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Linkage mapping and phenotypic analysis of autosomal dominant Pallister-Hall syndrome.

Pallister-Hall syndrome is a human developmental disorder that is inherited in an autosomal dominant pattern. The phenotypic features of the syndrome include hypothalamic hamartoma, polydactyly, imperforate anus, laryngeal clefting, and other anomalies. Here we describe the clinical characterisation of a family with 22 affected members and the genetic mapping of the corresponding locus. Clinical, radiographic, and endoscopic evaluations showed that this disorder is a fully penetrant trait with variable expressivity and low morbidity. By analysing 60 subjects in two families using anonymous STRP markers, we have established linkage to 7p13 by two point analysis with D7S691 resulting in a lod score of 7.0 at theta = 0, near the GLI3 locus. Deletions and translocations in GLI3 are associated with the Greig cephalopolysyndactyly syndrome. Although Greig cephalopolysyndactyly syndrome has some phenotypic overlap with Pallister-Hall syndrome, these two disorders are clinically distinct. The colocalisation of loci for these distinct phenotypes led us to analyse GLI3 for mutations in patients with Pallister-Hall syndrome. We have previously shown GLI3 mutations in two other small, moderately affected families with Pallister-Hall syndrome. The linkage data reported here suggest that these larger, mildly affected families may also have mutations in GLI3.

Abnormalities, Multiple↗

Assignment of fourteen microsatellite markers to the chicken linkage map.

A large mapping population, with 874 F2 individuals, was generated by reciprocally intercrossing 2 chicken lines. A genetic map of 2,426.6 cM comprising 25 linkage groups was established based on 145 microsatellite markers. Chromosome locations were assigned for 14 previously unmapped markers. The marker ADL0132 was previously mapped to chromosome 9; however, here close linkage to the MCW0091 marker on chromosome 4 was found. With this exception, the derived linkage map was in excellent agreement with the chicken consensus map. A comparison with the chicken genome assembly (http://genome.ucsc.edu; February 2004) suggested a few minor errors in the assembly. A PCR-RFLP test was used to genotype a single nucleotide polymorphism in the melanocortin receptor 3 (MC3R) gene in the intercross, and pyrosequencing was used to map the genes for Hemopoetic Cell Kinase (HCK) and Bone Morphogenic Protein 7 (BMP7). The HCK and BMP7 genes on linkage group E32 showed significant linkage to MC3R on the distal end of linkage group E47W24, consequently joining the 2 linkage groups. A comparison between the linkage data in the current study and the physical location of markers as revealed in the chicken genome sequence assembly (February 2004) showed a 3-fold higher recombination rate on microchromosomes than on macrochromosomes.

Animals↗

Exclusion of linkage of Crohn's disease to previously reported regions on chromosomes 12, 7, and 3 in the Belgian population indicates genetic heterogeneity.

Susceptibility to inflammatory bowel disease (IBD) is significantly determined by genetic factors. Linkage data from genome-wide searches have identified regions on chromosomes 16, 12, 7, and 3. Our goal was to replicate these four regions in a Belgian population of IBD families. Fifty-four IBD families were studied (47 with Crohn's disease [CD] and 7 with mixed CD and ulcerative colitis, containing 79 affected sibpairs (68 CD only, 11 mixed) for the regions previously implicated to chromosomes 16, 12, 7, and 3. In this study, no evidence for linkage was found on any of the four chromosomal regions studied for either the whole IBD dataset or the CD subgroup. The multipoint maximum logarithm of odds scores were less than 0.7 for all four regions. Exclusion mapping could significantly exclude chromosomes 3, 7, and 12. Despite earlier findings, we could significantly exclude linkage of CD with previously reported regions on chromosomes 12, 7, and 3, and could not find evidence for linkage to chromosome 16. It is important to report these findings in light of the genetic heterogeneity of IBD. A genome-wide search on a larger group of affected siblings is being analyzed to detect other possible susceptibility loci in the Belgian population.

