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Several projects have produced maps of the physical position of genes within the human genome, either on a genome-wide scale or of a more detailed subsection of a chromosome. However, these maps largely rely on the mapping of expressed sequences (cDNAs and ESTs) back onto physical maps by their localization onto specific fragments of DNA within the radiation hybrid panels. In this report we present a gene map of a section of chromosome 19 that has been derived by combining the use of a method of gene identification (exon trapping) that does not rely on expression patterns, with data available in the genome databases to produce a fine-detailed transcript map. This map also provides several potential candidates for disorders that map to this region of the genome. Details of the maps and more detailed descriptions of cosmid contigs, exon sequences, and expression patterns for the 96 exons that form the basis of this transcript map are available on a series of Web pages that are referenced in this report. These Web pages can be accessed from http://www.nottingham.ac.uk/~pdzmgh/tm/livemap19q.html .

Mice from the MRL strain are prone to develop systemic lupus erythematosus (SLE) and have demonstrated accelerated wound healing and scarless tissue regeneration; however, many of the mechanisms involved in these clinically relevant pathologies are unclear. Prior studies have described macrophage accumulation and functional defects in mice prone to lupus. Monocyte-macrophages have also been shown to have a high degree of plasticity. To determine whether there might be innate differences in the hematopoietic systems of MRL mice, we evaluated hematopoietic progenitor cell content in a variety of tissues and the proliferative responses of derived marrow and thioglycolate (TG)-elicited peritoneal macrophages. Our experiments reveal that MRL mice have significantly lower numbers of circulating blood leukocytes and platelets. Even more strikingly, we found that MRL blood and marrow contain an unusually robust number of unique and assayable macrophage colony-stimulating factor responsive cells which have the characteristics of macrophage colony-forming cell precursors. In culture, in contrast to cells derived from control C57BL/6 mice, this cell type and thioglycolate-elicited peritoneal macrophages from MRL mice can be extensively expanded with just macrophage colony-stimulating factor to acquire an in situ “f-mac-like” (see Y. Zhao, D. Glesne and E. Huberman, A human peripheral blood monocyte-derived subset acts as pluripotent stem cells. Proc. Natl. Acad. Sci. U.S.A. 100, (2003) 2426–2431.) morphology when plated on plastic surfaces. Our results suggest that these increased numbers of macrophage progenitor cells and their potential differentiation plasticity may play a functional role in the onset of systemic lupus erythematosus and may also contribute to the accelerated and scarless tissue regenerative repair response observed in MRL mice.

The relationship between gene expression profiles and cellular behavior in humans is largely unknown. Expression patterns of individual cell types have yet to be precisely measured, and, at present, we know or can predict the function of a relatively small percentage of genes. However, biomedical research is in the midst of an informational and technological revolution with the potential to increase dramatically our understanding of how expression modulates cellular phenotype and response to the environment. The entire sequence of the human genome will be known by the year 2003 or earlier. 1, 2 In concert, the pace of efforts to complete identification and full-length cDNA sequencing of all genes has accelerated, and these goals will be attained within the next few years. 3, 4, 5, 6, 7 Accompanying the expanding base of genetic information are several new technologies capable of global gene expression measurements. 8, 9, 10, 11, 12, 13, 14, 15, 16 Taken together, the expanding genetic database and developing expression technologies are leading to an exciting new paradigm in biomedical research known as molecular profiling.

The laboratory mouse is the premier model system for studies of mammalian development due to the powerful classical genetic analysis1 possible (see also the Jackson Laboratory web site, http://www.jax.org/ ) and the ever–expanding collection of molecular tools2,3. To enhance the utility of the mouse system, we initiated a program to generate a large database of expressed sequence tags (ESTs) that can provide rapid access to genes4,5,6,7,8,9,10,11,12,13,14,15,16. Of particular significance was the possibility that cDNA libraries could be prepared from very early stages of development, a situation unrealized in human EST projects7,12. We report here the development of a comprehensive database of ESTs for the mouse. The project, initiated in March 1996, has focused on 5´ end sequences from directionally cloned, oligo–dT primed cDNA libraries. As of 23 October 1998, 352,040 sequences had been generated, annotated and deposited in dbEST, where they comprised 93% of the total ESTs available for mouse. EST data are versatile and have been applied to gene identification17, comparative sequence analysis18,19, comparative gene mapping and candidate disease gene identification20, genome sequence annotation21,22, microarray development23 and the development of gene–based map resources24.

