Jean Morissette

The 1993-94 Généthon human genetic linkage map.

In 1992, we described a second-generation genetic linkage map of the human genome. Using 1,267 new microsatellite markers, we now present a new genetic linkage map containing a total of 2,066 (AC)n short tandem repeats, 60% of which show a heterozygosity of over 0.7. Statistical linkage analysis based on the genotyping of eight large CEPH families placed these markers in the 23 linkage groups. The map includes 1,266 intervals and spans a total distance of 3690 centiMorgans (cM). A total of 1,041 markers could be ordered with odds ratios greater than 1000:1. About 56% of this map is at a distance of 1 cM or less from one of its markers.

An STS-Based Map of the Human Genome

A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid map of the human genome containing 6193 loci and incorporated a genetic linkage map of the human genome containing 5264 loci. This information was combined with the results of STS-content screening of 10,850 loci against a yeast artificial chromosome library to produce an integrated map, anchored by the radiation hybrid and genetic maps. The map provides radiation hybrid coverage of 99 percent and physical coverage of 94 percent of the human genome. The map also represents an early step in an international project to generate a transcript map of the human genome, with more than 3235 expressed sequences localized. The STSs in the map provide a scaffold for initiating large-scale sequencing of the human genome.

Bio2RDF: Towards a mashup to build bioinformatics knowledge systems

Presently, there are numerous bioinformatics databases available on different websites. Although RDF was proposed as a standard format for the web, these databases are still available in various formats. With the increasing popularity of the semantic web technologies and the ever growing number of databases in bioinformatics, there is a pressing need to develop mashup systems to help the process of bioinformatics knowledge integration. Bio2RDF is such a system, built from rdfizer programs written in JSP, the Sesame open source triplestore technology and an OWL ontology. With Bio2RDF, documents from public bioinformatics databases such as Kegg, PDB, MGI, HGNC and several of NCBIs databases can now be made available in RDF format through a unique URL in the form of http://bio2rdf.org/namespace:id. The Bio2RDF project has successfully applied the semantic web technology to publicly available databases by creating a knowledge space of RDF documents linked together with normalized URIs and sharing a common ontology. Bio2RDF is based on a three-step approach to build mashups of bioinformatics data. The present article details this new approach and illustrates the building of a mashup used to explore the implication of four transcription factor genes in Parkinsons disease. The Bio2RDF repository can be queried at http://bio2rdf.org.

Recurrent Mutation of the Gene Encoding sequestosome 1 (SQSTM1/p62) in Paget Disease of Bone

Paget disease of bone (PDB) is a common disorder characterized by focal and disorganized increases of bone turnover. Genetic factors are important in the pathogenesis of PDB. We and others recently mapped the third locus associated with the disorder, PDB3, at 5q35-qter. In the present study, by use of 24 French Canadian families and 112 unrelated subjects with PDB, the PDB3 locus was confined to approximately 300 kb. Within this interval, two disease-related haplotype signatures were observed in 11 families and 18 unrelated patients. This region encoded the ubiquitin-binding protein sequestosome 1 (SQSTM1/p62), which is a candidate gene for PDB because of its association with the NF-kappaB pathway. Screening SQSTM1/p62 for mutations led to the identification of a recurrent nonconservative change (P392L) flanking the ubiquitin-associated domain (UBA) (position 394-440) of the protein that was not present in 291 control individuals. Our data demonstrate that two independent mutational events at the same position in SQSTM1/p62 caused PDB in a high proportion of French Canadian patients.

Genome-wide search for linkage of bipolar affective disorders in a very large pedigree derived from a homogeneous population in quebec points to a locus of major effect on chromosome 12q23-q24.

We completed a genome-wide scan for susceptibility loci for bipolar affective disorders in families derived from a rather homogeneous population in the Province of Québec. The genetic homogeneity of this population stems from the migration of founding families into this relatively isolated area of Québec in the 1830s. A possible founder effect, combined with a prevalence of very large families, makes this population ideal for linkage studies. Genealogies for probands can be readily constructed from a population database of acts of baptism and marriage from the early 1830s up to the present time (the BALSAC register). We chose probands with a DSM III diagnosis of bipolar affective disorder and who may be grouped within large families having genealogical origins with the founding population of the Saguenay-Lac-St-Jean area. Living members (n approximately 120) of a very large pedigree were interviewed using the Structured Clinical Interview for DSM III (SCID I), SCID II, and with a family history questionnaire. A diagnostic panel evaluated multisource information (interview, medical records, family history) and pronounced best-estimate consensus diagnoses on all family members. Linkage, SimAPM, SimIBD, and sib-pair analyses have been performed with 332 microsatellite probes covering the entire genome at an average spacing of 11 cM. GENEHUNTER and haplotype analyses were performed on regions of interest. Analysis of a second large pedigree in the same regions of interest permitted confirmation of presumed linkages found in the region of chromosome 12q23-q24.