Belgium↗

[The 'Beijing clinical database' on severe acute respiratory syndrome patients: its design, process, quality control and evaluation].

OBJECTIVE: To develop a large database on clinical presentation, treatment and prognosis of all clinical diagnosed severe acute respiratory syndrome (SARS) cases in Beijing during the 2003 "crisis", in order to conduct further clinical studies. METHODS: The database was designed by specialists, under the organization of the Beijing Commanding Center for SARS Treatment and Cure, including 686 data items in six sub-databases: primary medical-care seeking, vital signs, common symptoms and signs, treatment, laboratory and auxiliary test, and cost. All hospitals having received SARS inpatients were involved in the project. Clinical data was transferred and coded by trained doctors and data entry was carried out by trained nurses, according to a uniformed protocol. A series of procedures had been taken before the database was finally established which included programmed logic checking, digit-by-digit check on 5% random sample, data linkage for transferred cases, coding of characterized information, database structure standardization, case reviewe by computer program according to SARS Clinical Diagnosis Criteria issued by the Ministry of Health, and exclusion of unqualified patients. RESULTS: The database involved 2148 probable SARS cases in accordant with the clinical diagnosis criteria, including 1291 with complete records. All cases and record-complete cases showed an almost identical distribution in sex, age, occupation, residence areas and time of onset. The completion rate of data was not significantly different between the two groups except for some items on primary medical-care seeking. Specifically, the data completion rate was 73% - 100% in primary medical-care seeking, 90% in common symptoms and signs, 100% for treatment, 98% for temperature, 90% for pulse, 100% for outcomes and 98% for costs in hospital. CONCLUSION: The number of cases collected in the Beijing Clinical Database of SARS Patients was fairly complete. Cases with complete records showed that they could serve as excellent representatives of all cases. The completeness of data was quite satisfactory with primary clinical items which allowed for further clinical studies.

China↗

Estimation of the frequency of occult mutations for an autosomal recessive disease in the presence of genetic heterogeneity: application to genetic hearing loss disorders.

The routine testing for pathologic mutation(s) in a patient's DNA has become the foundation of modern molecular genetic diagnosis. It is especially valuable when the phenotype shows genetic heterogeneity, and its importance will grow as treatments become genotype specific. However, the technology of mutation detection is imperfect and mutations are often missed. This can be especially troublesome when dealing with a recessive disorder where the combination of genetic heterogeneity and missed mutation creates an imprecision in the genotypic assessment of individuals who do not appear to have the expected complement of two pathologic mutations. This article describes a statistical approach to the estimation of the likelihood of a genetic diagnosis under these conditions. In addition to providing a means of testing for missed mutations, it also provides a method of estimating and testing for the presence of genetic heterogeneity in the absence of linkage data. Gene frequencies as well as estimates of sensitivity and specificity can be obtained as well. The test is applied to GJB2 recessive nonsyndromic deafness, Usher syndrome types Ib and IIa, and Pendred-enlarged vestibular aqueduct syndrome.

Connexin 26↗

Positive association of the oxytocin receptor gene (OXTR) with autism in the Chinese Han population.

BACKGROUND: Previous research has suggested that the social impairments exhibited by individuals with autism are associated with changes in plasma oxytocin (OT) levels. The physiologic effects of oxytocin are mediated through its specific receptors (OTRs), and numerous studies have implicated OTRs in the regulation of social cognition and behavior. Animal models and linkage data from genome screens indicate that the oxytocin receptor gene (OXTR) is an excellent candidate for research concerning psychiatric disorders, particularly those involving social impairments, such as autism. METHODS: We genotyped four single nucleotide polymorphisms (SNPs) located within the OXTR gene of 195 Chinese Han autism trios, using polymerase chain reaction-restriction fragment length polymorphism analysis. RESULTS: The family-based association test (FBAT) revealed a significant genetic association between autism and two of the SNPs tested (rs2254298 A: Z = 2.287, p = .0222; rs53576 A: Z = 2.573, p = .0101). When haplotypes were constructed with two, three, and four markers, the haplotype-specific FBAT revealed that a number of haplotypes, particularly those involving rs53576, were significantly associated with autism. Furthermore, haplotypes constructed with all markers showed a significant excess transmission for the specific and global haplotype analyses (p = .0020 and .0289, respectively). CONCLUSIONS: These data suggest an involvement of OXTR in the susceptibility to autism, and replication is important.

