Generating linkage mapping files from Affymetrix SNP chip data

Bahlo, Melanie; Bromhead, Catherine J

doi:10.1093/bioinformatics/btp313

Cited by 60 publications

(49 citation statements)

References 24 publications

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“…Genotypes were called using the GenCall algorithm implemented in Illumina’s BeadStudio package. The LINKDATAGEN script 34 was used to select a subset of 11,913 SNP markers for analysis. These markers were chosen to be in approximate linkage equilibrium (spaced at least 0.15 cM apart) and to have high heterozygosity in the HapMap population of Utah residents with ancestry from northern and western Europe (CEU).…”

Section: Methodsmentioning

confidence: 99%

Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features

et al. 2014

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Age-related degenerative and malignant diseases represent major challenges for health care systems. Elucidation of the molecular mechanisms underlying carcinogenesis and age-associated pathologies is thus of growing biomedical relevance. We identified biallelic germline mutations in SPRTN (also called C1orf124 or DVC1)1–7 in three patients from two unrelated families. All three patients are affected by a new segmental progeroid syndrome characterized by genomic instability and susceptibility toward early onset hepatocellular carcinoma. SPRTN was recently proposed to have a function in translesional DNA synthesis and the prevention of mutagenesis1–7. Our in vivo and in vitro characterization of identified mutations has uncovered an essential role for SPRTN in the prevention of DNA replication stress during general DNA replication and in replication-related G2/M-checkpoint regulation. In addition to demonstrating the pathogenicity of identified SPRTN mutations, our findings provide a molecular explanation of how SPRTN dysfunction causes accelerated aging and susceptibility toward carcinoma.

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Section: Methodsmentioning

confidence: 99%

Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features

et al. 2014

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“…VCF2LINKDATAGEN [Smith et al, 2011] was then used to produce genotype data for both individuals in the style of SNP chip data using population allele frequencies from HapMap phase II SNPs. LINKDATAGEN [Bahlo and Bromhead, 2009] was used to obtain genotype data with SNPs in approximate linkage equilibrium and high heterozygosity according to the HapMap CEU population data.…”

Section: Methodsmentioning

confidence: 99%

Identical by descent L1CAM mutation in two apparently unrelated families with intellectual disability without L1 syndrome

Shaw¹,

Yap²,

Henden³

et al. 2015

European Journal of Medical Genetics

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Mutations in the L1 Cell Adhesion Molecule (L1CAM) gene (MIM#308840) cause a variety of X-linked recessive neurological disorders collectively called L1 syndrome. Using massively parallel sequencing (MPS) of the X-chromosome exome, we identified a novel missense variant in L1CAM in two Caucasian families with mild-moderate intellectual disability without obvious L1 syndrome features. These families were not known to be related. SNP data extracted from MPS identified a 5.6 cM tract of identity by descent (IBD), encompassing the L1CAM gene, between the DNA of the two probands. This cannot be explained by chance alone and strongly implies that the two families are related. It also suggests that the L1CAM (NM_000425.3, c.604G > A, p.D202N) variant is pathogenic. This report also demonstrates the usefulness of additional information, which can be extracted from exome sequencing data.

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“…Then, SNP 6.0 array data were subjected to homozygosity mapping using HomozygosityMapper software24. The linkage analysis was performed based on the model of autosomal recessive inheritance with complete penetrance, using the subset of 7860 SNPs with high heterozygosity extracted from the SNP 6.0 array data with the program Linkdatagen, setting the bin size to 0.5 cM25. To find a gene mutation within the loci, whole exome sequencing was performed on the proband.…”

Section: Methodsmentioning

confidence: 99%

Late-onset spastic ataxia phenotype in a patient with a homozygous DDHD2 mutation

Doi

Ushiyama²,

Baba

et al. 2014

Sci Rep

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Autosomal recessive cerebellar ataxias and autosomal recessive hereditary spastic paraplegias (ARHSPs) are clinically and genetically heterogeneous neurological disorders. Herein we describe Japanese siblings with a midlife-onset, slowly progressive type of cerebellar ataxia and spastic paraplegia, without intellectual disability. Using whole exome sequencing, we identified a homozygous missense mutation in DDHD2, whose mutations were recently identified as the cause of early-onset ARHSP with intellectual disability. Brain MRI of the patient showed a thin corpus callosum. Cerebral proton magnetic resonance spectroscopy revealed an abnormal lipid peak in the basal ganglia, which has been reported as the hallmark of DDHD2-related ARHSP (SPG 54). The mutation caused a marked reduction of phospholipase A1 activity, supporting that this mutation is the cause of SPG54. Our cases indicate that the possibility of SPG54 should also be considered when patients show a combination of adult-onset spastic ataxia and a thin corpus callosum. Magnetic resonance spectroscopy may be helpful in the differential diagnosis of patients with spastic ataxia phenotype.

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Generating linkage mapping files from Affymetrix SNP chip data

Abstract: LINKDATAGEN is available from http://bioinf.wehi.edu.au/software/linkdatagen/ with accompanying annotation files, reference manual and test dataset.

Cited by 60 publications

References 24 publications

Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features

Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features

Identical by descent L1CAM mutation in two apparently unrelated families with intellectual disability without L1 syndrome

Late-onset spastic ataxia phenotype in a patient with a homozygous DDHD2 mutation

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