Carrier detection of Batten disease (Juvenile neuronal ceroid-lipofuscinosis)

Batten disease, or the juvenile form of neuronal ceroid lipofuscinosis, is an autosomal recessive neurodegenerative disorder manifesting with progressive blindness, seizures, and dementia, leading to an early death. The CLN3 locus which is involved in Batten disease had been localized to chromosome 16p11.2. Linkage disequilibrium has been observed between CLN3 and polymorphic microsatellite markers D16S288, D16S299, and D16S298, making carrier detection and prenatal diagnosis by haplotype analysis possible. For the purpose of carrier detection, haplotypes from Dutch Batten patients and their families were constructed. Most patients share the same D16S298 allele, suggesting the presence of a founder effect in the Dutch population. In a large inbred Dutch family, in which Batten disease occurs with high frequency, haplotype analysis has been carried out with high accuracy for carrier detection. © 1995 Wiley-Liss, Inc.     

Physical mapping of the 5 Mb D9S196-D9S180 interval harboring the basal cell nevus syndrome gene and localization of six genes in this region

The basal cell nevus syndrome (Gorlin syndrome) is characterized by multiple basal cell carcinomas and diverse developmental defects. The gene responsible for this syndrome has been mapped previously to a 2 cM interval between D9S196 and D9S180 at 9q22.3, and very recently mutations of a candidate gene in this region—the human homolog of the Drosophila patched gene—have been identified. We report here on physical mapping studies integrating a contig of yeast artificial chromosomes and bacterial artificial chromosomes with a long-range map spanning approximately 5 Mb between the recombination-determined flanking markers. Six genes have been mapped to this interval. Genes Chromosom. Cancer 18:305–309, 1997. © 1997 Wiley-Liss, Inc.     

Physical map and haplotype analysis of 16q-linked autosomal dominant cerebellar ataxia (ADCA) type III in Japan

 Autosomal dominant cerebellar ataxia (ADCA) is a group of heterogeneous neurodegenerative disorders. We previously mapped a gene locus for ADCA with pure cerebellar syndrome (ADCA type III) to a 3-cM region in chromosome 16q, and found a common haplotype among affected individuals. This region was exactly within the locus for another ADCA, spinocerebellar ataxia type 4 (SCA4). To identify the gene causing 16q-linked ADCA type III, we constructed a contig with 38 bacterial artificial chromosome clones between D16S3043 and D16S3095. The size of this contig was estimated to be 4.8 Mb. We found more than 500 nucleotide tandem repeats, including 9 CAG/CTG repeats in this candidate region, although none of the 94 tandem repeats analyzed were expanded in affected individuals. However, we found 11 new polymorphic markers, giving 22 markers spanning the candidate region. By typing these markers on eight Japanese families with ADCA type III, including two new families, we found that a common “founder” haplotype is seen in a more restricted 3.8-Mb region, spanning markers GGAA05 and D16S3095. We present here a newly refined critical interval of 16q-ADCA type III/SCA4. Data of 11 new DNA markers on 16q22.1 would also be useful for other research of genes mapped to this region. Received: June 25, 2002 / Accepted: November 22, 2002 Correspondence to:H. Mizusawa     

Clinical and molecular aspects of nephropathic cystinosis

 Nephropathic cystinosis, an autosomal recessively inherited lysosomal storage disease, results from impaired transport of the disulfide amino acid cystine out of cellular lysosomes. The consequent accumulation and crystallization of cystine destroys tissues, causing growth retardation in infancy, renal failure at 10 years of age, and a variety of other complications. Early oral therapy with the cystine-depleting agent cysteamine prevents renal deterioration and enhances growth. Although the lysosomal cystine carrier has been extensively studied, its molecular structure remains unknown. The lysosomal cystine transporter gene has been mapped by linkage analysis to human chromosome 17p between polymorphic microsatellite markers D17S1583 and D17S1584. Pertinent recombination events and homozygosity by descent has verified that the cystinosis gene lies in the 3.6 cM genetic interval between these two markers. The cystinosis region has been substantially reduced in size by the observation of recombination events in cystinosis patients between markers D17S1828 and D17S2167. According to radiation hybrid analysis, these two markers are separated by 10.2 cR₈₀₀₀ (centirad using 8000 rad radiation hybrids). Estimates of the physical size of this interval range from 187 to 510 kb. Four yeast artificial chromosomes have been identified which form a contig covering the original cystinosis region. Two P1 clones together may span the new, smaller interval, meaning that the cystinosis gene would lie on one of them. Current efforts are being directed toward using these P1 clones to isolate candidate cDNAs by a variety of methods. The ultimate cloning of the cystinosis gene will reveal how functional lysosomal porters are synthesized, targeted, processed, and integrated into the lysosomal membrane. Received: 18 April 1997 / Accepted: 2 July 1997     