Asian People↗

Exclusion of the retinoblastoma gene and chromosome 13q as the site of a primary lesion for human breast cancer.

Chromosome 13q has been suggested as the site of a gene predisposing to human breast cancer, because loss of heterozygosity of alleles on this chromosome has been observed in some ductal breast tumors and because two breast cancer lines are altered at the retinoblastoma gene (RB1) at 13q14. To test this possibility, linkage of breast cancer susceptibility to 14 loci on chromosome 13q loci was assessed in extended families in which breast cancer is apparently inherited as an autosomal dominant trait. RB1 was excluded as the site of a breast cancer gene by a lod score of Z = -7.60 at close linkage for 13 families. Multipoint analysis yielded negative lod scores throughout the region between 13q12 and 13q34; over most of this distance, Z less than -2.0. Therefore, chromosome 13q appears to be excluded as the site of primary lesion for breast cancer in these families. In addition, comparison of tumor versus normal tissues of nonfamilial breast cancer patients revealed an alteration at the 5' end of RB1 in a mucoid carcinoma but no alterations of RB1 in five informative ductal adenocarcinomas. Linkage data and comparisons of tumor and normal tissues suggest that changes in the RBI locus either are secondary alterations associated with progression of some tumors or occur by chance.

Breast Neoplasms↗

Assignment of the gene for complete X-linked congenital stationary night blindness (CSNB1) to Xp11.3.

X-linked congenital stationary night blindness (CSNB) is a nonprogressive retinal disorder characterized by a presumptive defect of neurotransmission between the photoreceptor and bipolar cells. Carriers are not clinically detectable. A new classification for CSNB includes a complete type, which lacks rod function by electroretinography and dark adaptometry, and an incomplete type, which shows some rod function on scotopic testing. The refraction in the complete CSNB patients ranges from mild to severe myopia; the incomplete ranges from moderate hyperopia to moderate myopia. To map the gene responsible for this disease, we studied eight multigeneration families, seven with complete CSNB (CSNB1) and one with incomplete CSNB, by linkage analysis using 17 polymorphic X-chromosome markers. We found tight genetic linkage between CSNB1 and an Xp11.3 DNA polymorphic site, DXS7, in seven families with CSNB1 (LOD 7.35 at theta = 0). No recombinations to CSNB1 were found with marker loci DXS7 and DXS14. The result with DXS14 may be due to the small number of scored meioses (10). No linkage could be shown with Xq loci PGK, DXYS1, DXS52, and DXS15. Pairwise linkage analysis maps the gene for CSNB1 at Xp11.3 and suggests that the CSNB1 locus is distal to another Xp11 marker, TIMP, and proximal to the OTC locus. Five-point analysis on the eight families supported the order DXS7-CSNB1-TIMP-DXS225-DXS14. The odds in favor of this order were 9863:1. Removal of the family with incomplete CSNB (F21) revealed two most favored orders, DXS7-CSNB1-TIMP-DXS255-DXS14 and CSNB1-DXS7-TIMP-DXS255-DXS14. Heterogeneity testing using the CSNB1-M27 beta and CSNB1-TIMP linkage data (DXS7 was not informative in F21) was not significant to support evidence of genetic heterogeneity (P = 0.155 and 0.160, respectively).

Alleles↗

Health care provider quality improvement organization Medicare data-sharing: a diabetes quality improvement initiative.

