Top PDF Detecting rare variants in case-parents association studies.

Detecting rare variants in case-parents association studies.

Detecting rare variants in case-parents association studies.

In human medical genetics, one often hypothesizes that genetic susceptibility to common diseases such as diabetes is mainly due to the alleles that have moderate frequencies in the population. However, there is increasing evidence showing that there is extreme allelic and locus heterogeneity and multiple rare variants underlie susceptibility to such diseases. [1,2] So far, GWASs, focusing mainly on common single nucleotide polymorphisms (SNPs), have detected over 2000 loci associated with diseases and traits [3]. However, many identified SNPs have very small effect sizes and the proportion of heritability explained by common variants is only modest [4]. Recently, Cirulli and Goldstein [5] evaluated the evidence for an important role of rare variants of major effect in common diseases and suggested the hypothesis that multiple rare gene variants, each with moderate to high penetrance, could play an important role in common diseases [6–8]. Some studies have demonstrated that both common and rare alleles may lead to the same disease. For examples, multiple rare mutations were found to be related to early-onset Alzheimer’s disease [9]. Rare mutations in genes involved in immune response also confer a high risk for lupus [10]. An effective way to discover disease-associated rare variants is through direct sequencing of relevant regions (for examples, linkage regions, all exons, all promoters). Botstein and Risch [11] suggested study of nonsynon- ymous SNPs in common diseases. With the advances in resequencing technologies, many believed that it is possible to
Mostrar mais

9 Ler mais

A unified method for detecting secondary trait associations with rare variants: application to sequence data.

A unified method for detecting secondary trait associations with rare variants: application to sequence data.

Next-generation sequencing has made possible the detection of rare variant (RV) associations with quantitative traits (QT). Due to high sequencing cost, many studies can only sequence a modest number of selected samples with extreme QT. Therefore association testing in individual studies can be underpowered. Besides the primary trait, many clinically important secondary traits are often measured. It is highly beneficial if multiple studies can be jointly analyzed for detecting associations with commonly measured traits. However, analyzing secondary traits in selected samples can be biased if sample ascertainment is not properly modeled. Some methods exist for analyzing secondary traits in selected samples, where some burden tests can be implemented. However p-values can only be evaluated analytically via asymptotic approximations, which may not be accurate. Additionally, potentially more powerful sequence kernel association tests, variable selection-based methods, and burden tests that require permutations cannot be incorporated. To overcome these limitations, we developed a unified method for analyzing secondary trait associations with RVs (STAR) in selected samples, incorporating all RV tests. Statistical significance can be evaluated either through permutations or analytically. STAR makes it possible to apply more powerful RV tests to analyze secondary trait associations. It also enables jointly analyzing multiple cohorts ascertained under different study designs, which greatly boosts power. The performance of STAR and commonly used RV association tests were comprehensively evaluated using simulation studies. STAR was also implemented to analyze a dataset from the SardiNIA project where samples with extreme low-density lipoprotein levels were sequenced. A significant association between LDLR and systolic blood pressure was identified, which is supported by pharmacogenetic studies. In summary, for sequencing studies, STAR is an important tool for detecting secondary-trait RV associations.
Mostrar mais

13 Ler mais

Differing roles for TCF4 and COL8A2 in central corneal thickness and fuchs endothelial corneal dystrophy.

Differing roles for TCF4 and COL8A2 in central corneal thickness and fuchs endothelial corneal dystrophy.