The hASNA-I is a novel human arsenite-stimulated ATPase identified as the human paralogue of the ATPase component of the arsenite efflux system in E. coli. The hASNA-I has distinct biochemical properties and a dual nuclear and cytoplasmic distribution. Immunohistochemical staining showed a distinct pattern of hASNA-I expression in cells within normal tissues, and its overexpression in breast cancer. Recently, the yeast two-hybrid system has identified hASNA-I as a cellular partner of metallothionein II suggesting an additional role in Zn homeostasis and cellular detoxification. This report describes the assignment of hASNA-I to human chromosome 19 by somatic-cell hybrid PCR mapping, the isolation of a chromosome 19-specific cosmid clone, and the genomic structure and exon-intron boundaries of hASNA-I. Our results indicate that the coding region of hASNA-I consists of 4 exons spanning 6 kb on band 19q13.3. These data will facilitate molecular analysis of the role of hASNA-I in human disease.

The amino acid hypusine is formed post-translationally in a single cellular protein, the eukaryotic translation initiation factor 5A, by two enzymes, namely deoxyhypusine synthase and deoxyhypusine hydroxylase. Hypusine is found in all eukaryotes and in some archaebacteria, but not in eubacteria. The deoxyhypusine synthase cDNA was cloned and mapped by fluorescence in situ hybridization on chromosome 19p13.11-p13.12. Rare cDNAs containing internal deletions were also found. We localized the deoxyhypusine synthase gene on a high resolution cosmid/BAC contig map of chromosome 19 to a region in 19p13.2-distal 19p13.1 between MANB and JUNB. Analysis of the genomic exon/intron structure of the gene coding region showed that it consists of nine exons and spans a length of 6.6 kb. From observation of the genomic structure, it seems likely that the internally deleted forms of mature RNA are the result of alternative splicing, rather than of artifacts.

In a systematic effort for mapping of all the human ribosomal protein (rp) genes, we have found that an unusually large number (12) of rp genes are present on chromosome 19 and subsequently determined their locations on the chromosome by a radiation-hybrid procedure. For this, we isolated cosmid clones corresponding to each gene and placed nine of them on a metric physical map of chromosome 19. Although most genes are scattered over the chromosome, we found three genes are clustered in a 0.6-Mb region at 19q13.3 and two of them, RPL13A and RPS11, within a single cosmid only 4.3 kb apart. To explore a possible relationship between rp gene defects and human disease, we compared map positions of the rp genes and disease loci on chromosome 19, which led us to find RPS9 gene in the same interval as the gene for retinitis pigmentosa 11. The disease locus has previously been mapped to the 6-cM interval at 19q13.4 between markers D19S572 and D19S926, which corresponds to less than 2-Mb region on the metric physical map. We mapped RPS9 about 800 kb distal to D19S572.

Several studies have proposed the existence of susceptibility loci for bipolar disorder on chromosome 18. To identify possible candidate genes for this disease, we isolated brain-expressed transcripts by direct cDNA selection on chromosome 18-specific biotinylated cosmid clones. Longer cognate cDNA clones of the selected cDNAs were isolated from a normalized infant brain cDNA library. Physical mapping by PCR on a panel of somatic cell hybrids was conducted by the use of primers derived from partial sequences on either the 5' or 3' ends of the clones. In our initial analysis, 48 cDNA clones were found to be chromosome 18-specific, mapping to different subchromosomal regions. Sequence redundancy among these clones yielded 30 unique transcripts, five of which were represented in previously known genes. Further sequencing of the remaining 25 unique cDNA clones confirmed the absence of significant homology to known genes, indicating that these transcripts represented novel genes. Mapping with the use of a radiation hybrid panel positioned the brain cDNAs to within = 100 to 1100 kb from reference sequence tag sites (STSs) and assembled them into six high resolution linkage groups. The majority of the transcripts were found to cluster to discrete locations on 18p and 18q, previously hypothesized as susceptibility regions for bipolar disorder, identifying them as positional candidate genes.

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching.[All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.]