BACKGROUND: This paper describes a collaborative Medicare claims data linkage and sharing effort between the Baylor Health Care System (BHCS) and Texas Medical Foundation (TMF, the Texas Quality Improvement Organization) designed to assess the effect of three quality improvement interventions on care delivered to elderly patients with diabetes. The randomized controlled trial is being conducted among a network of primary care physician practices owned by BHCS and focuses on measures of care process and outcome. METHODS: Cohort definition and baseline measurement took place between January 1 and December 31, 2000. BHCS administrative data and TMF-supplied Medicare enrollment data were used to define the January 1, 2001 prevalence cohort of Medicare diabetic beneficiaries meeting study inclusion criteria. A total of 22 practices (with 92 physicians and 2,158 patients) were randomized to one of three interventions, each of which involved performance measurement feedback on three claims-based measures of care process. Physician profiles, generated by TMF using Medicare utilization files, were reported to study physicians via academic detailing sessions with a BHCS physician educator. RESULTS: The January 1 - December 31, 2000 baseline Medicare claims for the January 1, 2001 prevalence cohort were provided to HTPN by TMF in October 2001, representing a ten-month lag in the ability of Quality Improvement Organizations to provide Part B data relative to a specific episode of care time frame. Overall baseline rates for the claims-based process measures were: annual HbA1c testing (86.1%), annual eye examination (60.8%), and annual lipid profile (72.5%). As anticipated, medical-record based rates of annual eye examination were significantly underrepresented. Agreement between claims-based and medical record-based measures was very close for annual HbA1c and annual lipid profile. CONCLUSIONS: The use of Medicare claims data, through collaboration with a QIO, can help health care providers overcome a significant barrier associated with quality improvement initiatives. Limitations associated with the use of Medicare claims can impact implementation of intervention strategies, but do not prevent them from being a practical tool for improving care.

Aged↗

Linkage studies in X-linked Alport's syndrome.

Four kindreds segregating for Alport's syndrome (ASLN) compatible with a X-linked inheritance were studied for linkage with polymorphic markers of the human X chromosome. No recombinant was observed between the ASLN locus and the DXS101 and DXS94 loci, the maximum lod scores were z = 3.93 and 3.50 respectively. Linkage data between the ASLN locus and the other genetic markers used in the present study are in keeping with the assignment of the mutation to the proximal Xq arm.

Adult↗

Close linkage between Norrie disease, a cloned DNA sequence from the proximal short arm, and the centromere of the X chromosome.

Norrie disease (ND) is an X-linked recessive disorder with congenital blindness (atrophia bulborum hereditaria, pseudoglioma). Six kindreds segregating for ND were studied for linkage with polymorphic markers of the human X chromosome. No recombination was observed between the ND-locus (NDP) and the DXS7 locus, the latter followed as a DNA-restriction fragment length polymorphism, detected by the recombinant DNA probe L1.28, and assigned to the region Xp11.2-Xp11.3. The maximum lod scores are zeta = 3.81 at theta = 0.00. Linkage data between NDP and the other genetic markers used in the present study are in keeping with this assignment of the mutation to the proximal Xp.

Adolescent↗

A genome-wide screen for linkage in Nordic sib-pairs with multiple sclerosis.

Genetic factors influence susceptibility to multiple sclerosis but the responsible genes remain largely undefined, association with MHC class II alleles being the only established genetic feature of the disease. The Nordic countries have a high prevalence of multiple sclerosis, and to further explore the genetic background of the disease, we have carried out a genome-wide screen for linkage in 136 sibling-pairs with multiple sclerosis from Denmark, Finland, Norway and Sweden by typing 399 microsatellite markers. Seventeen regions where the lod score exceeds the nominal 5% significance threshold (0.7) were identified-1q11-24, 2q24-32, 3p26.3, 3q21.1, 4q12, 6p25.3, 6p21-22, 6q21, 9q34.3, 10p15, 10p12-13, 11p15.5, 12q21.3, 16p13.3, 17q25.3, 22q12-13 and Xp22.3. Although none of these regions reaches the level of genome-wide significance, the number observed exceeds the 10 that would be expected by chance alone. Our results significantly add to the growing body of linkage data relating to multiple sclerosis.

