Refinement of linkage of human severe combined immunodeficiency (SCIDX1) to polymorphic markers in Xq13.

The most common form of human severe combined immunodeficiency (SCID) is inherited as an X-linked recessive genetic defect, MIM 300400. The disease locus, SCIDX1, has previously been placed in Xq13.1-q21.1 by demonstration of linkage to polymorphic markers between DXS159 and DXS3 and by exclusion from interstitial deletions of Xq21.1-q21.3. We report an extension of previous linkage studies, with new markers and a total of 25 SCIDX1 families including female carriers identified by nonrandom X chromosome inactivation in their T lymphocytes. SCIDX1 was nonrecombinant with DXS441, with a lod score of 17.96. Linkage relationships of new markers in the SCIDX1 families were consistent with the linkage map generated in the families of the Centre d'Etude du Polymorphisme Humain (CEPH) and with available physical map data. The most likely locus order was DXS1-(DXS159,DXS153)-DXS106-DXS132-DXS4 53-(SCIDX1,PGK1, DXS325,DXS347,DXS441)-DXS447-DXS72-DXYS 1X-DXS3. The SCIDX1 region now spans approximately 10 Mb of DNA in Xq13; this narrowed genetic localization will assist efforts to identify gene candidates and will improve genetic management for families with SCID.     

X-linked severe combined immunodeficiency: localization within the region Xq13.1-q21.1 by linkage and deletion analysis.

X-linked severe combined immunodeficiency (SCID) (McKusick 30040; IMD4) is a disease of unknown pathogenesis characterized by severe and persistent infections from early in life that are due to absence of both cellular and humoral immune function. Although the disease has been provisionally mapped to proximal Xq, high lethality and lack of a carrier test have limited the number of scorable meioses. We performed linkage analysis in six new kindreds with X-linked SCID, using a random pattern of T-cell X inactivation to rule out the carrier state in at-risk women. Our linkage results, combined with analysis of Xq interstitial deletions, confirmed the regional assignment of X-linked SCID, narrowed the boundaries within which this locus lies to Xq13.1-q21.1, and established the locus order DXS159-(PGK1, SCID)-DXS72-DXS3, defining flanking markers for prenatal diagnosis and carrier testing.     

Multipoint linkage analysis of loci in the proximal long arm of the human X chromosome: application to mapping the choroideremia locus.

Choroideremia (McK30310), an X-linked retinal dystrophy, causes progressive night blindness, visual field constriction, and eventual central blindness in affected males by the third to fourth decade of life. The biochemical basis of the disease is unknown, and prenatal diagnosis is not available. Subregional localization of the choroideremia locus to Xq13-22 was accomplished initially by linkage to two restriction-fragment-length polymorphisms (RFLPs), DXYS1 (Xq13-q21.1) and DXS3 (Xq21.3-22). We have now extended our linkage analysis to 12 families using nine RFLP markers between Xp11.3 and Xq26. Recombination frequencies of 0%-4% were found between choroideremia and five markers (PGK, DXS3, DXYS12, DXS72, and DXYS1) located in Xq13-22. The families were also used to measure recombination frequencies between RFLP loci to provide parameters for the program LINKMAP. Multipoint analysis with LINKMAP provided overwhelming evidence for placing the choroideremia locus within the region bounded by DXS1 (Xq11-13) and DXS17 (Xq21.3-q22). At a finer level of resolution, multipoint analysis suggested that the choroideremia locus was proximal to DXS3 (384:1 odds) rather than distal to it. Data were insufficient, however, to distinguish between a gene order that puts choroideremia between DXS3 and DXYS1 and one that places choroideremia proximal to both RFLP loci. These results provide linkage mapping of choroideremia and RFLP loci in this region that will be of use for further genetic studies as well as for clinical applications in this and other human diseases.     

Linkage of PGK1 to X-linked severe combined immunodeficiency (IMD4) allows predictive testing in families with no surviving male

Summary We present a linkage map of DNA probes around the X-linked severe combined immunodeficiency (IMD4) locus at Xq11-13. DXS159 and PGK1 show no cross-overs with the disease locus (Lod 3.01 at = 0.00). The order of loci is DXS1-DXS106-(DXS159-PGK1-IMD4)-DXS72-DXYS1. Members of families whose carrier status has been established by X-inactivation patterns were included in the analysis. As the probe (pSPT/PGK), which is used for investigation of X-inactivation patterns, has been shown to be linked to the disease itself, it is possible to assign phase in mothers of sporadic cases who have been shown to be carriers, even when they have no surviving male offspring.     

