Allelic frequencies of twelve dinucleotide repeat marker loci on chromosome 13 in the normal Japanese population

Summary To establish a genotypic database for dinucleotide repeat marker loci in the Japanese population, we determined allelic frequencies of 12 such markers on chromosome 13 and compared them with data from Caucasians in the GDB archive. The average heterozygosity (79%) for the 12 loci was the same for the two populations. However, allelic distributions at two of the marker loci were quite different. These data will be useful for disease studies in the Japanese population that involve linkage or sibship-pair analyses, or association studies.     

Two dinucleotide repeat polymorphisms at the D8S1442 and D8S1443 loci

Two polymorphic dinucleotide (CA) repeat clones were isolated from cosmids, cCI8-1121 and cCI8-1199, mapped to chromosome 8p11.2-p12.     

Two dinucleotide repeat polymorphisms at the D8S1218 and D8S1219 loci

Summary Two polymorphic dinucleotide (CA) repeat dones were isolated from a CEPH mega-YAC clone (844E2), and were localized to chromosome 8 using a panel of 13 mouse/human somatic cell hybrids.     

Two dinucleotide repeat polymorphisms at the D8S1444 and D8S1445 loci

Summary Two polymorphic dinucleotide (CA) repeat clones were isolated from two P1 phage clones, 1239F3 and 8H11, and were localized to chromosome 8 using a panel of 13 mouse human somatic cell hybrids.     

Dinucleotide repeat polymorphism on chromosome 9q32

Summary A new microsatellite was developed from a cosmid clone (cCI9-246) assigned to human chromosome 9q32.     

Three dinucleotide repeat polymorphisms at the D8S1217, D8S1220, and D8S1221 loci

Three polymorphic dinucleotide (CA) repeat clones were isolated from a CEPH mega-YAC clone (936F7), and were localized to chromosome 8 using a panel of 13 mouse/human somatic cell hybrids.     

A highly polymorphic dinucleotide repeat at the D8S1222 locus

A highly polymorphic dinucleotide (CA) repeat clone was isolated from a CEPH mega-YAC clone (844E2), and was localized to chromosome 8 using a panel of 13 mouse/human somatic cell hybrids.     

Isolation of DNA from the centromere of human chromosome 7 by microdissection

Centromeres remain the least characterized regions of human chromosomes because they have a very high content of repetitive DNA. Here, we describe a micro-dissection library from the centromeric region of human chromosome 7 and its use for generating sequence tagged sites (STSs). The library contains about 1500 clones with an average insert size of 150 bp and only about 15% of the clones harbour repetitive human DNA. Seven clones hybridizing to alphoid DNA were found to correspond to a fragment of the D7Z2 alphoid array on chromosome 7, thus confirming the origin of the library. A number of clones not containing known repetitive DNA were used to generate STSs that identified yeast artificial chromosomes (YACs) and in turn allowed the STSs to be placed on the physical map. One STS is located between the two Genethon genetic markers closest to the centromere on the q side. Another STS was located 3–4 cM away in 7q11.2, while a third identified YACs containing both low-copy and alphoid sequences that are not yet mapped but are clearly centromeric. The library therefore comprises a collection of sequences from the centromeric region of chromosome 7 that can be used to generate STSs and to map the entire centromeric region.This revised version was published online in November 2005 with corrections to the Cover Date.     

Isolation and characterization of 19 dinucleotide repeat polymorphisms on chromosome 3p.

We have screened cosmids on chromosome 3p for (dC-dA)n.(dG-dT)n dinucleotide-repeat sequences. Eighty-nine of 155 cosmids (58%) contained (dC-dA)n.(dG-dT(n repeats as determined by colony hybridization with a (dG-dT)10 oligonucleotide probe; 29 of these were subcloned and the sequences flanking the dinucleotide repeats were determined. Nineteen of the 24 loci examined for polymorphisms by PCR were found to be polymorphic with heterozygosities ranging from 3% to 86%. These dinucleotide repeat polymorphisms will be useful markers for high-resolution mapping of genes that have been localized to 3p, including tumour suppressor genes associated with several types of cancer and genes responsible for various hereditary disorders, such as von Hippel-Lindau disease.     

Diagnosis of four chromosome abnormalities of unknown origin by chromosome microdissection and subsequent reverse and forward painting

A molecular cytogenetic method consisting of chromosome microdissection and subsequent reverse/forward chromosome painting is a powerful tool to identify chromosome abnormalities of unknown origin. We present 4 cases of chromosome structural abnormalities whose origins were ascertained by this method. In one MCA/MR patient with an add(5q)chromosome, fluorescence in situ hybridization (FISH), using probes generated from a microdissected additional segment of the add(5q) chromosome and then from a distal region of normal chromosome 5, confirmed that the patient had a tandem duplication for a 5q35-qter segment. Similarly, we ascertained that an additional segment of an add(3p) chromosome in another MCA/MR patient had been derived from a 7q32-qter segment. In a woman with a history of successive spontaneous abortions and with a minute marker chromosome, painting using microdissected probes from the whole marker chromosome revealed that it was i(15)(p10) or psu dic(15;15)(q11;q11). Likewise, a marker observed in a fetus was a ring chromosome derived from the paracentromeric region of chromosome 19. We emphasize the value of the microdissection-based chromosome painting method in the identification of unknown chromosomes, especially for marker chromosomes. The method may contribute to a collection of data among patients with similar or identical chromosome abnormalities, which may lead to a better clinical syndrome delineation. © 1996 Wiley-Liss, Inc.     

