Donor splice mutation (665 + 1 G_T) in familial hypobetalipoproteinemia with no detectable apoB truncation

We report a 49-member four-generation kindred in which 11 members express familial hypobetalipoproteinemia (FHBL). In other kindreds, various truncated apoB species cosegregate with the FHBL phenotype. In contrast, no truncated apoB proteins were found by immunoblotting of plasma samples in this kindred. Previous linkage analysis showed strong linkage of FHBL to apoB markers. Nucleotide sequence analysis demonstrated a 665 + 1 G_T transition in the splice donor site of intron 5. This probably alters the accuracy and efficiency of mRNA splicing leading to the extremely low apoB levels in plasma. In addition, we detected four novel polymorphisms in the apoB gene. Am. J. Med. Genet. 80:218–220, 1998. © 1998 Wiley-Liss, Inc.     

Familial hypomagnesemia maps to chromosome 9q, not to the X chromosome: genetic linkage mapping and analysis of a balanced translocation breakpoint

Familial hypomagnesemia with secondary hypocalcemia (HSH) (MIM 307600) was studied in three inbred Bedouin kindreds from Israel. The three kindreds, one extended and two nuclear families, contained 13 affected individuals, 11 males and two females. Assuming that the individuals affected with hypomagnesemia shared a chromosomal region inherited from a common ancestor, we used a DNA pooling strategy in a genome-wide search for loci which show homozygosity for shared alleles in affected individuals. DNA samples from affected individuals within a single kindred were pooled and used as the template for PCR amplification of short tandem repeat polymorphic markers (STRPs). Pooled DNA from unaffected siblings and parents were used as controls. A shift towards homozygosity was observed in the affected DNA pool compared with the control pools with D9S301 (GATA7D12). Genotyping of individual DNA samples with D9S301 and several flanking markers confirmed linkage to chromosome 9 with maximum LOD scores of 3.4 (theta = 0.05), 3.7 (theta = 0) and 2.3 (theta = 0) for the three families. We have identified a 14 cM interval on chromosome 9 (9q12-9q22.2), flanked by proximal marker D9S1874 and distal marker D9S1807, within which all affected individuals from the three kindreds are homozygous for a shared haplotype. The disease segregates with a common affected haplotype in the three families, suggesting that hypomagnesemia is caused by a common ancestral mutation in these families. Although HSH has been previously reported to be X linked, these linkage data demonstrate that the disorder is an autosomal recessive disease in these kindreds. Mapping of a chromosomal breakpoint in a somatic cell line established from a patient with HSH and a balanced X;9 translocation placed the chromosomal breakpoint in a 500 kb region flanked by D9S1844 and D9S273. Identification of the gene responsible for hypomagnesemia will provide insight into the regulation of this essential cation.      

Regional mapping of the gene for familial Mediterranean fever on human chromosome 16p13

Familial Mediterranean fever (FMF) is an autosomal recessively inherited inflammatory disorder characterized by recurrent short spisodes of fever, peritonitis, arthritis, and pleuritis. Recently, linkage was demonstrated between FMF and the VNTR probes 3′HVR and 5′HVR of the α-globin complex at 16p13.3 ( = 0.06?0.10, Lod_max = 9.76?14.47) and the insertion/deletion polymorphism detected by the probe CMM65 of D16S84 ( = 0.04, Lod_max = 9.17). WE have now mapped the FMF gene between the two flanking markers D16S283/D16S291 ( = 0.038) and D16S80 ( = 0.159). The proximity of the microsatellite markers in D16S283 and D16S291 to the FMF gene allows preclinical diagnosis in most pedigrees with affected individuals. © 1993 Wiley-Liss, Inc.     

