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SNP haplotype mapping in a small ALS family.

Krueger KA, Tsuji S, Fukuda Y, Takahashi Y, Goto J, Mitsui J, Ishiura H, Dalton JC, Miller MB, Day JW, Ranum LP - PLoS ONE (2009)

Bottom Line: The identification of genes for monogenic disorders has proven to be highly effective for understanding disease mechanisms, pathways and gene function in humans.New tools and approaches are needed to allow researchers to effectively tap into this genetic gold-mine.Our study illustrates how genetic information can be maximized using readily available tools as a first step in mapping single-gene disorders in small families.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America.

ABSTRACT
The identification of genes for monogenic disorders has proven to be highly effective for understanding disease mechanisms, pathways and gene function in humans. Nevertheless, while thousands of Mendelian disorders have not yet been mapped there has been a trend away from studying single-gene disorders. In part, this is due to the fact that many of the remaining single-gene families are not large enough to map the disease locus to a single site in the genome. New tools and approaches are needed to allow researchers to effectively tap into this genetic gold-mine. Towards this goal, we have used haploid cell lines to experimentally validate the use of high-density single nucleotide polymorphism (SNP) arrays to define genome-wide haplotypes and candidate regions, using a small amyotrophic lateral sclerosis (ALS) family as a prototype. Specifically, we used haploid-cell lines to determine if high-density SNP arrays accurately predict haplotypes across entire chromosomes and show that haplotype information significantly enhances the genetic information in small families. Panels of haploid-cell lines were generated and a 5 centimorgan (cM) short tandem repeat polymorphism (STRP) genome scan was performed. Experimentally derived haplotypes for entire chromosomes were used to directly identify regions of the genome identical-by-descent in 5 affected individuals. Comparisons between experimentally determined and in silico haplotypes predicted from SNP arrays demonstrate that SNP analysis of diploid DNA accurately predicted chromosomal haplotypes. These methods precisely identified 12 candidate intervals, which are shared by all 5 affected individuals. Our study illustrates how genetic information can be maximized using readily available tools as a first step in mapping single-gene disorders in small families.

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Comparison of Recombination Points Identified by Haploid Mapping and SNPs.Recombinations are depicted for the four founder chromosomes for chromosome 22. The four founder haplotypes are shown in blue, red, green and yellow and the unaffected chromosomes are shown in grey. Arrows point to deviations between the haploid (STRPs) (A) and SNP (B) methods. Regions that are designated by a hatched mixture of two colors result from markers that were not fully informative. The (1) and (5) arrows specify regions where the STRPs were not informative but the SNPs were able to accurately determine the correct haplotype. The (2) and (4) arrows show regions where a block of SNPs were not informative and the haplotypes could not be accurately designated. The (3) arrow represents a region where a double recombination over a small area occurred and was not detected by the STRPs due to marker spacing.
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pone-0005687-g005: Comparison of Recombination Points Identified by Haploid Mapping and SNPs.Recombinations are depicted for the four founder chromosomes for chromosome 22. The four founder haplotypes are shown in blue, red, green and yellow and the unaffected chromosomes are shown in grey. Arrows point to deviations between the haploid (STRPs) (A) and SNP (B) methods. Regions that are designated by a hatched mixture of two colors result from markers that were not fully informative. The (1) and (5) arrows specify regions where the STRPs were not informative but the SNPs were able to accurately determine the correct haplotype. The (2) and (4) arrows show regions where a block of SNPs were not informative and the haplotypes could not be accurately designated. The (3) arrow represents a region where a double recombination over a small area occurred and was not detected by the STRPs due to marker spacing.

Mentions: Diploid DNA samples from fourteen members of the ALS-A family were analyzed using the GeneChip™ Human Mapping 100 K Set (Affymetrix) and the resultant data were analyzed using the linkage program Allegro [22]. Specifically, haplotypes were determined in silico and were compared with the experimentally defined haplotypes from the haploid cell lines. Evaluation and comparison of recombination points revealed that the SNP arrays were able to precisely and accurately reconstruct haplotypes over large chromosomal regions. Figure 5 shows the comparison of the experimentally and predicted recombinations over the entire length of chromosome 22. While the recombination points are essentially the same, arrows point to deviations between the haploid and SNP methods. Arrows (1) and (5) specify sites where STRP markers were not informative but SNPs accurately defined the haplotype and excluded the regions. Arrows (2) and (4) show regions where a block of SNPs were not informative and the haplotypes could not be unambiguously defined. Arrow (3) represents a region where a double recombination over a small area occurred and was not detected by the STRPs due to marker spacing.


SNP haplotype mapping in a small ALS family.

