Thyroid carcinomas that occur in familial adenomatous polyposis patients recurrently harbor somatic variants in APC, BRAF, and KTM2D

Background: Familial adenomatous polyposis (FAP) is a condition typically caused by pathogenic germline mutations in the APC gene. In addition to colon polyps, individuals with FAP have a substantially increased risk of developing papillary thyroid cancer (PTC). Little is known about the events underlying this association, and the prevalence of somatic "second-hit" mutations in APC is controversial. Methods: Whole-genome sequencing was performed on paired thyroid tumor and normal DNA from 12 FAP patients who developed PTC. Somatic mutation profiles were compared with clinical characteristics and previously sequenced sporadic PTC cases. Germline variant profiling was performed to assess the prevalence of variants in genes previously shown to have a role in PTC predisposition. Results: All 12 patients harbored germline mutations in APC, consistent with FAP. Seven patients also had somatic mutations in APC, and seven patients harbored somatic mutations in KMT2D, which encodes a lysine methyl transferase. Mutation of these genes is extremely rare in sporadic PTCs. Notably, only two of the tumors harbored the somatic BRAF p.V600E mutation, which is the most common driver mutation found in sporadic PTCs. Six tumors displayed a cribriform-morular variant of PTC (PTC-CMV) histology, and all six had somatic mutations in APC. Additionally, nine FAP-PTC patients had rare germline variants in genes that were previously associated with thyroid carcinoma. Conclusions: Our data indicate that FAP-associated PTCs typically have distinct mutations compared with sporadic PTCs. Roughly half of the thyroid cancers that arise in FAP patients have somatic "second-hits" in APC, which is associated with PTC-CMV histology. Somatic BRAF p.V600E variants also occur in some FAP patients, a novel finding. We speculate that in carriers of heterozygous pathogenic mutations of tumor suppressor genes such as APC, a cooperating second-hit somatic variant may occur in a different gene such as KTM2D or BRAF, leading to differences in phenotypes. The role of germline variance in genes other than APC (9 of the 12 patients in this series) needs further research.Peer reviewe

Preservation Of Redundancy In The Existence Of Developmental Error Assignment Error

Conservation of functionally identical copies of the same gene throughout the generations is not an easy task. In this study, based on the biological evidence that suggests the existence of the developmental error as one of the ways to preserve redundancy, our goal is to investigate the impact of developmental error on a simple problem using a genetic algorithm(GA). Developmental errors exist during the biological development of an individual. The biological models with developmental errors have demonstrated that it is possible to maintain redundant copies in the existence of proper mutation rates and developmental error rates. Our preliminary results with a simple problem demonstrates that using developmental error helps preserving the redundant copies and maintaining a better solution quality for the redundant copies of a gene. Besides the developmental error, we propose a new error type that comes into play during the fitness assignment and enhances the quality of the solutions when used together with developmental error. Copyright 2005 ACM

Preservation of genetic redundancy in the existence of developmental error and fitness assignment error

Conservation of functionally identical copies of the same gene throughout the generations is not an easy task. In this study, based on the biological evidence that suggests the existence of the developmental error as one of the ways to preserve redundancy, our goal is to investigate the impact of developmental error on a simple problem using a genetic algorithm(GA). Developmental errors exist during the biological development of an individual. The biological models with developmental errors have demonstrated that it is possible to maintain redundant copies in the existence of proper mutation rates and developmental error rates. Our preliminary results with a simple problem demonstrates that using developmental error helps preserving the redundant copies and maintaining a better solution quality for the redundant copies of a gene. Besides the developmental error, we propose a new error type that comes into play during the fitness assignment and enhances the quality of the solutions when used together with developmental error

multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results.

Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), most with small or moderate effect sizes, making them difficult to detect. Second, many complex traits share a common genetic basis due to 'pleiotropy' and and though few methods consider it, leveraging pleiotropy can improve statistical power to detect genotype-trait associations with weaker effect sizes. Third, currently available statistical methods are limited in explaining the functional mechanisms through which genetic variants are associated with specific or multiple traits. We propose multi-GPA-Tree to address these challenges. The multi-GPA-Tree approach can identify risk SNPs associated with single as well as multiple traits while also identifying the combinations of functional annotations that can explain the mechanisms through which risk-associated SNPs are linked with the traits. First, we implemented simulation studies to evaluate the proposed multi-GPA-Tree method and compared its performance with existing statistical approaches. The results indicate that multi-GPA-Tree outperforms existing statistical approaches in detecting risk-associated SNPs for multiple traits. Second, we applied multi-GPA-Tree to a systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), and to a Crohn's disease (CD) and ulcertive colitis (UC) GWAS, and functional annotation data including GenoSkyline and GenoSkylinePlus. Our results demonstrate that multi-GPA-Tree can be a powerful tool that improves association mapping while facilitating understanding of the underlying genetic architecture of complex traits and potential mechanisms linking risk-associated SNPs with complex traits

A Description of Oral and Swallowing Characteristics in Pediatric Patients with Neuromuscular Diseases

Objective: The aim of our study was to put forth the existing problems about oral structure/function and swallowing function in patients with different pediatric neuromuscular diseases. Methods: Forty-five pediatric patients with NMD's aged 10.22 +/- 3.32 years were included in the study. Oral intake levels of patients were determined with Functional Oral Intake Scale. Oral structural and functional examination, assessment of complaints related to swallowing problems, and three-ounce water swallow test were performed to all patients. Results: In oral assessment, structural problems were determined at varying rates between 13.3% and 46.6%, problems related to oral functions between %4.4 and 26.6%, and complaints related to swallowing problems between 11.1% to 33.3%. Five patients (%11) failed the three-ounce water swallow test. Conclusion: The findings related to oral structure/function and swallowing function indicate a risk of swallowing dysfunction with different symptoms and problems in neuromuscular diseases. These symptoms may result in life-threatening complications added to their current neuromuscular problems

Reliability And Validity Of The Turkish Translation Of Pedsql (Tm) Multidimensional Fatigue Scale In Duchenne Muscular Dystrophy

Objectives: To perform the Turkish translation, reliability, and validity study of the PedsQL (TM) -3.0 Multidimensional Fatigue Scale (PcdsQL-MFS) in patients with Duchenne Muscular Dystrophy (DMD). Methods: This prospective, cross-sectional, observational study was held in Hacettepe University, Faculty of Physical Therapy and Rehabilitation between January 2016-August 2018. Turkish translation of the PedsQL-MFS was conducted based on the steps addressed in the translation manual of the original research. The psychometric features of the Turkish version of PedsQL-MFS including feasibility, internal consistency, and test-retest reliability, construct, and criterion-related validity as well as parent/child agreement were investigated on a total of 71 children and their parents. Results: The mean age of boys with DMD included in the study was 102.94 +/- 23.23 months with a mean 17.15 +/- 2.98 BMI. Internal consistencies of Child Self Report General Fatigue, Sleep/rest Fatigue, and Cognitive Fatigue items were 0.74, 0.65, and 0.83 while. 0.89, 0.84, and 0.91 in Parent Proxy Report. The ICC values of Child Self Report and Parent Proxy Report were 0.87 and 0.91. respectively. Parent Proxy Report succeded more acceptable fit indices than Child Self Report. A statistically significant correlation was found between PedsQL-MFS and PedsQL-Neuromuscular Module (p<0.05). Moderate agreement was detected between parent and child. Conclusion: The Turkish version of PedsQL-MFS was determined to be a reliable and valid tool to evaluate fatigue in 5-12 years old, ambulant children with DMD.WoSScopu

Identification of Medium-Sized Copy Number Alterations in Whole-Genome Sequencing