Tottering and leaner, two mutations of the mouse tottering locus, have been studied extensively as models for human epilepsy. Here we describe the isolation, mapping, and expression analysis of Cacnl1a4, a gene encoding the alpha subunit of a proposed P-type calcium channel, and also report the physical mapping and expression patterns of the orthologous human gene. DNA sequencing and gene expression data demonstrate that Cacnl1a4 mutations are the primary cause of seizures and ataxia in tottering and leaner mutant mice, and suggest that tottering locus mutations and human diseases, episodic ataxia 2 and familial hemiplegic migraine, represent mutations in mouse and human versions of the same channel-encoding gene.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al., [Background]: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. [Results]: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. [Conclusions]: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups., This work was supported by funds provided through the Gene Partnership and the Manton Center for Orphan Disease Research at Boston Children’s Hospital and the Center for Biomedical Informatics at Harvard Medical School and by generous donations in-kind of genomic sequencing services by Life Technologies (Carlsbad, CA, USA) and Complete Genomics (Mountain View, CA, USA).

Eleven unique cDNA fragments were identified from YAC B30H3, which spans 330 kb in the human major histocompatibility complex class I region. One fragment (CAT80) was mapped 80 kb telomeric to the HLA-A locus. Using this cDNA fragment as probe, Northern analysis reveals a ubiquitously expressed transcript of about 850 nt in all 16 tissues tested. Based on the cDNA fragment sequence, a full-length cDNA of 858 bp that contains an open reading frame of 378 bp was cloned. Within the putative polypeptide of 126 amino acids, two zinc-ribbon domains were identified: Cx2Cx15Cx2C at the N-terminal and Cx2Cx24Cx2C at the C-terminal. The C-terminal domain is well conserved throughout evolution, including archaea, yeast, Drosophila, nematodes, amphibians, and mammals. The conserved amino acid sequence, CxRCx6Yx3QxRSADEx2TxFxCx2C, is highly homologous to the yeast RNA polymerase A subunit 9 and transcription-associated proteins. Alignment with genomic DNA demonstrates that this gene spans 3.6 kb and consists of four exons and three introns. Cross-species Northern analysis reveals a mouse homolog of a similar size and with an expression profile similar to those of the human gene. We have named this gene ZNRD1 for zinc ribbon domain-containing 1 protein.

The intron-containing gene for human ribosomal protein RPL23A has been cloned, sequenced, and localized. The gene is approximately 4.0 kb in length and contains five exons and four introns. All splice sites exactly match the AG/GT consensus rule. The transcript is about 0.6 kb and is detected in all tissues examined. In adult tissues, the RPL23A transcript is dramatically more abundant in pancreas, skeletal muscle, and heart, while much less abundant in kidney, brain, placenta, lung, and liver. A full-length cDNA clone of 576 nt was identified, and the nucleotide sequence was found to match the exon sequence precisely. The open reading frame encodes a polypeptide of 156 amino acids, which is absolutely conserved with the rat RPL23A protein. In the 5' flanking region of the gene, a canonical TATA sequence and a defined CAAT box were found for the first time in a mammalian ribosomal protein gene. The intron-containing RPL23A gene was mapped to cytogenetic band 17q11 by fluorescence in situ hybridization.

CAG and CGG expansion is associated with 10 inherited neurological diseases and is thought to be involved in other human genetic diseases. To identify new candidate genes, we have undertaken a large-scale screening project for CAG/CTG ([CAG] n ) and CGG/GCC ([CGG] n ) repeats in human brain reference cDNAs. Here, we present the final classification for 597 cDNAs selected by CAG and CGG hybridization from two libraries (100,128 clones) and the updated characterization of [CAG] n - and [CGG] n -positive cDNAs (repeat polymorphism and cDNA localization). We have selected 124 CAG and 83 CGG hybridization-positive clones representing new genes, from which 49 CAG and 7 CGG repeats could be identified. New [CAG] n and [CGG] n with more than seven to nine units were rare (1/2000), and perfect [CAG] n 9 were more likely polymorphic. Overall, highly polymorphic to monomorphic new [CAG] n > 9 and [CGG] n > 7 were characterized. The comparison of our data with other [CAG] n and [CGG] n resources suggests that the screening of reference cDNAs leads to unique sources of new [CAG] n and [CGG] n and will enhance the study of enlarged triplet repeats in human genetic diseases.

