Correction: Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy-number variants.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy number variants.

Purpose: The ability of a single technology, next-generation sequencing, to provide both sequence and copy number variant (CNV) results has driven the merger of clinical cytogenetics and molecular genetics. Consequently, the distinction between the definition of a sequence variant and a CNV is blurry. As the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) standards and guidelines for interpretation of sequence variants address CNV classification only sparingly, this study focused on adapting ACMG/AMP criteria for single-gene CNV interpretation.

Inhibitory effect of atorvastatin on the cell growth of cardiac myxomas via the PTEN and PHLPP2 phosphatase signaling pathway.

Insulin-like growth factor 1 (IGF-1) is a molecule with strong proliferative effects, and statins have been reported to exhibit antitumor effects based on clinical and experimental studies. However, their effects on cardiac myxoma (CM) cells and the underlying signaling mechanism(s) are largely unknown. Therefore, we investigated whether the protein/lipid phosphatases and tensin homolog deleted on chromosome ten (PTEN) and pleckstrin homology domain leucine-rich repeat phosphatase 1 and 2 (PHLPP1 and 2) are involved in the proliferative effect of IGF-1 on CM cells and the pharmacological impact of atorvastatin.

Alcohol consumption and breast tumor mitochondrial DNA mutations.

Mitochondrial DNA (mtDNA) mutations are frequent in breast tumors, but the etiology of these mutations is unknown. We hypothesized that these mutations are associated with exposures that affect oxidative stress such as alcohol metabolism. Using archived tumor blocks from incident breast cancer cases in a case control study, the Western New York Exposures and Breast Cancer (WEB) study, analysis of mtDNA mutations was conducted on 128 breast cancer cases selected based on extremes of alcohol intake.

Toxicological analysis of low-nicotine and nicotine-free cigarettes.

Low-nicotine and nicotine-free cigarettes are commercially available under the brand-name Quest. Some consumers may believe that these are safer cigarettes, and they may smoke more cigarettes or inhale more smoke to compensate for low nicotine yields. Thus, we have studied the toxicological effects of these two cigarettes and compared them with the Kentucky reference cigarette 2R4F.

Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

DNA alterations in mitochondria are believed to play a role in carcinogenesis and are found in smoking-related cancers. We sought to replicate earlier findings for the association of smoking with increased mitochondrial DNA (mtDNA) content in buccal cells and further hypothesized that there would be an increased number of somatic mtDNA mutations in smokers. Buccal cells and blood lymphocytes were studied from 42 healthy smokers and 30 non-smokers.

Novel mitochondrial DNA mutations associated with myopathy, cardiomyopathy, renal failure, and deafness.

Patients with mitochondrial disease usually manifest multisystemic dysfunction with a broad clinical spectrum. When the tests for common mitochondrial DNA (mtDNA) point mutations are negative and the mtDNA defects are still hypothesized, it is necessary to screen the entire mitochondrial genome for unknown mutations in order to confirm the diagnosis. We report an 8-year-old girl who had a long history of ragged-red fiber myopathy, short stature, and deafness, who ultimately developed renal failure and fatal cardiac dysfunction.

Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer.

Background: The roles of mitochondria in energy metabolism, the generation of ROS, aging, and the initiation of apoptosis have implicated their importance in tumorigenesis. In this study we aim to establish the mutation spectrum and to understand the role of somatic mtDNA mutations in esophageal cancer.

Methods: The entire mitochondrial genome was screened for somatic mutations in 20 pairs (18 esophageal squamous cell carcinomas, one adenosquamous carcinoma and one adenocarcinoma) of tumor/surrounding normal tissue of esophageal cancers, using temporal temperature gradient gel electrophoresis (TTGE), followed by direct DNA sequencing to identify the mutations.

[Heteroplasmy: a common phenomenon of mitochondrial genome mutations in human tumor tissues].

To explore the status of heteroplasmy and homoplasmy of Mitochondrial DNA somatic mutations in different tumors. DNA from 149 tumors and corresponding normal tissues were extracted and entire mitochondrial genome was amplified using 32 pairs of overlapping primers. The somatic mutations were screened by temporal temperature gradient gel electrophoresis and their heteroplasmic statute were identified by sequencing.

[Evaluation of inheritable character in essential hypertension through reconstruction of neighbor-joining tree].