Localisation of the gene for multiple endocrine neoplasia type 2A to a 480 kb region in chromosome band 10q11.2

A YAC contig has been constructed spanning 1.1 Mb of human chromosomeband 10q11.2 which encompasses three markers (D10S141, RET,D10S94) closely linked to the gene for MEN 2A. This physicallinkage group is ordered cen-D10S141-RET-D10S94-qter, and mustinclude MEN2A, which lies in a 480 kb region between flankingmarkers D10S141 and D10S94.     

A linkage disequilibrium at the candidate gene locus for 16q-linked autosomal dominant cerebellar ataxia type III in Japan

We previously mapped the gene responsible for autosomal dominant cerebellar ataxia (ADCA) type III to a 10.9-cM interval between D16S3089 and D16S515 on chromosome 16q. This region, however, was identical to the candidate locus of spinocerebellar ataxia type 4 (SCA4). In this study, we extended our research to refine the gene locus of the disease by applying linkage disequilibrium with 20 microsatellite DNA markers. With 9 markers flanked by D16S3031 and D16S3107, we found that the affected individuals in six families had a common haplotype on their disease chromosomes. Furthermore, linkage disequilibrium was demonstrated with 5 informative markers: D16S3019 (P = 0.013), D16S3067 (P = 0.008), D16S3141 (P = 0.011), D16S496 (P = 0.032), and D16S3107 (P = 0.000). These results indicate that the disease could have originated from a common ancestor harboring a mutation within a less than 3-cM region between D16S3043 and D16S3095. The founder alleles were also observed in other patients with ADCA type III unrelated to the six families. Received: October 25, 2000 / Accepted: January 5, 2001     

Genome-wide search for CLN2, the gene causing late-infantile neuronal ceroid-lipofuscinosis (LNCL)

The loci for the juvenile (CLN3) and infantile (CLN1) neuronal ceroid lipofuscinosis (NCL) types have been mapped by genetic linkage analysis to chromosome arms 16p and 1p, respectively. The late-infantile defect CLN2 has not yet been mapped, although linkage analysis with tightly linked markers excludes it from both the JNCL and INCL loci. We have initiated a genome-wide search for the LNCL gene, taking advantage of the large collection of highly polymorphic markers that has been developed through the Human Genome Initiative. The high degree of heterozygosity of these markers makes it feasible to carry out successful linkage analysis in small nuclear families, such as found in LNCL. Our current collection of LNCL pedigrees includes 19 US families and 11 Costa Rican families. To date, we have completed typing with over 50 markers on chromosomes 2, 9, 13, and 18–22. The results of this analysis formally exclude about 10% of the human genome as the location of the LNCL gene. © 1995 Wiley-Liss, Inc.     

A yeast artificial chromosome contig from human chromosome 14q24 spanning the Alzheimer's disease locus AD3

Familial Alzheimer's disease has been previously linked to threegenetic loci on chromosomes 21, 19 and 14. The AD3 locus onchromosome 14 has not been cloned and the molecular defect inchromosome 14-linked AD3 families has yet to be identified.Genetic linkage analysis has placed the AD3 locus in band 14q24between the dinucleotide markers D14S61 and D14S289, a geneticdistance of approximately 6.4 cM. We have constructed a yeastartificial chromosome (YAC) contig that covers the entire minimalregion, encompassing all genetic markers that are non-recombinantfor the disease in AD3-linked families. This contig, constructedby using a combination of YAC end sequence walking and sequence-taggedsite (STS) mapping, consists of 63 YACs from three differentlibraries. The AD3 contig contains 12 polymorphic dinucleotiderepeat markers from D14S61 to D14S251, as well as an additional43 non-polymorphic STSs. This contiguous physical map of theregion will allow the physical distances between the markersto be determined, as well as providing a framework for the identificationof candidate genes.     

