The CEPH consortium linkage map of human chromosome 1

Molecular basis of the Duffy blood group system

ACKR1, located on chromosome 1q23.2, is the gene that encodes a glycoprotein expressing the Duffy blood group antigens. This gene is transcribed in two mRNA variants yielding two isoforms, encoding proteins with 338 and 336 amino acids. This review provides a general overview of the Duffy blood group to characterise and elucidate the genetic basis of this system. The Fy^a and Fy^b antigens are encoded by co-dominant FY*A (FY*01) and FY*B (FY*02) alleles, which differ by c.125G>A (rs12075), defining the Fy(a+b-), Fy(a-b+) and Fy(a+b+) phenotypes. The Fy(a-b-) phenotype that occurs in Africans provides an explanation for the apparent absence of Plasmodium vivax in this region: this phenotype arises from homozygosity for the FY*B allele carrying a point mutation c.1-67T>C (rs2814778), which prevents Fy^b antigen expression only in red blood cells. The same mutation has also been found on the FY*A allele, but it is very rare. The Fy(a-b-) phenotype in Europeans and Asians arises from mutations in the coding region of the FY*A or FY*B allele, preventing Duffy antigen expression on any cell in the body and thus are true Duffy null phenotypes. According to the International Society for Blood Transfusion, ten alleles are associated with the null expression of the Fy antigens. Furthermore, different allelic forms of FY*B modify Fy^b antigen expression, which may result in very weak or equivocal serology results. The mostly common found variants, c.265C>T (rs34599082) and c.298G>A (rs13962) -previously defined in combination only with the FY*B allele - have already been observed in the FY*A allele. Thus, six alleles have been recognised and associated with weak expression of the Fy antigens. Considering the importance of the Duffy blood group system in clinical medicine, additional studies via molecular biology approaches must be performed to resolve and clarify the discrepant results that are present in the erythrocyte phenotyping.

A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits

BACKGROUND

Genomic resources for the rabbit are still limited compared to many other livestock species. The genomic sequence as well as linkage maps have gaps that hamper their use in rabbit genome research. Therefore, the aims of this study were the improvement of existing linkage maps and the mapping of quantitative trait loci (QTL) for carcass and meat quality traits. The study was performed in a F2 population of an initial cross between Giant Grey (GG) and New Zealand White (NZW) rabbits. The population consisted of 363 F2 animals derived from 9 F1 bucks and 33 F1 does. 186 microsatellite and three SNP markers were informative for mapping.

RESULTS

Out of 189 markers, which could be assigned to linkage groups, 110 markers were genetically mapped for the first time. The average marker distance was 7.8 cM. The map across all autosomes reached a total length of 1419 cM. The maternal linkage map was 1.4 times longer than the paternal. All linkage groups could be anchored to chromosomes. On the basis of the generated genetic map, we identified a highly significant QTL (genome-wide significance p < 0.01) for different carcass weights on chromosome 7 with a peak position at 91 cM (157 Mb), a significant QTL (p < 0.05) for bone mass on chromosome 9 at 61 cM (65 Mb), and another one for drip loss on chromosome 12 at 94 cM (128 Mb). Additional suggestive QTL were found on almost all chromosomes. Several genomic loci affecting the fore, intermediate and hind parts of the carcass were identified. The identified QTL explain between 2.5 to 14.6% of the phenotypic variance in the F2 population.

CONCLUSIONS

The results present the most comprehensive genetic map and the first genome-wide QTL mapping study for carcass and meat quality traits in rabbits. The identified QTL, in particular the major QTL on chromosome 7, provide starting points for fine mapping and candidate gene search. The data contribute to linking physical and genetic information in the rabbit genome.

Red blood cell polymorphism and susceptibility to Plasmodium vivax

Resistance to Plasmodium vivax blood-stage infection has been widely recognised to result from absence of the Duffy (Fy) blood group from the surface of red blood cells (RBCs) in individuals of African descent. Interestingly, recent studies from different malaria-endemic regions have begun to reveal new perspectives on the association between Duffy gene polymorphism and P. vivax malaria. In Papua New Guinea and the Americas, heterozygous carriers of a Duffy-negative allele are less susceptible to P. vivax infection than Duffy-positive homozygotes. In Brazil, studies show that the Fy(a) antigen, compared to Fy(b), is associated with lower binding to the P. vivax Duffy-binding protein and reduced susceptibility to vivax malaria. Additionally, it is interesting that numerous studies have now shown that P. vivax can infect RBCs and cause clinical disease in Duffy-negative people. This suggests that the relationship between P. vivax and the Duffy antigen is more complex than customarily described. Evidence of P. vivax Duffy-independent red cell invasion indicates that the parasite must be evolving alternative red cell invasion pathways. In this chapter, we review the evidence for P. vivax Duffy-dependent and Duffy-independent red cell invasion. We also consider the influence of further host gene polymorphism associated with malaria endemicity on susceptibility to vivax malaria. The interaction between the parasite and the RBC has significant potential to influence the effectiveness of P. vivax-specific vaccines and drug treatments. Ultimately, the relationships between red cell polymorphisms and P. vivax blood-stage infection will influence our estimates on the population at risk and efforts to eliminate vivax malaria.

Utility of a C-Jun Microsatellite Marker in Determining Gene Dosage forfatty (fa)

The Zucker fatty (fa) mutation provides a genetic model for obesity and non-insulin dependent diabetes mellitus. The molecular pathogenesis of the metabolic phenotype of these animals is not known. Detailed molecular maps of the region surrounding the fa locus on rat chromosome 5 can be used for positional cloning experiments as well as to permit genotyping of animals from appropriate crosses before the confounding metabolic effects of obesity have occurred. We describe the development of a polymerase chain reaction (PCR) assay for a polymorphic simple sequence repeat (SSR) in the promoter region of the protooncogene c-Jun. This assay was used to position c-Jun 4.5cM proximal to the fa locus in 111 F2 progeny of a 13MBN fa/+ F1 intercross. Concurrent use of the c-Jun SSR with a previously described assay for a microsatellite in the glucose transporter, Glut1, permits rapid and accurate assessment of genotypes at the fa locus in animals of any age using minimal amounts of DNA. A strategy is described which minimizes the error rate in assigning genotype at the fatty locus for backcross and intercross progeny.

Acquired antibody responses against Plasmodium vivax infection vary with host genotype for duffy antigen receptor for chemokines (DARC)

Background

Polymorphism of the Duffy Antigen Receptor for Chemokines (DARC) is associated with susceptibility to and the severity of Plasmodium vivax malaria in humans. P. vivax uses DARC to invade erythrocytes. Individuals lacking DARC are ‘resistant’ to P. vivax erythrocytic infection. However, susceptibility to P. vivax in DARC+ individuals is reported to vary between specific DARC genotypes. We hypothesized that the natural acquisition of antibodies to P. vivax blood stages may vary with the host genotype and the level of DARC expression. Furthermore, high parasitemia has been reported to effect the acquisition of immunity against pre-erythrocytic parasites. We investigated the correlation between host DARC genotypes and the frequency and magnitude of antibodies against P. vivax erythrocytic stage antigens.