X-linked hypohidrotic ectodermal dysplasia: localization within the region Xq11-21.1 by linkage analysis and implications for carrier detection and prenatal diagnosis.

X-linked hypohidrotic ectodermal dysplasia (H.E.D.) is a disorder of abnormal morphogenesis of ectodermal structures and is of unknown pathogenesis. Neither relatively accurate carrier detection nor prenatal diagnosis has been available. Previous localization of the disorder by linkage analysis utilizing restriction-fragment polymorphisms, by our group and others, has placed the disorder in the general pericentromeric region. We have extended our previous study by analyzing 36 families by means of 10 DNA probes at nine marker loci and have localized the disorder to the region Xq11-Xq21.1, probably Xq12-Xq13. Three loci--DXS159 (theta = .01, z = 14.84), PGK1 (theta = .02, z = 13.44), and DXS72 (theta = .02, z = 11.38)--show very close linkage to the disorder, while five other pericentromeric loci (DXS146, DXS14, DXYS1, DXYS2, and DXS3) display significant but looser linkage. Analysis of the linkage data yields no significant evidence for nonallelic heterogeneity for the X-linked form of the disorder. Both multipoint analysis and examination of multiply informative meioses with known phase establish that the locus for H.E.D. is flanked on one side by the proximal long arm loci DXYS1, DXYS2, and DXS3 and on the other side by the short arm loci DXS146 and DXS14. Multipoint mapping could not resolve the order of H.E.D. and the three tightly linked loci. This order can be inferred from published data on physical mapping of marker loci in the pericentromeric region, which have utilized somatic cell hybrid lines established from a female with severe manifestations of H.E.D., and an X/9 translocation (breakpoint Xq13.1). If one assumes that the breakpoint of the translocation is within the locus for H.E.D. and that there has not been a rearrangement in the hybrid line, then DXS159 would be proximal to the disorder and PGK1 and DXS72 would be distal to the disorder. Both accurate carrier detection and prenatal diagnosis are now feasible in a majority of families at risk for the disorder.     

Multipoint linkage analysis in Menkes disease.

Linkage analyses were performed in 11 families with X-linked Menkes disease. In each family more than one affected patient had been diagnosed. Forty informative meioses were tested using 11 polymorphic DNA markers. From two-point linkage analyses high lod scores are seen for DXS146 (pTAK-8; maximal lod score 3.16 at recombination fraction [theta] = .0), for DXS1 (p-8; maximal lod score 3.44 at theta = .0), for PGK1 (maximal lod score 2.48 at theta = .0), and for DXS3 (p19-2; maximal lod score 2.90 at theta = .0). This indicates linkage to the pericentromeric region. Multilocus linkage analyses of the same data revealed a peak for the location score between DXS146(pTAK-8) and DXYS1X(pDP34). The most likely location is between DXS159 (cpX289) and DXYS1X(pDP34). Odds for this location relative to the second-best-supported region, between DXS146(pTAK-8) and DXS159 (cpX289), are better than 74:1. Visualization of individual recombinant X chromosomes in two of the Menkes families showed the Menkes locus to be situated between DXS159(cpX289) and DXS94(pXG-12). Combination of the present results with the reported absence of Menkes symptoms in male patients with deletions in Xq21 leads to the conclusion that the Menkes locus is proximal to DXSY1X(pDP34) and located in the region Xq12 to Xq13.3.     

The Juberg-Marsidi syndrome maps to the proximal long arm of the X chromosome (Xq12-q21).

Juberg-Marsidi syndrome (McKusick 309590) is a rare X-linked recessive condition characterized by severe mental retardation, growth failure, sensorineural deafness, and microgenitalism. Here we report on the genetic mapping of the Juberg-Marsidi gene to the proximal long arm of the X chromosome (Xq12-q21) by linkage to probe pRX214H1 at the DXS441 locus (Z = 3.24 at theta = .00). Multipoint linkage analysis placed the Juberg-Marsidi gene within the interval defined by the DXS159 and the DXYS1X loci in the Xq12-q21 region. These data provide evidence for the genetic distinction between Juberg-Marsidi syndrome and several other X-linked mental retardation syndromes that have hypogonadism and hypogenitalism and that previously. Finally, the mapping of the Juberg-Marsidi gene is of potential interest for reliable genetic counseling of at-risk women.     

Localization of the Aland Island eye disease locus to the pericentromeric region of the X chromosome by linkage analysis.

