Regions Of Suggestive Linkage Research Articles

Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment.

PurposeSpecific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping.MethodWe performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype.ResultsA suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis.ConclusionsThese results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI.Supplemental Material https://doi.org/10.23641/asha.13203218

Presence of knee osteophytes is heritable and linked to regions of CHR. 19 and 2 that contain TGFB1 and SPP2

Presence of knee osteophytes is heritable and linked to regions of CHR. 19 and 2 that contain TGFB1 and SPP2

Genome wide analysis in a family with sensorineural hearing loss, autism and mental retardation

Hearing loss is a common congenital anomaly with an incidence of 1 in 1000 live births. It has been described together with several other clinical features as fortuitous association or commune genetic syndrome. In this study, we investigated a consanguineous Tunisian family with moderate to profound congenital hearing loss, mental retardation and autistic behaviors. We performed a genome wide microarray analysis study using approximately 300,000 SNPs in a common set of 7 invidious of this family. We identified regions of suggestive linkage with hearing loss on chromosomes 6p12 and 7q34. In addition, we identified a deletion on chromosome 8p in the two autistic individuals. This report presents an illustration of how consanguinity could increase familial clustering of multiple hereditary diseases within the same family. The application of next generation sequencing for this family seems to be a good strategy for further analysis leading to the identification of candidate genes.

Genome-wide linkage and association scans for pulse pressure in Chinese twins

Elevated pulse pressure (PP) is associated with cardiovascular disorders and mortality in various populations. The genetic influence on PP has been confirmed by heritability estimates using related individuals. Recently, efforts have been made by mapping genes that are linked to the phenotype. We report the results of our gene mapping studies conducted in the Chinese population in mainland China. The genome-wide linkage and association scans were carried out on 63 middle-aged dizygotic twin pairs using high-density markers. The linkage analysis identified three significant linkage peaks (all with a single point P<1e(-05)) on chromosome 11 (LOD core 4.06 at 30.5 cM), chromosome 12 (LOD score 3.97 at 100.7 cM) and chromosome 18 (LOD score 4.01 at 70.7 cM), with the last two peaks closely overlapping with linkage peaks reported by two American studies. Multiple regions with suggestive linkages were identified, with many of the peaks overlapping with published linkage regions. The genome-wide association analysis detected a suggestive association on chromosome 4 (rs17031508, P<8.34e(-08)) located within a wide region of suggestive linkage. Our results provide some evidence for genetic linkages and associations with PP in the Chinese population. Further investigation is warranted to replicate the findings and to explore the susceptibility loci or genes for PP.

QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch

The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak have also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now, no genomic polymorphisms have been identified, which are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here, we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1404 informative single-nucleotide polymorphisms genotyped in a four-generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of 11 genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.

A Genome-Wide Linkage Analysis in 181 German Sarcoidosis Families Using Clustered Biallelic Markers

Sarcoidosis (SA) is a systemic granulomatous inflammatory disorder with complex etiology and strong clustering in families. Genome-wide association studies have been successful in the identification of common risk variants for the disease. To reveal susceptibility variants with low frequencies but strong effects, we performed a genome-wide linkage scan in a large sample of SA families. We genotyped 528 members of 181 German SA families for 3,882 single nucleotide polymorphism assays from the SNPlex System Human Linkage Mapping Set 4K. Nonparametric linkage analysis revealed one region of suggestive linkage on chromosome 12p13.31 at 20 cM (logarithm of odds [LOD] = 2.53; local P value = .0003) and another linkage peak of nearly suggestive linkage on 9q33.1 at 134 cM (LOD = 2.12; local P value = .0009). The latter has been reported to show suggestive evidence for linkage in a sample of 229 African American SA families previously. Analysis of acute and chronically affected families revealed a subphenotype-specific linkage pattern and an additional, nearly suggestive linkage peak on chromosome 16p13.11 at 38 cM (LOD = 2.09; local P value = .001), which was confined to acute SA. Our results propose that the respective regions might harbor yet-unidentified, possibly subphenotype-specific risk factors for the disease (eg, with immune-related functions like the tumor necrosis factor receptor 1). They should be proved to be important for SA pathogenesis and investigated in detail with an emphasis on rare variants. Subphenotype-specific risk factors might serve for prognosis of the clinical course of the disease.