The genome-wide discoveries such as detection of copy number alterations (CNA) from high-throughput whole-genome sequencing data enabled new developments in personalized medicine. The CNAs have been reported to be associated with various diseases and cancers including acute myeloid leukemia. However, there are multiple challenges to the use of current CNA detection tools that lead to high false-positive rates and thus impede widespread use of such tools in cancer research. In this paper, we discuss these issues and propose possible solutions. First, since the entire genome cannot be mapped due to some regions lacking sequence uniqueness, current methods cannot be appropriately adjusted to handle these regions in the analyses. Thus, detection of medium-sized CNAs is also being directly affected by these mappability problems. The requirement for matching control samples is also an important limitation because acquiring matching controls might not be possible or might not be cost efficient. Here we present an approach that addresses these issues and detects medium-sized CNAs in cancer genomes by (1) masking unmappable regions during the initial CNA detection phase, (2) using pool of a few normal samples as control, and (3) employing median filtering to adjust CNA ratios to its surrounding coverage and eliminate false positives

MiR-34a regulates the invasive capacity of canine osteosarcoma cell lines

<div><p>Background</p><p>Osteosarcoma (OSA) is the most common bone tumor in children and dogs; however, no substantial improvement in clinical outcome has occurred in either species over the past 30 years. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and play a fundamental role in cancer. The purpose of this study was to investigate the potential contribution of miR-34a loss to the biology of canine OSA, a well-established spontaneous model of the human disease.</p><p>Methodology and principal findings</p><p>RT-qPCR demonstrated that miR-34a expression levels were significantly reduced in primary canine OSA tumors and canine OSA cell lines as compared to normal canine osteoblasts. In canine OSA cell lines stably transduced with empty vector or pre-miR-34a lentiviral constructs, overexpression of miR-34a inhibited cellular invasion and migration but had no effect on cell proliferation or cell cycle distribution. Transcriptional profiling of canine OSA8 cells possessing enforced miR-34a expression demonstrated dysregulation of numerous genes, including significant down-regulation of multiple putative targets of miR-34a. Moreover, gene ontology analysis of down-regulated miR-34a target genes showed enrichment of several biological processes related to cell invasion and motility. Lastly, we validated changes in miR-34a putative target gene expression, including decreased expression of KLF4, SEM3A, and VEGFA transcripts in canine OSA cells overexpressing miR-34a and identified KLF4 and VEGFA as direct target genes of miR-34a. Concordant with these data, primary canine OSA tumor tissues demonstrated increased expression levels of putative miR-34a target genes.</p><p>Conclusions</p><p>These data demonstrate that miR-34a contributes to invasion and migration in canine OSA cells and suggest that loss of miR-34a may promote a pattern of gene expression contributing to the metastatic phenotype in canine OSA.</p></div

Ectopic expression of miR-34a in canine OSA cells does not affect cell proliferation or cell cycle distribution.

<p>(A) Canine OSA8 and Abrams cells were transduced with pre-miR-34a lentiviral constructs or empty control vector and sorted to greater than 95% purity based on GFP expression 72 hours following infection. Total RNA was isolated and RT-qPCR was performed as described above immediately prior to plating cells to confirm transduction efficiency miR-34a levels in wild-type (WT), empty vector (EV), and miR-34a expressing cells (*<i>p</i> < 0.05). Multiple group comparisons were analyzed by one-way ANOVA followed by Tukey-Kramer <i>post-hoc</i> comparison. (B) OSA8 and Abrams cells transduced with either empty control or pre-miR-34a lentiviral constructs were plated in complete media and the cell proliferation was assessed at 24, 48, and 72 hours using the BrdU incorporation assay. Cell proliferation was measured at 490 nm. Values of optical density (OD) are expressed as means +/- SD of 3 independent experiments. (C) OSA8 and Abrams cells expressing empty vector or pre-miR-34a lentivirus vector were incubated in complete media for 24 hours. Cells were then evaluated for effects on cell cycle using propidium iodide (PI) staining and flow cytometry. Three independent experiments were performed, and 1 representative result is presented. Linear mixed effects models were applied to OSA8 and Abrams cell line miR-34a expression, proliferation and cell cycling data to take account of the correlation among observations from the same replicates. No statistically significant difference in cell proliferation or cell cycle distribution was detected in OSA8 or Abrams cells expressing empty vector or pre-miR-34a vector for any of the tested time points (Student’s <i>t</i>-test).</p