Although several rare mutations causing familial, early-onset FECD and rare variants associated with late-onset FECD have been identified [13,14,27,30,38–40,56,57], our current knowledge of the heritable causes of late-onset FECD is severely limited. No causal variant has been identified that is common in the population and that is of relatively modest effect. To date, the locus most consistently replicated in association studies on late- onset FECD has been TCF4 [15–19]. In samples of European descent, highly significant association has been reported specifi- cally with a particular SNP, rs613872, with large per-allele ORs of between 4.0 and 5.5 [15–17,19], consistent with our estimate of 6.0 (Fig. 1). Because it resides in intron 3 of TCF4, the causal locus at or captured by rs613872 is most likely a regulatory locus and not a coding variant. Indeed, the G allele of rs613872 was absent in a small Chinese sample of FECD cases and controls, but another SNP in intron 3, rs17089887, showed significant association with an odds ratio of 2.57 for each minor allele T [18]. These findings point to either an unknown, shared causal variant in the Chinese and European populations, or a multiplicity of common variants. Linkage to a broader region encompassing TCF4 has also been reported [16,58], strengthening the case that the association signals reflect true linkage disequilibrium between this SNP and a causal variant, although the action of TCF4 may be independent of the FCD2 locus at chromosome 18q21.2–21.32 [17]. The gene product of TCF4, E2-2, is found in the developing corneal endothelium [15], but changes in the endothelial cell density associated with FECD are not apparent in carriers of the rs613872 G allele in early adulthood [59]. The precise mechanism by which E2-2 alters the structure of the cornea is unknown, but is likely to involve regulation of genes involved in cell growth and differentiation. E2-2, after binding to b-catenin, has been shown to maintain multipotency of corneal epithelial stem cells via the Wnt1 pathway [60], and to activate ZEB1, a zinc-finger transcription factor which in turn is involved in dedifferentiation of epithelial cells [61] as well as mediating collagen I deposition. We have confirmed the association and strong effect of the rs613872 variant on FECD and CCT in our multi-center sample of FECD cases and controls. However, while the association with FECD persisted when the phenotype was adjusted for independent effects on CCT, the association with CCT was lost when CCT was adjusted for FECD grade, suggesting that this SNP, or the causal variant tagged by it, affects CCT via its influence on FECD severity.
Mostrar mais

10 Ler mais

Utilizing mutual information for detecting rare and common variants associated with a categorical trait

Utilizing mutual information for detecting rare and common variants associated with a categorical trait

We propose the mutual information based test (MIT) and adjust one (aMIT) to detect the association between multiple genetic variants and a categorical trait, which are intuitive and easily implemented. More importantly, the relative distribution of genetic variants is across all sites, not based on genotype patterns of each site. Through a range of simulation studies with varied combinations of the numbers of variants of rare causal (RC), rare non-causal, common causal (CC), and common non-causal, deleterious and protective, various minor allele frequencies (MAF) and different levels of linkage disequilibrium (LD), we demonstrate that our methods have higher power than the existing ones in terms of detecting functional variants. The robustness of the proposed test statistics to the proportions of alleles of rare to common, causal to non-causal, deleterious to protective, and linkage disequilibrium amount from weak to strong, is also shown in the simulation results. To further manifest the benefit of the proposed tests, we apply them to the data from the Collaborative Study on the Genetics of Alcoholism (COGA) which focuses on detecting ethanol-associated genes. The outputs show that MIT and aMIT are effective and powerful for dealing with the categorical trait.
Mostrar mais

22 Ler mais

Blocking approach for identification of rare variants in family-based association studies.

Blocking approach for identification of rare variants in family-based association studies.

Investigators often use either population-based or family-based sampling designs to study the genetic basis of complex diseases. A population-based design samples affected and unaffected individ- uals who are unrelated, such as case-control samples. Almost all the methods proposed in the literature for detecting rare variant associations, including those discussed above, are for case-control studies. On the other hand, a family-based design treats a family as a sampling unit, which can be as simple as trios or as complex as large extended pedigrees with potentially multiple affected individuals per pedigree. For family studies, half of the offspring are expected to inherit a copy of the minor allele from a parent who has a copy of it. Therefore, variants that are rare in the general population could be quite common in certain families and are potentially more informative. Aggregation-based rare variant tests for analyzing family-data, however, are very limited and in fact only a handful have been proposed to date. Zhu et al. (2010) [13] propose a two-stage method that utilizes part of the data set to co-classify rare risk haplotypes either by unrelated-case or affected sibpair design, while the rest is used for association testing. It was demonstrated that the affected sibpair design has better power to co-classify rare risk haplotypes than the unrelated-case design due to the risk haplotype frequencies being more enriched in affected sibpairs than in affected cases. Similarly, Feng et al [14] developed a sibpair-based weighted sum statistic to detect both rare and common risk variants residing in a gene or a genomic region. Neither method models phenotypic or genetic correlations between related individuals and they cannot be used to analyze pedigree samples. Natural extensions of existing tests for popula- tion-based designs to family designs have also taken place in the literature. Two recent studies extended the idea of SKAT to family data [15,16], but they only deal with quantitative traits. There is also an extension of a popular family-based association test (FBAT) to test for variants jointly over a region of interest [17]. Although the method can be used for both quantitative and qualitative traits, it relies on sometimes unrealistic assumption that all variants have effects in the same direction.
Mostrar mais

11 Ler mais

Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants.

Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants.

Association tests that pool minor alleles into a measure of burden at a locus have been proposed for case-control studies using sequence data containing rare variants. However, such pooling tests are not robust to the inclusion of neutral and protective variants, which can mask the association signal from risk variants. Early studies proposing pooling tests dismissed methods for locus-wide inference using nonnegative single-variant test statistics based on unrealistic comparisons. However, such methods are robust to the inclusion of neutral and protective variants and therefore may be more useful than previously appreciated. In fact, some recently proposed methods derived within different frameworks are equivalent to performing inference on weighted sums of squared single-variant score statistics. In this study, we compared two existing methods for locus-wide inference using nonnegative single-variant test statistics to two widely cited pooling tests under more realistic conditions. We established analytic results for a simple model with one rare risk and one rare neutral variant, which demonstrated that pooling tests were less powerful than even Bonferroni-corrected single-variant tests in most realistic situations. We also performed simulations using variants with realistic minor allele frequency and linkage disequilibrium spectra, disease models with multiple rare risk variants and extensive neutral variation, and varying rates of missing genotypes. In all scenarios considered, existing methods using nonnegative single-variant test statistics had power comparable to or greater than two widely cited pooling tests. Moreover, in disease models with only rare risk variants, an existing method based on the maximum single-variant Cochran-Armitage trend chi-square statistic in the locus had power comparable to or greater than another existing method closely related to some recently proposed methods. We conclude that efficient locus-wide inference using single-variant test statistics should be reconsidered as a useful framework for devising powerful association tests in sequence data with rare variants.
Mostrar mais

15 Ler mais

A HuGE Review and Meta-Analyses of Genetic Associations in New Onset Diabetes after Kidney Transplantation.

A HuGE Review and Meta-Analyses of Genetic Associations in New Onset Diabetes after Kidney Transplantation.

New onset diabetes after transplantation (NODAT), also known as post transplantation diabe- tes mellitus (PTDM), is a serious complication of solid organ transplantation [1]. It affects 2–50%[1–3] of organ transplant recipients and is associated with greater healthcare costs and an increased risk of graft failure, cardiovascular complications and death [4]. The wide varia- tion in reported prevalence of NODAT in part reflects the varying clinical definitions of this disorder. In different clinical studies the NODAT phenotype has been defined by various crite- ria including elevated fasting blood glucose; abnormal oral glucose tolerance tests; elevated gly- cated haemoglobin (HbA1c) or absolute requirement for hypoglycaemic therapies following solid organ transplantation [5,6]. A number of modifiable and non-modifiable risk factors have been identified which may predict NODAT. Modifiable risk factors include obesity and choice of anti-rejection immunosuppression medication [7]. Patients receiving tacrolimus- based immunosuppressive regimens are at greater risk of developing NODAT compared to those prescribed ciclosporin-based immunosuppressive treatment [8]. However, choosing an immunosuppressive regimen to specifically avoid NODAT may have a damaging effect on the graft itself [1]. Non-modifiable risk factors include family history of diabetes mellitus, polycys- tic kidney disease, hepatitis C infection, female gender and older recipient age [9,10]. There is an established genetic component to NODAT, however the identification of genetic risk factors has proved challenging. It is well documented that ethnicity is an important risk factor; people of African American, Hispanic, or South Asian background are at a significantly increased risk of developing the disease [5]. Low plasma adiponectin concentration, a factor which is under significant genetic control [11], has also been demonstrated to be predictive for NODAT [12]. Genome-wide association studies (GWAS) are revealing SNPs associated with diabetes, which are replicated across multiple populations [13,14], but such robust multi-centre GWAS have not yet been published for NODAT. However, multiple publications have reported genetic associations with NODAT in the literature, often with inconsistent results [1]; this report describes an inclusive review and meta-analysis of existing data.
Mostrar mais