Methodology/Findings

We assessed the frequencies and magnitudes of antibody responses against P. vivax and P. falciparum sporozoite and erythrocytic antigens in Colombian donors from malaria-endemic regions. The frequency and level of naturally-acquired antibodies against the P. vivax erythrocytic antigens merozoite surface protein 1 (PvMSP1) and Duffy binding protein (PvDBP) varied with the host DARC genotypes. Donors with one negative allele (FY*B/FY*Bnull and FY*A/FY*Bnull) were more likely to have anti-PvMSP1 and anti-PvDBP antibodies than those with two positive alleles (FY*B/FY*B and FY*A/FY*B). The lower IgG3 and IgG1 components of the total IgG response may account for the decreased responses to P. vivax erythrocytic antigens with FY*A/FY*B and FY*B/FY*B genotypes. No such association was detected with P. falciparum erythrocytic antigens, which does not use DARC for erythrocyte invasion.

Conclusion/Significance

Individuals with higher DARC expression, which is associated with higher susceptibility to P. vivax infection, exhibited low frequencies and magnitudes of P. vivax blood-stage specific antibody responses. This may indicate that one of the primary mechanisms by which P. vivax evades host immunity is through DARC indirectly down-regulating humoral responses against erythrocytic invasion and development.

A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution

BACKGROUND

Genomic resources for the majority of free-living vertebrates of ecological and evolutionary importance are scarce. Therefore, linkage maps with high-density genome coverage are needed for progress in genomics of wild species. The Siberian jay (Perisoreus infaustus; Corvidae) is a passerine bird which has been subject to lots of research in the areas of ecology and evolutionary biology. Knowledge of its genome structure and organization is required to advance our understanding of the genetic basis of ecologically important traits in this species, as well as to provide insights into avian genome evolution.

RESULTS

We describe the first genetic linkage map of Siberian jay constructed using 117 microsatellites and a mapping pedigree of 349 animals representing five families from a natural population breeding in western Finland from the years 1975 to 2006. Markers were resolved into nine autosomal and a Z-chromosome-specific linkage group, 10 markers remaining unlinked. The best-position map with the most likely positions of all significantly linked loci had a total sex-average size of 862.8 cM, with an average interval distance of 9.69 cM. The female map covered 988.4 cM, whereas the male map covered only 774 cM. The Z-chromosome linkage group comprised six markers, three pseudoautosomal and three sex-specific loci, and spanned 10.6 cM in females and 48.9 cM in males. Eighty-one of the mapped loci could be ordered on a framework map with odds of >1000:1 covering a total size of 809.6 cM in females and 694.2 cM in males. Significant sex specific distortions towards reduced male recombination rates were revealed in the entire best-position map as well as within two autosomal linkage groups. Comparative mapping between Siberian jay and chicken anchored 22 homologous loci on 6 different linkage groups corresponding to chicken chromosomes Gga1, 2, 3, 4, 5, and Z. Quite a few cases of intra-chromosomal rearrangements within the autosomes and three cases of inter-chromosomal rearrangement between the Siberian jay autosomal linkage groups (LG1, LG2 and LG3) and the chicken sex chromosome GgaZ were observed, suggesting a conserved synteny, but changes in marker order, within autosomes during about 100 million years of avian evolution.

CONCLUSION

The constructed linkage map represents a valuable resource for intraspecific genomics of Siberian jay, as well as for avian comparative genomic studies. Apart from providing novel insights into sex-specific recombination rates and patterns, the described maps - from a previously genomically uncharacterized superfamily (Corvidae) of passerine birds - provide new insights into avian genome evolution. In combination with high-resolution data on quantitative trait variability from the study population, they also provide a foundation for QTL-mapping studies.

Proliferation and bone-related gene expression of osteoblasts grown on hydroxyapatite ceramics sintered at different temperature

Human osteoblast-like cells SaOS-2 (ATCC HTB85) were seeded onto three kinds of hydroxyapatite (HA) ceramics sintered at different temperature (1200 degrees C, 1000 degrees C and 800 degrees C). Scanning electron microscopy (SEM) was conducted to detect the surface microstructure. Cells were cultured on these substrates for 6 and 12 days and cell proliferation rate and mRNA expression for osteocalcin, osteonectin, type I collagen and alkaline phosphatase and protein production for osteocalcin, bone sialoprotein and osteonectin were detected with quantitative in situ hybridization and immunocytochemistry techniques. SEM revealed that crystal particle size was affected by sintering temperature. Result showed that cell proliferation rate on HA ceramics sintered at 1200 degrees C was the highest. Osteonectin and type I collagen mRNA expression was not altered by sintering temperature. After 12 days in culture, bone sialoprotein, osteocalcin and osteonectin proteins levels were significantly (p<0.05) higher when SaOS-2 cells were cultured on HA sintered at 1200 degrees C, compared to the other two surfaces, suggesting that HA sintered at high temperature may be a better candidate for in vivo implantation. This result provides valuable information concerning the clinic application of HA ceramics sintered at different temperature.

Phenotypic expression of bone-related genes in osteoblasts grown on calcium phosphate ceramics with different phase compositions

Calcium phosphate ceramics with different hydroxyapatite (HA) and tricalcium phosphate (TCP) ratios have different chemical properties. Does the difference in phase composition affect osteoblast behavior? In this study, osteoblasts were cultured on 4 kinds of calcium phosphate ceramics, i.e. pure (HA), HT1 (HA/TCP, 70/30), HT2 (HA/TCP, 35/65), and pure TCP. Cell proliferation of SaOS-2 cells together with bone-related genes' mRNA expression and protein production in osteoblasts cultured on different calcium phosphate ceramics were detected at different time points. Data suggested that cell proliferation rate on TCP ceramics was lower than that on the other substrates tested. Generally, mRNA expressions for osteonectin and osteocalcin were similar among the four kinds of ceramics in most circumstances, whereas at six days, alkaline phosphatase mRNA expression was higher on HA and HT1 surfaces than on the other two materials. Collagen I mRNA expression was also affected by the phase composition of substrates. Osteocalcin and bone sialoprotein production in SaOS-2 cells was very similar no matter which ceramic surface the cells were grown upon. This study revealed that calcium phosphate ceramics substrate could support osteoblast growth and bone-related gene expression and its gene expression pattern explained the basis of the biocompatibility and bioactivity for calcium phosphate ceramics.

