High-density SNP Map Research Articles

Application of Linkage Disequilibrium Mapping Methods to Detect QTL for Carcass Quality on Chromosome 6 Using a High Density SNP Map in Hanwoo

The purpose of this study was to detect QTL for carcass quality on bovine chromosome (BTA) 6 using a high density SNP map in a Hanwoo population. The data set comprised 45 sires and their 427 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers that were used for progeny testing in the Hanwoo Improvement Center in Seosan, Korea, were genotyped with the 2,535SNPs on BTA6 that were embedded in the Illumina bovine SNP 50K chip. Four different linkage disequilibrium (LD) mapping models were applied to detect significant SNPs for carcass quality traits; the fixed model with a single marker, the random model with a single marker, the random model with haplotype effects using two adjacent markers, and the random model at hidden state. A total of twelve QTL were detected, for which four, one, three and four SNPs were detected on BTA6 under the respective models (p

Localization of Type 1 Diabetes susceptibility in the ancestral haplotype 18.2 by high density SNP mapping

Previous studies have suggested that the ancestral haplotype 18.2 (AH18.2) carries additional susceptibility gene to Type 1 Diabetes (T1D) on the Major Histocompatibility Complex (MHC). We analyzed 10 DR3/TNFa1b5 homozygous subjects in order to establish the conservation of the AH18.2 and then compared this conserved region with other DR3 haplotype, the AH8.1. The Illumina's HumanHap550 Bead chip was used to perform an extensive genotyping of the MHC region. The AH18.2 was highly conserved between DDR1 and HLA-DQA1 genes; therefore most probably the second susceptibility gene is located within this region. We can exclude the region centromeric to HLA-DRA gene and telomeric to DDR1 gene. A comparison between the AH18.2 and AH8.1 haplotypes showed that 233 SNPs were different in the aforementioned conserved region. These data suggest that the 1.65 Mb MHC region between DDR1 and HLA-DRA genes is likely to carry additional susceptibility alleles for T1D on the AH18.2 haplotype.

The Primordial Growth Disorder 3-M Syndrome Connects Ubiquitination to the Cytoskeletal Adaptor OBSL1

3-M syndrome is an autosomal-recessive primordial growth disorder characterized by significant intrauterine and postnatal growth restriction. Mutations in the CUL7 gene are known to cause 3-M syndrome. In 3-M syndrome patients that do not carry CUL7 mutations, we performed high-density genome-wide SNP mapping to identify a second locus at 2q35-q36.1. Further haplotype analysis revealed a 1.29 Mb interval in which the underlying gene is located and we subsequently discovered seven distinct null mutations from 10 families within the gene OBSL1. OBSL1 is a putative cytoskeletal adaptor protein that localizes to the nuclear envelope. We were also able to demonstrate that loss of OBSL1 leads to downregulation of CUL7, implying a role for OBSL1 in the maintenance of CUL7 protein levels and suggesting that both proteins are involved within the same molecular pathway.

L005 Identification of genes involved in aortic elastic anomalies in the rat

The inbred Brown Norway (BN) rat presents several rare arterial phenotypes, including an aortic elastin deficit, a high incidence of PDA and the spontaneous formation of ruptures in the internal elastic lamina (RIEL) of the abdominal aorta (AA) and iliac arteries. Our previously performed genetic linkage study, using microsatellite markers, showed that these 3 arterial phenotypes do not correlate in the backcross population and so are independent, and are controlled by distinct genetic loci (Kota et al. Physiol. Genomics, 2007). The RIEL phenotype is of particular interest as it probably reflects a structural anomaly of the elastic network of the AA and the contiguous common iliac arteries. Since the human AA is highly susceptible to pathological alterations with aging, i.e. atherosclerosis and aneurysm formation, for reasons not entirely understood, the discovery of a gene influencing AA elastic network structure would be of interest. In the BN rat, RIEL is strongly linked to a locus on chromosome 5 (peak LOD score 27.4) but in this locus candidate genes are sparse and sequencing them gave negative results. We thus produced congenic rats, introgressing the chrom5 segment containing the RIEL locus from BN rats on a LOU (control) genetic background. These rats express the phenotype sufficiently (30 % of parental BN values) to permit further studies on recombinant offspring to try and locate the gene(s) responsible. We have analysed genotype-phenotype correlations in a large cohort of recombinants, obtained by crossing the congenic rat LOU.BN.D5Rat59-D5Rat131 with parental LOU and subsequent intercrossing, in order to further define the position of the gene(s) responsible. We also performed high-density SNP mapping on chosen, informative recombinants, using >5000 SNPs discriminative between BN and LOU, and demonstrated the purity of the LOU genetic background (>99.9 % outside the chr.5 congenic region). Further generations of recombinants produced from informative genitors and use of SNP genotyping in the congenic region has enabled us to locate the gene(s) responsible for a moderate RIEL phenotype in the first 6Mb region of chrom5. However, BN homozygosity down to 35 Mb causes increased severity of the phenotype.