Amish brittle hair syndrome gene maps to 7p14.1

The brittle hair syndrome (BHS) is characterized by short stature, intellectual impairment, brittle hair, and decreased fertility in 20 members from a large Amish consanguineous kindred previously reported affected with this syndrome. We mapped the BHS gene by genome scan to chromosome 7p14.1. Evidence of linkage was supported by a maximum multipoint LOD score of 6 obtained with GENEHUNTER for the linkage interval defined by markers D7S484-D7S2422 distant by 17.2 cM. Two-point linkage analysis performed with SUPERLINK yielded a LOD score of 9.02 at theta = 0 for marker D7S2497 located within that interval. Analysis of haplotypes homozygous-by-descent allowed fine mapping of the BHS gene within a 4.81 cM interval delimited by markers D7S2497 and D7S691, a region that spreads over 3.42 Mb.     

Development of a microsatellite-based approach to co-segregation analysis of familial hypercholesterolaemic kindreds

Co-segregation studies based on a selection of intragenic restriction fragment length polymorphisms of the low density lipoprotein receptor (LDLR) gene have been used extensively both for research and diagnostic studies of familial hypercholesterolaemia (FH) families, because direct mutation screening remains complex. Here we describe the development and application of a more efficient approach to co-segregation studies based on highly informative dinucleotide and tetranucleotide repeats flanking the LDLR gene. A series of microsatellites (D19S391, D19S394, D19S221 and D19S179) were selected for study on the basis of linkage analysis in the CEPH families using intragenic polymorphisms for a TA repeat (exon 18) in the LDLR gene, and earlier data for a Pvu II polymorphism (intron 15). A physical map of the region of chromosome 19 also contributed to this selection. One marker in particular, D19S394, sited 150 kilobases telomeric to the gene, was extremely useful, displaying 90% heterozygosity, robust PCR of tetranucleotide repeats without stutter bands, and no recombination with the LDLR gene (θ=0, LOD 68). Use of this marker in the families of twenty-three FH probands from Hampshire demonstrated co-segregation of the hyperlipidaemia phenotype with the LDLR gene region, except in one family with defective apolipoprotein B-100, and a family turning out to display familial combined hyperlipidaemia. This approach should facilitate the search for any families where FH does not co-segregate with the LDLR gene, and will enhance the repertoire of molecular diagnostic tools available for FH.     

The gene for spinal cerebellar ataxia 1 (SCA1) is flanked by two closely linked highly polymorphic microsatellite loci

The gene for one form of autosomal dominant spinal cerebellarataxia (SCA1), Is mapped by linkage to chromosome 6p, very closeto the microsatellite locus D6S89. Eight large Italian kindredssegregating SCA1, as defined by very close linkage to D6S89,were genotyped with five microsatellite markers linked closelyto D6S89, all mapping within a 6 cM Interval on 6p. Multipointlinkage analysis and haplotypes from recombinants map SCA1 betweentwo of these markers, D6S274, and D6S259, 5 – 6 cM apart.A single rare four marker haplotype within this Interval showslinkage disequilibrium with the disease locus in southern Italyand is transmitted with SCA1 In five kindreds originating fromthis area.     

Mapping of a disease locus for familial rapidly progressive frontotemporal dementia to chromosome 17q12-21

Familial frontotemporal dementia (FTD) is a complex disorder with lack of distinctive histopathological markers found in other types of dementia. Most of the linkage reports from FTD families map the disease loci to chromosome 17q21-22. However, FTD is genetically heterogeneous, as linkage also has been reported to chromosome 3. In the present study, we investigated the genetics of a Swedish family with an early-onset type of rapidly progressive FTD, associated with muscular rigidity and akinetic movements. Neuropathological features such as severe frontal lobe degeneration, spongy changes, and gliosis were present in affected family members. We here report probable linkage to chromosome 17q12-21 with a maximum two-point lod score of 2.76 at θ = 0 for marker D17S806, and a peak multipoint lod score of 2.86 for the same marker. Linkage to chromosome 3 was excluded, as two-point lod scores of −2.79, and −2.27 at θ = 0.01 for markers D3S1603 and D3S1552, respectively, were obtained. Sequencing of the translated exons of a strong candidate gene in the linked region of chromosome 17, the tau gene, failed to identify any mutations segregating with the disease. Am. J. Med. Genet. 74:380–385, 1997. © 1997 Wiley-Liss, Inc.     

