Cosmid mapping and locus linkage within the human chromosomal region 22q13.1

Many human meningiomas show loss of heterozygosity at distal loci but retain constitutional heterozygosity at one or more proximal loci of 22q. Molecular analysis indicted deletions involving at least the region 22q12.3-qter. In this region, distal to myoglobin, the putative meningioma locus ought to be expected. Long-range mapping was performed around two loci from 22q12.3–q13.1 (D22S16 and PDGFB, the most proximal locus to be lost in meningioma). D22S16, originally assigned to 22q13-qter by isotopic in situ hybridization, was placed in the vicinity of PDGFB by utilizing a set of somatic cell hybrids, an assignment confirmed by fluorescence in situ hybridization (FISH) of a cosmid clone containing the D22S16 locus. Moreover, pulsed field gel electrophoresis suggests a close linkage of both markers within 630 kb.     

Fine mapping supports previous linkage evidence for a bipolar disorder susceptibility locus on 13q32

A region between D13S71 and D13S274 on 13q32 showed linkage to bipolar disorder (BP) based on a genome scan using markers with an average spacing of approximately 6 cM and an average heterozygosity of approximately 60% [Detera-Wadleigh et al., 1999: Proc Natl Acad Sci USA 96:5604-5609]. In an attempt to confirm this finding and achieve fine mapping of the susceptibility region, nine additional microsatellite markers with average heterozygosity of approximately 86%, located between D13S71 and D13S274, were typed in the same sample. The strongest linkage evidence was detected by multipoint linkage analysis (ASPEX program) around D13S779-D13S225 with maximum LOD score of 3.25 under Affection Status Model II (ASM II; P = 0.0000546). Data from additional nine markers resulted in a decrease of the 95% confidence interval of the linkage region. Association analyses with GASSOC TDT and ASPEX/sib_tdt detect potential linkage disequilibrium with several markers, including D13S280 (ASPEX TDT P = 0.0033, ASM I). These data generated using a higher marker density within the proposed susceptibility region strengthen the validity of our previous findings and suggest a finer localization of the susceptibility gene(s) on 13q32.     

A follow-up linkage study supports evidence for a bipolar affective disorder locus on chromosome 21q22

Evidence for linkage between bipolar affective disorder (BP) and 21q22 was first reported by our group in a single large pedigree with a lod score of 3.41 with the PFKL locus. In a subsequent study, with denser marker coverage in 40 multiplex BP pedigrees, we reported supporting evidence with a two-point lod score of 2.76 at the D21S1260 locus, about 6 cM proximal to PFKL. For cost-efficiency, the individuals genotyped in that study comprised a subset of our large pedigree sample. To augment our previous analysis, we now report a follow-up study including a larger sample set with an additional 331 typed individuals from the original 40 families, improved marker coverage, and an additional 16 pedigrees. The analysis of all 56 pedigrees (a total of 862 genotyped individuals vs. the 372 genotyped previously), the largest multigenerational BP pedigree sample reportedly analyzed to date, supports our previous results, with a two-point lod score of 3.56 with D21S1260. The 16 new pedigrees analyzed separately gave a maximum two-point lod score of 1.89 at D21S266, less than 1 cM proximal to D21S1260. Our results are consistent with a putative BP locus on 21q22.     

Genetic refinement and physical mapping of a chromosome 16q candidate region for inflammatory bowel disease.

Crohn's disease (CD) is a complex genetic disorder for which a susceptibility gene, IBD1, has been mapped within the pericentromeric region of chromosome 16. In order to refine the location of IBD1, 77 multiplex CD families were genotyped for 26 microsatellite markers evenly spaced by approximately 1 cM. Nonparametric linkage analyses exhibited a maximum NPL score of 3.49 (P=2.37x10(-4)) in a region centred by markers D16S3136, D16S3117 and D16S770. Simulation studies showed that the probability for IBD1 to be located in a 5 cM region around these markers was 70%. A 2.5 Mb YAC and BAC contig map spanning this genetic region on chromosome band 16q12 was built. TDT analyses demonstrated suggestive association between the 207 bp allele of D16S3136 (P<0.05) and a new biallellic marker hb27g11f-end (P=0.01). These markers were located in the hb27g11 and hb87b10 BAC clones from the contig. Taken together, the present results provide a crucial preliminary step before an exhaustive linkage disequilibrium mapping of putatively transcribed regions to identify IBD1.     

