A cattle-human comparative map built with cattle BAC-ends and human genome sequence

As a step toward the goal of adding the cattle genome to those available for multispecies comparative genome analysis, 40,224 cattle BAC clones were end-sequenced, yielding 60,547 sequences (BAC end sequences, BESs) after trimming with an average read length of 515 bp. Cattle BACs were anchored to the human and mouse genome sequences by BLASTN search, revealing 29.4% and 10.1% significant hits (E < e-5), respectively. More than 60% of all cattle BES hits in both the human and mouse genomes are located within known genes. In order to confirm in silico predictions of orthologyand their relative position on cattle chromosomes, 84 cattle BESs with similarity to sequences on HSA11 were mapped using a cattle-hamster radiation hybrid (RH) panel. Resulting RH maps of BTA15 and BTA29 cover approximately 85% of HSA11 sequence, revealing a complex patchwork shuffling of segments not explained by a simple translocation followed by internal rearrangements. Overlay of the mouse conserved syntenies onto HSA11 revealed that segmental boundaries appear to be conserved in all three species. The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome.     

A comparative map of the zebrafish genome

Zebrafish mutations define the functions of hundreds of essential genes in the vertebrate genome. To accelerate the molecular analysis of zebrafish mutations and to facilitate comparisons among the genomes of zebrafish and other vertebrates, we used a homozygous diploid meiotic mapping panel to localize polymorphisms in 691 previously unmapped genes and expressed sequence tags (ESTs). Together with earlier efforts, this work raises the total number of markers scored in the mapping panel to 2119, including 1503 genes and ESTs and 616 previously characterized simple-sequence length polymorphisms. Sequence analysis of zebrafish genes mapped in this study and in prior work identified putative human orthologs for 804 zebrafish genes and ESTs. Map comparisons revealed 139 new conserved syntenies, in which two or more genes are on the same chromosome in zebrafish and human. Although some conserved syntenies are quite large, there were changes in gene order within conserved groups, apparently reflecting the relatively frequent occurrence of inversions and other intrachromosomal rearrangements since the divergence of teleost and tetrapod ancestors. Comparative mapping also shows that there is not a one-to-one correspondence between zebrafish and human chromosomes. Mapping of duplicate gene pairs identified segments of 20 linkage groups that may have arisen during a genome duplication that occurred early in the evolution of teleosts after the divergence of teleost and mammalian ancestors. This comparative map will accelerate the molecular analysis of zebrafish mutations and enhance the understanding of the evolution of the vertebrate genome.     

Integration of the cytogenetic map with the draft human genome sequence

Chemically staining metaphase chromosomes resulting in an alternating dark and light banding pattern provide a tool by which abnormalities in chromosomes from diseased cells can be identified. The localization of these aberrations to a chromosomal region provides clues as to which gene or genes may contribute to a particular disease. With the sequencing of the human genome, it became critical to determine the positions of these cytogenetic bands within the sequence in order to take advantage of vast amount of information now anchored to the sequence, especially the locations of genes. The molecular basis of cytogenetic bands is not well understood, therefore their positions cannot be determined solely based on sequence information. We developed a dynamic programming algorithm that employs results from approximately 9500 fluorescence in situ hybridization experiments to approximate the locations of the 850 high-resolution bands in the June 2002 version of the draft human genome sequence. These band predictions support previously identified correlations between band stain intensity and certain structural characteristics of chromosomes, namely GC content, repeat structure content, CpG island density, gene density and degree of condensation.     

A radiation hybrid map of the human genome

We have developed a panel of whole-genome radiation hybrids by fusing irradiated diploid human fibroblasts with recipient hamster cells. This panel of 168 cell lines has been typed with microsatellite markers of known genetic location. Of 711 AFM genetic markers 404 were selected to construct a robust framework map that spans all the autosomes and the X chromosome. To demonstrate the utility of the panel, 374 expressed sequence tags (ESTs) previously assigned to chromosomes 1, 2, 14 and 16 were localized on this map. All of these ESTs could be positioned by pairwise linkage to one of the framework markers with a LOD score of greater than 8. The whole genome radiation hybrid panel described here has been used as the starting material for the Genebridge4 panel that is being made widely available for genome mapping projects.      