Detecting low-quality markers using map expanders

Genetic marker data play a crucial role in gene mapping, and genotyping errors may have substantial influence on the power to detect and the precision to locate disease loci. Statistical methods can identify individuals, markers, or pedigrees with a high likelihood of containing genotyping errors, and the putative erroneous genotypes can then be rechecked and either verified, removed, or corrected to reduce the loss of power introduced by errors. We present a method to identify genetic markers with a high genotyping error rate. Genotyping errors are likely to appear as double recombinations which expand the genetic map around the marker. Markers flagged as map expanders (i.e., having an excessive number of double recombinations) can then be reread or regenotyped, or a replacement marker of higher quality can be used instead. The proposed method can be applied to any type of pedigree. Simulation studies of nuclear pedigrees and sib-pairs show that the proposed method generally has high power to identify map expanders when the set of markers is reasonably dense (average intermarker distance of 5 cM), even when the nominal genotyping error rate is low (2%). Not surprisingly, the power to detect map expanders increases with marker heterozygosity and genotyping error rate, and is reduced with increasing intermarker distance. When the method was applied to a real dataset consisting of 56 nuclear pedigrees genotyped for 20 microsatellite markers on chromosome 4, the method diagnosed three markers as map expanders. Subsequent examination of these markers proved that they all had high genotyping error frequencies.

Prosthetic particles modify the expression of bone-related proteins by human osteoblastic cells in vitro

Loss of bone near joint prostheses is thought to be caused by activation of recruited osteoclasts by osteolytic mediators induced by wear particles. It is proposed that particles inhibit osteogenesis during bone remodelling causing a reduction in the levels of peri-implant bone. This study explores whether prosthetic particles modulate bone formation by affecting osteoblastic bone-related mRNAs (alkaline phosphatase, pro-collagen Ialpha1, osteopontin, osteonectin, osteocalcin, bone sialoprotein and thrombospondin) or their translated proteins using titanium alloy, commercially pure titanium, and cobalt-chrome particles. The direct effect of the particles revealed no change to the expression of the bone-related mRNAs in human bone-derived cells (HBDC) at the time points investigated; although non-collagenous translated proteins expressed by these HBDC were significantly effected (p<0.05). Different patterns of expression for bone-related proteins were induced by the different particles both directly and indirectly. Inflammatory mediators (interleukin-1beta, tumor necrosis factor alpha, interleukin-6, and prostaglandin E2) had similar effects on HBDC to the media obtained from monocytes incubated with particles. This study shows that prosthetic wear particles can significantly modify the expression of bone-related proteins by osteogenic cells in vitro. These alterations in osteogenic activity at the interface of the implant and bone may be an important factor in the failure of many orthopaedic implants.

Chromosome bands 1p35-36 contain two distinct neuroblastoma tumor suppressor loci, one of which is imprinted

A previous loss of heterozygosity (LOH) study of a series of 91 neuroblastomas suggested that the 1p35-36 region encodes at least two tumor suppressor genes (TSGs) of importance in neuroblastoma development. Here we present the results of a study including 205 neuroblastomas that were analyzed for LOH at chromosome 1 and MYCN amplification. The results corroborate the existence of two TSGs on 1p. Distinct 1p loci seem to be involved in MYCN single copy vs. MYCN amplified neuroblastoma, as these tumors display a different type of shortest region of overlap (SRO). About 15% of MYCN single copy neuroblastomas show 1p deletions of variable length with an SRO of 47 cR at 1p36.3. The lost alleles are preferentially of maternal origin (P = 0.0002), suggesting parental imprinting of the locus. MYCN amplified neuroblastomas have a contrasting pattern of 1p loss. These tumors display much larger deletions of at least 89 cR comprising the region from 1p36.1 to the telomere. LOH of 1p is detected in 86% of the cases. The lost alleles are of random parental origin, suggesting inactivation of a non-imprinted TSG.

A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data

The identification of genes contributing to complex diseases and quantitative traits requires genetic data of high fidelity, because undetected errors and mutations can profoundly affect linkage information. The recent emphasis on the use of the sibling-pair design eliminates or decreases the likelihood of detection of genotyping errors and marker mutations through apparent Mendelian incompatibilities or close double recombinants. In this article, we describe a hidden Markov method for detecting genotyping errors and mutations in multilocus linkage data. Specifically, we calculate the posterior probability of genotyping error or mutation for each sibling-pair-marker combination, conditional on all marker data and an assumed genotype-error rate. The method is designed for use with sibling-pair data when parental genotypes are unavailable. Through Monte Carlo simulation, we explore the effects of map density, marker-allele frequencies, marker position, and genotype-error rate on the accuracy of our error-detection method. In addition, we examine the impact of genotyping errors and error detection and correction on multipoint linkage information. We illustrate that even moderate error rates can result in substantial loss of linkage information, given efforts to fine-map a putative disease locus. Although simulations suggest that our method detects Collapse

Key Words Collapse

MESH Headings

• Alleles
• Chromosome Mapping/methods
• Chromosome Mapping/statistics & numerical data
• Computer Simulation
• Gene Frequency/genetics
• Genetic Diseases, Inborn/genetics
• Genetic Linkage/genetics
• Genetic Markers/genetics
• Genotype
• Haplotypes/genetics
• Humans
• Lod Score
• Markov Chains
• Matched-Pair Analysis
• Models, Genetic
• Mutation/genetics
• Nuclear Family
• Research Design
• Sensitivity and Specificity

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Grants

• T32 HG00040 NHGRI NIH HHS
• R01 HG00376 NHGRI NIH HHS
• R01 HG000376 NHGRI NIH HHS
• T32 HG000040 NHGRI NIH HHS
• MH59490 NIMH NIH HHS
• R01 MH059490 NIMH NIH HHS
• R37 MH059490 NIMH NIH HHS
• R01 GM053275 NIGMS NIH HHS

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Affiliation(s)

Julie A. Douglas Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor; and Departments of Biomathematics and Human Genetics, University of California, Los Angeles
Michael Boehnke Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor; and Departments of Biomathematics and Human Genetics, University of California, Los Angeles
Kenneth Lange Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor; and Departments of Biomathematics and Human Genetics, University of California, Los Angeles

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The Duffy protein: a malarial and chemokine receptor