Mapping of the gene for cleidocranial dysplasia in the historical Cape Town (Arnold) kindred and evidence for locus homogeneity.

Cleidocranial dysplasia (CCD) is an autosomal dominant disorder, features of which include a patient anterior fontanelle, a bulging calvarium, hypoplasia or aplasia of the clavicles, a wide public symphysis, dental anomalies, vertebral malformation, and short stature. The Cape Town kindred which is under our genetic management was originally described more than four decades ago and now consists of more than 1000 people. Following reports of rearrangements on chromosomes 6 and 8 in people with CCD, we have carried out linkage analyses between highly information microsatellite dinucleotide repeat markers in the rearranged regions and the disorder in a branch of this South African CCD kindred, consisting of 38 subjects, 18 of whom are affected. Maximum lod scores (at theta = 0.00) of 7.14 (for marker D6S459), 4.32 (TCTE), 4.99 (D6S452), 5.97 (D6S269), and 3.95 (D6S465) confirm linkage of the disorder to the short arm of chromosome 6. Our data indicate that the CCD gene is located within a minimal region of approximately 10 cM flanked by the marker D6S451 distally and D6S466 proximally. This information is vital towards isolating and characterising the gene for CCD, and is being used to construct a physical map of 6p21.1-6p21.3. More importantly, mapping of the locus in the South African kindred of mixed ancestry, in which the "founder" of the disorder was of Chinese origin, suggests that a single locus is responsible for classic CCD.     

Linkage disequilibrium mapping of the Nova Scotia variant of Niemann–Pick disease

Niemann-Pick type D (NPD) disease is a severe degenerative disorder of the nervous system characterized by the accumulation of tissue cholesterol and sphingomyelin. Because of a founder effect, it is unusually common in southwestern Nova Scotia, Canada. We have confirmed that almost all patients from 20 affected sibships descended on both sides from a small group of Acadians who settled in this region in about the year 1767. Previously using classic linkage analysis of this large kindred, we defined the critical gene region to a 13-cM chromosome segment between D18S869 and D18S66. Seven ESTs have been positioned within this interval. Carstea et al. (Niemann Pick C disease gene: homology to mediators of cholesterol homeostasis. Science 1997: 277: 232-235) recently demonstrated that one of these ESTs is the Niemann-Pick type C (NPCI) gene, the gene disrupted in most patients with NPC disease, and we have shown that a G3097-->T mutation in the NPC1 gene is also responsible for NPD. Here we report the development of five new polymorphic microsatellite markers and the testing for complete linkage disequilibrium in our single large NPD kindred that allowed us to reduce the NPD critical region to a 1-cM (1.3-1.6 Mb) interval between D18S1398 and D18S1108. In contrast, Carstea et al., using classic linkage analysis, required more than 18 unrelated NPC families to reduce the NPC1 critical region to a 5-cM interval. Our work supports the finding that NPD is an allelic variant of NPC1, and illustrates the power of large kindreds, which are common in Atlantic Canada and other relatively isolated areas, for gene mapping and identification.     

An approach to identify new genes in autoimmune diseases: lessons from rheumatoid arthritis

We have searched the human genome for genes that predispose to rheumatoid arthritis using fluorescence-based microsatellite marker analysis and affected sib-pair linkage studies. A panel of 41 Japanese families, each with at least two affected siblings, was typed for genome-wide 358 polymorphic microsatellite marker loci. Three principal chromosome regions of linkage, D1S253/214, D8S556 and DX1232, have been assigned, which we call RA1, RA2 and RA3 for rheumatoid arthritis disease loci. We are now assigning the death receptor 3 as a candidate gene for RA1, and the truncated form of Dbl proto-oncogene, which does not contain the 23rd and 24th exons, as disease gene for RA3. Microsatellite marker analyses seem to be promising and new genes are now being identified by reference to sequence tag sites.     