Suggestive Linkage of the Child Behavior Checklist Juvenile Bipolar Disorder Phenotype to 1p21, 6p21, and 8q21

Several studies have documented a profile of elevated scores on the Attention Problems, Aggressive Behavior and Anxious/Depressed scales of the Child Behavior Checklist (CBCL) in youth with bipolar disorder. The sum of these scales, referred to as the CBCL Juvenile Bipolar Disorder (JBD) phenotype, has modest diagnostic utility, and high scores are associated with severity of psychopathology and poor outcome. Recently, a genomewide linkage scan of this measure in ADHD sibling pairs revealed a region of suggestive linkage on chromosome 2q21. The current study aimed to further identify quantitative trait loci that influence the CBCL-JBD phenotype by using a dense and thus, arguably, more powerful set of single-nucleotide polymorphism markers in a different ADHD sibling pair sample. Subjects were 765 individuals from 154 families with CBCL data enrolled in a linkage study of ADHD. Linkage analyses were completed using a multipoint maximum likelihood variance components approach implemented using the statistical program SOLAR. Heritability of the CBCL-JBD phenotype was estimated at .71. Although no regions of the genome surpassed empirically derived criteria for significant linkage (p = .000038), peaks on 1p21.1 (p = .00037; LOD = 2.76), 6p21.3 (p = .00054; LOD =2.60), and 8q21.13 (p = .00081; LOD = 2.44) surpassed the threshold for suggestive linkage (p = .002). These regions have been highlighted in genomewide scans of bipolar disorder in adults, schizophrenia, autism, and ADHD. Findings raise the possibility that genes in these regions influence variation on the CBCL-JBD scale and the emotional and behavioral dysregulation associated with severe psychopathology.

Heritable and non-genetic factors as variables of pharmacologic phenotypes in lymphoblastoid cell lines

Publicly available genetic and expression data on lymphoblastoid cell lines (LCLs) make them a unique resource for understanding the genetic underpinnings of pharmacological outcomes and disease. LCLs have been used for pharmacogenomic discovery and validation of clinical findings associated with drug response. However, variation in cellular growth rate, baseline Epstein-Barr virus (EBV) copy number and ATP levels can all be confounders in such studies. Our objective is to better define confounding variables that affect pharmacological end points in LCLs. To this end, we evaluated the effect of these three variables on drug-induced cytotoxicity in LCLs. The drugs evaluated included daunorubicin, etoposide, carboplatin, cisplatin, cytarabine, pemetrexed, 5'-deoxyfluorouridine, vorinostat, methotrexate, 6-mercaptopurine, and 5-fluorouracil. Baseline ATP or EBV copy number were not significantly correlated with cellular growth rate or drug-induced cytotoxicity. In contrast, cellular growth rate and drug-induced cytotoxicity were significantly, directly related for all drugs except vorinostat. Importantly, cellular growth rate is under appreciable genetic influence (h²=0.30-0.39) with five suggestive linkage regions across the genome. Not surprisingly, a percentage of SNPs that significantly associate with drug-induced cytotoxicity also associate with cellular growth rate (P ≤ 0.0001). Studies using LCLs for pharmacologic outcomes should therefore consider that a portion of the genetic variation explaining drug-induced cytotoxicity is mediated via heritable effects on growth rate.

A genome-wide linkage and association scan reveals novel loci for autism

SummaryAlthough autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1. Genome-wide association studies (GWAS) using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits (http://www.genome.gov/26525384). Consequently, we initiated a linkage and association mapping study using half a million genome-wide SNPs in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed a SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 × 10−7). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening while the discovery of a single novel association demonstrates the action of common variants.

