Physical and linkage mapping of human chromosome 17 loci to dog chromosomes 9 and 5

We performed fluorescein and indocyanine green (ICG) angiographies in 56 patients with central serous chorioretinopathy, and studied the choroidal lesions. In the early phase, choroidal filling with ICG was delayed in 77% in the area including focal leakage. Hypofluorescent findings around the site of focal leakage persisted through the phase in 23%, and we think this finding was caused by filling defect of the choriocapillaris. In the late phase, choroidal tissue staining by ICG was present in 82% in the area including focal leakage. Multiple areas of choroidal staining were also present in unaffected areas in 43% and in 62% of fellow eyes. Choroidal tissue staining by ICG was revealed in 48% in the area of choroidal filling delay, and this finding persisted after focal leakage had disappeared following photocoagulation. We think this finding was caused by choroidal vascular hyperpermeability. These findings suggest that choroidal circulatory disturbance and choroidal vascular hyperpermeability play a causative role in damage to the retinal pigment epithelium in central serous chorioretinopathy.     

Complete exon-intron organization of the human gene for the alpha1 chain of type XV collagen (COL15A1) and comparison with the homologous COL18A1 gene

The human gene for the alpha1 chain of type XV collagen (COL15A1) is about 145 kilobases in size and contains 42 exons. The promoter is characterized by the lack of a TATAA motif and the presence of several Sp1 binding sites, some of which appeared to be functional in transfected HeLa cells. Comparison with Col18a1, which encodes the alpha1(XVIII) collagen chain homologous with alpha1(XV), indicates marked structural homology spread throughout the two genes. The mouse Col18a1 contains one exon more than COL15A1, due to the fact that COL15A1 lacks sequences corresponding to exon 3 of Col18a1, which encodes a cysteine-rich sequence motif. Twenty-five of the exons of the two genes are almost identical in size, six of them contain conserved split codons, and the locations of the respective exon-intron junctions are identical or almost identical in the two genes. The homologous exons include the closely adjacent first pair of exons and the exons encoding a thrombospondin-1 homology found in the N-terminal noncollagenous domain 1, which are followed by the most variable part of the two genes, covering the C-terminal half of their noncollagenous domain 1 and the beginning of the collagenous portion, after which most of the exons are homologous. The lengths of the introns are not similar in these genes, with two exceptions, namely the first intron, which is very short, less than 100 base pairs, and the second intron, which is very large, about 50 kilobases, in both genes. It can be concluded that COL15A1 and Col18a1 are derived from a common ancestor.     

Mutations in the type IV collagen alpha 3 (COL4A3) gene in autosomal recessive Alport syndrome

A group of 22 unrelated patients with sporadic or non-X-linked Alport syndrome were screened for mutations in the non-collagenous domain of the type IV collagen alpha 3 (COL4A3) chain gene. The five 3'-exons of this gene, located on chromosome 2qter, were tested by single strand conformation polymorphism analysis and direct sequencing. One patient was heterozygous and another homozygous (Mochizuki et al., Nature Genetics, in press) for a deletion of five nucleotides. A third patient appeared to be a compound heterozygote for two different nonsense mutations. In two patients and the father of a deceased patient we found a heterozygous substitution of an evolutionary conserved leucine by proline. However, segregation data of the mutation and a COL4A3/COL4A4 CA-repeat marker in their families argued against a causative role of the missense mutation. Even drastic changes of strongly conserved amino acids, as in the Leu36Pro case, may not be significant. Autosomal recessive inheritance due to pathogenic COL4A3 mutations accounts for at least 13% of Alport syndrome cases in this sample. It is concluded that COL4A3 is a major gene in the genetically and clinically heterogeneous Alport syndrome.     

CA repeat polymorphism of the COL6A3 gene on chromosome 2q37

A CA dinucleotide repeat has been identified in an intron of the human alpha3(VI) collagen gene (COL6A3) located on chromosome 2q37. Analysis of 100 chromosomes in unrelated Caucasians has demonstrated the existence of eight alleles, and the allelic frequencies have been determined.     

Assignment of STK6 to human chromosome 20q13.2-->q13.3 and a pseudogene STK6P to 1q41-->q42

Fluorescence in situ hybridization analysis of human STK6 encoding a mitotic centrosomal protein kinase, Aik, revealed two signals in chromosome bands 20q13.2-->q13.3 and 1q41-->q42. Somatic cell hybrid panel analyses showed the existence of an identical sequence to STK6 cDNA on chromosome 20, and a processed pseudogene on chromosome 1. These results suggest that STK6 is localized at 20q 13.2-->q13.3 and a pseudogene STK6P at 1q41-->q42.     

