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Mapping genomic deletions down to the base: a quantitative copy number scanning approach used to characterise and clone the breakpoints of a recurrent 7p14.2p15.3 deletion

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@article{9d262e51f0034a57b052ded3bd9bacd3,
title = "Mapping genomic deletions down to the base: a quantitative copy number scanning approach used to characterise and clone the breakpoints of a recurrent 7p14.2p15.3 deletion",
abstract = "With the recent advances in genomic research, it has become apparent that a substantial part of human malformation and mental retardation is caused by imbalances in genomic content. Thus, there is an increasing need for versatile methods allowing a detailed mapping and cloning of the actual rearrangements. We have combined the flexibility of real-time quantitative PCR with the knowledge of human genome sequence to perform a copy number scanning in three patients known to harbour a deletion in the 7p14p15 locus. In two of the patients the actual breakpoints were cloned and sequenced, whereas the breakpoint of the third patient was mapped to a region previously predicted to be prone for rearrangements. One patient also harboured an inversion in connection with the deletion that disrupted the HDAC9 gene. All three patients showed clinical characteristics reminiscent of the hand-foot-genital syndrome and were deleted for the entire HOXA cluster. Two patients were also deleted for DFNA5, a gene implicated in dominant nonsyndromic hearing impairment, but neither patient showed signs of reduced hearing capabilities. The described copy number scanning approach is largely independent of the genomic locus and may be a valuable tool for characterising a large spectrum of deletions.",
keywords = "Child, Preschool, Chromosomes, Human, Pair 7, Cloning, Molecular, Cytogenetics, DNA, Facies, Female, Gene Deletion, Genome, Human, Histone Deacetylases, Humans, Intellectual Disability, Karyotyping, Male, Microsatellite Repeats, Models, Genetic, Multigene Family, Nucleic Acid Hybridization, Polymerase Chain Reaction, Receptors, Estrogen, Repressor Proteins, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Syndrome, Case Reports, Journal Article",
author = "Morten Dun{\o} and Hanne Hove and Maria Kirchhoff and Koenraad Devriendt and Marianne Schwartz",
year = "2004",
month = "11",
doi = "10.1007/s00439-004-1174-y",
language = "English",
volume = "115",
pages = "459--67",
journal = "Human Genetics",
issn = "0340-6717",
publisher = "Springer",
number = "6",

}

RIS

TY - JOUR

T1 - Mapping genomic deletions down to the base

T2 - a quantitative copy number scanning approach used to characterise and clone the breakpoints of a recurrent 7p14.2p15.3 deletion

AU - Dunø, Morten

AU - Hove, Hanne

AU - Kirchhoff, Maria

AU - Devriendt, Koenraad

AU - Schwartz, Marianne

PY - 2004/11

Y1 - 2004/11

N2 - With the recent advances in genomic research, it has become apparent that a substantial part of human malformation and mental retardation is caused by imbalances in genomic content. Thus, there is an increasing need for versatile methods allowing a detailed mapping and cloning of the actual rearrangements. We have combined the flexibility of real-time quantitative PCR with the knowledge of human genome sequence to perform a copy number scanning in three patients known to harbour a deletion in the 7p14p15 locus. In two of the patients the actual breakpoints were cloned and sequenced, whereas the breakpoint of the third patient was mapped to a region previously predicted to be prone for rearrangements. One patient also harboured an inversion in connection with the deletion that disrupted the HDAC9 gene. All three patients showed clinical characteristics reminiscent of the hand-foot-genital syndrome and were deleted for the entire HOXA cluster. Two patients were also deleted for DFNA5, a gene implicated in dominant nonsyndromic hearing impairment, but neither patient showed signs of reduced hearing capabilities. The described copy number scanning approach is largely independent of the genomic locus and may be a valuable tool for characterising a large spectrum of deletions.

AB - With the recent advances in genomic research, it has become apparent that a substantial part of human malformation and mental retardation is caused by imbalances in genomic content. Thus, there is an increasing need for versatile methods allowing a detailed mapping and cloning of the actual rearrangements. We have combined the flexibility of real-time quantitative PCR with the knowledge of human genome sequence to perform a copy number scanning in three patients known to harbour a deletion in the 7p14p15 locus. In two of the patients the actual breakpoints were cloned and sequenced, whereas the breakpoint of the third patient was mapped to a region previously predicted to be prone for rearrangements. One patient also harboured an inversion in connection with the deletion that disrupted the HDAC9 gene. All three patients showed clinical characteristics reminiscent of the hand-foot-genital syndrome and were deleted for the entire HOXA cluster. Two patients were also deleted for DFNA5, a gene implicated in dominant nonsyndromic hearing impairment, but neither patient showed signs of reduced hearing capabilities. The described copy number scanning approach is largely independent of the genomic locus and may be a valuable tool for characterising a large spectrum of deletions.

KW - Child, Preschool

KW - Chromosomes, Human, Pair 7

KW - Cloning, Molecular

KW - Cytogenetics

KW - DNA

KW - Facies

KW - Female

KW - Gene Deletion

KW - Genome, Human

KW - Histone Deacetylases

KW - Humans

KW - Intellectual Disability

KW - Karyotyping

KW - Male

KW - Microsatellite Repeats

KW - Models, Genetic

KW - Multigene Family

KW - Nucleic Acid Hybridization

KW - Polymerase Chain Reaction

KW - Receptors, Estrogen

KW - Repressor Proteins

KW - Reverse Transcriptase Polymerase Chain Reaction

KW - Sequence Analysis, DNA

KW - Syndrome

KW - Case Reports

KW - Journal Article

U2 - 10.1007/s00439-004-1174-y

DO - 10.1007/s00439-004-1174-y

M3 - Journal article

VL - 115

SP - 459

EP - 467

JO - Human Genetics

JF - Human Genetics

SN - 0340-6717

IS - 6

ER -

ID: 53438852