A major advance towards understanding the Duffy blood group system has been achieved with the cloning of FY, a single-copy gene located in the 1q22->q23 region of chromosome 1. The product of FY Is an acidic glycoprotein (gp-Fy), which spans the plasma membrane seven times and has an exocellular N-terminal domain and an endocellular C-terminal domain. The system consists of four alleles, five phenotypes, and five antigens. FYA, FYB, FYB(ES), and FYB(WK) are the alleles; Fy(a+b-), Fy(a-b+), Fy(a+b+), Fy(a-b+(wK)), and Fy(a-b-), are the phenotypes, and Fy(a), Fy(b), Fy3, Fy5, and Fy6 are the antigens. Fy(a-b-), or Duffy-negative individuals, lack the Duffy protein on erythrocytes and are predominantly African and American blacks. They have the FYB(Es) allele with a mutation in the promoter region, which abolishes the expression of the protein in erythrocytes only. In the few cases of non-black Fy(a-b-) individuals, a nonsense mutation prevents the synthesis of gp-Fy. In Fy(a-b+(wk)) erythrocytes, the Fy(b) antigen is weakly expressed due to a reduced amount of the protein. The Fy5 antigen includes the Rh protein, and the Fy6 antigen is defined by a murine monoclonal antibody. Gp-Fy is produced in several cell types, including endothellal cells of capillary and postcapillary venules, epithelial cells of kidney collecting ducts, and lung alveoli, as well as PurkinJe cells of the cerebellum. The Duffy protein plays a role in inflammation and in malaria Infection. The protein is a member of the superfamily of chemokine receptors and is the receptor to which certain malarial parasites bind to invade red blood cells. The parasite-specific binding site, the binding site of chemokines, and the major antigenic domains are located in overlapping regions at the exocellular N terminus of the Duffy protein.

An integrated transcript map of human chromosome 1p35-p36

The distal short arm of human chromosome 1 (1p) is rearranged in a variety of malignancies, and several genetic diseases also map to this region. We have constructed an integrated transcript map to precisely define the positions of genes and expressed sequence tags (ESTs) previously mapped to 1p35-p36, a region spanning approximately 40 Mb. To anchor the integrated map, a framework genetic map was constructed with 24 genetic markers and a marker order of 1000:1 odds, yielding an average resolution of 2.8 cM. An additional 106 genetic markers were localized relative to the framework genetic map. To place markers more precisely within 1p35-p36, a chromosome 1-specific, radiation-reduced hybrid (RH) panel was created. Individual DNA fragments of the RH panel were identified and ordered by PCR with the framework genetic map. A total of 250 markers, including 142 genes and ESTs, were mapped by PCR against the RH panel. The map has an observed resolution of 800 kb, and the results closely match and more precisely define previous mapping information for most markers. This map will help to identify candidate genes for genetic diseases mapping to distal 1p and is fully integrated with existing genetic and RH maps of the human genome.

A second-generation linkage map of the bovine genome

We report a bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens and serum proteins. The 2990-cM map consists of a sex-specific, X chromosome linkage group and 29 sex-averaged, autosomal linkage groups with an average interval size of 2.5 cM. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. Orientation and chromosomal assignment of all the linkage groups, except BTA20 and BTA22, was provided by 88 markers that were assigned previously to chromosomes. This map provides sufficient marker density for genomic scans of populations segregating quantitative trait loci (QTL) and subsequent implementation of marker-assisted selection (MAS) mating schemes.

European Gene Mapping Project (EUROGEM): breakpoint panels for human chromosomes based on the CEPH reference families. Centre d'Etude du Polymorphisme Humain

Meiotic breakpoint panels for human chromosomes 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 17, 18, 20 and X were constructed from genotypes from the CEPH reference families. Each recombinant chromosome included has a breakpoint well-supported with reference to defined quantitative criteria. The panels were constructed at both a low-resolution, useful for a first-pass localization, and high-resolution, for a more precise placement. The availability of such panels will reduce the number of genotyping experiments necessary to order new polymorphisms with respect to existing genetic markers. This paper shows only a representative sample of the breakpoints detected. The complete data are available on the World Wide Web (URL http:/(/)www.icnet.uk/axp/hgr/eurogem++ +/HTML/data.html) or by anonymous ftp (ftp.gene.ucl.ac.uk in/pub/eurogem/maps/breakpoints).

Genomic instability in 1p and human malignancies

Both cytogenetic and molecular genetic approaches have unveiled non-random genomic alterations in 1p associated with a number of human malignancies. These have been interpreted to suggest the existence of cancer-related genes in 1p. Earlier studies had employed chromosome analysis or used molecular probes mapped by in situ hybridization. Further, studies of the various tumor types often involved different molecular probes that had been mapped by different technical approaches, like linkage analysis, radioactive or fluorescence in situ hybridization, or by employing a panel of mouse x human radiation reduced somatic cell hybrids. The lack of maps fully integrating all loci has complicated the generation of a comparative and coherent picture of 1p damage in human malignancies even among different studies on the same tumor type. Only recently has the availability of genetically mapped, highly polymorphic loci at (CA)n repeats with sufficient linear density made it possible to scan genomic regions in different types of tumors readily by polymerase chain reaction (PCR) with a standard set of molecular probes. This paper aims at presenting an up-to-date picture of the association of 1p alterations with different human cancers and compiles the corresponding literature. From this it will emerge that the pattern of alterations in individual tumor types can be complex and that a stringent molecular and functional definition of the role that Ip alterations might have in tumorigenesis will require a more detailed analysis of the genomic regions involved.

Mapping of the OB receptor to 1p in a region of nonconserved gene order from mouse and rat to human

As part of an effort to identify informative molecular markers for genetic analysis of human pedigrees segregating for obesity, we have developed a genetic map of human 1p in the region of the OB receptor (OBR), the gene that is defective in murine diabetes (Obrdb) and rat Zucker fatty (Obrfa) mutations located on mid-chromosome 4 and chromosome 5, respectively. OBR was mapped 0.9 cR centromeric to WI-9515 and 2.2 cR telomeric of WI-7249 by radiation hybrid (RH) mapping. Ten yeast artificial chromosomes (YACs) containing OBR were identified, confirming the location of OBR centromeric to WI-9515 and telomeric to WI-7249. Additionally, five P1 artificial chromosomes (PACs) were identified that comprised a contiguous series of overlapping clones spanning the length of OBR. WI-5182 was contained within the two PACs that are 3' of OBR. Using a panel of 68 individuals from a single three-generation family and an additional nuclear family, we have mapped 18 polymorphic markers including phosphoglucomutase 1 (PGM1), which is centromeric to Obrdb / Obrfa, and D1S85, which is telomeric to Obrdb / Obrfa in the mouse and rat. The following composite map integrates these radiation hybrid, genetic, and physical maps: Centromere-@WI-7249-[OBR; WI-5182]-D1S198-[WI-9515; WI-6550; D1S2866]-D1S2825-[WI-3077; D1S2886]-[D1S515; DS1613; PGM1]-[D1S312; D1S473; D1S230; D1S246; D1S203]-D2S1643-[D1S1669; D1S1596;]UNCJ-D1S476- D1S85-D1S220-C8B-GTAT1A7. Unresolvable markers are within brackets. A comparison of gene order on mouse chromosome 4, rat chromosome 5, and human 1p indicates that between rodents and humans, there has been a rearrangement of the gene order in the region surrounding OBR.