Mutations in the Lipase H Gene Underlie Autosomal Recessive Woolly Hair/Hypotrichosis

Woolly hair (WH) is characterized by the presence of fine and tightly curled hair. WH can appear as a symptom of some systemic diseases, or without associated findings (nonsyndromic WH). Nonsyndromic WH is known to be inherited as either an autosomal-dominant (OMIM 194300) or recessive (ARWH; OMIM 278150) trait. In this study, we identified 11 consanguineous families of Pakistani origin with ARWH, as well as associated features including sparse and hypopigmented hair shafts. We first checked for mutations in the P2RY5 gene, which encodes an orphan G-protein-coupled receptor that we recently identified as a cause of ARWH. However, none of the 11 families had mutations in the P2RY5 gene. To identify the disease locus, we performed linkage studies in one of these families using the Affymetrix 10K array, and identified a region of suggestive linkage on chromosome 3q27. This region contains the lipase H (LIPH) gene which has been recently shown to underlie an autosomal-recessive form of hypotrichosis. Mutation analysis resulted in the identification of a total of 5 pathogenic mutations in the LIPH of all 11 families analyzed. These results show that LIPH is a second causative gene for ARWH/hypotrichosis, giving rise to a phenotype clinically indistinguishable from P2RY5 mutations.

Association of amyloid precursor protein-binding protein, family B, member 1 with nicotine dependence in African and European American smokers

Although epidemiological studies reveal that cigarette smoking is inversely associated with Alzheimer's disease (AD) and Parkinson's disease (PD), the underlying mechanism remains largely unknown. Considering the facts that amyloid precursor protein-binding protein, family B, member 1 (APBB1) is mapped to a suggestive linkage region on chromosome 11 for nicotine dependence (ND), and has been implicated in the pathogenesis of AD and PD, it represents a plausible candidate for genetic study of ND. Five single nucleotide polymorphisms (SNPs) within APBB1 were genotyped in a sample consisting of 2,037 participants of either African-American (AA) or European-American (EA) origin, and examined their associations with ND assessed by three commonly used measures: Smoking Quantity (SQ), the Heaviness of Smoking Index (HSI), and the Fagerström Test for ND (FTND). Individual SNP-based association analysis showed that all five SNPs are associated with at least one ND measure in one of the three samples; however, only the association of SNP rs4758416 with SQ and HSI remained significant after correction for multiple testing in the pooled sample. Haplotype analysis demonstrated three major haplotypes significantly associated with ND after Bonferroni correction. Formed by rs4758416-rs10839562-rs1079199, haplotype C-C-T showed positive association with FTND in the AA and pooled samples, and conversely, haplotype G-C-T showed negative association with SQ and HSI in AA and EA samples. Another haplotype, C-T-G, formed by rs10839562-rs1079199-rs8164, was significantly associated with HSI in the EA sample. Based on these findings, we conclude that APBB1 represents an important candidate gene in the genetic study on ND and neurodegenerative diseases and warrants further investigation in future.

Genetic Variation in the Dopamine Pathway and Smoking Cessation

Twin and family studies have established that genetic factors account for much of the variation in tobacco dependence. Therefore, identification of genetic variants predictive of successful smoking cessation has implications for the future prospect of personalized smoking cessation therapies. Converging data implicate the dopamine pathway as an important neural substrate for tobacco dependence. Several candidate genes within the dopamine pathway (e.g., DRD2 and COMT) have been reported to be associated with the efficacy of bupropion and nicotine replacement therapy, and others (e.g., SLC6A3 and DRD4) have been reported to be associated with smoking cessation independent of pharmacotherapy. However, few of these candidate genes are present within regions of suggestive or significant linkage or overlap with genome-wide linkage or association studies of tobacco dependence or smoking cessation. Future studies should seek to replicate genome-wide association analyses with individual-level genotyping, and use better-defined smoking cessation phenotypes. Once robust evidence for association is established, which may take several more years, further research into the likely cost-effectiveness, feasibility and acceptability of personalized medicine for smoking cessation will be necessary before it can be translated into practice.

The association of primary hyperparathyroidism and primary ovarian failure: a de novo t(X; 2) (q22p13) reciprocal translocation