强直性脊柱炎家系全基因组扫描基因定位的荟萃分析

目的 综合分析强直性脊柱炎（ankylosing spondylitis,AS）家系的全基因组扫描基因定位的结果,探讨进一步研究和确定AS的遗传易感位点的思路和方法.方法 采用基因组寻证荟萃分析（genome search meta analysis,GSMA）法,对符合该方法分析的4个AS家系的全基因组扫描结果包括参数连锁分析和非参数连锁分析的结果进行分析.根据连锁分析的最大值被赋值并按降序排列,从而计算出总的等级分值（Rsumrnk）.根据每个研究的受累个体数进行加权GSMA对结果进行修正.本研究共有479个家系,1151例AS患者.总的等级分析概率（Psumrnk）和有序的等级分析概率（Pord）＜0.05被认为可能含有易感区域;GSMA Psumrnk＜0.000417时,被认为在全基因组连锁中有显著意义.结果 GSMA显示10组结果的Psumrnk和Pord均小于0.05,表明这些组内最可能含有AS的易感基因位点,这些组分别是6.2、16.3、6.1、3.3、6.3、16.4、10.5、17.1、2.5、2.9.GSMA生成的具有显著意义的全基因组连锁分析的证据位于6p22.3-p21.1（BIN6.2,Psumrnk＜0.000417）,包含HLA位点.结论 本GSMA研究进一步证实了HLA位点是AS的主要易感区域,并初步提供非HLA区域包括16 q,3 p,10 q,2 p,17 p和2 q证据.     

强直性脊柱炎家系全基因组扫描基因定位的荟萃分析

目的 综合分析强直性脊柱炎(ankylosing spondylitis,AS)家系的全基因组扫描基因定位的结果,探讨进一步研究和确定AS的遗传易感位点的思路和方法.方法 采用基因组寻证荟萃分析(genome search meta analysis,GSMA)法,对符合该方法分析的4个AS家系的全基因组扫描结果包括参数连锁分析和非参数连锁分析的结果进行分析.根据连锁分析的最大值被赋值并按降序排列,从而计算出总的等级分值(Rsumrnk).根据每个研究的受累个体数进行加权GSMA对结果进行修正.本研究共有479个家系,1151例AS患者.总的等级分析概率(Psumrnk)和有序的等级分析概率(Pord)＜0.05被认为可能含有易感区域;GSMA Psumrnk＜0.000417时,被认为在全基因组连锁中有显著意义.结果 GSMA显示10组结果的Psumrnk和Pord均小于0.05,表明这些组内最可能含有AS的易感基因位点,这些组分别是6.2、16.3、6.1、3.3、6.3、16.4、10.5、17.1、2.5、2.9.GSMA生成的具有显著意义的全基因组连锁分析的证据位于6p22.3-p21.1(BIN6.2,Psumrnk＜0.000417),包含HLA位点.结论 本GSMA研究进一步证实了HLA位点是AS的主要易感区域,并初步提供非HLA区域包括16 q,3 p,10 q,2 p,17 p和2 q证据.     

A second-generation combined linkage physical map of the human genome

We have completed a second-generation linkage map that incorporates sequence-based positional information. This new map, the Rutgers Map v.2, includes 28,121 polymorphic markers with physical positions corroborated by recombination-based data. Sex-averaged and sex-specific linkage map distances, along with confidence intervals, have been estimated for all map intervals. In addition, a regression-based smoothed map is provided that facilitates interpolation of positions of unmapped markers on this map. With nearly twice as many markers as our first-generation map, the Rutgers Map continues to be a unique and comprehensive resource for obtaining genetic map information for large sets of polymorphic markers.     

A radiation hybrid map of the cat genome: implications for comparative mapping

Ordered gene maps of mammalian species are becoming increasingly valued in assigning gene variants to function in human and animal models, as well as recapitulating the natural history of genome organization. To extend this power to the domestic cat, a radiation hybrid (RH) map of the cat was constructed integrating 424 Type I-coding genes with 176 microsatellite markers, providing coverage over all 20 feline chromosomes. Alignment of parallel RH maps of human and cat reveal 100 conserved segments ordered (CSOs) between the species, nearly three times the number observed with reciprocal chromosome painting analyses. The observed number is equivalent to theoretical predictions of the number of conserved segments to be found between cat and human, implying that 300-400 Type I gene markers is sufficient to reveal nearly all conserved segments for species that exhibit the most frequently observed "slow" rate of genome reorganization. The cat-human RH map comparisons provide a new genomic tool for comparative gene mapping in the cat and related Felidae, and provide confirmation that the cat genome organization is remarkably conserved compared with human. These data demonstrate that ordered RH-based gene maps provide the most precise assessment of comparing genomes, short of contig construction or full-sequence determination.     