Krueger KA, Tsuji S, Fukuda Y, Takahashi Y, Goto J, Mitsui J, Ishiura H, Dalton JC, Miller MB, Day JW, Ranum LP - PLoS ONE (2009)

Comparison of Recombination Points Identified by Haploid Mapping and SNPs.Recombinations are depicted for the four founder chromosomes for chromosome 22. The four founder haplotypes are shown in blue, red, green and yellow and the unaffected chromosomes are shown in grey. Arrows point to deviations between the haploid (STRPs) (A) and SNP (B) methods. Regions that are designated by a hatched mixture of two colors result from markers that were not fully informative. The (1) and (5) arrows specify regions where the STRPs were not informative but the SNPs were able to accurately determine the correct haplotype. The (2) and (4) arrows show regions where a block of SNPs were not informative and the haplotypes could not be accurately designated. The (3) arrow represents a region where a double recombination over a small area occurred and was not detected by the STRPs due to marker spacing.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2682655&req=5

pone-0005687-g005: Comparison of Recombination Points Identified by Haploid Mapping and SNPs.Recombinations are depicted for the four founder chromosomes for chromosome 22. The four founder haplotypes are shown in blue, red, green and yellow and the unaffected chromosomes are shown in grey. Arrows point to deviations between the haploid (STRPs) (A) and SNP (B) methods. Regions that are designated by a hatched mixture of two colors result from markers that were not fully informative. The (1) and (5) arrows specify regions where the STRPs were not informative but the SNPs were able to accurately determine the correct haplotype. The (2) and (4) arrows show regions where a block of SNPs were not informative and the haplotypes could not be accurately designated. The (3) arrow represents a region where a double recombination over a small area occurred and was not detected by the STRPs due to marker spacing.
Mentions: Diploid DNA samples from fourteen members of the ALS-A family were analyzed using the GeneChip™ Human Mapping 100 K Set (Affymetrix) and the resultant data were analyzed using the linkage program Allegro [22]. Specifically, haplotypes were determined in silico and were compared with the experimentally defined haplotypes from the haploid cell lines. Evaluation and comparison of recombination points revealed that the SNP arrays were able to precisely and accurately reconstruct haplotypes over large chromosomal regions. Figure 5 shows the comparison of the experimentally and predicted recombinations over the entire length of chromosome 22. While the recombination points are essentially the same, arrows point to deviations between the haploid and SNP methods. Arrows (1) and (5) specify sites where STRP markers were not informative but SNPs accurately defined the haplotype and excluded the regions. Arrows (2) and (4) show regions where a block of SNPs were not informative and the haplotypes could not be unambiguously defined. Arrow (3) represents a region where a double recombination over a small area occurred and was not detected by the STRPs due to marker spacing.

Bottom Line: The identification of genes for monogenic disorders has proven to be highly effective for understanding disease mechanisms, pathways and gene function in humans.New tools and approaches are needed to allow researchers to effectively tap into this genetic gold-mine.Our study illustrates how genetic information can be maximized using readily available tools as a first step in mapping single-gene disorders in small families.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America.

ABSTRACT
The identification of genes for monogenic disorders has proven to be highly effective for understanding disease mechanisms, pathways and gene function in humans. Nevertheless, while thousands of Mendelian disorders have not yet been mapped there has been a trend away from studying single-gene disorders. In part, this is due to the fact that many of the remaining single-gene families are not large enough to map the disease locus to a single site in the genome. New tools and approaches are needed to allow researchers to effectively tap into this genetic gold-mine. Towards this goal, we have used haploid cell lines to experimentally validate the use of high-density single nucleotide polymorphism (SNP) arrays to define genome-wide haplotypes and candidate regions, using a small amyotrophic lateral sclerosis (ALS) family as a prototype. Specifically, we used haploid-cell lines to determine if high-density SNP arrays accurately predict haplotypes across entire chromosomes and show that haplotype information significantly enhances the genetic information in small families. Panels of haploid-cell lines were generated and a 5 centimorgan (cM) short tandem repeat polymorphism (STRP) genome scan was performed. Experimentally derived haplotypes for entire chromosomes were used to directly identify regions of the genome identical-by-descent in 5 affected individuals. Comparisons between experimentally determined and in silico haplotypes predicted from SNP arrays demonstrate that SNP analysis of diploid DNA accurately predicted chromosomal haplotypes. These methods precisely identified 12 candidate intervals, which are shared by all 5 affected individuals. Our study illustrates how genetic information can be maximized using readily available tools as a first step in mapping single-gene disorders in small families.

Show MeSH
Related in: MedlinePlus