Denmark↗

Consortium fine localization of X-linked Charcot-Marie-Tooth disease (CMTX1): additional support that connexin32 is the defect in CMTX1.

Charcot-Marie-Tooth (CMT) disease is the most common form of inherited motor and sensory neuropathy. X-linked CMT (CMTX1) has been localized to the pericentric region of the X chromosome. Recently, mutations have been defined in the connexin32 gene that cosegregate with the CMTX1 phenotype in several families. The present paper presents the results of an international consortium to fine map the gene for CMTX1 to a small segment of Xq12-13. The linkage data, together with the molecular genetic studies, support the hypothesis that connexin32 is the genetic defect in CMTX1.

Charcot-Marie-Tooth Disease↗

Risk prediction with linked markers: pedigree analysis.

Rogatko [1995: Am J Med Genet 59:14-23] has proposed a method for risk prediction with linked markers. The actual implementation of this method required that the analytical forms of likelihood and risk functions be specified. It is impractical to obtain the explicit analytical form of these functions in large phase unknown pedigrees. When large phase unknown pedigrees are encountered, the compound risk can be approximated by a transformation of the discrete distribution obtained by computing the likelihood and risk functions over a grid of points. We propose a method to compute genetic risks when the functional form of the pedigree likelihood is unknown. The method was evaluated using a simple pedigree by comparing the results when functional forms were and were not known. This method was also applied to estimate genetic risks for a single pedigree with nonsyndromal X-linked mental retardation using 3 genetic markers linked to the putative disease gene. Linkage data from an extended pedigree were combined with genome mapping data, and recurrence risk distributions were calculated for members of the pedigree. The results suggest that the proposed method provides accurate risk estimate for genetic diseases. Computer programs are available to apply this method whenever genetic markers are suspected of being linked to a disease gene.

Female↗

A physical linkage map of HLA-A, -G, -7.5p, and -F.

The class I region of the human leukocyte antigen (HLA) complex includes genes encoding the classical transplantation antigens (HLA-A, -B, -C), at least three nonclassical class I genes (HLA-E, -F, and -G), and many class I pseudogenes (including HLA-7.5p). We have used probes from DNA within or flanking the HLA -A, -F, -G, and -7.5p genes to construct a physical linkage map that places the HLA-F, -G, and -7.5p loci in order with respect to HLA-A. The map was constructed using clamped homogeneous electric field pulsed-field gel electrophoresis. DNA was isolated from LCL 721 (A1:B8, A2:B5), a human Epstein-Barr virus-transformed lymphoblastoid cell line (LCL), and from two gamma-irradiation-induced mutants of LCL 721 lacking complementary class I haplotypes. The physical linkage data place HLA-G closest to HLA-A and place HLA-7.5p between HLA-G and HLA-F. The map constructed supports a maximum distance of 490 kilobases between HLA-A and HLA-F.

Cell Line, Transformed↗

Genetic linkage of IgA deficiency to the major histocompatibility complex: evidence for allele segregation distortion, parent-of-origin penetrance differences, and the role of anti-IgA antibodies in disease predisposition.

Immunoglobulin A (IgA) deficiency (IgAD) is characterized by a defect of terminal lymphocyte differentiation, leading to a lack of IgA in serum and mucosal secretions. Familial clustering, variable population prevalence in different ethnic groups, and a predominant inheritance pattern suggest a strong genetic predisposition to IgAD. The genetic susceptibility to IgAD is shared with a less prevalent, but more profound, defect called "common variable immunodeficiency" (CVID). Here we show an increased allele sharing at 6p21 in affected members of 83 multiplex IgAD/CVID pedigrees and demonstrate, using transmission/diseqilibrium tests, family-based associations indicating the presence of a predisposing locus, designated "IGAD1," in the proximal part of the major histocompatibility complex (MHC). The recurrence risk of IgAD was found to depend on the sex of parents transmitting the defect: affected mothers were more likely to produce offspring with IgAD than were affected fathers. Carrier mothers but not carrier fathers transmitted IGAD1 alleles more frequently to the affected offspring than would be expected under random segregation. The differential parent-of-origin penetrance is proposed to reflect a maternal effect mediated by the production of anti-IgA antibodies tentatively linked to IGAD1. This is supported by higher frequency of anti-IgA-positive females transmitting the disorder to children, in comparison with female IgAD nontransmitters, and by linkage data in the former group. Such pathogenic mechanisms may be shared by other MHC-linked complex traits associated with the production of specific autoantibodies, parental effects, and a particular MHC haplotype.