A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping

The mapping of Hox clusters and many duplicated genes in zebrafish indicated an extra whole-genome duplication in ray-fined fish. However, to reconstruct the preduplication chromosomes (proto-chromosomes), the comparative genomic studies of more distantly related teleosts are essential. Medaka and zebrafish are ideal for this purpose, because their lineages separated from their last common ancestor approximately 140 million years ago. To reconstruct ancient vertebrate chromosomes, including the chromosomes of the vertebrate ancestor of humans from 450 million years ago, we mapped 818 genes and expressed sequence tags (ESTs) on a single meiotic backcross panel obtained from inbred strains of the medaka, Oryzias latipes. Comparisons of linkage relationships of orthologous genes among three species of vertebrates (medaka, zebrafish, and human) indicate the number and content of the chromosomes of the last common ancestor of ray-fined fish and lobe-fined fish (including humans), and the extra whole genome duplication event in the ray-fin lineage occurred in the common ancestor of perhaps all teleosts.     

A comparative gene map of the horse (Equus caballus)

A comparative gene map of the horse genome composed of 127 loci was assembled based on the new assignment of 68 equine type I loci and on data published previously. PCR primers based on consensus gene sequences conserved across mammalian species were used to amplify markers for assigning 68 equine type I loci to 27 horse synteny groups established previously with a horse-mouse somatic cell hybrid panel (SCHP, UC Davis). This increased the number of coding genes mapped to the horse genome by over 2-fold and allowed refinements of the comparative mapping data available for this species. In conjunction with 57 previous assignments of type I loci to the horse genome map, these data have allowed us to confirm the assignment of 24 equine synteny groups to their respective chromosomes, to provisionally assign nine synteny groups to chromosomes, and to further refine the genetic composition established with Zoo-FISH of two horse chromosomes. The equine type I markers developed in this study provide an important resource for the future development of the horse linkage and physical genome maps.     

A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics

Comparative nematode genomics has thus far been largely constrained to the genus Caenorhabditis, but a huge diversity of other nematode species, and genomes, exist. The Brugia malayi genome is approximately 100 Mb in size, and distributed across five chromosome pairs. Previous genomic investigations have included definition of major repeat classes and sequencing of selected genes. We have generated over 18,000 sequences from the ends of large-insert clones from bacterial artificial chromosome libraries. These end sequences, totalling over 10 Mb of sequence, contain just under 8 Mb of unique sequence. We identified the known Mbo I and Hha I repeat families in the sequence data, and also identified several new repeats based on their abundance. Genomic copies of 17% of B. malayi genes defined by expressed sequence tags have been identified. Nearly one quarter of end sequences can encode peptides with significant similarity to protein sequences in the public databases, and we estimate that we have identified more than 2700 new B. malayi genes. Importantly, 459 end sequences had homologues in other organisms, but lacked a match in the completely sequenced genomes of Caenorhabditis briggsae and Caenorhabditis elegans, emphasising the role of gene loss in genome evolution. B. malayi is estimated to have over 18,500 protein-coding genes.     

Cytogenetic alignment of the bovine chromosome 13 genome map by fluorescence in-situ hybridization of human chromosome 10 and 20 comparative markers

A bovine bacterial artificial chromosome (BAC) library was screened for the prescence of six genes (IL2RA, VIM, THBD, PLC-II, CSNK2A1 and TOP1) previously assigned to human chromosomes 10 or 20 (HSA10 or HSA20). Four of the genes were found repesented in the bovine BAC library by at least one clone. The identified BAC clones were used as probes in single-color fluorescence in-situ hybridization (FISH) to determine the chromosomal band location of each gene. As predicted by the human/bovine comparative map and comparative chromosome painting analysis, the four genes mapped to bovine chromosome 13 (BTA13). Dual-color FISH was then used to integrate these four type I markers into the existing BTA13 genome map. These FISH results anchor the BTA13 genome map from bands 14–23, and confirm the presence of a conserved HSA10 homologous synteny group on BTA13 centromeric to a HSA20 homologous segment. This revised version was published online in July 2006 with corrections to the Cover Date.     