A follow‐up linkage study supports evidence for a bipolar affective disorder locus on chromosome 21q22

Evidence for linkage between bipolar affective disorder (BP) and 21q22 was first reported by our group in a single large pedigree with a lod score of 3.41 with the PFKL locus. In a subsequent study, with denser marker coverage in 40 multiplex BP pedigrees, we reported supporting evidence with a two‐point lod score of 2.76 at the D21S1260 locus, about 6 cM proximal to PFKL. For cost‐efficiency, the individuals genotyped in that study comprised a subset of our large pedigree sample. To augment our previous analysis, we now report a follow‐up study including a larger sample set with an additional 331 typed individuals from the original 40 families, improved marker coverage, and an additional 16 pedigrees. The analysis of all 56 pedigrees (a total of 862 genotyped individuals vs. the 372 genotyped previously), the largest multigenerational BP pedigree sample reportedly analyzed to date, supports our previous results, with a two‐point lod score of 3.56 with D21S1260. The 16 new pedigrees analyzed separately gave a maximum two‐point lod score of 1.89 at D21S266, less than 1 cM proximal to D21S1260. Our results are consistent with a putative BP locus on 21q22. © 2001 Wiley‐Liss, Inc.     

Compelling evidence for a prostate cancer gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics

Previously, an analysis of 14 extended, high-risk Utah pedigrees localized in the chromosome 22q linkage region to 3.2 Mb at 22q12.3-13.1 (flanked on each side by three recombinants) contained 31 annotated genes. In this large, multi-centered, collaborative study, we performed statistical recombinant mapping in 54 pedigrees selected to be informative for recombinant mapping from nine member groups of the International Consortium for Prostate Cancer Genetics (ICPCG). These 54 pedigrees included the 14 extended pedigrees from Utah and 40 pedigrees from eight other ICPCG member groups. The additional 40 pedigrees were selected from a total pool of 1213 such that each pedigree was required to contain both at least four prostate cancer (PRCA) cases and exhibit evidence for linkage to the chromosome 22q region. The recombinant events in these 40 independent pedigrees confirmed the previously proposed region. Further, when all 54 pedigrees were considered, the three-recombinant consensus region was narrowed down by more than a megabase to 2.2 Mb at chromosome 22q12.3 flanked by D22S281 and D22S683. This narrower region eliminated 20 annotated genes from that previously proposed, leaving only 11 genes. This region at 22q12.3 is the most consistently identified and smallest linkage region for PRCA. This collaborative study by the ICPCG illustrates the value of consortium efforts and the continued utility of linkage analysis using informative pedigrees to localize genes for complex diseases.     

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.     

Genetic refinement and physical mapping of a chromosome 18q candidate region for bipolar disorder.

Recent genetic studies have implicated chromosome 18 in bipolar disorder (BP) with putative loci in the pericentromeric region and on 18q. We reported linkage to chromosome 18q21.33-q23 in a large family. In this study we typed additional markers in the family and were able to reduce the candidate region significantly. All affected family members are sharing alleles for markers spanning a genetic distance of maximal 8.9 cM. Haplotype analysis provided a marker order in agreement with published genetic and physical maps. Using yeast artificial chromosomes, we constructed a contig map that will help to identify positional candidate genes for bipolar disorder.     

Meta-analysis for linkage to asthma and atopy in the chromosome 5q31-33 candidate region

Asthma is a common, complex human disease. Gene discovery inasthma has been complicated by substantial etiological heterogeneity,the possibility of genes of small effect and the concomitantrequirement for large sample sizes. Linkage to asthma phenotypeshas been investigated most intensively in the 5q chromosomalregion, although results have been inconsistent across studiesand all studies have had modest sample sizes. One potentialsolution to these issues is to combine data from multiple studiesin a retrospective meta-analysis by pooling either summary statisticsor raw data. The International Consortium on Asthma Genetics combined data from 11 data sets (n = 6277 subjects) to investigateevidence for linkage of 35 markers spanning the cytokine clusteron chromosome 5q31–33 to ‘asthma’ dichotomyand total serum immunoglobulin E (IgE) levels. Chromosome 5qmarkers typed in different centers were integrated into a consensusmap to facilitate effective data pooling. Multipoint linkageanalyses using a new Haseman–Elston method were performedwith all data sets pooled together, and also separately withthe resulting linkage statistics pooled by meta-analytic methods.Our results did not provide any evidence significant at the5% level that loci conferring susceptibility to asthma or atopyare present in the 5q31–33 region; however, there wassome weak evidence (empirical P = 0.077) of linkage toasthma affection. This study suggests that loci in 5q31–33have at most a modest effect on susceptibility to asthma ortotal serum IgE levels, may not be detectable or present inall human populations and are difficult to detect even usingcombined linkage evidence from 2400–2600 full siblingpairs. ⁺ To whom correspondence should be addressed. Tel: +1 617 5250872; Fax: +1 617 525 0958; Email: reljp@channing.harvard.edu.     

