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BMC Medical Genomics

Jie-Qiong Li, Xiang-Zhen Yuan, Hai-Yan Li, Xi-Peng Cao, Jin-Tai Yu, Lan Tan, Wei-An Chen
BACKGROUND: Plasma neurofilament light (NFL) is a promising biomarker for Alzheimer disease (AD), which increases in the early stage of AD and is associated with the progression of AD. We performed a genome-wide association study (GWAS) of plasma NFL in Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort to identify novel variants associated with AD. METHODS: This study included 179 cognitively healthy controls (HC), 176 patients with mild cognitive impairment (MCI), and 172 patients with AD...
May 10, 2018: BMC Medical Genomics
Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Moon Young Kim, So Yeon Park, Youl-Hee Cho, Hyun Mee Ryu
BACKGROUND: The most frequent chromosomal aneuploidy is trisomy 21 (T21) that is caused by an extra copy of chromosome 21. The imbalance of whole genome including genes and microRNAs contributes to the various phenotypes of T21. However, the integrative association between genes and microRNAs in the T21 placenta has yet to be determined. METHODS: We analyzed the expressions of genes and microRNAs in the whole genomes of chorionic villi cells from normal and T21 human fetal placentas based on our prior studies...
May 9, 2018: BMC Medical Genomics
Julia Wynn, Katie Lewis, Laura M Amendola, Barbara A Bernhardt, Sawona Biswas, Manasi Joshi, Carmit McMullen, Sarah Scollon
BACKGROUND: Current medical practice includes the application of genomic sequencing (GS) in clinical and research settings. Despite expanded use of this technology, the process of disclosure of genomic results to patients and research participants has not been thoroughly examined and there are no established best practices. METHODS: We conducted semi-structured interviews with 21 genetic and non-genetic clinicians returning results of GS as part of the NIH funded Clinical Sequencing Exploratory Research (CSER) Consortium projects...
May 8, 2018: BMC Medical Genomics
Jiaxuan Liu, Wei Zhao, Erin B Ware, Stephen T Turner, Thomas H Mosley, Jennifer A Smith
BACKGROUND: Genetic variations in apolipoprotein E (APOE) and proximal genes (PVRL2, TOMM40, and APOC1) are associated with cognitive function and dementia, particularly Alzheimer's disease. Epigenetic mechanisms such as DNA methylation play a central role in the regulation of gene expression. Recent studies have found evidence that DNA methylation may contribute to the pathogenesis of dementia, but its association with cognitive function in populations without dementia remains unclear...
May 8, 2018: BMC Medical Genomics
C S Paththinige, N D Sirisena, U G I U Kariyawasam, R C Ediriweera, P Kruszka, M Muenke, V H W Dissanayake
BACKGROUND: Parental balanced reciprocal translocations can result in partial aneuploidies in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and molecular cytogenetic characterization of a 2 years and 4 months old female child with partial trisomy 7q22 → qter. This is the first such reported case resulting from a parental balanced translocation involving the long arms of chromosomes 7 and 14. The phenotype of the proband was compared with that of previously reported cases of trisomy 7q21 → qter or 7q22 → qter resulting from parental balanced translocations...
May 8, 2018: BMC Medical Genomics
Mitsuko Furuya, Hironori Kobayashi, Masaya Baba, Takaaki Ito, Reiko Tanaka, Yukio Nakatani
BACKGROUND: Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder caused by germline mutations in the folliculin gene (FLCN). Nearly 150 pathogenic mutations have been identified in FLCN. The most frequent pattern is a frameshift mutation within a coding exon. In addition, splice-site mutations have been reported, and previous studies have confirmed exon skipping in several cases. However, it is poorly understood whether there are any splice-site mutations that cause translation of intron regions in FLCN...
May 2, 2018: BMC Medical Genomics
Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B Ekici, André Reis, Rami Jamra, Fulvia Ferrazzi
BACKGROUND: Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown that EDC3 plays a role in mRNA decapping, however its function is not well understood. Previously, we have associated a homozygous variant in EDC3 with autosomal recessive intellectual disability. Here, we investigate the functional role of EDC3. METHODS: We performed transcriptome analyses in patients' samples...
April 23, 2018: BMC Medical Genomics
Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M Przytycka, Chee Keong Kwoh, Jie Zheng
BACKGROUND: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots...
April 20, 2018: BMC Medical Genomics
Tony Kuo, Martin C Frith, Jun Sese, Paul Horton
BACKGROUND: Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning sequencing reads to the reference genome. In practice a variety of ad hoc quality filtering methods are employed to produce more reliable lists of putative variants, but the resulting lists typically still include numerous false positives. Thus it would be desirable to be able to rigorously evaluate the degree to which each putative variant is supported by the data...
April 20, 2018: BMC Medical Genomics
Joowon Lee, Seungyeoun Lee, Jin-Young Jang, Taesung Park
BACKGROUND: Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e.g., burden tests and variance-component tests) rely on large sample sizes. Notwithstanding, due to its-still high cost, NGS data is generally restricted to small sample sizes, that cannot be analyzed by most existing methods. METHODS: In this work, we propose a new exact association test for sequencing data that does not require a large sample approximation, which is applicable to both common and rare variants...