The gene responsible for Clouston hidrotic ectodermal dysplasia maps to the pericentromeric region of chromosome 13q

Hidrotic ectodermal dysplasia (HED), Clouston type, is an autosomal dominant skin disorder which is most common in the French-Canadian population and is characterized by hair defects, nail dystrophy and palmoplantar hyperkeratosis. Biophysical and biochemical studies conducted in HED suggested a molecular abnormality of keratins. We tested eight French-Canadian families segregating HED for linkage to microsatellite markers flanking the known keratin genes and were able to exclude linkage to these loci. Therefore, a genome-wide search for the HED gene was initiated. The first lod score above 3.00 was obtained with the marker D13S175 located in the pericentromeric region of chromosome 13q (Zmax = 8.12 at zero recombination). The cumulative lod scores were above 3.00 for six other markers in the region. A multipoint linkage analysis using the markers D13S175, D13S141 and D13S143 gave a maximum lod score of 11.12 at D13S141 with the one-lod- unit support interval spanning a 12.7 cM region which includes D13S175 and D13S141. Haplotype analysis allowed us to establish D13S143 as the telomeric flanking marker for the HED candidate region.      

Atrichia with papular lesions maps to 8p in the region containing the human hairless gene

Atrichia with papular lesions (APL) (OMIM 209500) is a hereditary form of alopecia. Hair loss occurs soon after birth and is followed years later by the development of a diffuse papular eruption. Its mode of transmission is still uncertain. A related but clinically distinct form of alopecia, known as alopecia universalis (OMIM 203655), has recently been found to be associated with a mutation in the human hairless gene. The present report describes the largest consanguineous kindred of APL reported to date and provides strong evidence for autosomal recessive inheritance of this rare disorder. On the basis of a linkage analysis of this kindred using six microsatellite markers spanning the human hairless gene region, we found that the APL locus maps to chromosome region 8p12 in a 5 cM interval between marker D8S560 and marker D8S1739. A maximum lodscore of 3.7 was obtained with marker D8S1786, at a recombination fraction of 0. Our results suggest phenotypic variability at the hairless locus although they do not rule out the existence of a gene cluster associated with hair disorders in the same region. Am. J. Med. Genet. 80:546–550, 1998. © 1998 Wiley-Liss, Inc.     

Exclusion of BMP6 as a candidate gene for cleidocranial dysplasia

Cleidocranial dysplasia (CCD) is an autosomal dominant, generalized skeletal dysplasia in humans that has been mapped to the short arm of chromosome 6. We report linkage of a CCD mutation to 6p21 in a large family and exclude the bone morphogenetic protein 6 gene (BMP6) as a candidate for the disease by cytogenetic localization and genetic recombination. CCD was linked with a maximal two-point LOD score of 7.22 with marker D6S452 at θ = 0. One relative with a recombination between D6S451 and D6S459 and another individual with a recombination between D6S465 and CCD places the mutation within a 7 cM region between D6S451 and D6S465 at 6p21. A phage P1 genomic clone spanning most of the BMP6 gene hybridized to chromosome 6 in band region p23–p24 using FISH analysis, placing this gene cytogenetically more distal than the region of linkage for CCD. We derived a new polymorphic marker from this same P1 clone and found recombinations between the marker and CCD in this family. The results confirm the map position of CCD on 6p21, further refine the CCD genetic interval by identifying a recombination between D6S451 and D6S459, and exclude BMP6 as a candidate gene. Am. J. Med. Genet. 71:292–297, 1997. © 1997 Wiley-Liss, Inc.     

Identification of a common low density lipoprotein receptor mutation (R329X) in the south of England: complete linkage disequilibrium with an allele of microsatellite D19S394.