F.33. The IMAGEN Consortium: A High-density SNP Map of the MHC in Lupus Identifies Multiple Independent Disease-associated Variants

F.33. The IMAGEN Consortium: A High-density SNP Map of the MHC in Lupus Identifies Multiple Independent Disease-associated Variants

Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

BackgroundFlow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification.ResultsHere we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA). Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA) for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H.ConclusionThe results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which considerably expands the potential of chromosome flow sorting in plant genomics.

Initial study of candidate genes on chromosome two for relative hand skill

Relative hand skill (HSR) is a trait of potential use as a physical characteristic in forensic analysis. The HSR gene has not been discovered but is mapped to chromosome 2p12-q11. Using high density SNP mapping we aim to refine the linkage signal and detect the gene.

ZBTB7 HapMap in a worldwide population study

The ZBTB7 gene is aberrantly overexpressed in human tumours [1] and is an obvious candidate for a breast cancer low-penetrance gene. Here we aimed to analyze the SNP and haplotypic variability of the ZBTB7 gene in human populations. The information available in SNPs databases is still limited; for example, HapMap contains information of only four ethnic groups, two of them from East Asia [2,3]. The inference of the portability of tagSNPs using this limited amount of information is therefore still under debate. We have thus selected 22 validated polymorphisms covering the ZBTB7 gene and flanking regions using public and private SNP databases. There are more than 1200 worldwide DNA samples (40 human populations), which include those contained in the CEPH Genome Diversity Cell Line Panel. Genotyping was performed using the MassARRAY SNP genotyping system (Sequenom Inc., San Diego, CA, USA). Briefly, it involves multiplex PCR and minisequencing assays, designed with Spectro DESIGNER software (Sequenom Inc.), followed by mass spectrometry analysis with the Bruker Bi-flex MALDI-TOF mass spectrometer (Bruker Daltonics, Billerica, MA, USA). Spectral output was analyzed using SpectroTYPER–RT 3.1 software (Sequenom Inc.) and by manual review. The present high-density SNP mapping study will facilitate a map of specific population variation and patterns of linkage disequilibrium at the ZBTB7 region in different human populations, and will facilitate the adequate selection of a highly efficient set of tag SNPs that will capture the bulk of the (potentially pathogenic) variation. We have found that patterns of LD and haplotype diversity at the ZBTB7 gene vary considerably among different populations. Thus, sub-Saharan African populations showed higher levels of haplotype diversity and shorter blocks, while non-Africans showed a higher level of LD and lower haplotype diversity, as expected according to population history. According to these patterns, we will discuss the efficiency of these LD patterns and tagSNPs to capture candidate SNPs at the ZBTB7 gene in tumor association studies.

A 6.9-Mb High-Resolution BAC/PAC Contig of Human 4p15.3–p16.1, a Candidate Region for Bipolar Affective Disorder

Bipolar affective disorder (BPAD) is a complex disease with a significant genetic component and a population lifetime risk of 1%. Our previous work identified a region of human chromosome 4p that showed significant linkage to BPAD in a large pedigree. Here, we report the construction of an accurate, high-resolution physical map of 6.9 Mb of human chromosome 4p15.3–p16.1, which includes an 11-cM (5.8 Mb) critical region for BPAD. The map consists of 460 PAC and BAC clones ordered by a combination of STS content analysis and restriction fragment fingerprinting, with a single ∼300-kb gap remaining. A total of 289 new and existing markers from a wide range of sources have been localized on the contig, giving an average marker resolution of 1 marker/23 kb. The STSs include 57 ESTs, 9 of which represent known genes. This contig is an essential preliminary to the identification of candidate genes that predispose to bipolar affective disorder, to the completion of the sequence of the region, and to the development of a high-density SNP map.

Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28

Linkage disequilibrium (LD), or the non-random association of alleles, is poorly understood in the human genome. Population genetic theory suggests that LD is determined by the age of the markers, population history, recombination rate, selection and genetic drift. Despite the uncertainties in determining the relative contributions of these factors, some groups have argued that LD is a simple function of distance between markers. Disease-gene mapping studies and a simulation study gave differing predictions on the degree of LD in isolated and general populations. In view of the discrepancies between theory and experimental observations, we constructed a high-density SNP map of the Xq25-Xq28 region and analysed the male genotypes and haplotypes across this region for LD in three populations. The populations included an outbred European sample (CEPH males) and isolated population samples from Finland and Sardinia. We found two extended regions of strong LD bracketed by regions with no evidence for LD in all three samples. Haplotype analysis showed a paucity of haplotypes in regions of strong LD. Our results suggest that, in this region of the X chromosome, LD is not a monotonic function of the distance between markers, but is more a property of the particular location in the human genome.