High-resolution cytogenetic-based physical map of human chromosome 16

Callen, David F.; Doggett, Norman A.; Stallings, Raymond L.; Chen, L.Z.; Whitmore, Scott A.; Lane, Sharon; Nancarrow, J.K.; Apostolou, Sinoula; Thompson, Andrew; Lapsys, Naras M.; Eyre, Helen J.; Baker, Elizabeth; Shen, Yang; Holman, Katherine; Phillips, Hilary; Richards, Robert I.; Sutherland, G. R.

doi:10.1016/0888-7543(92)90035-q

Cited by 48 publications

(26 citation statements)

References 35 publications

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“…This particular chromosome was in part targeted for sequencing because of the localization of the DNA repair gene ERCC4 to the p arm of chromosome 16 (ref. 1), the availability of a unique flowsorted chromosome-specific cosmid library 2 , and access to a mouse-human hybrid cell panel enabling the localization of clones to discrete cytogenetic intervals 3 . Further interest in human chromosome 16 stemmed from the clustering of metallothionein genes on this chromosome, which participate in heavy metal transport and detoxification, coinciding with important biological interests of the DOE 4,5 .…”

mentioning

confidence: 99%

The sequence and analysis of duplication-rich human chromosome 16

Martin

Han

Gordon

et al. 2004

Nature

153

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confidence: 99%

The sequence and analysis of duplication-rich human chromosome 16

Martin

Han

Gordon

et al. 2004

Nature

153

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“…FISH mapping, coupled with previous somatic cell hybrid mapping results (Callen et al, 1992), has also provided exten sive verification of contig integrity. Table IV lists 13 of these contigs for which more than one clone has been analyzed, either by FISH mapping or by hybridization to somatic cell hybrid DNA.…”

Section: Discussionmentioning

confidence: 95%

“…Although the majority of cosmid contigs hybridized to single sites on chromosome 16. a sig nificant fraction (23%) hybridized to multiple regions on chro mosome 16; a subset of these also hybridized to other human chromosomes. In most instances, clones that mapped to multi ple locations were found to contain low-abundance repetitive DNA sequcnces.The FISH data presented here, coupled with published mapping data from somatic cell hybrids (Callen et al" 1992). permits independent verification of the integrity of chromosome 16 cosmid contigs.…”

mentioning

confidence: 85%

“…Thirty-one of the 48 contigs were also mapped by a panel of 51 somatic cell hybrids containing different breakpoints on chromosome 16 (Callen et al" 1992). Table III lists these con tigs in the order (from the terminus of the short arm to that of the long arm) that they were mapped by the hybrid panel.…”

Section: Comparison O F Fish and Somatic Cell Hybrid Mappingmentioning

confidence: 99%

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In situ hybridization mapping of human chromosome 16: evidence for a high frequency of repetitive DNA sequences

Okumura

Menninger²,

Stallings³

et al. 1994

Cytogenet Genome Res

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Fluorescence in situ hybridization (FISH) provides a rapid approach to regional localization of overlapping clone sets (contigs) developed by various fingerprinting approaches. We have used 70 cosmid clones derived from 48 different contigs, part of the developing contig map of chromosome 16 (Stallings et al., 1990, 1992a), to cytogenetically map an estimated 8.6 million base pairs (Mbp) of chromosome 16 DNA (∼8–9 % total coverage). Although the majority of cosmid contigs hybridized to single sites on chromosome 16, a significant fraction (23 %) hybridized to multiple regions on chromosome 16; a subset of these also hybridized to other human chromosomes. In most instances, clones that mapped to multiple locations were found to contain low-abundance repetitive DNA sequences.The FISH data presented here, coupled with published mapping data from somatic cell hybrids (Callen et al., 1992), permits mdependent verification of the integrity of chromosome 16 cosmid contigs. The order of clones derived by FISH agrees closely with the cell hybrid mapping data and can be correlated with chromosome bands and specific chromosomal translocation breakpoints.

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“…In addition, Southern hybridization of clone inserts to EcoRI digests of DNA from cosmids, chromosome 16-specific somatic cell breakpoint hybrids (Callen et al 1992), and total human genomic DNA was performed on most of the clones to confirm their mapping to the FMF region. Assignment to the FMF region required either >90% sequence identity with the FMF region finished/sample sequence database or comparable hybridization patterns on total human genomic and somatic cell hybrid or cosmid DNA.…”

Section: Cdna Selectionmentioning

confidence: 99%

Construction of an ∼700-kb Transcript Map Around the Familial Mediterranean Fever Locus on Human Chromosome 16p13.3

Centola

Chen²,

Sood

et al. 1998

Genome Res.

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We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA around D16S3370, a marker showing a high degree of linkage disequilibrium with FMF, was sequenced to completion, and the sequence annotated. A transcript map reflecting the minimal number of genes encoded within the ∼700 kb of genomic DNA surrounding the FMF locus was assembled. This map consists of 27 genes with discreet messages detectable on Northerns, in addition to three olfactory-receptor genes, a cluster of 18 tRNA genes, and two putative transcriptional units that have typical intron-exon splice junctions yet do not detect messages on Northerns. Four of the transcripts are identical to genes described previously, seven have been independently identified by the French FMF Consortium, and the others are novel. Six related zinc-finger genes, a cluster of tRNAs, and three olfactory receptors account for the majority of transcribed sequences isolated from a 315-kb FMF central region (between D16S468/D16S3070 and cosmid 377A12). Interspersed among them are several genes that may be important in inflammation. This transcript map not only has permitted the identification of the FMF gene (MEFV), but also has provided us an opportunity to probe the structural and functional features of this region of chromosome 16.Saturating the human genome with mapped genes so that the structure and function of each can be determined is an ultimate goal of the human genome project (Collins and Galas 1993). In addition

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High-resolution cytogenetic-based physical map of human chromosome 16

Cited by 48 publications

References 35 publications

The sequence and analysis of duplication-rich human chromosome 16

The sequence and analysis of duplication-rich human chromosome 16

In situ hybridization mapping of human chromosome 16: evidence for a high frequency of repetitive DNA sequences

Construction of an ∼700-kb Transcript Map Around the Familial Mediterranean Fever Locus on Human Chromosome 16p13.3

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