Report of the first workshop on the genetic map of bovine chromosome 23

A report of the first workshop on the genetic map of bovine chromosome 23 (BTA23) is given. Five laboratories contributed data from 29 loci, including a total 11586 informative genotypes. The combined pedigrees represented 1930 potentially informative meioses. Eighteen of the 29 loci were common to two or more data sets and were used to construct a framework linkage map of BTA23. Twelve of the 18 could be ordered on the linkage map with a likelihood ratio of greater than 1000:1. Thus, a low resolution consensus map was constructed with a high level of support for order. The sex-averaged, female and male maps span 54.5, 52.7 and 55.8 cM, respectively. Sex-specific differences in recombination frequency were identified for eight pairs of framework loci. Average genetic distance between framework loci on the sex-averaged map is 5.0 cM.

A novel technique for quantitative detection of mRNA expression in human bone derived cells cultured on biomaterials

A nonisotopic and quantitative in situ hybridization technique was adapted to investigate the effect of biomaterials on the cellular expression of mRNA from human bone derived cells (HBD cells). HBD cells were cultured for 24 or 48 h on tissue culture plastic, alumina, and ion modified alumina. Osteocalcin, osteopontin, alkaline phosphatase, type I collagen alpha 1, and type I collagen alpha 2 mRNAs were quantified. Protein expression for collagen types I, III, and V, and for anti-human macrophages CD68 (DAKO-CD68, KP1) and CD68 (PG-M1), and anti-human myeloid/histiocyte antigen (DAKO-MAC 387) were determined immunohistochemically using monoclonal antibodies. At 24 and 48 h, levels of mRNA for alkaline phosphatase and osteonectin were greater than mRNA levels for osteopontin, osteocalcin, collagen type I alpha 1, and collagen type I alpha 2 for cells grown on the three substrata. However, at 48 h mRNA levels for alkaline phosphatase and osteonectin were significantly higher on the modified ceramic substrata relative to the native alumina. HBD cells appear to express CD68-KP1 when cultured for 24 h. The techniques provide a sensitive and reproducible assay to evaluate gene and protein expression of cells grown on different substrata.

Development of a genetic map of the chicken with markers of high utility

Microsatellites are tandem duplications with a simple motif of one to six bases as the repeat unit. Microsatellites provide an excellent opportunity for developing genetic markers of high utility because the number of repeats is highly polymorphic, and the assay to score microsatellite polymorphisms is quick and reliable because the procedure is based on the polymerase chain reaction (PCR). We have identified 404 microsatellite-containing clones of which 219 were suitable as microsatellite markers. Primers for 151 of these microsatellites were developed and used to detect polymorphisms in DNA samples extracted from the parents of two reference populations and three resource populations. Sixty, 39, 46, 49, and 61% of the microsatellites exhibited length polymorphisms in the East Lansing reference population, the Compton reference population, resource population No. 1 (developed to identify resistance genes to Marek's disease), resource population No. 2 (developed to identify genes involved in abdominal fat), and resource population No. 3 (developed to identify genes involved in production traits), respectively. The 91 microsatellites that were polymorphic in the East Lansing reference population were genotyped and 86 genetic markers were eventually mapped. In addition, 11 new random amplified polymorphic DNA (RAPD) markers and 24 new markers based on the chicken CR1 element were mapped. The addition of these markers increases the total number of markers on the East Lansing genetic map to 273, of which 243 markers are resolved into 32 linkage groups. The map coverage within linkage groups is 1,402 cM with an average spacing of 6.7 cM between loci. The utility of the genetic map is greatly enhanced by adding 86 microsatellite markers. Based on our current map, approximately 2,550 cM of the chicken genome is within 20 cM of at least one microsatellite marker.

Integrated genetic map of human chromosome 2

A framework genetic map of human chromosome 2 is described, integrating data from the Centre d'Etude du Polymorphisme Humain (CEPH) version 6 database, the CEPH chromosome 2 consortium database, the National Institute of Health (NIH)/CEPH Collaborative Mapping group and other laboratories. A comprehensive map is also presented, showing regional locations of a large number of additional loci. The framework map is used to identify an informative set of meiotic breakpoints within the CEPH families, and the utility of this information for mapping new markers is discussed. The degree of typing error within the data set is estimated, as are the sex-specific interference parameters. A location database for these genetic and additional cytogenetic data is constructed using algorithms which map genetic distances on to a physical scale, and the potential for this approach to aid the integration of genetic and physical data is examined.

Integration of gene maps: updating chromosome 1

The first integrated map of chromosome 1 was published in 1992. We present an updated summary map of 371 loci constructed from a location database that includes physical and genetic data. The summary map subsumes a composite physical location, sex-specific genetic location, cytogenetic assignment, mouse homology, rank and references to physical maps. The genetic length is 208 cM for the male map, in close agreement with the chiasma map, and 371 cM for the female map. There is evidence for a high level of interference on chromosome 1. The location database comprising both data and analytical software is discussed in relation to alternative approaches and possible enhancements.

Frequent loss of chromosome arm 1p DNA in parathyroid adenomas

Two molecular defects have been described in parathyroid adenomas: rearrangement and overexpression of the PRAD1/cyclin D1 oncogene and allelic loss of chromosome 11 DNA, often including the multiple endocrine neoplasia type 1 (MEN1) putative tumor suppressor gene region. In an effort to identify additional parathyroid tumor suppressor genes, we examined 25 parathyroid adenomas for tumor-specific allelic loss of polymorphic DNA loci located near known or candidate tumor suppressor genes. Control leukocyte DNA from all 25 patients was heterozygous for 1 or more of the 9 chromosome 1 markers examined. Allelic loss at 1 or more of these informative loci on chromosome 1 was observed in 10 of 25 (40%) adenomas. Although many tumors lost extensive regions on chromosome 1, all but one of these tumors had allelic loss of distal 1p (1p32-pter); four tumors also lost loci on 1q. Allelic loss at 11q13, the site of the MEN1 gene, was detected in 5 of 21 (24%) informative cases, including 3 with 1p loss. In contrast, allelic loss was rarely observed at loci on 9q and 10p and was not observed at loci on 3p, 3q, 4p, 5q, 12q, 14q, 18q, 22q, or Xp. In summary, clonal allelic loss of loci on chromosome arm 1p is a frequent feature of parathyroid adenomas, implying that inactivation of a tumor suppressor gene(s) on 1p commonly contributes to their pathogenesis.