Positive association to IgE levels and a physical map of the 13q14 atopy locus

Linkage of atopy and associated traits to a locus on chromosome 13q14 has been identified by several studies in diverse populations. We have previously shown the putative atopy gene to be contained within an interval of approximately 5 Mb flanked by D13S328 and D13S1269 and centred on D13S273. We have now extended this work using a top-down approach to physical mapping. A YAC contig was constructed covering the D13S328 and D13S1269 interval. Thirty-one ESTs were mapped to the contig. We constructed a BAC and PAC contig flanking D13S273 by approximately 750 kb in either direction. The interval contained 27 of the 31 ESTS from the YAC contig. Seven previously unknown microsatellites were recovered and then typed in two subject panels. A positive association between the total serum Immunoglobulin E concentration and the novel USAT24G1 microsatellite was discovered (P(corrected)<0.005) and replicated in a second panel of families. The discovery of a region of positive association within the BAC/PAC contig will permit identification of the atopy gene from this locus.     

Genetic refinement and physical mapping of a chromosome 16q candidate region for inflammatory bowel disease.

Crohn's disease (CD) is a complex genetic disorder for which a susceptibility gene, IBD1, has been mapped within the pericentromeric region of chromosome 16. In order to refine the location of IBD1, 77 multiplex CD families were genotyped for 26 microsatellite markers evenly spaced by approximately 1 cM. Nonparametric linkage analyses exhibited a maximum NPL score of 3.49 (P=2.37x10(-4)) in a region centred by markers D16S3136, D16S3117 and D16S770. Simulation studies showed that the probability for IBD1 to be located in a 5 cM region around these markers was 70%. A 2.5 Mb YAC and BAC contig map spanning this genetic region on chromosome band 16q12 was built. TDT analyses demonstrated suggestive association between the 207 bp allele of D16S3136 (P<0.05) and a new biallellic marker hb27g11f-end (P=0.01). These markers were located in the hb27g11 and hb87b10 BAC clones from the contig. Taken together, the present results provide a crucial preliminary step before an exhaustive linkage disequilibrium mapping of putatively transcribed regions to identify IBD1.     

Refinement of the RP17 locus for autosomal dominant retinitis pigmentosa, construction of a YAC contig and investigation of the candidate gene retinal fascin

The RP17 locus for autosomal dominant retinitis pigmentosa has previously been mapped to chromosome 17q by linkage analysis. Two unrelated South African families are linked to this locus and the identification of key recombination events assigned the RP17 locus to a 10 cM interval on 17q22. The work reported here refines the mapping of the locus from a 10 cM to a 1 cM interval between the microsatellite markers D17S1604 and D17S948. A physical map of this interval was constructed using information from the Whitehead/MIT YAC contig WC 17.8. Sequence-tagged site (STS) content mapping of seven overlapping YACs from this contig was employed in order to build the map. A BAC library was screened to cover a gap in the YAC contig and two positive BACs were identified. Intragenic polymorphisms in the retinal fascin gene provided evidence for the exclusion of this candidate as the RP17 disease gene.     

Saturating density of STSs (1/6 kb) in a 1.1 Mb region on 3q28-q29: a valuable resource for cloning of disease genes

We have fine mapped 29 ESTs of Genemap'99 to YACs and radiation hybrids covering 8 cM of the chromosomal region of 3q28-q29. Focusing on the genetic interval of approximately 1 Mb between markers D3S3669 and D3S3562 we established a sequence-ready PAC contig which covers the OPA1 locus containing the gene causing autosomal dominant optic atrophy (ADOA; OMIM*165500). The fidelity of the contig was increased by the generation of 181 PAC end sequences, 84 of which resulted in PCR-able STSs. Sequence content evaluation of the PAC ends by BLAST analysis identified two novel ESTs localising to the OPA1 crucial interval.     