Aland Island eye disease (AIED) is an X-chromosomal disorder characterized by reduced visual acuity, progressive axial myopia, regular astigmatism, latent nystagmus, foveal hypoplasia, defective dark adaptation, and fundus hypopigmentation. The syndrome was originally reported in 1964 in a family on the Aland Islands. To determine the localization of the AIED gene, linkage studies were performed in this family. total of 37 polymorphisms, covering loci on the entire X chromosome, were used. By two-point analysis the strongest evidence for linkage was obtained between AIED and DXS255 (maximum lod score [Zmax] 4.92 at maximum recombination fraction [theta max] .00). Marker loci DXS106, DXS159, and DXS1 also showed no recombination with AIED. Other positive lod scores at theta max .00 were obtained with markers localized in the XY homologous region in Xq13-q21, but the numbers of informative meioses were small. Multilocus linkage analysis indicated that the most probable location of AIED is in the pericentromeric region between DXS7 and DXS72. These results rule out localizations of AIED more distal on Xp that have been proposed by others. Our data do not exclude the possibility that AIED and incomplete congenital stationary night blindness are caused by mutations in the same gene. This question should be resolved by careful clinical comparison of the disorders and ultimately by the molecular dissection of the genes themselves.     

Genetic mapping of anhidrotic ectodermal dysplasia: DXS159, a closely linked proximal marker

Summary Three families with anhidrotic ectodermal dysplasia (AED) have been studied by linkage analysis with seven polymorphic DNA markers from the Xp11-q21 region. Previously reported linkage to DXYS1 (Xq13-q21) has been confirmed (z()=4.08 at =0.05) and we have also established linkage to another polymorphic locus, DXS159, located in Xq11-q12 (z()=4.28 at =0.05). Physical mapping places DSX159 proximal to the Xq12 breakpoint of an X autosome translocation found in a female with clinical signs of ectodermal dysplasia. Of all markers that have been used in linkage analysis of AED, DXS159 would appear the closest on the proximal side of the disease locus.     

X-linked alpha-thalassemia/mental retardation (ATR-X) syndrome: localization to Xq12-q21.31 by X inactivation and linkage analysis.

We have examined seven pedigrees that include individuals with a recently described X-linked form of severe mental retardation associated with alpha-thalassemia (ATR-X syndrome). Using hematologic and molecular approaches, we have shown that intellectually normal female carriers of this syndrome may be identified by the presence of rare cells containing HbH inclusions in their peripheral blood and by an extremely skewed pattern of X inactivation seen in cells from a variety of tissues. Linkage analysis has localized the ATR-X locus to an interval of approximately 11 cM between the loci DXS106 and DXYS1X (Xq12-q21.31), with a peak LOD score of 5.4 (recombination fraction of 0) at DXS72. These findings provide the basis for genetic counseling, assessment of carrier risk, and prenatal diagnosis of the ATR-X syndrome. Furthermore, they represent an important step in developing strategies to understand how the mutant ATR-X allele causes mental handicap, dysmorphism, and down-regulation of the alpha-globin genes.     

Linkage localization of X-linked Charcot-Marie-Tooth disease.

Charcot-Marie-Tooth disease (CMT), also known as hereditary motor and sensory neuropathy, is a heterogeneous group of slowly progressive, degenerative disorders of peripheral nerve. X-linked CMT (CMTX) (McKusick 302800), a subdivision of type I, or demyelinating, CMT is an X-linked dominant condition with variable penetrance. Previous linkage analysis using RFLPs demonstrated linkage to markers on the proximal long and short arms of the X chromosome, with the more likely localization on the proximal long arm of the X chromosome. Available variable simple-sequence repeats (VSSRs) broaden the possibilities for linkage analysis. This paper presents new linkage data and recombination analysis derived from work with four VSSR markers--AR, PGKP1, DXS453, and DXYS1X--in addition to analysis using RFLP markers described elsewhere. These studies localize the CMTX gene to the proximal Xq segment between PGKP1 (Xq11.2-12) and DXS72 (Xq21.1), with a combined maximum multipoint lod score of 15.3 at DXS453 (theta = 0).     

The gene for Aarskog syndrome is located between DXS255 and DXS566 (Xp11.2-Xq13).

Aarskog syndrome has been mapped to Xq13 on the basis of a patient carrying an Xq13:8p21.2 translocation. We have identified a new microsatellite marker in a clone mapping to this region (HX60;DXS566). Using primers flanking this microsatellite along with primers detecting a microsatellite at PGK1P1 and DXS255, and DXS72, we have performed a multipoint analysis in a large kindred with Aarskog syndrome. Our results suggest that the Aarskog locus lies proximal to Xq13. This is supported by the recent redefining of the breakpoint of the original translocation as between DXS14 (Xp11.21-p11.1) and DXS146 (Xp11.23-p11.22).     

