Significant Linkage Results Research Articles

Intra-Familial Tests of Association between Familial Idiopathic Scoliosis and Linked Regions on 9q31.3–q34.3 and 16p12.3–q22.2

Objective: Custom genotyping of markers in families with familial idiopathic scoliosis were used to fine-map candidate regions on chromosomes 9 and 16 in order to identify candidate genes that contribute to this disorder and prioritize them for next-generation sequence analysis. Methods: Candidate regions on 9q and 16p–16q, previously identified as linked to familial idiopathic scoliosis in a study of 202 families, were genotyped with a high-density map of single nucleotide polymorphisms. Tests of linkage for fine-mapping and intra-familial tests of association, including tiled regression, were performed on scoliosis as both a qualitative and quantitative trait. Results and Conclusions: Nominally significant linkage results were found for markers in both candidate regions. Results from intra-familial tests of association and tiled regression corroborated the linkage findings and identified possible candidate genes suitable for follow-up with next-generation sequencing in these same families. Candidate genes that met our prioritization criteria included FAM129B and CERCAM on chromosome 9 and SYT1, GNAO1, and CDH3 on chromosome 16.

Phenotype evaluation and genomewide linkage study of clinical variables in schizophrenia

Genetic factors are likely to influence clinical variation in schizophrenia, but it is unclear which variables are most suitable as phenotypes and which molecular genetic loci are involved. We evaluated clinical variable phenotypes and applied suitable phenotypes in genome-wide covariate linkage analysis. We ascertained 170 affected relative pairs (168 sibling-pairs and two avuncular pairs) with DSM-IV schizophrenia or schizoaffective disorder from the United Kingdom. We defined psychotic symptom dimensions, age at onset (AAO), and illness course using the OPCRIT checklist. We evaluated phenotypes using within sibling-pair correlations and applied suitable phenotypes in multipoint covariate linkage analysis based on 372 microsatellite markers at ∼10 cM intervals. The statistical significance of linkage results was assessed by simulation. The positive and disorganized symptom dimensions, AAO, and illness course qualified as suitable phenotypes. There were no genome-wide significant linkage results. There was suggestive evidence of linkage for the positive dimension on chromosomes 2q32, 10q26, and 20q12; the disorganized dimension on 8p21 and 17q21; and illness course on 2q33 and 22q11. The linkage peak for disorganization on 17q21 remained suggestive after correction for multiple testing. To our knowledge, this is the first study to integrate phenotype evaluation and genome-wide covariate linkage analysis for symptom dimensions and illness history variables in sibling-pairs with schizophrenia. The significant within-pair correlations strengthen the evidence that some clinical variables within schizophrenia are suitable phenotypes for molecular genetic investigations. At present there are no genome-wide significant linkage results for these phenotypes, but a number of suggestive findings warrant further investigation.

A Novel Locus for Congenital Simple Microphthalmia Family Mapping to 17p12-q12

To investigate the etiology in a family with autosomal-dominant congenital simple microphthalmia of Chinese origin. A whole-genome scan was performed by using 382 microsatellite DNA markers after the exclusion of reported candidates linked to microphthalmia. Additional fluorescent markers were genotyped for fine mapping. To find out the novel predisposing gene, 14 candidate genes including CRYBA1 and NCOR1 were selected to screen for the mutation by the PCR direct-sequencing method. Genome-wide single-nucleotide polymorphism (SNP) genotyping was performed to find out the pathogenetic copy number variation, as well. The most statistically significant linkage results were obtained at D17S1824 (maximum LOD score, 4.97, at recombination fraction 0.00). Haplotype analyses supported the location of the disease-causing gene to a 21.57-cM interval between loci D17S900 and D17S1872 of chromosome 17, region p12-q12. However, no mutation or CNV (copy number variation) was identified to be responsible for the microphthalmia phenotype of this pedigree. A novel suggestive linkage locus for congenital microphthalmia was detected in a Chinese family. This linkage region provides a target for susceptibility gene identification.

Genome Scan for Locus Involved in Mandibular Prognathism in Pedigrees from China

BackgroundIt is well known that genetic components play an important role in the etiology of mandibular prognathism, but few susceptibility loci have been mapped.MethodologyIn order to identify linkage regions for mandibular prognathism, we analyzed two Chinese pedigrees with 6,090 genome-wide single-nucleotide polymorphism (SNP) markers from Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM). Multipoint parametric and non-parametric (model-free) linkage analyses were used for the pedigrees.Principal FindingThe most statistically significant linkage results were with markers on chromosome 4 (LOD = 3.166 and NPL = 3.65 with rs 875864, 4p16.1, 8.38 cM). Candidate genes within the 4p16.1 include EVC, EVC2.ConclusionWe detected a novel suggestive linkage locus for mandibular prognathism in two Chinese pedigrees, and this linkage region provides target for susceptibility gene identification, a process that will provide important insights into the molecular and cellular basis of mandibular prognathism.