Biochemical composition of human saliva in relation to other mucosal fluids

This paper describes several salivary components and their distribution in other mucosal secretions. Histatins are polypeptides which possess exceptional anti-fungal and anti-bacterial activities, but are nevertheless present only in saliva. Proline-rich proteins (PRPs) are members of a closely related family, of which the acidic PRPs are found solely in saliva, whereas the basic PRPs are also found in other secretions. Mucins are a group of glycoproteins that contribute to the visco-elastic character of the mucosal secretions. Despite the similarities in their structure and behavior, mucins have distinct tissue distributions and amino acid sequences. Other salivary proteins are present in one or more mucosal secretions. Lysozyme is an example of a component belonging to an ancient self-defense system, whereas secretory immunoglobulin A (sIgA) is the secreted part of a sophisticated adaptive immune system. Cystatins are closely related proteins which belong to a multigene family. Alpha-Amylase is a component that is believed to play a specific role in digestion, but is nevertheless present in several body fluids. Kallikrein and albumin are components of blood plasma. But whereas albumin diffuses into the different mucosal secretions, kallikrein is secreted specifically by the mucosal glands. The presence of these proteins specifically in saliva, or their distribution in other mucosal secretions as well, may provide important clues with respect to the physiology of those proteins in the oral cavity.

Identification of YAC clones for human chromosome 1p32 and physical mapping of the infantile neuronal ceroid lipofuscinosis (INCL) locus

Infantile neuronal ceroid lipofuscinosis (INCL, CLN1) is a neurodegenerative disorder in which the biochemical defect is unknown. We earlier assigned the disease locus to chromosome 1p32 in the immediate vicinity of the highly informative HY-TM1 marker by linkage and linkage disequilibrium analysis. Here we report the construction of PFGE maps on the CLN1 region covering a total of 4 Mb of this relatively poorly mapped chromosomal region. We established the order of loci at 1p32 as tel-D1S57-L-myc-HY-TM1-rlf-COL9A2-D1S193-D1S6 2-D1S211-cen by combining data obtained from analysis of a chromosome 1 somatic cell hybrid panel, PFGE, and interphase FISH. We isolated YACs and constructed two separate YAC contigs, the loci L-myc, HY-TM1, rlf, and COL9A2 being present on a 1000-kb contig and the markers D1S193, D1S62, and D1S211 on a YAC contig spanning a maximum of 860 kb. Within the 1000-kb contig we were able to identify five CpG islands in addition to those associated with the earlier cloned genes. The YAC contigs as well as the physical map provide us with tools for the identification of the INCL gene.

High-resolution cytogenetic mapping of the short arm of chromosome 1 with newly isolated 411 cosmid markers by fluorescence in situ hybridization: the precise order of 18 markers on 1p36.1 on prophase chromosomes and "stretched" DNAs

A high-resolution cytogenetic map of the short arm of chromosome 1 with newly isolated 411 cosmid markers was constructed by fluorescence in situ hybridization (FISH). These markers were scattered throughout chromosome 1p, but they were preferentially concentrated on R-band dominant regions such as 1p36, 1p34, 1p32, 1p22, and 1p13. Among these markers, 197 were localized on chromosome band 1p36, a region frequently deleted in neuroblastoma. Of these, 18 were precisely ordered on 1p36.1 by multicolor FISH of prophase chromosomes and "stretched" DNAs as follows: 1pter-163-41-11-1-226-586-568-614-631-665-451-199-190-561-241-74-1 76-652-1cen. The high-density map of chromosome 1p constructed here can provide useful landmarks for constructing a contig map of the short arm of chromosome 1 with YACs and cosmid clones and will expedite the identification of breakpoints and/or tumor suppressor gene(s) associated with several types of malignant tumors that frequently exhibit chromosomal aberrations or deletions of chromosome 1p.

Characterisation of the chromosome breakpoints in a patient with a constitutional translocation t(1;17)(p36.31-p36.13;q11.2-q12) and neuroblastoma

Cytogenetic and molecular studies in neuroblastoma suggest the presence of a tumour suppressor gene at the distal chromosome band 1p36. Previously, we hypothesised that a constitutional translocation involving the region 1p36 [t(1;17)(p36;q12-q21)] in a patient with neuroblastoma predisposed him to tumour development. Here we report the molecular delineation of the translocation breakpoints. Somatic cell hybrids containing the derivative chromosomes were used to determine the position of chromosome 1p and 17q DNA probes respective to the breakpoints using fluorescence in situ hybridisation. The 1p breakpoint was localised between the PND and D1S56 loci. The chromosome 17q breakpoint is flanked by NF1 and SCYA7, as proximal and distal marker, respectively. We redefined the translocation as t(1;17)(p36.31-13;q11.2-q12). The identification of flanking markers of the breakpoints is a prerequisite for breakpoint cloning and identification of a putative neuroblastoma suppressor gene.

Genetic map of rat chromosome 5 including the fatty (fa) locus

Thirteen loci, including the obesity gene fatty (fa), were incorporated into a linkage map of rat Chromosome (Chr) 5. These loci were mapped in obese (fa/fa) progeny of a cross between BN x 13M-fal+F1 animals. Obese rats were scored for BN and 13M alleles at four loci (Ifna, D1S85h, C8b, and Lck1) by restriction fragment length polymorphisms and at eight additional loci (Glut1, Sv4j2, R251, R735, R980, R252, R371, and R1138) by simple sequence length polymorphisms (SSLP). The resulting map spans 67.3 cM of Chr5, presenting nine previously unmapped loci and one locus (Lck1) previously assigned to Chr 5 by use of somatic cell hybrid lines. Seven of the eight SSLP loci are newly identified; the SSLP linkage group alone spans 56.8 cM. The order of the loci is Sv4j2-R251-R735-R980-R1138-Ifna-fa-+ ++D1S85h-C8b-(Glut1-R252-R371)-Lck1. One locus, D1S85h, was found to lie only 0.4 cM from fa, close enough to serve as a reliable marker for the prediction of phenotype from genotype, and will be useful also for studies on the development of obesity in the fatty rat.

Molecular cytogenetic analysis of 1;17 translocations in neuroblastoma

Loss of chromosome 1 short arm material, resulting from terminal deletions or unbalanced translocations, is a frequent finding in advanced neuroblastoma. In translocations, often relatively small portions of a second chromosome are translocated to the chromosome 1 short arm. The chromosomal origin of this translocated material could often not be identified using banding analysis only. Recent studies, applying fluorescent in situ hybridisation, showed that in the majority of these translocations, chromosome 17 is involved. In this study, the nonrandom occurrence of unbalanced 1;17 translocations is further supported by their presence in 3/7 neuroblastoma cell lines. Analysis of the 1p breakpoints extends our earlier observation of breakpoint heterogeneity. A similar scattering of 17q breakpoints was observed. The 1p and 17q breakpoints of the constitutional 1;17 translocation did not coincide with any of the 1;17 translocation breakpoints found in neuroblastoma cell lines. Cell lines, not containing 1;17 translocations, contained other chromosome 17 rearrangements. As a result, extra copies of 17q are found in all cell lines, suggesting a role for genes on 17q in neuroblastoma development. The possible significance of 1;17 translocations in neuroblastoma is discussed.