Choroidoretinal dystrophies are incurable and essentially untreatable, representing the most common cause of genetic visual loss in childhood (1). They are a clinically and genetically heterogeneous group of disorders. Dystrophies which primarily affect rod function such as retinitis pigmentosa have been extensively studied and a number of genes have been implicated in the disease pathogenesis (2). In contrast dystrophies which primarily affect cone photoreceptors have been less well studied and examples of this group of diseases includes cone dystrophies and cone-rod dystrophies. Cone dystrophies are characterised by photophobia, loss of visual acuity and colour vision defects associated with reduced cone photoreceptor ERG responses. Abnormal pigmentation with atrophy is often seen at the macula. Cone-rod dystrophies are distinct from cone dystrophies in that abnormalities of cone dysfunction is seen with progressive peripheral retinal disease. Diminished visual acuity and loss of colour discrimination is followed by nyctalopia, progressive peripheral visual field deficit and decreasing rod photoreceptor ERG amplitudes from an early age. Advancing chorioretinal atrophy of the central and peripheral retina is characteristic (3). Autosomal dominant, recessive and X-linked patterns of inheritance for cone dystrophies and cone-rod dystrophy (CRD) have been described and studies have implicated a number of loci for the disease-causing genes. Loci associated with cone dystrophies include a balanced translocation on chromosome 6q which was reported in a patient with mental retardation and cone dystrophy (4), an X-linked cone dystrophy mapping to Xp21.1–p11.3 (5) and two independent studies have used linkage analysis to identify an autosomal dominant cone dystrophy locus on chromosome 17p (6–7). Loci implicated in CRD include two case reports that have suggested localisation of CRD genes on chromosome 18q (8) and 17q (9), an autosomal dominant form of CRD mapping to chromosome 19q (10) and a transverse mutation in the peripherin/RDS gene (Asn244His) has been found in one Japanese CRD family (11).

We isolated the human homologue, SUPT5H, of the yeast transcription factor, SPT5. The human homologue is 1088 aa long compared to 1063 aa for the yeast gene. SUPT5H maps to 19q13, near the ryanodine receptor. Like its family member, SUPT6H, and like yeast SPT5, SUPT5H has a very acidic 5' domain. Like its family member, SUPT6H, but unlike yeast SPT5 or SPT6, SUPT5H has seven MAP kinase sites at its 5' end. In addition, SUPT5H lacks the novel 6-amino-acid repeat (consensus is S-T/A-W-G-G-A/Q) at the C-terminus of yeast SPT5. This argues that while there is functional similarity between SPT5 and SUPT5H, the molecules differ in the signals to which they respond.

We describe an effort to share resources such that the maximum amount of gene-related data is obtained with the last redundancy. Specifically, we describe the I.M.A.G.E. Consortium effort to share arrayed cDNA libraries, to have the data derived from the use of these common reagents placed in public databases, and to use these data to create master arrays containing a representative cDNA clone from each gene. 8 refs.

We have used exon amplification to identify putative transcribed sequences from an 823-kb contig consisting of 28 cosmids that form a minimum tiling path from the interval 19p12-p13.1. This region contains the genes responsible for multiple epiphyseal dysplasia (MED) and pseudoachondroplasia (PSACH). We have trapped 66 exons (an average of 2.4 exons per cosmid) from pools of 2 or 3 cosmids. The majority of exons (51.5%) show only weak similarity or no similarity (36.3%) to sequences in current databases. Six of 8 exons examined from these groups, however, show cross-species sequence conservation, indicating that many of them probably represent authentic exons. Eight exons show identity or significant similarity to ESTs or known genes, including the human TNF receptor 3{prime}-flanking region gene, human epoxide hydrolase (EPHX), human growth/differentiation factor (GOF-1), human myocyte-specific enhancer factor 2, the rat neurocan gene, and the human cartilage oligomeric matrix protein gene (COMP). Mutations in this latter gene have recently been shown to be responsible for MED and PSACH. 33 refs., 4 figs., 2 tabs.