A 40-year-old female presented with primary amenorrhoea at 17 years of age. She was tall at 98th centile for height with eunuchoidal body habitus. Her breast development was Tanner stage 3, pubic and axillary hair Tanner stage 4 with normal external genitalia. Her bone age was 13.4 years at a chronological age of 17.8 years. Gonadotrophins were elevated indicating primary ovarian failure. A diagnostic laparotomy revealed hypoplastic, infantile uterus with bilateral streak gonads. Chromosomal analysis showed a balanced reciprocal translocation 46X, t(X; 2) (q22 p13). She became pregnant by in vitro fertilization with egg donation at the age of 36 years. At 13 weeks of gestation, she presented with intractable vomiting. She had raised corrected serum calcium and parathyroid hormone concentrations consistent with the diagnosis of primary hyperparathyroidism (PHPT). She underwent parathyroidectomy at 24 weeks of gestation with removal of a large left inferior parathyroid adenoma which normalized her serum calcium. Multipoint linkage from a genome-wide screen has identified a region of suggestive linkage on chromosome 2p13.3-14 in some cases of familial isolated hyperparathyroidism (FIHP). To our knowledge, this is the first case of primary amenorrhoea due to reciprocal translocation involving chromosome 2 and the X chromosome associated with PHPT. PHPT in this case is most likely to be as a result of chromosome 2 involvement where a locus for FIHP has been identified. Identification of the gene involved on chromosome 2p13.3-14 will be of considerable interest.

Linkage analysis of attention deficit hyperactivity disorder

Results of behavioral genetic and molecular genetic studies have converged to suggest that both genes contribute to the development of ADHD. Although prior linkage studies have produced intriguing results, their results have been inconsistent, with no clear pattern of results emerging across studies. We genotyped 5,980 SNPs across the genome in 1,187 individuals from families with children diagnosed with ADHD. We then performed two nonparametric linkage analyses on ADHD families: (1) an affected sibling pair linkage analysis on 217 families with 601 siblings diagnosed with ADHD and (2) a variance components linkage analysis using the number of ADHD symptoms as the phenotype on 260 families with 1,100 phenotyped siblings. The affection status linkage analysis had a maximum LOD score of 1.85 on chromosome 8 at 54.2 cM. The maximum LOD score in the variance components linkage analysis was 0.8 on chromosome 8 at 93.4 cM. The absence of regions of significant or suggestive linkage in these data suggest that there are no genes of large effect contributing to the ADHD phenotype.

Evidence of linkage to chromosome 1 for early age of onset of rheumatoid arthritis and HLA marker DRB1 genotype in NARAC data

Focusing on chromosome 1, a recursive partitioning linkage algorithm (RP) was applied to perform linkage analysis on the rheumatoid arthritis NARAC data, incorporating covariates such as HLA-DRB1 genotype, age at onset, severity, anti-cyclic citrullinated peptide (anti-CCP), and life time smoking. All 617 affected sib pairs from the ascertained families were used, and an RP linkage model was used to identify linkage possibly influenced by covariates. This algorithm includes a likelihood ratio (LR)-based splitting rule, a pruning algorithm to identify optimal tree size, and a bootstrap method for final tree selection.The strength of the linkage signals was evaluated by empirical p-values, obtained by simulating marker data under null hypothesis of no linkage. Two suggestive linkage regions on chromosome 1 were detected by the RP linkage model, with identified associated covariates HLA-DRB1 genotype and age at onset. These results suggest possible gene x gene and gene x environment interactions at chromosome 1 loci and provide directions for further gene mapping.

Comment on: Chang et al. (2007) Association Study of the Genetic Polymorphisms of the Transcription Factor 7-like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population: Diabetes 56:2631–2637

We read with interest the article by Chang et al. (1), who were the first group to report a novel allelic association (rs290487) of the TCF7L2 gene with type 2 diabetes in the Han Chinese population (1). The link between the TCF7L2 gene and type 2 diabetes in Caucasians was first reported by deCODE genetics through the fine-mapping of a previously identified suggestive linkage region on chromosome 10q. Two highly significant single nucleotide polymorphisms (SNPs), rs12255372 T-allele and rs7903146 T-allele, were reported to be in strong linkage disequilibrium with the microsatellite DG10S478. Therefore, the deCODE genetics authors recommended that these two SNPs be genotyped …

A genome‐wide linkage study in families with major depression and co‐morbid unexplained swelling

