A PCR-Based Genetic Map for Human Chromosome 3

O’Connell, P.; Leach, Robin J.; Rains, D. W.; Taylor, T. D.; Garcia, Dawn; Ballard, L.; Holik, P.; Weissenbach, Jean; Sherman, S.L.; Wilkie, Patricia J.; Weber, J. L.; Naylor, Susan L.

doi:10.1006/geno.1994.1666

Cited by 7 publications

(4 citation statements)

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“…Genotypes were collected primarily by PCR assays with radiolabeled oligonucleotide primers. The antisense primer was 5 -radiolabeled in a standard polynucleotide kinase reaction by 3,000 Ci/mmol [g 32 P]-adenosine triphosphate (ATP; from NEN) at a molar ratio of 18 [g 32 P]-ATP:1 primer, as described elsewhere (O'Connell et al 1994;Duggirala et al 1996). Thirty cycles of PCR (denaturing at 94ЊC for 30 s, annealing at 55ЊC for 1 min, and extension at 72ЊC for 1 min) were done in a 15-ml assay containing 50 ng of DNA template, 10 mM Tris-HCl, pH 8.3, 50 mM KCl, 1-4 mM MgCl 2 , 0.1 M spermidine (Sigma), 0.1 mM of each PCR primer, 0.1 mM dNTPs (Gibco BRL), and 0.5 U of Taq polymerase (PE Biosystems).…”

Section: Genotypingmentioning

confidence: 99%

A Major Susceptibility Locus Influencing Plasma Triglyceride Concentrations Is Located on Chromosome 15q in Mexican Americans

Duggirala¹,

Blangero

Almasy

et al. 2000

The American Journal of Human Genetics

101

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Although several genetic forms of rare or syndromic hypertriglyceridemia have been reported, little is known about the specific chromosomal regions across the genome harboring susceptibility genes for common forms of hypertriglyceridemia. Therefore, we conducted a genomewide scan for susceptibility genes influencing plasma triglyceride (TG) levels in a Mexican American population. We used both phenotypic and genotypic data from 418 individuals distributed across 27 low-income, extended Mexican American families. For the analyses, TG values were log transformed (ln TG). We used a variance-components technique to conduct multipoint linkage analyses for localizing susceptibility genes that determine variation in TG levels. We used an approximately 10-15-cM map, which was made on the basis of information from 295 microsatellite markers. After accounting for the effects of sex and sex-specific age terms, we found significant evidence for linkage (LOD = 3.88) of ln TG levels to a genetic location between the markers GABRB3 and D15S165 on chromosome 15q. This putative locus explains 39.7+/-7% (P=.000012) of total phenotypic variation in ln TG levels. Suggestive evidence was found for linkage of ln TG levels to two different locations on chromosome 7, which are approximately 85 cM apart from each other. Also, there is some evidence for linkage of high-density lipoprotein cholesterol concentrations to a genetic location near one of the regions on chromosome 7. In conclusion, we found strong evidence for linkage of ln TG levels to a genetic location on chromosome 15q in a Mexican American population, which is prone to disease conditions such as type 2 diabetes and the insulin-resistance syndrome that are associated with hypertriglyceridemia. This putative locus appears to have a major influence on ln TG variation.

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Section: Genotypingmentioning

confidence: 99%

A Major Susceptibility Locus Influencing Plasma Triglyceride Concentrations Is Located on Chromosome 15q in Mexican Americans

Duggirala¹,

Blangero

Almasy

et al. 2000

The American Journal of Human Genetics

101

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“…Although the first published genomewide human linkage map was based primarily on low-informativeness diallelic polymorphisms (Donis-Keller et al 1987), it was the more informative and easier to type multiallelic short tandem-repeat (microsatellite) polymorphisms (STRPs) (Weber and May 1989) that permitted costeffective construction of dense human genetic maps. Many human genetic maps covering individual chromosomes or segments of chromosomes have been described (e.g., see Tomfohrde et al 1992;O'Connell et al 1994;Shen et al 1994;Zahn and Kwiatkowski 1995;Fain et al 1996). Several human genomewide genetic maps also have been published, some of which include markers developed in only one laboratory (Buetow et al 1994;Gyapay et al 1994;Utah Marker Development Group 1995;Dib et al 1996) and some of which include markers from many labs (NIH/ CEPH Collaborative Mapping Group 1992; Matise et al 1994;Murray et al 1994).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Human Genetic Maps: Individual and Sex-Specific Variation in Recombination

Broman

Murray

Sheffield

et al. 1998

The American Journal of Human Genetics

1,023

916

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Comprehensive human genetic maps were constructed on the basis of nearly 1 million genotypes from eight CEPH families; they incorporated >8,000 short tandem-repeat polymorphisms (STRPs), primarily from Généthon, the Cooperative Human Linkage Center, the Utah Marker Development Group, and the Marshfield Medical Research Foundation. As part of the map building process, 0.08% of the genotypes that resulted in tight double recombinants and that largely, if not entirely, represent genotyping errors, mutations, or gene-conversion events were removed. The total female, male, and sex-averaged lengths of the final maps were 44, 27, and 35 morgans, respectively. Numerous (267) sets of STRPs were identified that represented the exact same loci yet were developed independently and had different primer pairs. The distributions of the total number of recombination events per gamete, among the eight mothers of the CEPH families, were significantly different, and this variation was not due to maternal age. The female:male ratio of genetic distance varied across individual chromosomes in a remarkably consistent fashion, with peaks at the centromeres of all metacentric chromosomes. The new linkage maps plus much additional information, including a query system for use in the construction of reliably ordered maps for selected subsets of markers, are available from the Marshfield Website.

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“…Chromosome 3 maps are available at two centers. The University of Texas Health Center at San Antonio offers an STS content map based on YACs, as well as a radiation hybrid map (O'Connell et al, 1996). Their Web site provides a graphical "clickable" interface to the mapping data, as well as a query-based mechanism.…”

Section: Example 2: Généthon Genotyping Informationmentioning

confidence: 99%

“…There are now high‐quality genetic maps of the human genome based on simple sequence repeat polymorphisms (Murray et al, ; Dib et al, ) that provide mapping information at 1‐ to 5‐Mb resolution. In addition, there exist a variety of physical maps that provide mapping resolutions in the sub‐megabase range (see Hudson et al, and O'Connell et al, , among others); a map of ∼16,000 expressed sequences (ESTs; Schuler et al, ) is also available. By taking advantage of these maps, a researcher can, in many cases, focus in on a candidate region by searching public mapping databases in a matter of hours rather than by performing laboratory experiments over a course of months.…”

mentioning

confidence: 99%

Navigating Public Physical Mapping Databases

Stein

1997

CP Human Genetics

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This unit provides concise overviews of the many physical mapping resources available and relates them to the genetic and transcript maps. Useful information on resolution of the maps, how to access them, and how to interpret them is compiled and presented in a clear fashion. Especially useful is a set of detailed protocols describing how to construct an STS marker and how to map it by means of available yeast artificial chromosomes (YACs). An additional protocol describes accessing EST marker maps.

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A PCR-Based Genetic Map for Human Chromosome 3

Cited by 7 publications

References 0 publications

A Major Susceptibility Locus Influencing Plasma Triglyceride Concentrations Is Located on Chromosome 15q in Mexican Americans

A Major Susceptibility Locus Influencing Plasma Triglyceride Concentrations Is Located on Chromosome 15q in Mexican Americans

Comprehensive Human Genetic Maps: Individual and Sex-Specific Variation in Recombination

Navigating Public Physical Mapping Databases

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