GeneHunter protocols

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Associated diseases

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GeneHunter specifications

Information


Unique identifier OMICS_09397
Name GeneHunter
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for GeneHunter

GeneHunter in pipelines

 (2)
2014
PMCID: 4310431
PMID: 25713721
DOI: 10.1093/ckj/sfu129

[…] search using affymetrix genechip® human mapping 250k sty arrays according to the manufacturer's protocol (http://www.affymetrix.com) in six affected members and two unaffected members of the family. genehunter software was used to calculate a multipoint parametric logarithm of odds (lod) score, assuming an autosomal dominant mode of inheritance. ibd across the genome was estimated using […]

2011
PMCID: 3223203
PMID: 22132174
DOI: 10.1371/journal.pone.0027940

[…] genescan 3.1 software (abi) for genotype assessment., families a-e and data of markers ca7, ren256f13, ca5, ca1, ca8, ren177b24, ca3 and fh2885 were used for multipoint lod score calculation with genehunter 2.1 software . we assumed a genetic distance of 1 cm per mbp and the observed alleles of each marker were assumed to have equal frequencies. the calculation was based on a recessive […]


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GeneHunter in publications

 (159)
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w

[…] for genome-wide homozygosity mapping the genechip® human mapping 250 k styi array from affymetrix was used. non-parametric lod scores were calculated using a modified version of the program genehunter 2.1, through stepwise use of a sliding window with sets of 110 snps and the program allegro in order to identify regions of homozygosity as described, using a disease allele frequency […]

PMCID: 5891035
PMID: 29590100
DOI: 10.1371/journal.pgen.1007269

[…] dna lysates. all genotyping pcrs were performed with the kapa genotyping kit (kapa biosystems). in some cases, alleles were sequenced with sequence-specific primers to verify mutation homozygosity (genehunter and etonbioscience)., confocal microscopy of mutants on the by250 strain background was performed using a nikon a1r confocal microscope in the fau brain institute cell imaging core using […]

PMCID: 5812614
PMID: 29444168
DOI: 10.1371/journal.pone.0192696

[…] has been shown to be more powerful than model-free methods [], even when the exact mode of inheritance is unknown and when genetic heterogeneity is present. hlod and mmls were calculated using the genehunter program [] under dominant and recessive models. disease allele frequencies were set to 0.006 and 0.1 for the dominant and recessive models respectively. as in the previous study by lipner […]

PMCID: 5774751
PMID: 29351342
DOI: 10.1371/journal.pone.0191224

[…] for genome-wide homozygosity mapping, the genechip human mapping 250k styi array from affymetrix was used. nonparametric lod scores were calculated using a modified version of the program genehunter 2 through stepwise use of a sliding window with sets of 110 snps [,]. the program allegro was employed to identify regions of homozygosity by descent as described using a disease allele […]

PMCID: 5732689
PMID: 29262523
DOI: 10.18632/oncotarget.21800

[…] checked for consistency by using pedcheck []. homozygosity tests were performed to further check marker quality and genotyping errors. model-dependent multipoint lod scores were generated using genehunter v2.1 [] complemented by linkmap of fastlink [-]. two-point lod scores were performed using the mlink of the fastlink package because multipoint lod scores are always affected by flanking […]


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GeneHunter institution(s)
Whitehead Institute for Biomedical Research, Cambridge, UK

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