Comparative mapping of 9 human chromosome 22q loci in the laboratory mouse

We present a comparative map of genes on human chromosome 22q and homologous loci in the mouse genome. Gene order in humans was established using a panel of somatic cell hybrids. Genetic maps spanning homologous segments on three mouse chromosomes were generated using an interspecific backcross. The conserved linkage between human chromosome 22 and mouse chromosome 16 includes two closely linked loci, Comt and IgI-1. The second conserved linkage involves human chromosome 22 and mouse chromosome 11 and contains two genetically and physically linked loci, Lif and Nfh. Finally, conserved synteny involving mouse chromosome 15 and human chromosome 22 spans 30 cM and contains five loci (Acr, Bzrp, Dia-1, Il2rb and Pdgfb). Loci within this conserved synteny have been sublocalized to different portions of human chromosome 22. The order of genes on mouse chromosome 15 and human chromosome 22 provides further evidence for chromosomal rearrangements within the conserved synteny that have occurred since the divergence of lineages leading to mice and humans.     

Molecular linkage of the human alpha 1-antitrypsin and corticosteroid-binding globulin genes on chromosome 14q32.1

The genes encoding alpha 1-antitrypsin (alpha 1AT; gene symbol PI) and corticosteroid-binding globulin (CBG) are part of a cluster of structurally related serine protease inhibitor (serpin) genes on human Chromosome (Chr) 14q32.1. This cluster also includes the genes encoding alpha 1-antichymotrypsin (AACT) and protein C inhibitor (PCI), as well as an alpha 1-antitrypsin-related sequence (ATR; gene symbol PIL). In this report we present a detailed restriction map of a 110-kb region of genomic DNA that includes the alpha 1AT, ATR, and CBG genes. Gene order in this interval is tel-alpha 1AT-ATR-CBG-cen, and all three genes are transcribed in a distal-to-proximal orientation. Within the gene cluster, ATR is approximately 12 kb downstream of alpha 1AT, and CBG is about 57 kb downstream of alpha 1AT. Repetitive DNA sequences have been mapped throughout the interval, and several new restriction site polymorphisms in the region are described.     

Genome scan for human obesity and linkage to markers in 20q13

Obesity is a highly prevalent, multigenic trait that predicts increased morbidity and mortality. Here we report results from a genome scan based on 354 markers in 513 members of 92 nuclear families ascertained through extreme obesity and normal body weight. The average marker interval was approximately 10 cM. We examined four correlated obesity phenotypes, including the body-mass index (BMI) (both as a quantitative trait and as a discrete trait with a threshold of BMI > or /=30 kg/m2) and percentage of fat (both as a quantitative trait and as a discrete trait with a threshold of 40%) as assessed by bioelectrical impedance. In the initial stage of the genome scan, four markers in 20q gave positive evidence for linkage, which was consistent across most obesity phenotypes and analytic methods. After saturating 20q with additional markers (25 markers total) in an augmented sample of 713 members from 124 families, we found linkage to several markers in a region, 20q13, previously implicated in both human and animal studies. Three markers (D20S107, D20S211, and D20S149) in 20q13 had empirical P values (based on Monte Carlo simulations, which controlled for multiple testing) < or /=. 01 for single-point analysis. In addition, the parametric, affecteds-only analysis for D20S476 yielded a LOD score of 3.06 (P=. 00009), and the affected-sib-pair test yielded a LOD score of 3.17 (P=.000067). Multipoint analyses further strengthened and localized these findings. This region includes several plausible candidate genes for obesity. Our results suggest that one or more genes affecting obesity are located in 20q13.     

Structure of the human paralemmin gene (PALM), mapping to human chromosome 19p13.3 and mouse chromosome 10, and exclusion of coding mutations in grizzled, mocha, jittery, and hesitant mice

OBJECTIVES: To assess the correlation of total prostatic size and prostate transition zone dimensions with various measurements of the severity of bladder outlet obstruction secondary to benign prostatic hyperplasia. METHODS: Prostate-specific antigen, creatinine, American Urological Association symptom score, bother score, urinary history, uroflowmetry, and post-void residual urine volume determination was followed by measurement of the prostate gland and transition zone on transrectal ultrasound images in 136 men undergoing systematic prostate biopsies. Patients were divided into five groups based on past urinary tract treatment history and the presence of prostate cancer on the biopsies. The total prostate and transition zone dimensions, as well as calculated prostate and transition zone volumes, were compared by Pearson correlation with both the subjective and objective voiding parameters in each patient group. RESULTS: The transition zone dimensions correlated positively with American Urological Association symptom score, bother score, and post-void residual urine volume and correlated negatively with maximum and mean flow rates, particularly in patients with no history of prostate surgery, alpha-blocker administration, urinary infections, irritative voiding symptoms, or prostate cancer. CONCLUSIONS: Transrectal ultrasound measurements of transition zone dimensions correlate better than total prostatic dimensions or calculated prostatic or transition zone volumes with the severity of benign prostatic hyperplasia. Of these, the transverse transition zone dimension demonstrated the best correlation; however, this correlation is probably not adequate for clinical utility.     

