Genetic mapping with SNP markers in Drosophila

Berger, Jürg; Suzuki, Takashi; Senti, Kirsten-André; Stubbs, Janine; Schaffner, G.; Dickson, Barry J.

doi:10.1038/ng773

Cited by 146 publications

(136 citation statements)

References 23 publications

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“…For example, flies with troponin I or ␦sg S151A mutation can be used as a cardiomyopathic sensitizer gene and backcrossed into either Canton-S or Oregon-R strains to derive recombinant inbred strains to examine the impact of genetic strain differences on dilated cardiomyopathy. Then, singlenucleotide polymorphism mapping strategies can be conducted to identify quantitative trait loci corresponding to genomic regions that contain protective or detrimental genetic modifiers of dilated cardiomyopathy (41,42). Identification of candidate genes from these modifier screens can be tested in populations of individuals with heart failure and thereby provide an unbiased avenue using Drosophila to find potential markers that correspond to human disease progression.…”

Section: Discussionmentioning

confidence: 99%

Drosophila as a model for the identification of genes causing adult human heart disease

Wolf

Amrein

Izatt

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

233

226

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Drosophila melanogaster genetics provides the advantage of molecularly defined P-element insertions and deletions that span the entire genome. Although Drosophila has been extensively used as a model system to study heart development, it has not been used to dissect the genetics of adult human heart disease because of an inability to phenotype the adult fly heart in vivo. Here we report the development of a strategy to measure cardiac function in awake adult Drosophila that opens the field of Drosophila genetics to the study of human dilated cardiomyopathies. Through the application of optical coherence tomography, we accurately distinguish between normal and abnormal cardiac function based on measurements of internal cardiac chamber dimensions in vivo. Normal Drosophila have a fractional shortening of 87 ؎ 4%, whereas cardiomyopathic flies that contain a mutation in troponin I or tropomyosin show severe impairment of systolic function. To determine whether the fly can be used as a model system to recapitulate human dilated cardiomyopathy, we generated transgenic Drosophila with inducible cardiac expression of a mutant of human ␦-sarcoglycan (␦sg S151A ), which has previously been associated with familial dilated cardiomyopathy. Compared to transgenic flies overexpressing wild-type ␦sg, or the standard laboratory strain w 1118 , Drosophila expressing ␦sg S151A developed marked impairment of systolic function and significantly enlarged cardiac chambers. These data illustrate the utility of Drosophila as a model system to study dilated cardiomyopathy and the applicability of the vast genetic resources available in Drosophila to systematically study the genetic mechanisms responsible for human cardiac disease.optical coherence tomography ͉ cardiomyopathy

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Section: Discussionmentioning

confidence: 99%

Drosophila as a model for the identification of genes causing adult human heart disease

Wolf

Amrein

Izatt

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

233

226

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“…At least some of these alternative forms of variation, such as insertion and deletion (INDEL) polymorphisms, are abundant in the genomes of model organisms and are expected to be abundant in humans as well. For example, studies of genetic variation in Drosophila melanogaster and Caenorhabditis elegans have shown that INDELs represent between 16% and 25% of all genetic polymorphisms in these species (Berger et al 2001;Wicks et al 2001). A study of genetic variation on human chromosome 22 has suggested that humans harbor similar levels of INDEL variation (INDELs represented 18% of the polymorphisms on this chromosome; Dawson et al 2001).…”

mentioning

confidence: 99%

An initial map of insertion and deletion (INDEL) variation in the human genome

et al. 2006

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Although many studies have been conducted to identify single nucleotide polymorphisms (SNPs) in humans, few studies have been conducted to identify alternative forms of natural genetic variation, such as insertion and deletion (INDEL) polymorphisms. In this report, we describe an initial map of human INDEL variation that contains 415,436 unique INDEL polymorphisms. These INDELs were identified with a computational approach using DNA re-sequencing traces that originally were generated for SNP discovery projects. They range from 1 bp to 9989 bp in length and are split almost equally between insertions and deletions, relative to the chimpanzee genome sequence. Five major classes of INDELs were identified, including (1) insertions and deletions of single-base pairs, (2) monomeric base pair expansions, (3) multi-base pair expansions of 2-15 bp repeat units, (4) transposon insertions, and (5) INDELs containing random DNA sequences. Our INDELs are distributed throughout the human genome with an average density of one INDEL per 7.2 kb of DNA. Variation hotspots were identified with up to 48-fold regional increases in INDEL and/or SNP variation compared with the chromosomal averages for the same chromosomes. Over 148,000 INDELs (35.7%) were identified within known genes, and 5542 of these INDELs were located in the promoters and exons of genes, where gene function would be expected to be influenced the greatest. All INDELs in this study have been deposited into dbSNP and have been integrated into maps of human genetic variation that are available to the research community.