HOMOZYGOTES CARRYING AN AUTOSOMAL DOMINANT TIGR MUTATION DO NOT MANIFEST GLAUCOMA

nature genetics volume 19 august 1998 319 Autosomal dominant disorders typically result in more severe clinical manifestations in mutant homozygotes than in heterozygotes1. Huntington disease is the only reported non-neoplastic human pathology in which no phenotypic variance has been detected between these two types of carriers, and where the mutant allele is truly dominant over its wild-type counterpart2. Primary openangle glaucoma (POAG), a leading cause of blindness worldwide, is characterized by progressive degeneration of the optic nerve and is usually associated with intraocular hypertension3 (OHT). Several loci involved in glaucoma have been localized4,5. Recently, mutations in the trabecular meshwork-inducible glucocorticoid response (TIGR) gene, also known as myocilin6, mapping to the GLC1A locus at 1q23−q25, were identified in families affected by autosomal dominant POAG (refs 7−10). We investigated a FrenchCanadian family, pedigree GV-001, in which POAG was transmitted as an autosomal dominant trait linked to the GLC1A locus11. The large size of this kindred and its relative isolation in eastern Québec allowed us to assess the effects of a TIGR mutation present in double dosage in four adult homozygotes. These individuals were asymptomatic for the disorder, with POAG affecting only the heterozygotes. The pedigree currently contains 622 individuals, of which 83 manifested either juvenile-onset (JOAG), a subset of POAG that has an early age at onset3, or adultonset POAG. Ten individuals also displayed OHT, which often preceded POAG by several years11. A marriage in branch GV-510 between two affected seconddegree cousins, mother V-1 and her spouse, father V-2 (Fig. 1a), resulted in 10 children, now 33−50 years of age. It was expected that these siblings would carry two wild-type copies of TIGR in a proportion of approximately 25%, and approximately 75% would harbour at least one mutant allele. It was also anticipated that a high proportion of these adults would be affected. Phenotypic evaluation showed only two sibs to be affected: son VI-3 and daughter VI-4 (Fig. 1a). The other eight sibs disHomozygotes carrying an autosomal dominant TIGR mutation do not manifest glaucoma

Sequestosome 1: mutation frequencies, haplotypes, and phenotypes in familial Paget's disease of bone.

Mutations of the SQSTM1/p62 gene are commonly observed in PDB. Screening an updated sample from Quebec and using previously published data from other populations, we compared frequency estimates for SQSTM1/p62 mutations and haplotype distribution. The P392L mutation was the most prevalent, embedded in two different haplotypes, possibly shared by other populations. We also examined the phenotype and penetrance of P392L.

Useful parameters to predict the eventual mental outcome of hypothyroid children

ABSTRACT: The Quebec Network for Genetic Medicine has followed the development of some 100 hypothyroid children treated by 1 month of age and evaluated at 18 months, 3 and 5 yr and the Griffiths Mental Development Scales, then at 7 and 9 yr with the Wechsler Intelligence Scale for Children Revised. Results show that the children as a group reach scores within the normal range of the tests. However, a few patients have low scores at each evaluation. Previously, we showed a correlation between a low serum thyroxine concentration, or a relatively retarded bone maturation before treatment, and low mental scores. To better characterize the significance of this relationship we correlated these pretreatment factors and the Wechsler Intelligence Scale for Children Revised results of 43 subjects reaching the age of 7 yr. Again, the same correlation was observed. Calculating a predictive factor (low thyroxine, <2 μg/dl and retarded bone surface, <0.05 cm2) from data recorded before therapy initiation, 10 of 13 children were correctly predicted to have I.Q. values <90. The use of these parameters might permit early intervention, and allow specific guidance of the more affected subjects.

Preliminary results on the mental development of hypothyroid infants detected by the Quebec Screening Program

A prospective study of the mental development of hypothyroid infants detected by the Quebec Network for Genetic Medicine began in January, 1976. The mean age at initiation of thyroid hormone therapy was 27 days. Forty-five hypothyroid infants and 37 normal control subjects were assessed at age 12 months with the Griffiths mental development test; 77 and 41, respectively, were assessed at age 18 months, and 59 and 40, respectively, at 36 months. There were no statistically significant differences in the various test scores between the two populations at age 12 months, but at age 18 and 36 months the hypothyroid infants had lower scores in hearing-speech performance scales and practical reasoning (36 months) which also decreased their global quotient. The mean scores were still above 100 and only nine were below 85. Further assessment of the influence of early therapy on mental development at age 6 years is needed before definitive statements can be made about the long-term mental development in these subjects.

The p62 P392L Mutation Linked to Paget’s Disease Induces Activation of Human Osteoclasts

Mutations of the gene encoding p62/SQSTM1 have been described in Pagets disease of bone (PDB), identifying p62 as an important player in osteoclast signaling. We investigated the phenotype of osteoclasts differentiated from peripheral blood monocytes obtained from healthy donors or PDB patients, all genotyped for the presence of a mutation in the p62 ubiquitin-associated domain. The cohort included PDB patients carrying or not the p62 P392L mutation and healthy donors carrying or not this mutation. Osteoclasts from PDB patients were more numerous, contained more nuclei, were more resistant to apoptosis, and had a greater ability to resorb bone than their normal counterparts, regardless of whether the p62 mutation was present or not. A strong increase in p62 expression was observed in PDB osteoclasts. The presence of the p62(P392L) gene in cells from healthy carriers conferred a unique, intermediate osteoclast phenotype. In addition, we report that two survival-promoting kinases, protein kinase Czeta and phosphoinositide-dependent protein kinase 1, were associated with p62 in response to receptor activator of NF-kappaB ligand (RANKL) stimulation in controls and before RANKL was added in PDB osteoclasts. In transfected osteoclasts derived from cord blood monocytes, the p62 P392L mutation contributed to increased activation of kinases protein kinase Czeta/lambda and phosphoinositide-dependent protein kinase 1, along with basal activation of NF-kappaB, independently of RANKL stimulation. These findings clearly indicate that the overexpression of p62 in PDB patients induces important shifts in the pathways activated by RANKL and up-regulates osteoclast functions. Moreover, the most-commonly reported p62 mutation, P392L, certainly contributes to the overactive state of osteoclasts in PDB.