Initial Genome Scan of the NIMH Genetics Initiative Bipolar Pedigrees: Chromosomes 4, 7, 9, 18, 19, 20, and 21q

An initial genome scan was performed on 540 individuals from 97 families segregating bipolar disorder, collected through the National Institutes of Mental Health Genetics Initiative. We report here affected-sib-pair (ASP) data on 126 marker loci (≈68,000 genotypes) mapping to chromosomes 4, 7, 9, 18, 19, 20, and 21q, under three affection status models. Modest increases in identical-by-descent (IBD) allele sharing were found at the following loci: D4S2397 and D4S391 ( P < 0.05) on 4p, D4S1647 ( P < 0.05) on 4q, D7S1802 and D7S1869 (low P = 0.01) on 7p, D9S302 ( P = 0.004) on 9q, and D20S604 on 20p and D20S173 on 20q ( P ≤ 0.05). In addition, five markers on 7q displayed increased IBD sharing ( P = 0.046–0.002). Additional ASP analyses on chromosomes 18 and 21q marker data were performed using disease phenotype models defined previously. On chromosome 18, only D18S40 on 18p and D18S70 on 18q yielded a slight elevation in allele sharing ( P = 0.02), implying that the reported linkages in these regions were not confirmed. On chromosome 21q, a cluster of markers within an ≈9 cM interval: D21S1254, D21S65, D21S1440, and D21S1255 exhibited excess allele sharing ( P = 0.041–0.008). Multilocus data on overlapping marker quartets, from D21S1265 to D21S1255, which were consistent with increased IBD sharing ( P < 0.01, with a low of 0.0009), overlapped a broad interval of excess allele sharing reported previously, increasing support for a susceptibility locus for bipolar disorder on 21q. Am. J. Med. Genet. 74:254–262, 1997. © 1997 Wiley-Liss, Inc.     

Comparative mapping of 9 human chromosome 22q loci in the laboratory mouse

We present a comparative map of genes on human chromosome 22qand homologous loci In the mouse genome. Gene order in humanswas established using a panel of somatic cell hybrids. Geneticmaps spanning homologous segments on three mouse chromosomeswere generated using an Interspecific backcross. The conservedlinkage between human chromosome 22 and mouse chromosome 16Includes two closely linked loci, Comt and Igl-1. The secondconserved linkage involves human chromosome 22 and mouse chromosome11 and contains two genetically and physically linked loci,Lif and Nfh. Finally, conserved synteny involving mouse chromosome15 and human chromosome 22 spans 30 cM and contains five loci(Acr, Bzrp, Dia-1, II2rb and Pdgfb). Loci within this conservedsynteny have been sublocalized to different portions of humanchromosome 22. The order of genes on mouse chromosome 15 andhuman chromosome 22 provides further evidence for chromosomalrearrangements within the conserved synteny that have occurredsince the divergence of lineages leading to mice and humans.     

A high frequency polymorphism in the candidate region for Tuberous Sclerosis 1 (TSC1) at 9q34

The Surfeit locus contains at least six tightly clustered housekeeping genes (Surf-1 to -6) with novel features (Huxley & Fried, 1990). In contrast to the tens to hundreds of kilobases found between most adjacent mammalian genes only a small region separates any two adjacent Surfeit genes. The organization of the Surfeit locus and the juxtaposition of the Surfeit genes is conserved between mouse, human and chicken (600 million years of divergent evolution) (Williams et al. 1988; Yon et al. 1993; Colombo et al. 1992) indicating that the Surfeit locus gene organization may have biological significance. The Surfeit locus has been mapped to human chromosome band 9q34, within the candidate region for Tuberous Sclerosis 1 (TSC1) (Yon et al. 1993). In the process of screening for mutations correlated with TSC1 by single strand conformation polymorphism (SSCP) (Orita et al. 1989) in this genomic region we detected a polymorphism which occurs at a high frequency.     

Candidate gene discovery procedure after follow-up confirmatory analyses of candidate regions of interests for Alzheimer's disease in the NIMH sibling dataset

The objective of this research was to develop a procedure to identify candidate genes under linkage peaks confirmed in a follow-up of candidate regions of interests (CRIs) identified in our original genome scan in the NIMH Alzheimer's diseases (AD) Initiative families (Blacker et al. [1]). There were six CRIs identified that met the threshold of multipoint lod score (MLS) of >or= 2.0 from the original scan. The most significant peak (MLS = 7.7) was at 19q13, which was attributed to APOE. The remaining CRIs with 'suggestive' evidence for linkage were identified at 9q22, 6q27, 14q22, 11q25, and 3p26. We have followed up and narrowed the 9q22 CRI signal using simple tandem repeat (STR) markers (Perry et al. [2]). In this confirmatory project, we have followed up the 6q27, 14q22, 11q25, and 3p26 CRIs with a total of 24 additional flanking STRs, reducing the mean interval marker distance (MID) in each CRI, and substantially increase in the information content (IC). The linkage signals at 6q27, 14q22 and 11q25 remain 'suggestive', indicating that these CRIs are promising and worthy of detailed fine mapping and assessment of candidate genes associated with AD. We have developed a bioinformatics approach for identifying candidate genes in these confirmed regions based on the Gene Ontology terms that are annotated and enriched among the systematic meta-analyzed genes, confirmed by at least three case-control samples, and cataloged in the "AlzGene database" as potential Alzheimer disease susceptibility genes (http://www.alzgene.org).     