A dominant gene for developmental dyslexia on chromosome 3

Developmental dyslexia is a neurofunctional disorder characterised by an unexpected difficulty in learning to read and write despite adequate intelligence, motivation, and education. Previous studies have suggested mostly quantitative susceptibility loci for dyslexia on chromosomes 1, 2, 6, and 15, but no genes have been identified yet. We studied a large pedigree, ascertained from 140 families considered, segregating pronounced dyslexia in an autosomal dominant fashion. Affected status and the subtype of dyslexia were determined by neuropsychological tests. A genome scan with 320 markers showed a novel dominant locus linked to dyslexia in the pericentromeric region of chromosome 3 with a multipoint lod score of 3.84. Nineteen out of 21 affected pedigree members shared this region identical by descent (corrected p<0.001). Previously implicated genomic regions showed no evidence for linkage. Sequencing of two positional candidate genes, 5HT1F and DRD3, did not support their role in dyslexia. The new locus on chromosome 3 is associated with deficits in all three essential components involved in the reading process, namely phonological awareness, rapid naming, and verbal short term memory.


Keywords: reading disability; linkage analysis; chromosome 3     

A supernumerary marker chromosome originating from two different regions of chromosome 18

By random amplification of a microdissected chromosome using the degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and forward painting (microFISH), we characterised an extra structurally abnormal chromosome (ESAC) or supernumerary marker chromosome in a mentally retarded girl with a pattern of dysmorphic features. It could be clearly shown that the small marker chromosome originates from two different regions of chromosome 18, 18p11.1-->18q11.1 and 18q12.3-->18q21.1 respectively. Maternal origin of the de novo ESAC and biparental origin of the normal homologues of chromosome 18 were shown by PCR of several highly polymorphic microsatellites. In this case, application of microFISH was a prerequisite for rapid and precise characterisation of an ESAC. A definite identification of this discontinuous supernumerary marker chromosome would not have been possible using FISH with centromere specific probes or multicolour FISH approaches.     

Origins of accessory small ring marker chromosomes derived from chromosome 1

Three patients with accessory small ring chromosomes derived from chromosome 1 are presented together with additional clinical details and cytogenetic analyses of a previously reported patient. Cytogenetic analysis was undertaken by FISH using a reverse painting probe generated from one of the patients by microdissection of the r(1) chromosome and with a BAC923C6 which maps to 1p12. Results indicated that patients with r(1) chromosomes consisting of 1q12 heterochromatin and short arm pericentric euchromatin which extends to at least the BAC923C6 were associated with a normal or mild phenotype. Patients with abnormal phenotypes possessed two types of rings. One patient had evidence for contiguous pericentric short arm euchromatin which extended from the centromere to beyond the BAC923C6. Two patients showed molecular cytogenetic results which were compatible with non-contiguous chromosome 1 euchromatin. The diversity of origin of r(1)s will hamper attempts to define phenotype/genotype relationships.     

A novel locus for autosomal dominant non-syndromic deafness, DFNA53, maps to chromosome 14q11.2-q12

Background

Non‐syndromic hearing loss is among the most genetically heterogeneous traits known in humans. To date, at least 50 loci for autosomal dominant non‐syndromic sensorineural hearing loss (ADNSSHL) have been identified by linkage analysis.

Objective

To report the mapping of a novel autosomal dominant deafness locus on the long arm of chromosome 14 at 14q11.2‐q12, DFNA53, in a large multigenerational Chinese family with post‐lingual, high frequency hearing loss that progresses to involve all frequencies.

Results

A maximum multipoint LOD score of 5.4 was obtained for marker D14S1280. The analysis of recombinant haplotypes mapped DFNA53 to a 9.6 cM region interval between markers D14S581 and D14S1021. Four deafness loci (DFNA9, DFNA23, DFNB5, and DFNB35) have previously been mapped to the long arm of chromosome 14. The critical region for DFNA53 contains the gene for DFNA9 but does not overlap with the regions for DFNB5, DFNA23, or DFNB35. Screening of the COCH gene (DFNA9), BOCT, EFS, and HSPC156 within the DFNA53 interval did not identify the cause for deafness in this family.

Conclusions

Identifying the DFNA53 locus is the first step in isolating the gene responsible for hearing loss in this large multigeneration Chinese family.     

Physical and genetic mapping of human chromosome 3 loci containing microsatellite repeats

One hundred and six microsatellite repeat-containing loci, including 59 CA-containing repeats from the CEPH/Genethon collection, were regionally assigned on human chromosome 3 using a somatic cell hybrid mapping panel, dividing the chromosome into 14 intervals. The others were dinucleotide and tetranucleotide repeat-containing loci newly developed for human chromosome 3, of which 26 were also localized by means of genetic linkage analysis against selected CEPH microsatellites. The regional assignment of these two marker sets in a common mapping panel facilitates their integration. Incorporation of these highly polymorphic loci into the developing physical and genetic maps should provide useful information for studies of various diseases involving chromosome 3.     

Isolation and mapping of microsatellites from a library microdissected from the Werner syndrome region, 8p11.2–p22

Summary We have constructed a new genetic linkage map of the Werner syndrome (WRN) region, using microsatellites from a library which was developed by a chromosome microdissection and enzymatic amplification method. These microsatellites were used to genotype members of CEPH families using a simplified detection system of polymerase chain reaction (PCR) products. Two-point analysis was used to assign 4 microsatellite markers relative to each marker and other markers reported in the CEPH public data base. We confirmed that these 4 markers are located to the WRN region, 8p11.2–p22. Such microsatellites microdissected from the definite chromosome region may be useful for positional cloning.