13 Ler mais

Systemic sclerosis, a rare case

Systemic sclerosis, a rare case

Systemic sclerosis (SS) is a rare severe autoimmune disease involving the connective tissue. The patho- physiology is not clearly understood. It is charac- terized by a remarkable clinical heterogeneity, and virtually all organs can be affected. Concerning diag nosis, the presence of antinuclear antibodies (ANA) can be found in more than 90% of patients, but the diagnosis is made gathering clinical mani- festations, autoimmune panel, nailfold capil- laroscopy and in some cases biopsy of the organ in- volved. The disease course is also weakly under- stood, although some serological patterns can be distinguished. Current therapeutic options target few aspects of pathologic mechanism and clinical management remains a challenge.
Mostrar mais

5 Ler mais

Rare association between pernicious anemia and neurogenic bladder : a case report and literature review

Rare association between pernicious anemia and neurogenic bladder : a case report and literature review

Laboratory tests at admission evidenced a macrocytic and normochromic anemia (Hb 8.26g/dL, MCV 121fL, MCH 45.2pg, MCHC 37.4g/dL), accentuated decreased vitamin B 12 levels (< 100 pg/mL), increased erythrocyte sedimentation rate (52mm), positive rheumatoid factor (46 IU/mL) and normal renal function. An uretero-cystography revealed a flaccid and distended bladder (Figure 2). The diagnosis of neurogenic bladder was then stated. Serologies for syphilis, toxoplasmosis, viral hepatitis, HIV and CMV were all Fig.-1: Rheumatoid arthritis findings - ulnar deviation in both hands and swan neck deformity in left fingers.
Mostrar mais

4 Ler mais

Sao Paulo Med. J.  vol.132 número4

Sao Paulo Med. J. vol.132 número4

a well-defined, heterogeneous, ovoid mass with fat com- ponent and peripheral speckled calcifications, which mea- sured 5.3 × 4.6 × 6 cm, located at the upper pole of the right kidney (Figures 1A and 1B). Contrast-enhanced computed tomography showed slight enhancement of the solid compo- nent of the mass in the portal venous phase. On December 12, 2012,  the patient underwent laparoscopic right adrenal gland resection because the possibility of malignant tumors could not be ruled out clinically. Pathological examination revealed a smoothly and completely encapsulated and mod- erately firm oval mass, measuring 6 × 5 × 4.5 cm and weigh- ing 150 g, with a cross-section of reddish-brown and ash-gray organized hematoma (Figure 1C). The  opened mass con- tained some areas of necrosis, and the tissue was extremely heterogeneous. Histopathological evaluation showed a cav- ernous hemangioma with erythrocytes filling the lacu- nae, which was lined with a single layer of endothelial cells (Figures 1D and 1E). Areas of hemorrhage and small focal calcifications were observed. Atrophy of the adrenal cortex was present under the tumor capsule. There was no evidence of malignancy. Immunohistochemical examination revealed vessels lined with vascular endothelial cells that were spe- cifically positive for CD31, CD34 and blood coagulation factor VIII (Figures 1F, 1G and 1H), demonstrating their endothelial nature. On December 17, 2012, the patient was discharged from the hospital.
Mostrar mais

4 Ler mais

A Rare Case of Mucormycosis in the Scalp

A Rare Case of Mucormycosis in the Scalp

Early diagnosis, the patient’s immune status and ac- companying factors play significant roles in successful treatment of patients with mucormycosis. The use of am- photericin-B is highly effective for the treatment of cutane- ous lesions as in our case. In our case, despite the visual loss, deepening of invasion was prevented by the treatment of Amphotericin B, and the patient’s life was saved. How- ever Melsom et al. were presented a case with non-insulin Figure 3 - Lactophenol cotton blue staining of cultivated mold (origi-

5 Ler mais

Rev. Bras. Reumatol.  vol.53 número6 en v53n6a13

Rev. Bras. Reumatol. vol.53 número6 en v53n6a13

Although there was no molecular verii cation, this patient likely has type 1, in which the deformities are uncommon and there may not be i nal height impairment. The altera- tions observed in extremities are characteristic of JIA without adequate treatment (Figs. 2A and 2B). Additionally, deafness is observed in only 30% of cases. 8

3 Ler mais

Challenges in whole exome sequencing: an example from hereditary deafness.