Major depressive disorder (MDD) is a common heritable condition. The diversity of the phenotype coupled with aetiological and genetic heterogeneity present formidable obstacles in the search for causative genetic loci. Studies of large families with many affected individuals, and the selection of well-defined clinical subgroups of depression, are two ways to reduce this complexity. Unexplained swelling symptoms (USS) are common in women and many patients give a strong personal and family history of depression. Co-morbid depression and swelling symptoms define a useful sub-phenotype for investigating genetic factors in depression. We have completed a genome-wide linkage analysis using 371 microsatellite markers in four families where MDD is co-morbid with USS. Of 47 affected individuals, 28 had both MDD and unexplained swelling, 11 had symptoms of swelling alone, and 8 had MDD alone. Parametric marker-specific analysis identified one suggestive locus, D8S260 (LOD = 2.02) and non-parametric multipoint variance component analysis identified a region on 7p (LOD = 2.10). A 47 cM suggestive linkage region on chromosome 14q (identified by both parametric and non-parametric methods) was identified and investigated further with fine-mapping markers but the evidence for linkage to this region decreased with increased marker information content.

The association analysis of RELN and GRM8 genes with autistic spectrum disorder in chinese han population

The region on chromosome 7q stands out as the region of suggestive linkage to aetiology of autism with the greatest concordance in many independent genome-wide scans. RELN and GRM8, the two genes selected in this study, are located within this region. The protein products of both genes are considered to play a pivotal role in the development of the central nervous system. In addition, biochemical and neuroanatomical data indicated that RELN and GRM8 genes are likely involved in the pathogenesis of autistic disorder. Therefore, both RELN and GRM8 genes are considered to be not only the positional but also the functional candidate genes to autism for association research. In this study, we genotyped 12 single nucleotide polymorphisms (SNPs) located within the RELN and GRM8 genes in 213 children with autistic spectrum disorder (ASD) and 160 controls. A significant genetic association between SNP2 (located in intron 59 of RELN) and ASD was observed, and the log-additive model was accepted as the best inheritance model fitting this data (OR: 0.72, 95% CI: 0.54-0.97, P = 0.03). Haplotype-specific association analysis revealed that the result was consistent with the individual SNP study; the combination of SNP1/SNP2/SNP3/SNP4 which are in strong linkage disequilibrium (LD) (D' > 0.75) showed significant association with ASD (P = 0.027). Neither the single SNP nor the haplotype analysis showed significant association between ASD and the markers of GRM8 gene. Hence, our study suggested the possible involvement of RELN gene in the susceptibility to ASD. Future replications are warranted before definitive conclusion can be drawn.

Genome-Wide Linkage Scan of a Large Family with IgA Nephropathy Localizes a Novel Susceptibility Locus to Chromosome 2q36

IgA nephropathy (IgAN) is the most common glomerulonephritis worldwide and an important cause of ESRD. Familial clustering of cases suggests genetic predisposition to this disease. Two recent genome-wide studies in IgAN have identified a major susceptibility locus on chromosome 6q22 (IGAN1) and two additional loci with suggestive linkage signals on chromosomes 4q26-31 and 17q12-22. A large four-generation family with 14 affected individuals has been clinically ascertained and excluded from linkage to these loci. A genome-wide linkage scan was performed on this family with GeneChip Mapping 10K 2.0 Arrays using an "affected-only" strategy. By nonparametric analysis, two regions of suggestive linkage (multipoint logarithm of odds [LOD] scores >2) were identified on chromosomes 2q36 and 13p12.3. By parametric analysis (assuming an autosomal dominant inheritance, a disease allele frequency of 0.001, phenocopy rate of 0.01, and penetrance of 75%), a significant linkage to chromosome 2q36 (maximum multipoint LOD score 3.47) was found. Nine simple sequence repeat markers then were genotyped in 21 members (included all of the affected individuals), and significant linkage to chromosome 2q36 over a region of 12.2 cM (maximum multipoint LOD score 3.46) was confirmed. Recombination events in two affected individuals, as detected by haplotype analysis, delineated a critical interval of approximately 9 cM (equivalent to approximately 7 Mb) between D2S1323 and D2S362. Taken together, these data provide strong evidence for a novel disease susceptibility locus for familial IgAN.

Episodic vertical oscillopsia with progressive gait ataxia: clinical description of a new episodic syndrome and evidence of linkage to chromosome 13q

We describe four families with late onset episodic vertical oscillopsia and progressive gait ataxia. Probands presented between the ages of 40 and 64 years with initial symptoms of episodic vertical...