Peutz-Jeghers syndrome: confirmation of linkage to chromosome 19p13.3 and identification of a potential second locus, on 19q13.4

Peutz-Jeghers syndrome (PJS) is an autosomal dominant disease with variable expression and incomplete penetrance, characterized by mucocutaneous pigmentation and hamartomatous polyposis. Patients with PJS have increased frequency of gastrointestinal and extraintestinal malignancies (ovaries, testes, and breast). In order to map the locus (or loci) associated with PJS, we performed a genomewide linkage analysis, using DNA polymorphisms in six families (two from Spain, two from India, one from the United States, and one from Portugal) comprising a total of 93 individuals, including 39 affected and 48 unaffected individuals and 6 individuals with unknown status. During this study, localization of a PJS gene to 19p13.3 (around marker D19S886) had been reported elsewhere. For our families, marker D19S886 yielded a maximum LOD score of 4.74 at a recombination fraction (theta) of .045; multipoint linkage analysis resulted in a LOD score of 7.51 for the interval between D19S886 and 19 pter. However, markers on 19q13.4 also showed significant evidence for linkage. For example, D19S880 resulted in a maximum LOD score of 3.8 at theta = .13. Most of this positive linkage was contributed by a single family, PJS07. These results confirm the mapping of a common PJS locus on 19p13.3 but also suggest the existence, in a minority of families, of a potential second PJS locus, on 19q13.4. Positional cloning and characterization of the PJS mutations will clarify the genetics of the syndrome and the implication of the gene(s) in the predisposition to neoplasias.     

Genetic mapping of the spinocerebellar ataxia type 2 gene on human chromosome 12

The dominant spinocerebellar ataxias are a genetically heterogeneous group of diseases leading to premature death of neurons in the cerebellum and other parts of the nervous system. The mutation causing SCA1 is on human chromosome (CHR) 6p and SCA3 is on CHR 14q. To refine the location of the SCA2 gene on CHR 12q, we performed genetic linkage analysis between the SCA2 locus and nine Ioci (D12S58, D12S78, D12S317, D12S330, D12S353, D12S84, D12S105, D12S79, and PLA2) in three SCA2 families. The highest pairwise lod scores were obtained between SCA2 and D12S84/D12S105 and D12S79. We determined the best order and genetic distances among these loci in ten multigenerational families by multipoint linkage analysis and established the following order: D12S101-D12S58/IGF1- D12S78-D12S317-D12S330/D12S353-D12S84/D 12S105-D12S79-PLA2. Using this genetic map, multipoint linkage analysis placed SCA2 between D12S84/D12S105 and D12S79.     

Cloning of a highly conserved human protein serine-threonine phosphatase gene from the glioma candidate region on chromosome 19q13.3

Allelic loss studies have suggested that a glioma tumor suppressor gene resides in a 425-kb region of chromosome 19q, telomeric to D19S219 and centromeric to D19S112. Exon amplification of a cosmid contig spanning this region yielded four exons with high homology to a rat protein serine-threonine phosphatase from a cosmid approximately 100 kb telomeric to D19S219. Isolation of a near full-length cDNA from a human fetal brain cDNA library revealed a protein serine-threonine phosphatase with a tetratricopeptide motif, almost identical to human PPP5C (PP5) and highly homologous to rat PPT. Northern blotting demonstrated expression in most tissues, including brain. Primary and cultured gliomas were studied for genetic alterations in this gene using pulsed-field gel electrophoresis, routine Southern blots, and genomic DNA-and RNA-based single-strand conformation polymorphism analysis. Genomic alterations were were not detected in any of the gliomas, and all studied gliomas expressed the gene, suggesting that this phosphatase is not the putative chromosome 19q glioma tumor suppressor gene.     

Localization of a gene for M?bius syndrome to chromosome 3q by linkage analysis in a Dutch family

M?bius syndrome (MIM no. 157900) consists of a congenital paresis or paralysis of the VIIth cranial nerve, frequently accompanied by paralysis of other cranial nerves, orofacial and limb malformations, defects of the musculoskeletal system and mental retardation. Although most patients are sporadic cases, familial recurrence is not rare. Different pedigrees suggest different modes of inheritance. We performed linkage analysis in a large family with autosomal dominantly inherited M?bius syndrome, consisting essentially of asymmetric bilateral facial pareses. After exclusion of the candidate region for M?bius syndrome on 13q12.2-q13, we localized the gene to chromosome 3q21-22, indicating genetic heterogeneity of M?bius syndrome. This heterogeneity is further proven by the exclusion of both loci in a second family with M?bius syndrome.