Challenges in whole exome sequencing: an example from hereditary deafness.

results of the exome sequencing. For the five autozygous regions much variation on the read depth was observed. Using a minimum depth of 8 as a filter, the chromosome 8 region has high average read depth of 1016 with 92% coverage compared to the chromosome 19 region which has low average read depth of 156 with 38% coverage (Figure 2A). There was a strong negative correlation (r = 20.96) between the percentage of gunanine cytosine (GC) bases and the read depth or coverage of autozygous regions (Figure 2B). We focused on exonic and flanking intronic variants within these five autozygous regions. Table 2 shows the four novel homozygous missense, nonsense, splice site and frame shift variants (not reported in dbSNP132) in the five autozygous regions when we used a filter of minimum 86 read depth. Sanger sequencing confirmed one novel missense variant in the second longest autozygous region on chr8 (76476256A.T) in HNF4G (MIM 605966) and one novel missense variant in the third longest autozygous region on chr19 (2917947C.T) in ZNF57 (no MIM number available) (nucelotide numbers are according to Hg19). We then recruited additional family members who were not typed with Affymetrix 6.0 chips to evaluate co-segregation of these variants. The novel variant c.1263A.T (p.Q421H) in HNF4G did not co-segregate with the phenotype in the entire family but variant c.1328C.T (p.T443M) in ZNF57 did (Figure 1A and C). For the variant in ZNF57 PolyPhen2 classification was possibly damaging with a score of 0.938, MutPred predicted that T443M amino acid substitution caused a gain of catalytic residue at V439 (p = 0.0472) and predicted the g score (probability of deleterious mutation) of 0.497 [15,22]. Four coding exons and intron-exon
Mostrar mais

7 Ler mais

Pulmonary Lymphangioleiomyomatosis: A Rare Case

Pulmonary Lymphangioleiomyomatosis: A Rare Case

Macroscopically, the specimen from the let lower lobe was 4 x 2.5 x 1.5 cm and from the upper lobe was 4 x 1.8 x 1.5cm, both with cystic features on the cut surface (Figure 2). On microscopic examination, proliferating LAM cells, heterogeneous epithelioid and spindle-shaped immature muscle-like proliferating cells, were found in the cystic space of the lung parenchyma (Figure 3). An immunohistochemical stain was positive for contractile proteins (smooth muscle actin and desmin), the melanocytic marker HMB-45 (Figure 4), estrogen receptor (ER), progesterone receptor (PR), and CD56 in the LAM cells. Pan cytokeratin, EMA, CEA, S-100 protein, chromogranin, and CD34 stains were negative. he Ki-67 proliferation index was 1%.
Mostrar mais

4 Ler mais

CASE REPORT: Chorangiophagus Parasiticus: A Rare Case Report

CASE REPORT: Chorangiophagus Parasiticus: A Rare Case Report

Malformations are common in twin pregency compared to singleton pregnancy. One such rare anomaly is Chorangiophagus parasiticus also known as twin to twin transfusion which is an asymmetric abnormality of monozygotic twins, where asymmetric twin survive by parasitisizing normal twin. It’s a rare condition with an inci- dence of 1 in 35.000 deliveries. We report such a case with complete autopsy findings.

3 Ler mais

SUBLINGUAL DERMOID CYST A RARE CASE – CASE REPORT

SUBLINGUAL DERMOID CYST A RARE CASE – CASE REPORT

INTRODUCTION: Development of face, head and neck is a very balanced and co-ordinated process during which the process from pharyngeal arches fuses in midline. A small piece of epidermis may get entrapped deep in the mid line, during the mandibular processes from both sides fuses together. This residual entrapped epidermis later in life may proliferate under some stimulus to form a cystic enlargement either above or below the tongue. The term sublingual dermoid cysts was first used Roser (1859) maintained that many cases of ranula and sebaceous cysts on the base of the tongue were dermoid cysts. 1
Mostrar mais

4 Ler mais

Case studies in chemistry teacher education.

