) allotype itself, or due to genes that are closely linked to, and in linkage disequilibrium with, the locus encoding the G2m(23) allotype.