Linkage disequilibrium in the 13q12 region in Finnish late onset Alzheimer's disease patients.

Alzheimer's disease (AD) is a complex neurodegenerative disorder, for which several disease-associated loci have been located on different chromosomes. We have used a population-based linkage disequilibrium mapping approach in order to find potential AD-associated loci on chromosome 13. To avoid population stratification, late onset AD patients and age-matched controls were carefully chosen from the same geographical area in Eastern Finland, where the population is mainly descended from a small group of original founders. During the initial screening with chromosome 13-specific microsatellite markers, tetranucleotide marker D13S787 was found to be in linkage disequilibrium in the 13q12 region. Screening this region with additional microsatellite markers revealed that marker D13S292 was also significantly associated with AD. Stratification of the AD patients and controls into groups according to apolipoprotein E, sex, and familial/sporadic status indicated that the 13q12 locus was associated with female familial AD patients regardless of ApoE genotype. Based on the physical data from the region 13q12, markers D13S292 and D13S787 were estimated to reside in a 810kb long YAC clone 754h7 together with two infant brain-derived ESTs and the H,K-ATPase alpha-subunit protein gene (ATP1AL1). The localisation of these sequences at the linkage disequilibrium region suggests that they may be candidate genes involved in a sex-specific effect during development of AD.     

No evidence of linkage to chromosome 9q21-22 in a Swedish family with frontotemporal dementia and amyotrophic lateral sclerosis

Frontotemporal dementia (FTD) is a neurodegenerative disorder, sometimes occurring together with amyotrophic lateral sclerosis (ALS) within the same family. Recently, a region on chromosome 9q21–22 was reported to harbour a locus that may participate in both disorders [Hosler, B.A., et al., JAMA., 284 (2000) 1664-1669]. In the present study, a Swedish pedigree with both ALS and FTD segregating in the family was investigated by linkage analysis with five markers on chromosome 9q21–22. The pedigree included 17 individuals in two generations, with five affected cases available for analysis. As two-point logarithm of odds scores close to zero were obtained for all markers tested, the region on chromosome 9q21–22 is suggested to be excluded as candidate region in this Swedish FTD/ALS family. Our conclusion is therefore that additional loci involved in these two disorders must be operating.     

Further evidence for linkage of low-mid frequency hearing impairment to the candidate region on chromosome 4p16.3

We have investigated a three-generation family with an autosomal dominant low-mid frequency hearing loss. Audiograms show consistently a hearing threshold of 50+/-20 db hearing loss (HL) between 250 Hz and 1-2 kHz. Normal hearing level was reached between 3 and 6 kHz in all examined children. Adult patients show an additional hearing impairment (HI) in the mid and higher frequencies that seems to differ from presbyacusis. The HI is always bilateral and symmetrical. Genes causing non-syndromic autosomal-dominant deafness with HI in the low and mid frequencies were previously mapped to chromosome 4p16.3 (DFNA6, DFNA14) and chromosome 5q31 (DFNA1). After exclusion of linkage to DFNA1 on chromosome 5, we mapped the candidate gene region to the DFNA14 and DFNA6 loci, between the genetic markers D4S432 and D4S431, located on chromosome 4. This is a further family in which evident linkage of low-mid frequency HI to the candidate region on chromosome 4p16.3 has been found.     

Linkage analysis of infantile pyloric stenosis and markers from chromosome 9q11-q33: no evidence for a major gene in this candidate region.

A genetic component in the aetiology of infantile pyloric stenosis (PS) is well established. Segregation analysis is compatible with a multifactorial sex modified threshold model of inheritance but a major gene of low penetrance has not been excluded. PS has been reported to occur in 57% (four of seven) of cases with duplication of chromosome 9q11-q33. Twenty families with PS were studied using genetic markers at loci D9S55, D9S111, D9S15, D9S12, D9S56, D9S59, and ASS from this region of chromosome 9. Pairwise lod scores of -2 were obtained with all these markers at recombination fractions greater or equal to 0.04 under both autosomal dominant and autosomal recessive models of inheritance. This provides evidence against the existence of a major locus predisposing to PS within chromosome 9q11-q33.