Global Genetic Analysis

Elahi, Elahe; Kumm, Jochen; Ronaghi, Mostafa

doi:10.5483/bmbrep.2004.37.1.011

Cited by 12 publications

(7 citation statements)

References 160 publications

(116 reference statements)

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“…A CAPS marker is a PCR-amplified sequence that corresponds to a defined genomic region and includes a polymorphic restriction endonuclease site, which allows one to distinguish the parent of origin. Because CAPS markers lack bias in the amplification step (both parental genotypes are amplified), these markers are readily amenable to bulked segregant analysis (Elahi et al, 2004;Jenkins, 2003;Michelmore et al, 1991;Vignal et al, 2002). For our purposes, CAPS markers distinguish between Oak Ridge-and Mauriceville-inherited sequences.…”

Section: Marker Developmentmentioning

confidence: 99%

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Rapid genetic mapping in Neurospora crassa

Jin

Allan

Baber

et al. 2007

Fungal Genetics and Biology

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Forward genetic analysis is the most broadly applicable approach to discern gene functions. However, for some organisms like the filamentous ascomycete Neurospora crassa, genetic mapping frequently represents a limiting step in forward genetic approaches. We describe an efficient method for genetic mapping in N. crassa that makes use of a modified bulked segregant analysis and PCR-based molecular markers. This method enables mapping with progeny from a single cross, and requires only 90 PCR amplifications. Genetic distances between syntenic markers have been determined to ensure complete coverage of the genome and to allow interpolation of linkage data. As a result, most mutations should be mapped in less than one month to within 1-5 map units, a level of resolution sufficient to initiate map-based cloning efforts. This system also will facilitate analyses of recombination at a genome-wide level, and is applicable to other perfect fungi when suitable markers are available.

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Section: Marker Developmentmentioning

confidence: 99%

“…PCR-based molecular markers have been widely adopted for genetic mapping purposes (Elahi et al, 2004;Jenkins, 2003). The main advantages of molecular markers are that they seldom affect the fitness of an organism (selectively neutral) and are much more numerous than phenotypic markers.…”

Section: Introductionmentioning

confidence: 99%

Rapid genetic mapping in Neurospora crassa

Jin

Allan

Baber

et al. 2007

Fungal Genetics and Biology

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“…The identification of SNPs is rapidly progressing in many species in conjunction with their use as genetic markers in population, linkage, and genome-wide association studies (Elahi et al 2004). The number of SNPs that are deposited in the official database (dbSNP: http://www.ncbi.nlm.…”

Section: Introductionmentioning

confidence: 99%

Porcine Single Nucleotide Polymorphism (SNP) Development and Population Structure of Pigs Assessed by Validated SNPs

Matsumoto¹,

Okumura²,

Uenishi

et al. 2011

Biochem Genet

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In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.

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“…STRs have been the workhorse of human genetic analysis since the late 1980s. Their polymorphism is due to variations in the number of tandem repeats of short sequence units typically ranging from two to four nucleotides in size [2].…”

Section: Introductionmentioning

confidence: 99%

Homozygosity Analysis in Autoimmunity Affected Individuals and Multiplex Autoimmune Disease Families

Castiblanco¹,

Anaya²

2017

Immunome Res

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Autoimmune diseases (AD) are responsible for a substantial amount of disability and morbidity worldwide. Research generally focuses on a single disease, although autoimmune phenotypes could represent pleiotropic outcomes of non-specific disease genes underlying similar immunogenetic mechanisms. This report examined the effect and importance of the homozygosity status, using genome-wide interspersed markers, in individuals and multiplex families affected with AD. This study presented two approaches: (I) a case-control comparison and evaluation on the effect of homozygosity at the genome-wide level and per marker, including 453 unrelated individuals (121 late-, 79 early-onset AD, 40 polyautoimmunity (PolyA), 30 multiple autoimmune syndrome (MAS) and 183 healthy control individuals); and (II) a model-free affected pair linkage approach which included 35 MAS, 49 polyA, 104 late-, and 83 early-onset multiplex families. A total of 372 genome-wide markers were used in the analysis. The standardized observed homozygosity (S OH ) was calculated and the association of the homozygosity status and the autoimmune trait was evaluated. The multipoint model-free linkage analysis was applied by using RELPAL from S.A.G.E v6.3. Results for the S OH showed significant differences between controls and early-onset individuals, where early-onset affected individuals showed lower homozygosity relative to controls. No differences were observed relative to controls for MAS, polyA and late-onset disease at the genome-wide level. The local marker homozygosity effect showed share and specific risk and/or protective effects for 24 markers. The model-free affected pair linkage approach lacked any suggestive linkage signals, but marginal signals displayed excess allele sharing for extreme phenotypes in autoimmunity. This study presumed autoimmunity as a trait rather than a clinical phenotype and tried to approach AD as a continuous trait presenting extreme phenotypes. Future approaches would be expected to dwell on the data presented here to corroborate and expand on sample size, marker coverage and their effects.

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Global Genetic Analysis

Cited by 12 publications

References 160 publications

Rapid genetic mapping in Neurospora crassa

Rapid genetic mapping in Neurospora crassa

Porcine Single Nucleotide Polymorphism (SNP) Development and Population Structure of Pigs Assessed by Validated SNPs

Homozygosity Analysis in Autoimmunity Affected Individuals and Multiplex Autoimmune Disease Families

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