A new autosomal recessive retinitis pigmentosa locus maps on chromosome 2q31-q33.

Autosomal recessive retinitis pigmentosa (ARRP) is a genetically heterogeneous disease. To date, mutations in four members of the phototransduction cascade have been implicated in ARRP. Additionally, linkage of the disease to three loci on 1p, 1q, and 6p has been described. However, the majority of cases are still uncharacterised. We have performed linkage analysis in a large nuclear ARRP family with five affected sibs. After exclusion of several regions of the genome known to contain loci for retinal dystrophies, a genomic search for linkage to ARRP was undertaken. Positive lod scores were obtained with markers on 2q31-q33 (Zmax at theta = 0.00 of 4.03, 4.12, and 4.12 at D2S364, D2S118, and D2S389, respectively) defining an interval of about 7 cM for this new ARRP locus, between D2S148 and D2S161. Forty-four out of 47 additional ARRP families, tested with markers on 2q32, failed to show linkage, providing evidence of further genetic heterogeneity.     

Primary palmar hyperhidrosis locus maps to 14q11.2-q13

Primary palmar hyperhidrosis (PPH) is a unique disorder of unknown cause. It is characterized by excessive perspiration of the eccrine sweat gland in the palm, sole, and the axilla. It is presumed that PPH results from overactivation of the cholinergic sympathetic nerve or dysfunction of the autonomic nervous system. There have been no genetic studies on the disease. We performed a linkage analysis of 11 families including 42 affected and 40 unaffected members using genome-wide DNA polymorphic markers to identify the disease locus. Diagnosis of their PPH was made by direct inspection, interviewing and measurement of the sweating rate with perspirometer. Consequently, from data of three of the 11 families examined, the combined maximum two-point LOD scores of 3.08 and 3.16 (recombination fraction = 0) were obtained at the D14S283 and D14S264 loci, respectively, on chromosome 14q11.2-q13, under an assumption that two liability conditions depend on age. These regions were ruled out in eight other families. Haplotype analysis of the three families supported that one of the PPH locus is assigned at minimum to about a 6-cM interval between D14S1070 and D14S990 and at maximum to about a 30-cM interval between D14S1070 and D14S70. This is the first report of systemic mapping of the PPH locus.     

A novel locus for parietal foramina maps to chromosome 4q21-q23

Parietal foramina [PFM], inherited usually in an autosomal dominant mode, is an extremely rare developmental defect characterized by a symmetrical, oval hole in the parietal bone. It can be present as either an isolated or a syndromic feature. PFM types 1 and 2 (PFM1 and PFM2) have been found to be caused by mutations in the MSX2 and ALX4 genes, located to chromosomes 5 and 11, respectively. After exclusion of both the above loci in a large Chinese pedigree with autosomal dominant PFM, a genome-wide search revealed a linkage of the PFM to markers at the 4q21-q23 region. The maximum LOD score from two-point linkage analysis is 3.87 for marker D4S2961. Analysis of co-segregated haplotype localized the region to a 20-cM interval that flanks D4S392 and D4S2945. Therefore, we concluded that the PFM in the family is a new PFM locus. Although three genes, BMPR1B, PP1 and IBSP, are located to 4q21-q25 and their functions are related to bone morphogenesis, no mutations were identified by sequencing analysis of their exons.     

A locus for congenital preauricular fistula maps to chromosome 8q11.1-q13.3

The incidence of congenital preauricular fistula (CPF) is >1.1% in both Chinese and Caucasians, but it is even higher in Blacks. We mapped the locus for CPF to chromosome 8q11.1-q13.3 by linkage analysis of a family composed of 7 affected and 11 nonaffected members. The two-point LOD score was 2.40, shown by markers D8S285 and D8S1113 at a recombination fraction (theta) of 0.00. Results from three other markers (D8S1110, D8S260, and D8S1136) in the same region further support the linkage. Haplotype analysis for this family confined the locus to within an interval of approximately 26.7 cM, flanked by markers D8S532 and D8S279. A LOD score of <3 is likely due to the limitation of family size.     