Haplotype analysis of two recurrent genomic rearrangements in the BRCA1 gene suggests they are founder mutations for the Greek population

Pertesi M, Konstantopoulou I, Yannoukakos D. Haplotype analysis of two recurrent genomic rearrangements in the BRCA1 gene suggests they are founder mutations for the Greek population. The deletions of 4.4 and 3.2 kb identified in exons 24 and 20, respectively, are two of the four most common mutations in the BRCA1 gene in Greek breast cancer patients. They have been reported previously six and three times, respectively, in unrelated Greek families. A total of 11 more families have been identified in the present study. In order to characterize these recurrent mutations as founder mutations, it is necessary to identify the disease‐associated haplotype and prove that it is shared by all the mutation carriers, suggesting that it occurred only once in a common ancestor. Haplotype analysis was performed on 24 mutation carriers and 66 healthy individuals using 10 short tandem repeat markers located within and flanking the BRCA1 gene locus, spanning a 5.9 Mb interval. Results indicate that most of the carriers of the exon 24 deletion share a common core haplotype ‘4‐7‐6‐6‐1‐3’ between markers D17S951 and D17S1299, for a stretch of 2.9 Mb, while the common haplotype for the exon 20 deletion is ‘6‐7‐4‐2‐6‐7‐1‐3’ between markers D17S579 and D17S1299, for a stretch of 3.9 Mb. Both genomic rearrangements in BRCA1 gene are Greek founder mutations, as carriers share the same, for each mutation, disease‐associated haplotype, suggesting the presence of a distinct common ancestor for both mutations.     

A novel candidate tumour suppressor locus at 9q32-33 in bladder cancer: localization of the candidate region within a single 840 kb YAC

Loss of heterozygosity (LOH) on chromosome 9q is the most frequent genetic alteration in transitional cell carcinoma (TCC) of the bladder, implicating the presence of a tumour suppressor gene or genes on 9q. To define the location of a tumour suppressor locus on 9q in TCC, we screened 156 TCCs of the bladder and upper urinary tract by detailed deletion mapping using 31 microsatellite markers on 9q. Partial deletions of 9q were found in 10 TCCs (6%), and LOH at all informative loci on 9q was found in 77 TCCs (49%). In five low grade superficial bladder tumours, the partial deletion was localized to D9S195 located at 9q32-33, with retention of heterozygosity at all other informative loci including D9S103, D9S258, D9S275 and GSN. We constructed a yeast artificial chromosome (YAC) contig covering the deleted region in these five tumours and placed another four unmapped microsatellite markers on this contig map. Using these markers, we further defined the common deleted region to the interval between D9S1848 and AFMA239XA9. The region is covered by a single YAC (852e11), whose size is estimated to be 840 kb. Our data should expedite further fine mapping and identification of the candidate tumour suppressor gene at 9q32-33.      

The isolation of a yeast artificial chromosome (YAC) contig extending for 2 megabases in the vicinity of the Von Hippel Lindau disease gene

Von Hippel LIndau disease (VHL) is a rare autosomal dominantdisease associated with tumors and cysts in multiple organ systems.The VHL disease gene is tightly linked to the polymorphic DNAmarker 233E2 (D3S720) and flanked by 479H4 (D3S719) on its telomericand RAF1 on its centromeric side. Two additional markers, D3S1038and D3S601, have also been identified, and these markers, likeD3S720, are very tightly linked to VHL. Previously 93 cosmidclones were mapped to the larger region, 3p24.2 - pter, surroundingthe VHL disease gene (1). Using a Southern-based screening strategyon pools of YAC clones we have Isolated a contig of overlappingYAC clones that extends about 0.7 megabase centromeric, andabout 1.3 megabases telomeric of D3S720 and contains all threetightly linked VHL markers. Individual YACs In this contig werehybridized to grids containing cosmids localized between 3p24.2-pterand to several cosmids localized by fluorescent in situ hybridization(FISH) to 3p25. A total of 28 cosmids were positioned on thiscontig of overlapping YAC clones. We have also identified homologousYAC clones to many additional cosmid clones localized between3p24.2–p25, although these have not yet been preciselylocalized relative to the contig of YAC clones. This contigof YAC clones probably contains the VHL disease gene and shouldfacilitate the isolation and characterization of this gene.     

Mapping the gene for juvenile onset neuronal ceroid lipofuscinosis to chromosome 16 by linkage analysis