A human cell-surface antigen defined by a monoclonal antibody and controlled by a gene on human chromosome 1

An antigen expressed by most human cells, but not erythrocytes, has been defined by a murine monoclonal antibody, TRA-2–10. This antigen is expressed on the surface of human-mouse somatic cell hybrids, and segregation analysis indicates that it is controlled by a gene located on human chromosome 1. From lysates of most human cells, surface-labelled with ¹²⁵I, TRA-2–10 immunoprecipitates two polypeptides with molecular weights in the range of about 55000 to 73000 depending upon the cell line. Since the TRA-2–10 polypeptides from a fibroblast cell strain and a hepatoma cell line from one individual differ, we conclude that the observed difference in molecular weight has an epigenetic origin.     

BLOCK-based PCR markers to find gene family members in human and comparative genome analysis

Degenerate primer pairs that include consensus sequences ofevolutionary conserved portions of protein families (BLOCKsor ancient conserved regions) can be used to screen by polymerasechain reaction (PCR) for cognate cDNAs and YACs through muchof phylogeny. Nine such primer pairs were developed, and fivewith sites on human chromosomes 7 or X were shown to identifyYACs from chromosome-specific locations, including a candidatefor a new zinc finger gene in Xq28. When linked to contig-basedgenomic maps, such BLOCK-based PCR assays may provide a routeto recover the members and study the development of familiescontaining up to 40% of genes, In genomes as diverse as humans,nematodes, and yeast.     

A gene dosage map of Chromosome 18: A map with clinical utility

PurposeMicroarray technology has revolutionized the field of clinical genetics with the ability to detect very small copy number changes. However, challenges remain in linking genotype with phenotype. Our goal is to enable a clinical geneticist to align the molecular karyotype information from an individual patient with the annotated genomic content, so as to provide a clinical prognosis.MethodsWe have combined data regarding copy number variations, microdeletion syndromes, and classical chromosome abnormalities, with the sparse but growing knowledge about the biological role of specific genes to create a genomic map of Chromosome 18 with clinical utility.ResultsWe have created a draft model of such a map, drawing from our long-standing interest in and data regarding the abnormalities of Chromosome 18.ConclusionWe have taken the first step toward creating a genomic map that can be used by the clinician in counseling and directing preventive or symptomatic care of individuals with Chromosome 18 abnormalities.     

A human cell-surface antigen defined by a monoclonal antibody and controlled by a gene on chromosome 12

A murine monoclonal antibody 602-29, subclass IgG1, that recognizes an antigenic determinant expressed by most human cells is described. Immunoprecipitation and sodium dodecyl sulfate-gel electrophoresis analysis indicate that the antigenic determinant is carried by a protein with an apparent molecular weight of 21,000. The antigen is expressed by human-mouse somatic cell hybrids, and analysis of segregants that have lost human chromosomes indicates that the gene controlling expression of the 602-29 antigen is on chromosome 12.     

Linking the human cytogenetic map with nucleotide sequence: the CCAP clone set

We present the completed dataset and clone repository of the Cancer Chromosome Aberration Project (CCAP), an initiative developed and funded through the intramural program of the U.S. National Cancer Institute, to provide seamless linkage of human cytogenetic markers with the primary nucleotide sequence of the human genome. Spaced at 1-2 Mb intervals across the human genome, 1,339 bacterial artificial chromosome (BAC) clones have been localized to chromosomal bands through high-resolution fluorescence in situ hybridization (FISH) mapping. Of these clones, 99.8% can be positioned on the primary human genome sequence and 95% are placed at or close to their precise nucleotide starts and stops. This dataset can be studied and manipulated within generally available public Web sites. The clones are available from a commercial repository. The CCAP BAC clone set provides anchors for the interrogation of gene and sequence involvement in oncogenic and developmental disorders when the starting point is the recognition of a structural, numerical, or interstitial chromosomal aberration. This dataset also provides a current view of the quality and coherence of the available genome sequence and insight into the nucleotide and three-dimensional structures that manifest as Giemsa light and dark chromosomal banding patterns.     

A human X-linked antigen defined by a monoclonal antibody

We have constructed hybrids between human thymocytes and the mouse thymoma BW5147. These hybrids, and others, have been used to show that the expression of a thymocyte antigen is controlled by an X-linked gene.