The CEPH consortium linkage map of human chromosome 16

A Centre d'Etude du Polymorphisme Humain (CEPH) consortium map of human chromosome 16 has been constructed. The map contains 158 loci defined by 191 different probe/restriction enzyme combinations or primer pairs. The marker genotypes, contributed by 9 collaborating laboratories, originated from the CEPH families DNA. A total of 60 loci, with an average heterozygosity of 68%, have been placed on the framework genetic map. The genetic map contains 7 genes. The length of the sex-averaged map is 165 cM, with a mean genetic distance between loci of 2.8 cM; the median distance between markers is 2.0 cM. The male map length is 136 cM, and the female map length is 197 cM. The map covers virtually the entire chromosome, from D16S85, within 170 to 430 kb of the 16p telomere, to D16S303 at 16qter. The markers included in the linkage map have been physically mapped on a partial human chromosome 16 somatic cell hybrid panel, thus anchoring the genetic map to the cytogenetic-based physical map.

Initial report of a genome search for the affective disorder predisposition gene in the old order Amish pedigrees: chromosomes 1 and 11

Family data have suggested that some forms of major affective disorder are genetic. Certain of the Old Order Amish pedigrees have a familial form of the disease. In this report we present the results of genetic analyses under autosomal dominant mode of transmission with reduced penetrance and three different disease hierarchies. The pedigrees were genotyped with 28 markers from chromosome 1 and 23 markers from chromosomes 11. None of the markers result in a significantly positive lod score.

A comprehensive human linkage map with centimorgan density. Cooperative Human Linkage Center (CHLC)

In the last few years there have been rapid advances in developing genetic maps for humans, greatly enhancing our ability to localize and identify genes for inherited disorders. Through the collaborative efforts of three large groups generating microsatellite markers and the efforts of the 110 CEPH collaborators, a comprehensive human linkage map is presented here. It consists of 5840 loci, of which 970 are uniquely ordered, covering 4000 centimorgans on the sex-averaged map. Of these loci, 3617 are polymerase chain reaction-formatted short tandem repeat polymorphisms, and another 427 are genes. The map has markers at an average density of 0.7 centimorgan, providing a resource for ready transference to physical maps and achieving one of the first goals of the Human Genome Project--a comprehensive, high-density genetic map.

Integrated human genome-wide maps constructed using the CEPH reference panel

High resolution linkage maps have proven to be invaluable tools in genetic investigations. We have assembled a collection of genetic maps constructed from primary data collected from investigators performing genotyping using the Centre Etude Polymorphism Humain (CEPH) reference pedigree panel. These maps were constructed using a rigorous, semi-automated map construction algorithm that evaluates the integrity of the maps during construction. Two classes of maps were produced: a high confidence "skeletal" set composed of 544 PCR based markers, and a more highly annotated "framework" set containing maps of 1,123 markers. Genetic map locations within the framework maps are provided for an additional 1,758 loci without statistically unique interval assignments.

Genomic scan for genes predisposing to schizophrenia

We initiated a genome-wide search for genes predisposing to schizophrenia by ascertaining 9 families, each containing three to five cases of schizophrenia. The 9 pedigrees were initially genotyped with 329 polymorphic DNA loci distributed throughout the genome. Assuming either autosomal dominant or recessive inheritance, 254 DNA loci yielded lod scores less than -2.0 at theta = 0.0, 101 DNA markers gave lod scores less than -2.0 at theta = 0.05, while 5 DNA loci produced maximum lod scores greater than 1: D4S35, D14S17, D15S1, D22S84, and D22S55. Of the DNA markers yielding lod scores greater than 1, D4S35 and D22S55 also were suggestive of linkage when the Affected-Pedigree-Member method was used. The families were then genotyped with four highly polymorphic simple sequence repeat markers; possible linkage diminished with DNA markers mapping nearby D4S35, while suggestive evidence of linkage remained with loci in the region of D22S55. Although follow-up investigation of these chromosomal regions may be warranted, our linkage results should be viewed as preliminary observations, as 35 unaffected persons are not past the age of risk.

Mapping of the hypokalaemic periodic paralysis (HypoPP) locus to chromosome 1q31-32 in three European families

Hypokalaemic periodic paralysis (HypoPP) is an autosomal dominant muscle disease thought to arise from an abnormal function of ion channels. Performing a genome-wide search using polymorphic dinucleotide repeats, we have localized the HypoPP locus in three families of different geographic origin to chromosome 1q31-32, by linkage analysis. Using an intragenic microsatellite, we also demonstrate that the gene encoding the muscle DHP-sensitive calcium channel alpha 1 subunit (CACNL1A3) maps to the same region, sharing a 5 centiMorgan (cM) interval with the HypoPP locus. Moreover, CACNL1A3 co-segregates with HypoPP without recombinants in the two informative families, and is therefore a good candidate for the HypoPP gene.

Chromosome instability and the FAMMM syndrome

Our study involved two extended familial atypical multiple mole melanoma (FAMMM) kindreds wherein a sufficient number of informative, high genetic risk, and affected patients enabled collection of pertinent tissue samples (normal skin/fibroblasts and atypical nevi/melanocytes) for cytogenetic analysis, and peripheral blood lymphocytes for DNA usage for linkage studies. We observed marked chromosome instability, as evidence by increased frequencies of cells with chromosomal rearrangements (translocations, deletions, and inversions) in cell cultures from atypical nevi and normal skin. There was no evidence of linkage of the FAMMM disease locus to any of the markers for the short arm of chromosome 1p in these two families. Well-characterized FAMMM kindreds provide an opportunity for biomarker investigations for elucidating heterogeneity and, ultimately, improving cancer control.

Genetic heterogeneity of Usher syndrome type II

Usher syndrome is an autosomal recessive disorder characterised by retinitis pigmentosa and congenital sensorineural hearing loss. A gene for Usher syndrome type II (USH2) has been localised to chromosome 1q32-q41. DNA from a family with four of seven sibs affected with clinical characteristics of Usher syndrome type II was genotyped using markers spanning the 1q32-1q41 region. These included D1S70 and D1S81, which are believed to flank USH2. Genotypic results and subsequent linkage analysis indicated non-linkage of this family to these markers. The A test analysis for heterogeneity with this family and 32 other Usher type II families was statistically significant at p < 0.05. Further clinical evaluation of this family was done in light of the linkage results to determine if any phenotypic characteristics would allow for clinical identification of the unlinked type. No clear phenotypic differences were observed; however, this unlinked family may represent a previously unreported subtype of Usher type II characterised by a milder form of retinitis pigmentosa and mild vestibular abnormalities. Heterogeneity of Usher syndrome type II complicates efforts to isolate and clone Usher syndrome genes using linkage analysis and limits the use of DNA markers in early detection of Usher type II.