The ceroid-lipofuscinoses are a group of inherited neurodegenerative disorders characterised by the accumulation of autofluorescent lipopigment in neurones and other cell types. The underlying biochemical defect is unknown. Juvenile onset neuronal ceroidlipofuscinosis (Batten disease; Spielmeyer-Vogt disease) is an autosomal recessive trait. Linkage studies were undertaken to determine the location of the Batten disease (CLN3) mutation. Studies were carried out on 205 members of 42 families in which there were 76 affected individuals. Families originated from 7 North European countries and Canada. Serum samples from 23 families, including a total of 48 affected children, were tested for a set of “classical markers.” A positive lod score was found with the haptoglobin (Hp) system. The combined male and female maximum lod score was 3.00 at θ = 0.00 and θ = 0.26, respectively. This provided an indication of localisation to the long arm of chromosome 16. Linkage analysis was then carried out in 42 families using DNA markers for loci on human chromosome 16. The maximal lod score between Batten disease and the locus D16S148 calculated for combined sexes was 6.05. No recombinants were observed. Multilocus analysis using 5 loci indicated the most likely order to be HP–D16S151–D16S150–CLN3–D16S148–D16S147. Work is in progress to refine the genetic and physical localisation of the Batten disease gene using additional markers in this region and a panel of somatic cell hybrids. Methods are now available which should allow the gene to be isolated and characterised.     

Molecular genetic characterization and comparative mapping of the humanPCP4 gene

The mousePcp4 gene is highly expressed in brain, primarily in cerebellar Purkinje cells. It maps to chromosome 16 (Chr 16), in a region of conserved synteny with human chromosome 21 (Chr 21). To further characterizePCP4 and its possible contribution to cerebellar hypoplasia in trisomy 21, or Down Syndrome (DS), we cloned and sequenced the full length human cDNA, isolated a YAC which carries the entire gene, determined the gene structure, and characterized its expression. The gene spans at least 55 kb and contains two introns, the placement of which is the same in mouse. Expression in the mouse brain during development was detected at embryonic day 10, and thereafter through development. ThePCP4 YAC was placed on the human Chr 21 YAC contig by a link to a YAC carrying the markersD21S15 andD21S349. This placement distal toETS2 was confirmed by mapping on a somatic cell hybrid panel of Chr 21 translocations. This position caused an apparent break in gene order with mouse Chr 16. However, mapping in the mouse was reassessed, andPcp4 and a linked marker,D16Mit71, were both moved distal toEts2, corresponding to the position ofPCP4 on Chr 21.     

A novel CLN8 mutation in late‐infantile‐onset neuronal ceroid lipofuscinosis (LINCL) reveals aspects of CLN8 neurobiological function

The late‐infantile‐onset forms of neuronal ceroid lipofuscinosis (LINCL) are the most genetically heterogeneous group among the autosomal recessive neuronal ceroid lipofuscinoses (NCLs), with causative mutations found in CLN1, CLN2, CLN5, CLN6, CLN7 (MFSD8), and CLN8 genes. Homozygous mutations in CLN8 are associated with two distinct phenotypes: progressive epilepsy and mental retardation (EPMR), first identified in Finland; and a variant of late‐infantile NCL (v‐LINCL) described in a subset of Turkish and Italian patients. The function of the protein encoded by CLN8 is currently unknown. Here we report the identification of an Italian v‐LINCL patient with a complete isodisomy of chromosome 8, leading to homozygosity of a maternally‐inherited 3‐bp deletion in CLN8 gene (c.180_182delGAA, p.Lys61del). Notably, uniparental disomy (UPD) has never been described associated with the NCLs. In addition, we provide evidence of the biological role of CLN8 characterized by expressing in different neuronal cell models the native protein, the protein carrying the mutation identified here, or three additional missense mutations previously described. Our results, validated through a gene silencing approach, indicate that CLN8 plays a role in cell proliferation during neuronal differentiation and in protection against cell death. Hum Mutat 30:1–13, 2009. © 2009 Wiley‐Liss, Inc.     

Refinement of the DFNA4 locus to a 1.44 Mb region in 19q13.33

Many forms of autosomal dominant non-syndromic hearing impairment are known. While the underlying gene defects and causative mutations have been discovered for some forms, the gene responsible for DFNA4 has remained elusive to date. Examination of a German four-generation kindred led to the identification of a 1.44 Mb map segment in contig NT_011109 as being the most likely DFNA4 candidate region in 19q13.33. The recombination breakpoints in this family and the intervals of two previously reported DFNA4 families allowed us to delineate a minimum consensus region between the markers D19S879 and D19S246. In our family, a maximum two-point LOD score of 4.5 was obtained at theta =0 for the marker D19S867. Within the refined DFNA4 interval the public databases list more than 50 genes, from which several appear to be promising DFNA4 candidates due to similarities with animal models and with other causative genes involved in hearing disability.Abbreviations DFNA Deafness, autosomal dominant - DFNB Deafness, autosomal recessive