Cosmid assembly and anchoring to human chromosome 21

Soeda, Eiichi; Hou, De‐Xing; Osoegawa, Kazutoyo; Atsuchi, Yasuo; Yamagata, Tetsushi; Shimokawa, Takanori; Kishida, Haruo; Soeda, E.; Okano, Satoshi; Chumakov, Ilya; Cohen, Daniel; Raff, Malcolm; Gardiner, Katheleen; Graw, Sharon; Patterson, David; Jong, Pieter J. de; Ashworth, Linda K.; Slezak, Tom; Carrano, A.V.

doi:10.1016/0888-7543(95)80111-x

Cited by 40 publications

(29 citation statements)

References 31 publications

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“…Cosmids taken at random from the chromosome 21-specific library LL21NCO2-Q (Soeda et al 1995) were used for identification of genes throughout the entire chromosome. A total of 1194 cosmids were used.…”

Section: Resultsmentioning

confidence: 99%

Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.

Chen

Chrast²,

Rossier³

et al. 1996

Genome Res.

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Chromosome 21 represents -1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes {YACs} and cosmids have been developed. We have used exon trapping to identify portions of genes from randomly picked chromosome 21-specific cosmids, to contribute to the creation of the transcription [genic} map of this chromosome and the cloning of its genes. A total of 559 different sequences were identified after elemination of false-positive clones and repetitive elements. Among these, exons for 13 of the 30 known chromosome 21 genes have been "trapped." In addition, a considerable number of trapped sequences showed homologies to genes from other species and to human expressed sequence tags [ESTs}. One hundred thirty-three trapped sequences were mapped, and every one mapped back to chromosome 21. We estimate that we have identified portions of up to -40% of all genes on chromosome 21. The genic map of chromosome 21 provides a valuable tool for the elucidation of function of the genes and will enhance our understanding of the pathophysiology of Down syndrome and other disorders of chromosome 21 genes.

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Section: Resultsmentioning

confidence: 99%

Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.

Chen

Chrast²,

Rossier³

et al. 1996

Genome Res.

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“…Although this region of Chr. 21 is covered by YAC maps (Chumakov et al 1992;Gardiner et al 1995;Korenberg et al 1995) and almost completely converted to sequence-ready template (Soeda et al 1995;Hubert et al 1997), marker spacing in human has not been measured accurately. It will be interesting to determine the basis for differences in the physical map at the sequence level in areas where there is no discrepancy in gene content or order.…”

Section: Discussionmentioning

confidence: 99%

Physical and Comparative Mapping of Distal Mouse Chromosome 16

Cabin¹,

McKee-Johnson²,

Matesic³

et al. 1998

Genome Res.

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Distal mouse Chromosome 16 (Chr. 16) includes a region of conserved linkage with human Chromosome 21 (Chr. 21). Mouse models of Down syndrome based on trisomy of distal Chr. 16 have several phenotypes similar to those seen in human patients and have proven useful for correlating dosage imbalance of specific genes with specific developmental anomalies. The degree to which such findings can be related to Down syndrome depends on how well the conserved synteny is maintained. Twenty-four genes have been mapped in both species and there are no discordancies, but the region could carry hundreds of genes. Comparative sequence represents the ultimate comparative map and will aid in identification of genes and their regulatory sequences. A physical map of the distal 4.5 Mb of Chr. 16 has been assembled as an essential step toward a map of sequence-ready templates. The map consists of 51 YACs and 15 BACs and includes 18 transcripts, 9 of which are mapped for the first time in mouse, and 3 of which are, for the first time, described in either species. YAC fragmentation was used to precisely localize the 49 markers on the map. Comparison of this physical map with that of the corresponding region on Chr. 21 shows conservation not only of gene order but of size in the 3 Mb fromCbr1 to Ets2; distal to Ets2, the human map is expanded.[The sequence data described in this paper have been submitted to GenBank. See Tables 1 and 2 for accession nos.]

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“…To reduce this problem and anchor contigs, investigators used markers in conjunction with fingerprints in which a marker can be a sequence tag site (STS), polymerase chain reaction (PCR), hybridization, etc. Cosmid maps ordered by Alu-PCR have been constructed for 40% of human chromosome 21 (Soeda et al 1995), and cosmid maps anchored to yeast artificial chromosomes (YAC) by STSs were constructed for 72.5% of the Y chromosome (Taylor et al 1996).…”

mentioning

confidence: 99%

Contigs Built with Fingerprints, Markers, and FPC V4.7

Soderlund

Humphray²,

French³

2000

Genome Research

304

299

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Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

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Cosmid assembly and anchoring to human chromosome 21

Cited by 40 publications

References 31 publications

Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.

Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.

Physical and Comparative Mapping of Distal Mouse Chromosome 16

Contigs Built with Fingerprints, Markers, and FPC V4.7

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