Genetic heterogeneity of synpolydactyly: a novel locus SPD3 maps to chromosome 14q11.2-q12

Syndactyly type II or synpolydactyly (SPD) is the second most frequent syndactyly type and is inherited in an autosomal dominant fashion. The cardinal features of this malformation are the cutaneous or bony fusion of third and fourth fingers, and fourth and fifth toes associated with additional digital elements within the web. It shows incomplete penetrance and high inter- and intrafamilial phenotypic variability. Two loci are known for SPD (MIM 186000, MIM 608180) associated with mutations in HOXD13 and FBLN1, respectively. Here, we report further genetic heterogeneity for SDP. Employing a whole genomic screen, we demonstrate, in a large Pakistani kindred, that the classical phenotype of SPD maps on a new locus at chromosome 14q11.2-q12. The highest LOD score (Z(max) = 4.06) was obtained with microsatellite marker D14S264, and the multipoint LOD score reached a maximum of 5.01. Haplotype analysis revealed that the disease interval is flanked by microsatellite markers D14S283 and D14S1060, encompassing a physical distance of 10.72 Mb. We propose to allocate to this locus the symbol SPD3 (synpolydactyly 3), and to name the loci associated with HOXD13 or FBLN1 mutations SPD1 and SPD2, respectively.     

Fine mapping of the CELIAC2 locus on chromosome 5q31-q33 in the Finnish and Hungarian populations

Celiac disease is a chronic inflammation of the small intestine, arising in genetically predisposed individuals as a result of ingestion of dietary gluten. The only confirmed and functionally characterised genetic risk factors for celiac disease are the DQ2 or DQ8 heterodimers at the major histocompatibility complex (MHC) class II locus ( CELIAC1 ). These genes are necessary but alone not sufficient for disease onset. Genome-wide linkage scans have suggested chromosome 5q31-q33 ( CELIAC2 ) as an important risk locus for celiac disease. This region has also been associated to other inflammatory disorders, although as yet, no clear gene associations have been found. In the current study, 11 celiac disease candidate loci were screened for genetic linkage in the Hungarian population. As the CELIAC2 locus showed the strongest evidence for linkage, this locus was selected for follow-up. Seventeen candidate genes were selected from the CELIAC2 locus, and genotyped using 48 haplotype tagging single nucleotide polymorphisms (SNPs) in large Finnish and Hungarian family materials. A subset of these, 40 tagging SNPs in 15 genes, were genotyped in an independent set of Finnish and Hungarian cases and controls. We confirmed linkage of this region with celiac disease and report strong linkage in both the Finnish and Hungarian populations. The association analysis showed modest associations throughout the whole region. These association findings were not replicated in the case–control datasets. Our study strongly supports the role of the CELIAC2 locus in celiac disease, but it also highlights the need for a more powerful study design in the region, to locate the true disease risk variants.     

A novel locus for dHMN with pyramidal features maps to chromosome 4q34.3-q35.2

The distal hereditary motor neuropathy (dHMN) is a rare genetically and clinically heterogeneous disorder characterized by weakness and wasting of distal limb muscles in absence of overt sensory abnormalities. Recently, pyramidal signs have been also described in some patients with dominant or recessive dHMN, and two different loci have been identified in families affected by dHMN complicated with pyramidal dysfunction. We investigated an Italian family affected by an autosomal dominant dHMN complicated by pyramidal signs in order to map a new gene locus. The disease maps to a novel locus in a 26-cM region flanked by D4S1552 and D4S2930 on chromosome 4q34.3-35.2. Three candidate genes ( SNX25 , CASP3 and TUBB4Q ) located in the critical region were screened for the presence of mutations by heteroduplex analysis. No mutations have been detected in the analyzed genes. In conclusion, the new private genetic locus we reported further confirms the wide heterogeneity of dHMN.     

A new locus for arrhythmogenic right ventricular cardiomyopathy (ARVD2) maps to chromosome 1q42-q43

Autosomal dominant arrhythmogenic right ventricular cardiomyopathy(ARVD, MIM 107970 [OMIM] ) is one of the major causes of juvenile suddendeath. We have previously assigned the disease locus to chromosome14q23–q24. Here we report on a novel variant of ARVD,which is transmitted associated to 1q42–q43 and is characterizedby a concealed form, showing effort-induced polymorphic tachycardias.Since both loci ARVD1 and ARVD2 map in proximity of a-actiningenes, the possible implication of these myofibrillar proteinsin the pathogenesis of ARVD is discussed. Two additional ARVDfamilies, tested with markers of chromosomes 1q42–q43and 14q23–q24, failed to show linkage, providing evidenceof further genetic heterogeneity.     