High-resolution mapping of the X-linked hypohidrotic ectodermal dysplasia (EDA) locus

The X-linked hypohidrotic ectodermal dysplasia (EDA) locus has been previously localized to the subchromosomal region Xq11-q21.1. We have extended our previous linkage studies and analyzed linkage between the EDA locus and 10 marker loci, including five new loci, in 41 families. Four of the marker loci showed no recombination with the EDA locus, and six other loci were also linked to the EDA locus with recombination fractions of .009-.075. Multipoint analyses gave support to the placement of the PGK1P1 locus proximal to the EDA locus and the DXS453 and PGK1 loci distal to EDA. Further ordering of the loci could be inferred from a human/rodent somatic cell hybrid derived from an affected female with EDA and an X;9 translocation and from studies of an affected male with EDA and a submicroscopic deletion. Three of the proximal marker loci, which showed no recombination with the EDA locus, when used in combination, were informative in 92% of females. The closely linked flanking polymorphic loci DXS339 and DXS453 had heterozygosities of 72% and 76%, respectively, and when used jointly, they were doubly informative in 52% of females. The human DXS732 locus was defined by a conserved mouse probe pcos169E/4 (DXCrc169 locus) that cosegregates with the mouse tabby (Ta) locus, a potential homologue to the EDA locus. The absence of recombination between EDA and the DXS732 locus lends support to the hypothesis that the DXCrc169 locus in the mouse and the DXS732 locus in humans may contain candidate sequences for the Ta and EDA genes, respectively.     

Linkage analysis of X-linked cleft palate and ankyloglossia in Manitoba Mennonite and British Columbia Native kindreds

A locus (CPX) responsible for X-linked cleft palate and ankyloglossia was previously mapped to the proximal long arm of the X chromosome through DNA marker linkage studies in two large kindreds: an Icelandic family and a British Columbia (B.C.) Native family. In this study, additional linkage analyses have been performed in the B.C. family and in a newly identified Manitoba Mennonite family with X-linked cleft palate and ankyloglossia. The Manitoba CPX locus maps to the same region as Icelandic and B.C. CPX. Two-point disease-tomarker linkage analyses in the Manitoba family indicate a maximum lod score (Z_max) between CPX and DXS349 (Z_max=3.33 at ). In multipoint linkage analysis, combined data from the B.C. and Manitoba families suggest that the most likely location for CPX is at DXS447 in Xq21.1 (multipoint Z=13.5). The support interval for CPX at DXS447 extends approximately from PGK1 to DXYS1 and includes a newly isolated polymorphic locus DXS1109.     

Regional localization of polymorphic DNA loci on the proximal long arm of the X chromosome using deletions associated with choroideremia

Summary In two unrelated families, males have been identified who suffer from choroideremia and at the same time have an interstitial deletion on the proximal long arm of the X chromosome. By high-resolution banding we have characterized the deletion chromosomes as del(X)(q21.1-q21.33) and del(X)(q21.2-q21.31) respectively. By Southern blot analysis we have mapped ten different polymorphic DNA loci relative to the position of the deletion and the choroideremia locus TCD. One probe, p31, was shown to cover one of the breakpoints of the smallest deletion. The following order of the loci was suggested by deletion mapping: cen-DXS106-DXS72-TCD-(DXYS1/DXYS23/DXYS5)-DXYS2-(DXYS12/DXS3)-(DXS17/DXS101)-Xqter.     

Localization of a mutant gene for cleft palate and ankyloglossia in an X-linked Icelandic family.

Common congenital malformations such as cleft lip and cleft palate are in most cases multifactorial in origin, involving both environmental and genetic components. Molecular biology techniques have enabled the successful chromosomal localization of many mutant genes from disorders that exhibit simple Mendelian segregation, whether autosomally dominant (e.g., Huntington's disease), autosomal recessive (e.g., cystic fibrosis), or X-linked (e.g., Duchenne muscular dystrophy). Studying the genetic aspect of multifactorial disorders is more complex. It requires a model family or families within which the common multifactorial phenotype is displayed as a single gene defect. Such a model has been recently exploited in the form of a large Icelandic family (over 280 members) exhibiting X-linked secondary cleft palate (CP) and ankyloglossia (A) (tongue-tied) as a single gene mutation. Using this family and the large bank of well-characterized DNA probes available for the human X chromosome, the gene for CP + A was localized by linkage analysis to Xq13-q21.1 (LOD score = 3.07, linked to anonymous probe DXYS1). Further fine mapping, using other X probes from this region (confirmed by analysis of DNA from a deletion cell-line) has placed the gene between markers DXYS12 and DXS17 (LOD score = 4.1) at Xq21.3-q22. The approximate distance between these two probes is 5 centimorgans (cM), equivalent to approximately 5 million base pairs. Now that the limits of genetic linkage have been fully tested and there are two markers flanking the defect locus, strategies are being pursued to clone the gene responsible.(ABSTRACT TRUNCATED AT 250 WORDS)     