Case studies in chemistry teacher education.

Esta proposta consistiria em uma boa oportunidade para o li- cenciando testar as suas competências didáticas, sua capacidade de planejamento e levaria a uma sistemática do Ensi[r]

7 Ler mais

Cognitive manic symptoms in bipolar disorder associated with polymorphisms in the DAOA and COMT genes.

Cognitive manic symptoms in bipolar disorder associated with polymorphisms in the DAOA and COMT genes.

The dopaminergic pathway is implicated in the neurobiology of cognitive function, and there are genetic associations with functional COMT genotypes related to performance on the neuropsychological tests in bipolar disorder, schizophrenia, ADHD, and in the general population [4,36,39]. Bipolar 1 disorder patients assessed during depressive and manic episodes showed the methionine (Met) allele of COMT to be related to lower test scores compared to healthy controls [4]. The Egan study examined schizophrenic patients, healthy siblings and healthy controls, investigating genetic effects of COMT related to neuropsychological test performance. The methionine (Met) variant of Val158Met COMT genotype was associated with enhanced cognitive performance and more efficient response in PFC. Furthermore, there was no significant difference between patients, siblings, or controls, thus the COMT genotype association with cognitive manic symptoms was found to be independent of psychiatric diagnosis or risk [36]. This finding was replicated by Malhotra in healthy subjects [38]. There are similar findings of cognitive manic symptoms in working memory in schizophrenic patients, healthy siblings, and controls [37]. However, in children diagnosed with ADHD, examined in a family-based control design, the low activity Met allele was associated with reduced performance [39], opposed to the finding in the Egan study. In addition, it has been shown that COMT polymorphisms have pleiotropic effect in PFC [41,42].
Mostrar mais

7 Ler mais

Cisto ósseo simples de mandíbula: um caso raro de ocorrência bilateral

Cisto ósseo simples de mandíbula: um caso raro de ocorrência bilateral

A 22-year-old male patient was refer- red by an orthodontist because of asymptoma- tic radiolucent areas on routine radiographs. The physical examination showed no bulging of the mandibular cortex, displa- cement, mobility, or loss of vitality of teeth adjacent to the pathologic areas. The patient reported no local trauma. Blood work-up (serum calcium, phosphorous, alkaline phos- phatase, and PTH) were within normal limits. Radiographic findings consisted of two unilocular radiolucent areas with a sclerotic halo that did not cause absorption of tooth roots, and that were located in the left parasymphyseal region in the mandible (measuring about 2.5 cm) and the right body of the mandible (diameter of about 2 cm) (Figure 1).
Mostrar mais

1 Ler mais

A RARE CASE OF BILATERAL MICROSPHEREPHAKIA

A RARE CASE OF BILATERAL MICROSPHEREPHAKIA

ABSTRACT: Microspherophakia is rare bilateral congenital anamoly of the crystalline lens. The condition may be isolated, familial or it may be associated with systemic affections like Marfan's syndrome, Weil-Marchesani syndrome, hyperlysinemia and congenital rubella. Microspherophakia results in lenticular myopia, lens dislocation, usually inferiorly and inverse glaucoma. We present a case in a 8 year old child who presented with bilateral microspherophakia and anterior dislocation of lens of right eye. visual acuity in right eye was counting fingers close to face and in left eye 6/60.IOP with perkins applanation tonometer was 30mmHg in right eye 22mmHg in left eye, cornea was hazy due to edema, anterior chamber was shallow in both eye patient was managed with emergency lens extraction of right eye and secondary ACIOL implantation. Left eye was managed by laser peripheral iridotomy. IOP was within normal limits postoperatively in both eyes without any antiglaucoma medications. Postoperatively best corrected visual acuity in right was 6/18 and 6/9 in left eye.
Mostrar mais

4 Ler mais

Show all 10000 documents...