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“…Aside from the SNP assays, the difference between the two strategies is that Martin et al describe a one-step process resulting in medium resolution, whereas our method is divided into a low-and high-resolution step. The two-step strategy has also been applied by Berger et al (2), who followed an all-molecular sequence-based approach. Our protocol guarantees maximal resolution with a minimal number of recombinants, because choosing closely linked markers provides a recombination event in the region of interest.…”

Section: Discussionmentioning

confidence: 99%

“…These are widespread, even in regions devoid of phenotypic markers, usually genetically inert, and dominant. An all-molecular approach to recombination mapping is aided by genome-wide SNP maps that have been established for some Drosophila strains (2,3). However, the resolution of these maps (114-1,000 kb) is in many cases not sufficient to localize the candidate gene and also is not much higher than the resolution attained by classical techniques.…”

Section: G Enome-wide Genetic Screens In Model Organisms Likementioning

confidence: 99%

High-resolution SNP mapping by denaturing HPLC

Nairz

Stocker

Schindelholz

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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With the availability of complete genome sequences, new rapid and reliable strategies for positional cloning become possible. Single-nucleotide polymorphisms (SNPs) permit the mapping of mutations at a resolution not amenable to classical genetics. Here we describe a SNP mapping procedure that relies on resolving polymorphisms by denaturing HPLC without the necessity of determining the nature of the SNPs. With the example of mapping mutations to the Drosophila nicastrin locus, we discuss the benefits of this method, evaluate the frequency of closely linked and potentially misleading second site mutations, and demonstrate the use of denaturing high-performance liquid chromatography to identify mutations in the candidate genes and to fine-map chromosomal breakpoints. Furthermore, we show that recombination events are not uniformly dispersed over the investigated region but rather occur at hot spots.SNP detection ͉ recombination mapping ͉ DHPLC ͉ nicastrin ͉ recombination hot spots G enome-wide genetic screens in model organisms like Drosophila facilitate the identification of genetic loci involved in biological processes (1). However, the isolation of the affected gene is a tedious process, particularly because the most commonly used mutagen, EMS, primarily induces point mutations. Standard procedures to localize point mutations involve (i) identification of the affected chromosome (arm); (ii) mapping by noncomplementation with chromosomal deficiencies; and (iii) recombination mapping relative to visible markers. In this way, it is generally possible to map mutations to a region of a few hundred kilobase pairs (kb). Limiting factors are the resolution of the meiotic map, the accuracy of determined deficiency breakpoints, and misleading effects caused by second site lethal mutations.To meiotically map mutations to the level of a single gene, sequence polymorphisms such as single-nucleotide polymorphisms (SNPs), nucleotide insertions, or deletions are exploited as genetic markers. These are widespread, even in regions devoid of phenotypic markers, usually genetically inert, and dominant. An all-molecular approach to recombination mapping is aided by genome-wide SNP maps that have been established for some Drosophila strains (2, 3). However, the resolution of these maps (114-1,000 kb) is in many cases not sufficient to localize the candidate gene and also is not much higher than the resolution attained by classical techniques. Moreover, in contrast to more recently introduced model organisms like Arabidopsis thaliana and Caenorhabditis elegans, for which clearly defined lines exist, the genetic backgrounds of Drosophila strains are often heterogeneous and difficult to trace, such that SNP maps cannot readily be applied to other strains. Furthermore, the complete reliance on sequence polymorphisms requires PCR amplification of the genomic DNA, which becomes a rate-limiting factor (4). A mapping strategy combining visible and molecular markers for recombination mapping can reduce efforts and costs (5).When a genetic lo...

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Genetic mapping with SNP markers in Drosophila

Cited by 146 publications

References 23 publications

Drosophila as a model for the identification of genes causing adult human heart disease

Drosophila as a model for the identification of genes causing adult human heart disease

An initial map of insertion and deletion (INDEL) variation in the human genome

High-resolution SNP mapping by denaturing HPLC

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