Genome Scan, Fine-Mapping, and Candidate Gene Analysis of Non-Syndromic Cleft Lip with or without Cleft Palate Reveals Phenotype-Specific Differences in Linkage and Association Results

Objectives: Non-syndromic orofacial clefts, i.e. cleft lip (CL) and cleft palate (CP), are among the most common birth defects. The goal of this study was to identify genomic regions and genes for CL with or without CP (CL/P). Methods: We performed linkage analyses of a 10 cM genome scan in 820 multiplex CL/P families (6,565 individuals). Significant linkage results were followed by association analyses of 1,476 SNPs in candidate genes and regions, utilizing a weighted false discovery rate (wFDR) approach to control for multiple testing and incorporate the genome scan results. Results: Significant (multipoint HLOD ≥3.2) or genome-wide-significant (HLOD ≥4.02) linkage results were found for regions 1q32, 2p13, 3q27-28, 9q21, 12p11, 14q21-24 and 16q24. SNPs in IRF6 (1q32) and in or near FOXE1 (9q21) reached formal genome-wide wFDR-adjusted significance. Further, results were phenotype dependent in that the IRF6 region results were most significant for families in which affected individuals have CL alone, and the FOXE1 region results were most significant in families in which some or all of the affected individuals have CL with CP. Conclusions: These results highlight the importance of careful phenotypic delineation in large samples of families for genetic analyses of complex, heterogeneous traits such as CL/P.

Dissecting the locus heterogeneity of autism: significant linkage to chromosome 12q14

Autism is a common neurodevelopmental disorder with a significant genetic component and locus heterogeneity. To date, 12 microsatellite genome screens have been performed using various data sets of sib-pair families (parents and affected children) resulting in numerous regions of potential linkage across the genome. However, no universal region or consistent candidate gene from these regions has emerged. The use of large, extended pedigrees is a recognized powerful approach to identify significant linkage results, as these families potentially contain more potential linkage information than sib-pair families. A genome-wide linkage analysis was performed on 26 extended autism families (65 affected, 184 total individuals). Each family had two to four affected individuals comprised of either avuncular or cousin pairs. For analysis, we used a high-density single-nucleotide polymorphism genotyping assay, the Affymetrix GeneChip Human Mapping 10K array. Two-point analysis gave peak heterogeneity limit of detection (HLOD) of 2.82 at rs2877739 on chromosome 14q. Suggestive linkage evidence (HLOD>2) from a two-point analysis was also found on chromosomes 1q, 2q, 5q, 6p,11q and 12q. Chromosome 12q was the only region showing significant linkage evidence by multipoint analysis with a peak HLOD=3.02 at rs1445442. In addition, this linkage evidence was enhanced significantly in the families with only male affected (multipoint HLOD=4.51), suggesting a significant gender-specific effect in the etiology of autism. Chromosome-wide haplotype analyses on chromosome 12 localized the potential autism gene to a 4 cM region shared among the affected individuals across linked families. This novel linkage peak on chromosome 12q further supports the hypothesis of substantial locus heterogeneity in autism.

Genomewide Scan for Anal Atresia in Swine Identifies Linkage and Association With a Chromosome Region onSus scrofaChromosome 1

Anal atresia is a rare and severe disorder in swine occurring with an incidence of 0.1-1.0%. A whole-genome scan based on affected half-sibs was performed to identify susceptibility loci for anal atresia. The analysis included 27 families with a total of 95 animals and 65 affected piglets among them. Animals were genotyped for 126 microsatellite markers distributed across the 18 autosomal porcine chromosomes and the X chromosome, covering an estimated 2080 cM. Single-point and multipoint nonparametric linkage scores were calculated using the computer package ALLEGRO 1.0. Significant linkage results were obtained for chromosomes 1, 3, and 12. Markers on these chromosomes and additionally on chromosomes for which candidate genes have been postulated in previous studies were subjected to the transmission disequilibrium test (TDT). The test statistic exceeded the genomewide significance level for adjacent markers SW1621 (P = 7 x 10(-7)) and SW1902 (P = 3 x 10(-3)) on chromosome 1, supporting the results of the linkage analysis. A specific haplotype associated with anal atresia that could prove useful for selection against the disorder was revealed. Suggestive linkage and association were also found for markers S0081 on chromosome 9 and SW957 on chromosome 12.

Genome search for additional human loci controlling infection levels by Schistosoma mansoni.

Schistosomiasis is a major public health problem in many developing countries. Previous studies have shown that infection levels by Schistosoma mansoni in a Brazilian population is controlled by a major gene, denoted as SM1, which was mapped to chromosome 5q31-q33 by use of a model-based (logarithm of the odds [lod] score) analysis method. The present study is an autosome-wide scan searching for additional human loci implicated in the regulation of S. mansoni infection intensities. The weighted pairwise correlation model-free linkage method was used in order to consider large pedigrees and to conduct a 2-locus analysis (i.e., to search for a second locus taking into account linkage to 5q31-q33). The most significant linkage results were again obtained in the 5q31-q33 region. Two additional regions provided linkage results with significance levels around 0.001, 1p21-q23 (results independent of 5q31-q33) and 6p21-q21 (results in interaction with 5q31-q33). The investigation of these regions, which contain some candidate genes, is ongoing in other populations to confirm the role of these regions.