A second autosomal split hand/split foot locus maps to chromosome 10q24-q25

Ectrodactyly (split hand/split foot malformation, SHSF) is ahuman limb malformation characterized by absent central digitalrays, deep median cleft, and syndactyly of remaining digits.The disorder is genetically heterogeneous, with at least twoloci thus far determined: an autosomal locus at 7q21 designatedSHFM1 and an X-linked locus at Xq26 designated SHFM2. Cytogeneticanalysis of sporadic SHSF patients and linkage studies in extendedpedigrees both suggest more than one autosomal locus exists.We report a novel SHSF locus suggested by a stillborn infantwith ectrodactyly and other malformations who inherited an unbalancedtranslocation resulting in monosomy 4p15.1–4pter and trisomyfor 10q25.2-qter. To investigate 10q25 as a possible split hand/splitfoot locus, microsatellite markers spanning 52 cM of 10q wereutilized for linkage analysis of a large autosomal dominantSHSF pedigree in which the region encompassing SHFM1 previouslywas excluded as containing the causative mutation. The markerD10S583 was fully informative in the family, giving a maximumLOD score of 4.21 at recombination     

A novel locus for syndromic chronic idiopathic intestinal pseudo-obstruction maps to chromosome 8q23-q24

Chronic idiopathic intestinal pseudo-obstruction (CIIP) is a rare and severe clinical syndrome characterized by symptoms and signs of intestinal occlusion, in the absence of any mechanical obstruction of the gut lumen. In the attempt to identify the genetic basis of CIIP, we analyzed a Turkish pedigree with a high degree of consanguinity in which three siblings presented with a syndromic form of CIIP. All affected family members were characterized by recurrent, self-limiting subocclusive episodes, long-segment Barrett esophagus, and a variety of minor cardiac valve or septal defects. In some patients full-thickness intestinal biopsy samples were obtained and tissues were processed for immunohistochemistry using antibodies to different markers of the intestinal neuromuscular tract. Full-thickness biopsies of the gut wall showed abnormalities of both the neural and muscular components suggesting an underlying intestinal neuro-myopathy. Blood samples were collected for DNA extraction from each available family member and DNAs were genotyped using 382 microsatellites spanning the entire genome with the aim to take advantage of the homozygosity mapping approach. Linkage analysis identified a new syndromic locus on chromosome 8q23-q24 (multipoint LOD score=5.01). Our data strongly support the presence of a new genetic locus associated with CIIP, long-segment Barrett esophagus, and cardiac involvement on chromosome 8.     

X-linked congenital ataxia: a new locus maps to Xq25-q27.1

We report clinical and molecular studies on a large American family of Norwegian descent with X-linked nonprogressive congenital ataxia (XCA) in six affected males over three generations. Neuroimaging showed global cerebellar hypoplasia without evidence of supratentorial anomalies. Linkage analysis resulted in a maximum LOD score Z = 3.44 for marker DXS1192 at Theta = 0.0 with flanking markers DXS1047 and DXS1227 defining a region of 12 cM in Xq25-q27.1. The clinical and neuroradiological findings in the present family are very similar to those described in two reported X-linked families [Illarioshkin et al., 1996; Bertini et al., 2000]; however, the newly identified locus does not overlap with the one defined previously, indicating that there are at least two genes responsible for this rare form of X-linked congenital cerebellar ataxia with normal intelligence.     

Three region-specific microdissection libraries for the long arm of human chromosome 2, regions q33-q35, q31-q32, and q23-q24

Three region-specific libraries have been constructed from the long arm of human chromosome 2, including regions 2q33-35 (2Q2 library), 2q31-32 (2Q3) and 2q23-24 (2Q4). Chromosome microdissection and the Mbol linker-adaptor microcloning techniques were used in constructing these libraries. The libraries comprised hundreds of thousands of microclones in each library. Approximately half of the microclones in the library contained unique or low-copy number sequence inserts. The insert sizes ranged between 50 and 800 bp, with a mean of 130–190 bp. Southern blot analysis of individual unique sequence microclones showed that 70–94% of the microclones were derived from the dissected region. 31 unique sequence microclones from the 2Q2 library, 31 from 2Q3, and 30 from 2Q4, were analyzed for insert sizes, the hybridizing genomic HindIII fragment sizes, and cross-hybridization to rodent species. These libraries and the short insert microclones derived from the libraries should be useful for high resolution physical mapping, sequence-ready reagents for large scale genomic sequencing, and positional cloning of disease-related genes assigned to these regions, e.g. the recessive familial amyotrophic lateral sclerosis assigned to 2q33-q35, and a type I diabetes susceptibility gene to 2q31-q33.     