April 20, 2018: BMC Medical Genomics
Seonggyun Han, Dongwook Kim, Youngjun Kim, Kanghoon Choi, Jason E Miller, Dokyoon Kim, Younghee Lee
BACKGROUND: The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TCGA cancer genome data into integrated knowledge can be useful to promote cancer research. Alternative splicing (AS) is a key regulatory mechanism of genes in human cancer development and in the interaction with epigenetic factors. Therefore, AS-guided integration of existing TCGA data sets will make it easier to gain insight into the genetic architecture of cancer risk and related outcomes...
April 20, 2018: BMC Medical Genomics
Hye-Young Jung, Sangseob Leem, Taesung Park
BACKGROUND: Gene-gene interactions (GGIs) are a known cause of missing heritability. Multifactor dimensionality reduction (MDR) is one of most commonly used methods for GGI detection. The generalized multifactor dimensionality reduction (GMDR) method is an extension of MDR method that is applicable to various types of traits, and allows covariate adjustments. Our previous Fuzzy MDR (FMDR) is another extension for overcoming simple binary classification. FMDR uses continuous member-ship values instead of binary membership values 0 and 1, improving power for detecting causal SNPs and more intuitive interpretations in real data analysis...
April 20, 2018: BMC Medical Genomics
Je-Keun Rhee, Tae-Min Kim
BACKGROUND: It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely unknown. METHODS: In this study, we built a population-based statistical framework to infer the temporal sequence of acquisition of somatic mutations. Using the model, we analyzed the mutation profiles of 1954 tumor specimens across eight tumor types...
April 20, 2018: BMC Medical Genomics
Jennifer D Hintzsche, Minjae Yoo, Jihye Kim, Carol M Amato, William A Robinson, Aik Choon Tan
BACKGROUND: With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we can now correlate specific variants and/or structural changes with actionable therapeutics known to inhibit these variants. We introduce the creation of the IMPACT Web Portal, a new online resource that connects molecular profiles of tumors to approved drugs, investigational therapeutics and pharmacogenetics associated drugs...
April 20, 2018: BMC Medical Genomics
Raissa T Relator, Aika Terada, Jun Sese
BACKGROUND: Survival analysis methods have been widely applied in different areas of health and medicine, spanning over varying events of interest and target diseases. They can be utilized to provide relationships between the survival time of individuals and factors of interest, rendering them useful in searching for biomarkers in diseases such as cancer. However, some disease progression can be very unpredictable because the conventional approaches have failed to consider multiple-marker interactions...
April 20, 2018: BMC Medical Genomics
Yeongjun Jang, Taekjin Choi, Jongho Kim, Jisub Park, Jihae Seo, Sangok Kim, Yeajee Kwon, Seungjae Lee, Sanghyuk Lee
BACKGROUND: Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex nature of genomic information presents a huge challenge for clinicians in interpreting the patient's genomic alterations and selecting the optimum approved or investigational therapy. An elaborate and practical information system is urgently needed to support clinical decision as well as to test clinical hypotheses quickly...
April 20, 2018: BMC Medical Genomics
Sunkyu Kim, Heewon Lee, Keonwoo Kim, Jaewoo Kang
BACKGROUND: Embedding techniques for converting high-dimensional sparse data into low-dimensional distributed representations have been gaining popularity in various fields of research. In deep learning models, embedding is commonly used and proven to be more effective than naive binary representation. However, yet no attempt has been made to embed highly sparse mutation profiles into densely distributed representations. Since binary representation does not capture biological context, its use is limited in many applications such as discovering novel driver mutations...
April 20, 2018: BMC Medical Genomics
Sungyoung Lee, Sungkyoung Choi, Dandi Qiao, Michael Cho, Edwin K Silverman, Taesung Park, Sungho Won
BACKGROUND: A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies-from heritability estimations to genetic association analyses. With the advance in genotyping technologies, whole-genome sequence data can be utilized for genetic epidemiological studies, and family-based samples may become more useful for detecting de novo mutations. However, genetic analyses employing family-based samples usually suffer from the complexity of the computational/statistical algorithms, and certain types of family designs, such as incorporating data from extended families, have rarely been used...
April 20, 2018: BMC Medical Genomics
Lining Su, Chunjie Wang, Chenqing Zheng, Huiping Wei, Xiaoqing Song
BACKGROUND: Parkinson's disease (PD) is a long-term degenerative disease that is caused by environmental and genetic factors. The networks of genes and their regulators that control the progression and development of PD require further elucidation. METHODS: We examine common differentially expressed genes (DEGs) from several PD blood and substantia nigra (SN) microarray datasets by meta-analysis. Further we screen the PD-specific genes from common DEGs using GCBI...
April 13, 2018: BMC Medical Genomics
Zhongzhong Chen, Yunping Lei, Xuanye Cao, Yufang Zheng, Fang Wang, Yihua Bao, Rui Peng, Richard H Finnell, Ting Zhang, Hongyan Wang
BACKGROUND: Mouse homozygous mutants in Wnt/planar cell polarity (PCP) pathway genes have been shown to cause neural tube defects (NTDs) through the disruption of normal morphogenetic processes critical to neural tube closure (NTC). Knockout mice that are heterozygotes of single PCP genes likely fail to produce NTD phenotypes, yet damaging variants detected in human NTDs are almost always heterozygous, suggesting that other deleterious interacting variants are likely to be present. Nonetheless, the Wnt/PCP pathway remains a genetic hotspot...
April 4, 2018: BMC Medical Genomics
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