Sample size requirements to control for stochastic variation in magnitude and location of allele‐sharing linkage statistics in affected sibling pairs

Typically, genome scans for complex disease have produced linkage peaks which have proved difficult to replicate in additional independent studies. Here we confirm that this may be due to the large variance in magnitude and position of the linkage statistics when maximized across a region. Simulations suggest that for genes of moderate effect (locus‐specific sibling relative risks λsin the range 1.23–1.39), sample sizes of less than 500 affected sib pairs will give unacceptably large standard errors in the magnitudes and locations of significant linkage results. For genes of small effect (λs≤ 1.13), sample sizes in the region of 1000–2000 pairs may be required to achieve consistency of results between different studies. These figures have important implications for our confidence in location estimates for disease genes obtained from linkage studies of modest size. In particular, collection of larger data sets and/or analysis strategies such as conditioning or narrowing the phenotype definition, in order to increase the relative effect size, may be required before embarking on positional cloning.

Sample size requirements to control for stochastic variation in magnitude and location of allele-sharing linkage statistics in affected sibling pairs.

Typically, genome scans for complex disease have produced linkage peaks which have proved difficult to replicate in additional independent studies. Here we confirm that this may be due to the large variance in magnitude and position of the linkage statistics when maximized across a region. Simulations suggest that for genes of moderate effect (locus-specific sibling relative risks lambda s in the range 1.23-1.39), sample sizes of less than 500 affected sib pairs will give unacceptably large standard errors in the magnitudes and locations of significant linkage results. For genes of small effect (lambda s < or = 1.13), sample sizes in the region of 1000-2000 pairs may be required to achieve consistency of results between different studies. These figures have important implications for our confidence in location estimates for disease genes obtained from linkage studies of modest size. In particular, collection of larger data sets and/or analysis strategies such as conditioning or narrowing the phenotype definition, in order to increase the relative effect size, may be required before embarking on positional cloning.

A Genomewide Analysis Provides Evidence for Novel Linkages in Inflammatory Bowel Disease in a Large European Cohort

Inflammatory bowel disease (IBD) is characterized by a chronic relapsing intestinal inflammation, typically starting in early adulthood. IBD is subdivided into two subtypes, on the basis of clinical and histologic features: Crohn disease and ulcerative colitis (UC). Previous genomewide searches identified regions harboring susceptibility loci on chromosomes 1, 3, 4, 7, 12, and 16. To expand our understanding of the genetic risk profile, we performed a 9-cM genomewide search for susceptibility loci in 268 families containing 353 affected sibling pairs. Previous linkages on chromosomes 12 and 16 were replicated, and the chromosome 4 linkage was extended in this sample. New suggestive evidence for autosomal linkages was observed on chromosomes 1, 6, 10, and 22, with LOD scores of 2.08, 2.07, 2.30, and 1.52, respectively. A maximum LOD score of 1.76 was observed on the X chromosome, for UC, which is consistent with the clinical association of IBD with Ullrich-Turner syndrome. The linkage finding on chromosome 6p is of interest, given the possible contribution of human leukocyte antigen and tumor necrosis-factor genes in IBD. This genomewide linkage scan, done with a large family cohort, has confirmed three previous IBD linkages and has provided evidence for five additional regions that may harbor IBD predisposition genes.

Genetic contributions to quantitative lipoprotein traits associated with coronary artery disease: analysis of a large pedigree from the Bogalusa Heart Study.

A pedigree of a large family with high prevalence of heart disease is subjected to association and sib-pair linkage analysis to investigate the role of 5 candidate genes in the regulation of lipoprotein metabolism and the development of coronary artery disease. At the 5% nominal significance level, the apolipoprotein B locus (APOB) was found to be linked to high-density lipoprotein cholesterol level (HDL-C), low-density lipoprotein cholesterol level (LDL-C), the ratio HDL-C/LDL-C, and apolipoprotein AI level times this ratio (apoAI x LDL-C/HDL-C). APOB (PvuII) was strongly associated with apolipoprotein B levels (apoB) (P = 0.006) and the VNTR region of the APOB locus showed highly significant association between allele 7 and low triglyceride levels (P = 0.004). No significant linkage results were found with cholesterol ester transfer protein (CETP). At the 1% nominal significance level, CETP [TaqI(B)] showed significant association with LDL-C, apoB, and HDL-C/LDL-C. There was significant linkage of lipoprotein lipase (LPL) with very-low-density lipoprotein cholesterol and the ratio apoAI/HDL-C, and strong association results between LPL (HindIII) and triglyceride levels (P = 0.005). At the 5% nominal significance level, haptoglobin (HPA) was associated with HDL-C, HDL-C/LDL-C, apoAI/HDL-C and apoAI x LDL-C/HDL-C. The apolipoprotein AI locus did not show any significant linkages or associations. The study thus indicated that genetic variation of APOB, LPL, CETP, and lecithin cholesterol acyl transferase (which is linked to HPA and CETP) may play an important role in the regulation of lipoprotein metabolism and could contribute to the risk of coronary artery disease.