Familial hypercholesterolaemia is commonly caused by mutations in the low density lipoprotein receptor (LDLR) gene and more than 300 different mutations have been described worldwide. Some mutations occur at relatively higher frequency in certain populations, reflecting both chance and demography, most evident in founder populations. As part of a study of kindreds of 78 probands from Southampton and south west Hampshire, we identified the same mutation (R329X) in 9/78 (11.5%) probands. In all (100%) of these probands, length allele 259nt of the 17 allele microsatellite D19S394, sited approximately 250 kilobases telomeric and 5' to the LDLR gene, was observed, although in the general population this allele has a prevalence of only 16.1%. A simple diagnostic assay for R329X was constructed in conjunction with more detailed family studies. Both the R329X and linked D19S394 allele also cosegregated with the FH phenotype within each kindred. Although R329X involves a CpG site, it is highly likely that the families are identical by descent for R329X, we surmise with a common ancestor within 500 to 1000 years, although the mutation is not restricted to this geographical area. This relationship illustrates that the linkage disequilibrium of gene LDLR with marker D19S394 will enable rapid recognition using D19S394 genotype of possible common FH mutation(s) within a cohort of FH patients from a particular locality or ethnic group.     

Evidence for a major susceptibility locus at 11q22.1-23.3 has been detected in a large Chinese family with pure grand mal epilepsy

Pure grand mal epilepsy (PGME) is a common subtype of idiopathic generalized epilepsy (IGE) with an unclear mode of inheritance. Several studies with the multiple families have provided evidence for the disorder to be linked to chromosome 8q24 and 8p. In this work, we performed an autosomal-wide scan linkage analysis using microsatellite markers in a large Chinese family with PGME and found seven markers with likelihood of odds (LOD), scores >/=1.0 (theta=0) in chromosome 11q22.1-23.3. The highest LOD score for two-point and multi-point linkage analysis are 1.99 (theta=0) at marker D11S4159 and 2.18 between markers D11S1782 and D11S3178, respectively, which reached the level of a suggested positive linkage LOD score (Z>/=1.9), under an autosomal dominant manner of inheritance with a penetrance of 65% but no significant positive LOD score (Z>/=3.3) was found after high density of microsatellite markers used in the regions. Obviously, our data do not support the linkage of the disease to chromosome 8q24 and 8p but implicate that chromosome 11q22.1-23.3 may be a new locus linked to PGME, which indicates the existence of genetic heterogeneity in the disorder.     

A genomewide linkage study of age at onset in schizophrenia.

There is strong evidence for a genetic contribution to age at onset of schizophrenia, which probably involves both susceptibility loci for schizophrenia and modifying loci acting independent of disease risk. We sought evidence of linkage to loci that influence age at onset of schizophrenia in a sample of 94 affected sibling pairs with DSM-IV schizophrenia or schizoaffective disorder, and age at first psychiatric contact of 45 years or less. Individuals were genotyped for 229 microsatellite markers spaced at approximately 20 cM intervals throughout the genome. Loci contributing to age at onset were sought by a quantitative maximum-likelihood multipoint linkage analysis using MAPMAKER/SIBS. A nonparametric multipoint analysis was also performed. The genomewide significance of linkage results was assessed by simulation studies. There were six maximum-likelihood LOD score peaks of 1.5 or greater, the highest being on chromosome 17q (LOD = 2.54; genomewide P = 0.27). This fulfils Lander and Kruglyak's [1995: Nat Genet 11:241-247] criteria for suggestive linkage in that it would be expected to occur once or less (0.3 times) per genome scan. However, this finding should be treated with caution because the LOD score appeared to be almost solely accounted for by the pattern of ibd sharing at one marker (D17S787), with virtually no evidence of linkage over flanking markers. None of the linkage results achieved genomewide statistical significance, but the LOD score peak on chromosome 13q (LOD = 1.68) coincided with the region showing maximum evidence for linkage in the study by Blouin et al. [1998: Nat Genet 20:70-73] of categorical schizophrenia.     

