Genome scanning by two‐dimensional DNA typing: The use of repetitive DNA sequences for rapid mapping of genetic traits

Uitterlinden, André G.; Slagboom, P. Eline; Mullaart, E.; Meulenbelt, Ingrid; Vijg, Jan

doi:10.1002/elps.1150120206

Cited by 14 publications

(9 citation statements)

References 111 publications

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“…A second approach fractionates DNA on the basis of size in the first dimension and by sequence in the second by using sequential agarose gel and denaturing gel electrophoresis steps. The twoFdimensionally resolved DNA is then hybridized to a repetitive element to produce a spot pattern (Vitterlinden et al, 1991).…”

Section: Discussionmentioning

confidence: 99%

Genome scanning detects genetic alterations in human ovarian carcinoma

Magliocco

Brilliant²

1994

Hum. Mutat.

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Genome scanning, originally used to detect mouse mutations, is a technique which can rapidly identify differences between genomic DNA samples. The procedure is essentially a high resolution Southern analysis using a probe that hybridizes to a medium copy number (1000-2000 copies per haploid genome) repetitive element naturally dispersed throughout the genome. This technique detects genetic changes (primarily large scale genetic changes, e.g., amplifications and deletions) as differences in hybridization band intensity. The use of a probe derived from an endogenous human retroviral-like repetitive sequence, the RTVL-H element, has made genome scanning in humans feasible. In this report, the genome scanning technique was used to evaluate genomic DNA extracted from 14 frozen ovarian tumors. These included 8 high grade serous cystadenocarcinomas, 2 endometrioid carcinomas, one malignant mixed mullerian tumor, 2 Krukenberg tumors, and one tumor where histological classification was unavailable. Band amplifications were identified in 11 cases, with the most prominent amplifications observed in the high grade serous cystadenocarcinomas. In some of the cases, the amplifications involved bands of identical molecular size suggesting that similar underlying changes occurred in different tumors and are potentially associated with specific histological tumor types or clinical behavior. Band deletions were also observed in one endometrioid tumor where blood leukocyte genomic DNA was available from the same patient, allowing a direct comparison.

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Section: Discussionmentioning

confidence: 99%

Genome scanning detects genetic alterations in human ovarian carcinoma

Magliocco

Brilliant²

1994

Hum. Mutat.

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“…1994. On the basis of results pre viously presented (Uitterlinden et al, 1991a) and the linkage study presented here, it can be estimated that if each probe detects 150 (+ -x -)-informative spot variants in a family, about 5 probes are necessary for a 5 million bp resolution genet ic map, supposing a random genomic distribution of the loci detected and a 5-10% overlap in identical loci detected by dif ferent probes. For the practical management of this amount of 2-D DNA typings and segregation information, a more auto mated 2-D DNA typing system and computerized image analy sis is needed.…”

Section: Discussionmentioning

confidence: 99%

“…Previously it has proved possible to re-find parental 2-D spots detected by the minisatellite core probe 33.6 (Jeffreys et al. 1985b) in 2-D DNA typings of their offspring (Uitterlinden et al, 1991a;te Meeiman et al, 1993), and sug gestive linkage has been presented between a 2-D spot and coatcolor in cattle assuming Mendelian inheritance and correct scoring of the segregation patterns of the 2-D spots (te .…”

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confidence: 99%

“…This is done by using the same kinds of probes as in DNA fingerprinting but extending the gel electrophoresis to two dimensions: Firstly according to size, and then, in the sec ond dimension, by denaturing gradient gel electrophoresis (DGGE) according to base-pair sequence. Depending on the core probe used in the hybridization analysis, between 150 and 700 restriction fragments are detected as spots in the 2-D DNA typing patterns (for review, see Uitterlinden et al, 1991a), and many of the loci corresponding to these spots are polymorphic possibly as a result of variable number of tandem repeat (VNTR) polymorphisms.…”

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Two-dimensional DNA typing as a genetic marker system in humans

Børglum

Mullaart

Kvistgaard

et al. 1995

Cytogenet Genome Res

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By two-dimensional (2-D) DNA typing several hundred genomic loci can be analysed simultaneously in a two-dimensional pattern as spots detected by micro- or minisatellite core probes. Many of these loci display DNA sequence polymorphisms, and we have examined whether it is possible to extract genetic information from the rather complex but potentially very informative 2-D DNA typing patterns. To do so, the segregation of 9 spots detected by the microsatellite core probe (CAC) _n was followed in a large CEPH pedigree, and by linkage analysis it was possible to obtain chromosomal assignments of the corresponding (CAC)_n loci in all cases except one. Furthermore, a regional, physical localization of these loci emerged from analysis of the existing genetic and physical localization data of DNA markers flanking the (CAC)_n loci. We have hereby obtained evidence that the spots detected by the microsatellite core probe (CAC)_n segregate in a Mendelian manner and that it is possible to reliably score the segregation of single spots within a family. These results indicate that the large amount of potential information inherent in 2-D DNA typing may be used as a genetic marker system; an important prerequisite for its application as a genome scanning method, e.g. in detection of genomic alterations in cancer and in mapping of genetic traits.

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“…These usually consist of different classes of repetitive sequences which can be detected by either hybridization analysis or PCR amplification (for a review see [8] and [lo]). The discriminating power is the possibility to distinguish the almost identical DNA sequences in a normal and diseased cell.…”

Section: Genome Scanningmentioning

confidence: 99%

Gene and genome scanning by two‐dimensional DNA typing

Uitterlinden

1995

Electrophoresis

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A major effort in the analysis of DNA currently focuses on identifying genes and their pathological variants underlying disease. Once such disease genes have been isolated a major task of molecular medicine is to identify the spectrum of DNA sequence variations responsible for the aberrant function of such genes. These efforts, however, are hindered by the vast amount of genetic information to scan for variations and the limited capacity of analytical techniques in terms of accuracy and speed. Recently, a number of techniques were developed, so-called "genome scanning" techniques, which allow complete genomes to be analyzed for sequence variation in parallel, i.e., at multiple sites or loci simultaneously rather than serially at predefined loci. Here we present the background and applications of a particular electrophoretic parallel processing approach, generically termed two-dimensional DNA typing. The approach is based on separating DNA fragments by two-dimensional electrophoresis [1], including denaturing gradient gel electrophoresis, thus allowing hundreds of fragments to be simultaneously assessed by comparative analysis for variations in size and sequence. The method is suitable for hybridization analysis with locus-specific and multilocus probes of genomic DNA restriction fragments derived from human and other DNA, and for analysis of polymerase chain reaction (PCR) fragments derived from large genes. Two-dimensional DNA typing has been applied, e.g., in linkage analysis of pedigrees, analysis of tumor genomes for rearrangements, and to scan the cystic fibrosis transmembrane regular gene for sequence variations such as point mutations.

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Genome scanning by two‐dimensional DNA typing: The use of repetitive DNA sequences for rapid mapping of genetic traits

Cited by 14 publications

References 111 publications

Genome scanning detects genetic alterations in human ovarian carcinoma

Genome scanning detects genetic alterations in human ovarian carcinoma

Two-dimensional DNA typing as a genetic marker system in humans

Gene and genome scanning by two‐dimensional DNA typing

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