To explore the inheritable character in essential hypertension and to evaluate the role of mitochondrial DNA (mtDNA) variations of the D-loop region in the pathogenesis of hypertension, the entire genome of the D-loop region from the hypertensive and the normotensive (20 cases, each) was amplified using 3 pairs of overlapping primers and followed by sequencing. We reconstructed the Neighbor-Joining tree and analyzed the mtDNA variations in the D-loop region. The results exhibited that one clustering branch harbored some hypertensive, who had significantly higher frequency and density of mtDNA variations (both P<0.

Somatic mitochondrial DNA mutations in neurofibromatosis type 1-associated tumors.

Neurofibromatosis type 1 is an autosomal dominantly inherited disease predisposing to a multitude of tumors, most characteristically benign plexiform neurofibromas and diffuse cutaneous neurofibromas. We investigated the presence and distribution of somatic mitochondrial DNA (mtDNA) mutations in neurofibromas and in nontumor tissue of neurofibromatosis type 1 patients. MtDNA alterations in the entire mitochondrial genome were analyzed by temporal temperature gradient gel electrophoresis followed by DNA sequencing.

Detection of mitochondrial DNA mutations using temporal temperature gradient gel electrophoresis.

Mitochondrial disorders are a group of clinically and genetically heterogeneous diseases. Common recurrent mitochondrial DNA (mtDNA) point mutations account for the molecular defects of a small proportion of patients. In order to identify mtDNA mutations, comprehensive mutational analysis of the entire mitochondrial genome is necessary.

Somatic mitochondrial DNA mutations in oral cancer of betel quid chewers.

Somatic mitochondrial DNA alteration is a general phenomenon that occurs in cancerous cells. Although numerous mtDNA mutations have been identified in various tumors, the pathogenic significance of these mutations remains unclear. In order to better understand the role of mtDNA mutations in the neoplastic process of oral cancer, the occurrence of mtDNA mutations in oral squamous cell carcinomas was screened by temporal temperature gradient gel electrophoresis (TTGE).

[Somatic mutation detection in complete mitochondrial DNA of lung cancer patients].

Background: To detect the somatic mutations in complete mitochondrial genome and to investigate the role of mtDNA mutation in the tumorigenesis of lung cancer.

Methods: DNA were extracted from sixteen lung cancer and corresponding normal tissues. The entire mitochondrial genome was amplified with 32 pairs of overlapping primers.

Novel heteroplasmic frameshift and missense somatic mitochondrial DNA mutations in oral cancer of betel quid chewers.

Mitochondrial DNA (mtDNA) has been proposed to be involved in carcinogenesis because of its high susceptibility to oxidative DNA damage and limited repair mechanisms. For investigation of the potential role of somatic mtDNA mutations in the tumorigenesis of oral cancer, we screened the occurrence of mtDNA mutations by the temporal temperature gradient gel electrophoresis method. We amplified the entire mitochondrial genome by use of 32 pairs of overlapping primers, and to identify the mutations, we sequenced DNA fragments showing different banding patterns between normal and tumor mtDNA.

Comprehensive scanning of the entire mitochondrial genome for mutations.

Background: Definitive molecular diagnosis of mitochondrial disorders has been greatly hindered by the tremendous clinical and genetic heterogeneity, the heteroplasmic condition of pathogenic mutations, and the presence of numerous homoplasmic mitochondrial DNA (mtDNA) variations with unknown significance. We used temporal temperature gradient gel electrophoresis (TTGE) to detect heteroplasmic mutations from homoplasmic variations in the whole mitochondrial genome.

Methods: We screened 179 unrelated patients by TTGE with use of 32 overlapping primer pairs.

Analysis of the mitochondrial DNA genome in the peripheral blood leukocytes of HIV-infected patients with or without lipoatrophy.

Objective: To investigate the molecular mechanisms of nucleoside analogue reverse transcriptase inhibitor (NRTI)-associated mitochondrial dysfunction.

Methods: Peripheral blood samples were collected from 10 healthy individuals, 10 HIV-infected, NRTI-treated patients with lipoatrophy, and four HIV-infected patients naive to all antiretrovirals. DNA was isolated from the leukocytes and the mitochondrial genome analyzed for DNA depletion, deletions and point mutations.

Comprehensive scanning of somatic mitochondrial DNA mutations in breast cancer.

To investigate the role of mitochondrial DNA (mtDNA) in tumorigenesis, a temporal temperature gradient gel electrophoresis method was used to analyze the somatic mtDNA mutations in breast cancer. The entire mitochondrial genomes in 19 tumor samples and paired normal tissues from the same patients were amplified using 32 pairs of overlapping primers. DNA fragments showing different banding patterns between normal and tumor mtDNA were sequenced to identify the mutations.