Fine mapping of a schizophrenia susceptibility locus at chromosome 6q23: increased evidence for linkage and reduced linkage interval

We previously reported an autosomal scan for schizophrenia susceptibility loci in a systematically recruited sample of Arab Israeli families. The scan detected significant evidence for linkage at chromosome 6q23 with a nonparametric LOD score (NPL) of 4.60 (P=0.000004) and a multipoint parametric LOD score of 4.16. In order to refine this finding we typed 42 additional microsatellite markers on chromosome 6q between D6S1570 (99.01 cM from the pter) and D6S281 (190.14 from the pter) in the same sample (average intermarker distance approximately 1.7 cM). In the 23 cM region between D6S1715 and D6S311, markers were more closely spaced ( approximately 1.1 cM). Multipoint nonparametric and parametric and single point linkage analyses were performed. The peak NPL rose to 4.98 (P=0.00000058) at D6S1626 (136.97 cM), immediately adjacent to D6S292 (NPL 4.98, P=0.00000068), the marker that gave the highest NPL in the original genome scan, under the broad diagnostic category. The putative susceptibility region (NPL-1) was reduced from 12.0 to 4.96 cM. The peak multipoint parametric LOD score was 4.63 at D6S1626 under a dominant genetic model, core diagnostic category and the LOD-1 interval was 2.10 cM. The maximum single point LOD score (3.55, theta=0.01) was also at D6S1626 (dominant model, core diagnostic category). Increased evidence for linkage in the same sample as in the original genome scan and consistent localization of the linkage peak add further support for the presence of a schizophrenia susceptibility locus at chromosome 6q23. Moreover, the markedly reduced linkage interval greatly improves prospects for identifying a schizophrenia susceptibility gene within the implicated region.     

A novel autosomal recessive nonsyndromic hearing impairment locus (DFNB42) maps to chromosome 3q13.31-q22.3

A consanguineous family with autosomal recessive nonsyndromic hearing impairment (NSHI) was ascertained in Pakistan and displayed significant evidence of linkage to 3q13.31-q22.3. The novel locus (DFNB42) segregating in this kindred, maps to a 21.6 cM region according to a genetic map constructed using data from both the deCode and Marshfield genetic maps. This region of homozygosity is flanked by markers D3S1278 and D3S2453. A maximum multipoint LOD score of 3.72 was obtained at marker D3S4523. DFNB42 represents the third autosomal recessive NSHI locus to map to chromosome 3.     

A mutation in cartilage oligomeric matrix protein (COMP) causes early-onset osteoarthritis in a large kindred study

We performed a genome-wide linkage analysis to identify susceptibility loci in a large six-generation extended family previously reported with early-onset osteoarthritis (OA) DNA sequencing was performed to investigate involvement of the COMP (Cartilage oligomeric matrix protein) gene in this family. The region covering D19S884, D19S226, and D19S414 on chromosome 19p following genome-wide scan from 70 individuals of this kindred showed significant linkage, with a maximum point LOD (logarithm of the odds ratio) score of 2.51 at D19S226. Direct sequencing of the COMP gene, the most plausible candidate gene in the region, identified a c.2152C>T substitution in exon 18 which resulted in a substitution of tryptophan for arginine at position 718 located in the C terminal globular domain of the gene product. A total of 26 individuals were identified with this mutation of which 21 affected individuals had the mutation, and the other five younger individuals (18.6 ± 11.3 years of age) carried the mutation without symptoms. The results indicate that COMP is the disease susceptibility gene and the c.2152C>T mutation in exon 18 could cause early-onset OA phenotypes in this kindred, which is compatible with a previous report that this mutation also causes a mild form of multiple epiphyseal dysplasia (MED).