Alleles↗

High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33.

We have completed a genome wide linkage scan using >5700 informative single-nucleotide polymorphism (SNP) markers (Illumina IV SNP linkage panel) in 642 Caucasian families containing affected sibling pairs with rheumatoid arthritis (RA), ascertained by the North American Rheumatoid Arthritis Consortium. The results show striking new evidence of linkage at chromosomes 2q33 and 11p12 with logarithm of odds (LOD) scores of 3.52 and 3.09, respectively. In addition to a strong and broad linkage interval surrounding the major histocompatibility complex (LOD>16), regions with LOD>2.5 were observed on chromosomes 5 and 10. Additional linkage evidence (LOD scores between 1.46 and 2.35) was also observed on chromosomes 4, 7, 12, 16 and 18. This new evidence for multiple regions of genetic linkage is partly explained by the significantly increased information content of the Illumina IV SNP linkage panel (75.6%) compared with a standard microsatellite linkage panel utilized previously (mean 52.6%). Stratified analyses according to whether or not the sibling pair members showed elevated anticyclic citrullinated peptide titers indicates significant variation in evidence for linkage among strata on chromosomes 4, 5, 6 and 7. Overall, these new linkage data should reinvigorate efforts to utilize positional information to identify susceptibility genes for RA.

Arthritis, Rheumatoid↗

Cytogenetics and molecular genetics of nervous system tumors.

Cytogenic and molecular genetic analyses of the major histological subtypes of nervous system tumors, gliomas, meningiomas, and neurinomas, have provided interesting information on the mechanisms responsible for or contributing to their origin and development. Regarding malignant gliomas, a complex pattern of chromosomal involvement has been documented at the cytogenetic level: gains of chromosome 7 and losses of chromosome 10, 9p, 17p, and 22; further molecular characterization of these abnormalities has shown that mutational alterations of the p53 gene, together with the loss of alleles at 17p, seem to be the earliest abnormalities occurring during the genesis and progression of these neoplasms. The losses of regions on chromosomes 22 and 13 might also be relatively early events, perhaps characterizing subgroups of low grade gliomas. The mutations of the p53 gene in low grade tumors leads to a selective advantage in vivo and seems to be a critical step in the transformation from low grade to high grade gliomas. The loss of sequences on chromosome 10 and the deletions of 9p (that is loss of tumor suppressor genes on these locations), and epidermal growth factor receptor gene amplification, have been proposed as sequential abnormalities participating in glioblastoma tumorigenesis. The available data on meningiomas and neurinomas show that loss of regions on chromosome 22 is the main characteristic feature. Thus, tumor suppressor genes located in this chromosome are non-randomly involved in both neoplasms, and may present as solitary, sporadic tumors or as multiple associated lesions in neurofibromatosis type 2 (NF-2). The molecular analysis of a large series of meningiomas to determine the common chromosome 22 region lost has revealed that a putative meningioma tumor suppressor gene should be located at the distal 22q12.3-qter region. In parallel, the linkage data on the mapping of the NF-2 gene suggest that the NF-2 and meningioma loci are separate entities. However, some evidence exists on a possible participation of the NF-2 locus in the genesis of some meningiomas. The efforts to identify and isolate the genes involved, as well as their functional analysis, will contribute to a better understanding of the mechanisms of oncogenesis in these neoplasms and will doubtless have a clinical impact in the diagnosis, treatment and prognosis of nervous system tumors in patients.

Chromosome Aberrations↗