Linkage and association between Plasmodium falciparum blood infection levels and chromosome 5q31-q33

We have previously mapped a locus controlling Plasmodium falciparum blood infection levels (PFBI) to chromosome 5q31-q33. We genotyped 19 microsatellite markers on chromosome 5q31-q33 in a new sample of 44 pedigrees comprising 84 nuclear families and 292 individuals living in a P. falciparum endemic area. Using a nonparametric multipoint variance-component approach (by GENEHUNTER), we evidenced a peak of linkage close to D5S636 (P=0.0069), with a heritability of 0.46. Using a variance-component method for linkage-disequilibrium mapping of quantitative traits (by QTDT) and the Bonferroni correction for multiple testing, we further detected allelic association in the presence of linkage between blood infection levels and D5S487 (P=6 x 10(-5); P(c)=0.0011), which is located on the distal part of the peak. These results confirm the importance of chromosome 5q31-q33 in the genetic control of PFBI levels.     

Re-assigning the DFNB33 locus to chromosome 10p11.23-q21.1

Homozygosity mapping is a powerful resource for mapping and identifying loci and genes responsible for autosomal recessive disorders. Nevertheless, it could result in the identification of several homozygous regions unrelated to the disease locus or non-informative regions. Previously, a genome-wide screen in a large consanguineous Jordanian family allowed us to assign the DFNB33 locus to chromosome 9q34.3. Sequencing of 23 candidate genes showed 11 SNPs in a heterozygous state in affected individuals. These results ruled out the candidate region on chromosome 9. Using additional markers, we were able to restrict the disease locus to an approximately 14 cM region at chromosome 10, located between markers D10S193 and D10S1784. A maximum LOD score of 3.99 was obtained with two markers, D10S199 and D10S220. The screening of two candidate genes, CX40.1 and FXYD4, failed to reveal any disease-causing mutations.     

Localization of a novel autosomal recessive hypotrichosis locus (LAH3) to chromosome 13q14.11-q21.32

Autosomal recessive hypotrichosis is a rare form of alopecia characterized by sparse hair on scalp, sparse to absent eyebrows and eyelashes, and sparse auxiliary and body hair. Previously, for this form of hypotrichosis, two loci LAH (localized hereditary hypotrichosis) and AH (autosomal recessive hereditary hypotrichosis) have been mapped on chromosome 18q12.1 and 3q27.2, respectively. In the study presented here, we report the localization of a third locus for autosomal recessive form of hypotrichosis in two large Pakistani families. The patients in the two families exhibited typical features of the hereditary hypotrichosis. Genome scan using polymorphic microsatellite markers mapped the gene on chromosome 13q14.11-q21.32. A maximum combined two-point logarithm of odds (LOD) score of 4.79 at theta= 0.0 was obtained for several markers. Multipoint linkage analysis resulted in a maximum LOD score of 5.9, which further supports the linkage. Haplotype analysis defined the linkage interval of 17.35 cM flanked by markers D13S325 and D13S1231 according to the Rutgers combined linkage-physical map. This region contains 24.41 Mb according to the build 36 of the human genome sequence-based physical map.     

A locus for asphyxiating thoracic dystrophy,ATD, maps to chromosome 15q13

Asphyxiating thoracic dystrophy (ATD), or Jeune syndrome, is a multisystem autosomal recessive disorder associated with a characteristic skeletal dysplasia and variable renal, hepatic, pancreatic, and retinal abnormalities. We have performed a genome wide linkage search using autozygosity mapping in a cohort of four consanguineous families with ATD, three of which originate from Pakistan, and one from southern Italy. In these families, as well as in a fifth consanguineous family from France, we localised a novel ATD locus (ATD) to chromosome 15q13, with a maximum cumulative two point lod score at D15S1031 (Zmax=3.77 at theta=0.00). Five consanguineous families shared a 1.2 cM region of homozygosity between D15S165 and D15S1010. Investigation of a further four European kindreds, with no known parental consanguinity, showed evidence of marker homozygosity across a similar interval. Families with both mild and severe forms of ATD mapped to 15q13, but mutation analysis of two candidate genes, GREMLIN and FORMIN, did not show pathogenic mutations.