International audience; Expansion of polymorphic CAG and CTG repeats in transcripts is the cause of six inherited origin. neurodegenerative or neuromuscular diseases and may be involved in several other genetic disorders of the central nervous system. To identify new candidate genes, we have undertaken a large-scale screening project for CAG and CTG repeats in human reference cDNAs. We screened 100 128 brain cDNAs by hybridization. We also scanned GenBank expressed sequence tags for the presence of long CAG/CTG repeats in the extremities of cDNAs from several human tissues, Of the selected clones, 286 were found to represent new genes, and 72 have thus far been shown to contain CAG/CTG repeats, Our data indicate that CAG/CTG repeated 10 or more times are more likely to be polymorphic, and that new 3'-directed cDNAs with such repeats are very rare (1/2862). Nine new cDNAs containing polymorphic (observed heterozygote frequency: 0.05-0.90) CAG/CTG repeats have been currently identified in cDNAs, Ail of the cDNAs have been assigned to chromosomes, and six of them could be mapped with YACs to 1q32-q41, 3p14, 4q28, 3p21 and 12q13.3, 13q13.1-q13.2, and 19q13.43, Three of these clones are highly polymorphic and represent the most likely candidate genes for inherited neurodegenerative diseases and, perhaps, neuropsychiatric disorders of multifactorial origin.

We report the construction of a high-resolution physical map of a 17-Mb region that encompasses the entire q12, q13.1, and q13.2 bands of human chromosome 19. The continuous map extends from a region approximately 400 kb centromeric of the D19S7 marker to the excision repair cross-complementing rodent repair deficiency complementation group 1 (ERCC1) locus. The ordered clone map has been obtained starting from a foundation of cosmid contigs assembled by automated fingerprinting and localized to the cytogenetic map by fluorescence in situ hybridization (FISH). Clonal continuity of the map has been achieved by binning and linking the premapped cosmid contigs by means of yeast artificial chromosomes (YACs). The map consists of a single contig composed of 169 YAC members (minimal spanning path of 18 YACs) linking 165 cosmid contigs. Eighty percent, or about 13.2 Mb of the entire region spanned by the map, has been resolved to the EcoRI restriction map level. Twenty-nine sequence-tagged sites associated with genetic markers or derived from FISH-mapped cosmids have been placed on the map. In addition to the ERCC1 gene area, the map includes the location of the creatine kinase muscle locus (CKM), imidazoledipetidase (PEPD), glucophosphate isomerase (GPI), myelin-associated glycoprotein (MAG), the apolipoprotein E and C (APOE and APOC) genes, and the ryanodine receptor (RYR1) gene. This type of map provides a source of continuously overlapping DNA segments at a level of resolution two orders of magnitude higher than that obtained using YACs alone. In addition, it provides ready-to-use reagents for detailed analyses at the gene level, FISH studies of chromosomal aberrations, and DNA sequencing.

By adapting a commercially available, general purpose laboratory robot, it is possible to produce high-density gridded hybridization filters of clone colonies or DNA products. We are using this system to produce 60-90, 8 x 12 cm filters in an 8-hour day, each containing 3,456 clones arranged in 96, 6 x 6 grids.

The mapping position of human endopeptidase 24.15 (THOP1) has previously been reported to be within the linkage region for the late-onset Alzheimer disease AD2 locus on chromosome 19q13.3. After localizing THOP1 to the high-resolution cosmid contig map of human chromosome 19, we found that the previous report was incorrect. Results of the hybridization and FISH mapping of positive clones indicated localization of THOP1 to chromosome 19p13.3 and not 19q13. 3. This localization is a correction of wrong chromosomal delegation and excludes THOP1 from the region that shows evidence of linkage to late-onset familial Alzheimer disease.

We have determined the genome-wide gene expression profile of Hodgkin disease, the most common cancer of young adult Americans. Sequences were obtained from approximately 40,000 ESTs (20,000,000 bases) from Hodgkin disease sources. These included cell lines, primary tissue and living, single Reed-Sternberg cells — the exceedingly rare but biologically active malignant cell of Hodgkin lymphoma. Results of the high throughput sequencing increased the number of named, expressed genes in Hodgkin disease from 100 to 2666. We devised an algorithm to globally compare the gene expression profile of Hodgkin's disease to 100,000 ESTs from different hematopoetic cell types. The analysis supports a B cell lineage of the elusive Reed-Sternberg cell and provides a public database of the gene expression profile of Hodgkin lymphoma1 (http://www.hodgkins.georgetown.edu).