Physical mapping in the region of human Xq12-21.1 using pulsed field gel electrophoresis

A number of human disease genes have been localised to Xq12-21.1. A genetic map of this region has previously been constructed using family linkage studies and has been complemented by physical mapping studies using hybrid and deletion cell lines. We have constructed a preliminary long-range physical map of the region, which incorporates thirteen polymorphic and non-polymorphic probes, using pulsed field gel electrophoresis. The order of loci that can be inferred from all the genetic and physical mapping data is: cen-DXS133-[DXS153, DXS159]-DXS132-DXS135-[DXS131, DXS162]-[DXS325, DXS-347, DXS441]-PGKl-DXS447-DXS72-tel. The detection of several large non-overlapping MluI fragments by these probes implies that the minimum extent of the genomic DNA containing these loci is 16Mb. This information should be useful in the eventual identification and isolation of the genes responsible for diseases that map to this region.     

Assignment of the dystonia-parkinsonism syndrome locus, DYT3, to a small region within a 1.8-Mb YAC contig of Xq13.1.

A YAC contig was constructed of Xq13.1 in order to sublocalize the X-linked dystonia-parkinsonism (XDP) syndrome locus, DYT3. The contig spans a region of approximately 1.8 Mb and includes loci DXS453/DXS348/IL2R gamma/GJB1/CCG1/DXS559. For the construction of the contig, nine sequence-tagged sites and four short tandem repeat polymorphisms (STRPs) were isolated. The STRPs, designated as 4704#6 (DXS7113), 4704#7 (DXS7114), 67601 (DXS7117), and B4Pst (DXS7119) were assigned to a region flanked by DXS348 proximally and by DXS559 distally. Their order was DXS348/4704 #6/4704 #7/67601/B4Pst/DXS559. They were applied to the analysis of allelic association and of haplotypes in 47 not-obviously-related XDP patients and in 105 Filipino male controls. The same haplotype was found at loci 67601 (DXS7117) and B4Pst (DXS7119) in 42 of 47 patients. This percentage of common haplotypes decreased at the adjacent loci. The findings, together with the previous demonstration of DXS559 being the distal flanking marker of DYT3, assign the disease locus to a small region in Xq13.1 defined by loci 67601 (DXS7117) and B4Pst (DXS7119). The location of DYT3 was born out by the application of a newly developed likelihood method for the analysis of linkage disequilibrium.     

Tightly linked flanking markers for the Lowe oculocerebrorenal syndrome, with application to carrier assessment.

The Lowe oculocerebrorenal syndrome (OCRL) is characterized by congenital cataract, mental retardation, and defective renal tubular function. A map assignment of OCRL to Xq24-q26 has been made previously by linkage analysis with DXS42 at Xq24-q26 (theta = 0, z = 5.09) and with DXS10 at Xq26 (theta = 0, z = 6.45). Two additional families were studied and three additional polymorphisms were identified at DXS42 by using a 35-kb sequence isolated with the probe detecting the original polymorphism at DXS42. With additional OCRL families made informative for DXS42, theta remained 0 with z = 6.63; and for DXS10 theta = 0.03 and z = 7.07. Evidence for placing OCRL at Xq25 also comes from a female with Lowe syndrome and an X;3 translocation. We have used the Xq25 breakpoint in this patient to determine the position of OCRL relative to the two linked markers. Each derivative chromosome was isolated away from its normal counterpart in somatic cell hybrids. DXS42 was mapped to the derivative chromosome X containing Xpterq25, and DXS10 was mapped to the derivative chromosome 3 containing Xq25-qter. The markers DXS10 and DXS42 therefore show tight linkage with OCRL in six families and flank the Xq25 breakpoint in a female patient with an X;3 translocation. Linkage analysis with flanking markers was used to assess OCRL carrier status in women at risk. Results, when compared with carrier determination by ophthalmologic examination, indicated that the slit-lamp exam can be a sensitive and specific method of carrier determination in many cases.