Deletion of the serine 34 codon from the major peripheral myelin protein P0 gene in Charcot-Marie-Tooth disease type 1B

Charcot-Marie-Tooth disease type 1B (CMT1B) is genetically linked to chromosome 1q21-23. The major peripheral myelin protein gene, P0, has been cloned and localized to the same chromosomal region. P0 is a 28 kDa glycoprotein involved in the compaction of the multilamellar myelin sheet and accounts for more than half of the peripheral myelin protein content. We checked whether P0 is altered in CMT1B, and show here that a 3 basepair deletion in exon 2 of the P0 gene is present in all affected individuals of a CMT1B family. The mutation results in the deletion of serine 34 in the extracellular domain of P0, suggesting that alterations of P0 cause CMT1B.

Allelic loss of chromosome 1p36 in neuroblastoma is of preferential maternal origin and correlates with N-myc amplification

Neuroblastomas frequently have deletions of chromosome 1p and amplification of the N-myc oncogene. We analysed 53 neuroblastomas for the N-myc copy number, loss of heterozygosity (LOH) of chromosome 1p36 and the parental origin of the lost alleles. Allelic loss of 1p36 was found in 15 tumours. All N-myc amplified tumours belonged to this subset. In 13/15 tumours with LOH of 1p36 the lost allele was of maternal origin. This non-random distribution implies that the two alleles of the putative neuroblastoma suppressor gene on chromosome 1p36 are functionally different, depending on their parental origin. This is the first evidence as far as we know for genomic imprinting on chromosome 1p.

Deletion mapping of chromosome 1p and 22q in pheochromocytoma

To identify the localization of tumor suppressor genes, 22 pheochromocytomas (9 hereditary and 13 sporadic) were examined for loss of heterozygosity (LOH) on the short arm of chromosome 1 and on the long arm of chromosome 22 by using 11 polymorphic DNA markers on each chromosome arm. LOH on 1p was observed in 12 of 22 informative cases (55%) and on 22q in 8 of 20 informative cases (40%). There was no significant difference in the frequency of LOH on 1p or 22q between hereditary and sporadic cases. We could localize the commonly deleted regions as distal to D1S73 and proximal to D1S63 on 1p and distal to D22S24 and proximal to D22S1 on 22q. In addition, the relationship between LOH on 1p and 22q was studied in 20 pheochromocytomas which were informative for probes on both chromosome arms. Of eight tumors that showed LOH on 22q, allelic loss on 1p was also detected in seven. Thus, LOH on 22q was correlated significantly with LOH on 1p (P = 0.0249; Fisher's exact test). These results suggest that inactivation of multiple tumor suppressor genes may be required for development and progression of hereditary and non-hereditary pheochromocytoma.

A disease locus for familial hypertrophic cardiomyopathy maps to chromosome 1q3

Familial hypertrophic cardiomyopathy (FHC) is caused by missense mutations in the beta cardiac myosin heavy chain (MHC) gene in less than half of affected individuals. To identify the location of another gene involved in this disorder, a large family with FHC not linked to the beta MHC gene was studied. Linkage was detected between the disease in this family and a locus on chromosome 1q3 (maximum multipoint lod score = 8.47). Analyses in other families with FHC not linked to the beta MHC gene, revealed linkage to the chromosome 1 locus in two and excluded linkage in six. Thus mutations in at least three genetic loci can cause FHC. Three sarcomeric contractile proteins--troponin I, tropomyosin and actin--are strong candidate FHC genes at the chromosome 1 locus.

Exclusion of familial dysautonomia from more than 60% of the genome

Familial dysautonomia (FD) is a recessive neurological disorder that affects the development of the sensory and autonomic nervous system. The gene defect appears to be limited to the Ashkenazi Jewish population, where the carrier frequency is 1 in 30. One hundred and ninety-one marker loci representing all autosomes were tested for linkage with the FD genetic defect in 23 families. A combination of pairwise and multipoint analyses excluded the FD gene from at least 60% of the autosomal genome. The program EXCLUDE predicted regions of chromosomes 2, 4, 5q, 9, or 10 as the most promising locations for future analyses.

Identification and genetic mapping of the murine gene and 20 related sequences encoding chromosomal protein HMG-17

HMG-17 is an abundant, nonhistone chromosomal protein that binds preferentially to nucleosomal core particles of mammalian chromatin. The human gene for HMG-17 has been localized to Chromosome (Chr) 1p, but the murine gene has not been previously mapped. Here we identify the murine functional gene, Hmg17, from among more than 25 related sequences (probably processed pseudogenes) and show that it is located on mouse Chr 4, in a region known to have conserved linkage relationships with human Chr 1p. We also report the map locations of 20 additional Hmg17-related sequences on mouse Chrs 1, 2, 3, 5, 7, 8, 9, 13, 15, 16, 17, 18, and X. The multiple, dispersed members of the Hmg17 multigene family can be detected efficiently with a single cDNA probe and provide useful markers for genetic mapping studies in mice.

Molecular genetics of human malignant melanoma

Due to a variety of known and unknown control mechanisms, the human genome is remarkably stable when compared to most other species. The long latency periods of most solid tumors, during which the cell undergoes malignant transformation, are presumably due to this stability. The molecular basis responsible for the induction of genetic instability and the resultant biological characteristics manifest in tumor populations is not well understood. The discovery of both oncogenes and tumor suppressor genes, however, has placed the phenomenon of human genome stability on a more solid conceptual footing. These types of genes clearly place multiple barriers to oncogenic transformation, and traversing these barriers apparently requires both time and the accumulation of genetic defects that cannot be corrected. The evolution of neoplasias can, therefore, be predicted to be due to: (1) consistent and progressive loss of tumor suppressor genes; (2) gene amplification, resulting in the over-expression of proteins that aid in tumor progression; (3) gene mutation, which alters the orderly biochemistry of the normal cell; (4) genes that allow a cell like the melanocyte to escape the confining nature of the epidermis and to invade through the dermis into the circulatory and lymphatic systems in order to disseminate itself to other organs (e.g., proteolytic enzymes, enzyme inhibitors, integrins, metastases genes, chemotactic factors etc.); (5) factors, perhaps such as TGF beta 2, that may impact negatively on MHC antigens and confuse host defense mechanisms; and (6) S.O.S.-type genes, which may be expressed as a direct response to the accumulating damage in an attempt to correct the damage, but that may then become part of the problem instead of the solution. The extraordinary plasticity and instability of the genome of a melanoma cell suggests an inordinate amount of genetic flux. In addition to activating and inactivating various genes, this constant shuffling and rearranging of the genome in neoplasms such as MM may be constantly altering gene dose. Cytogenetic and molecular biological studies have been the Rosetta stone for understanding the etiological relevant genetic events in human cancers. Genetic alterations fundamental to the pathology of MM have begun to be defined. Studies designed to understand these perturbations at the biochemical and organismic level are underway.(ABSTRACT TRUNCATED AT 400 WORDS)