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BMC Medical Genomics

Matthew Yen, Zongtai Qi, Xuhua Chen, John A Cooper, Robi D Mitra, Michael D Onken
BACKGROUND: BAP1 is a histone deubiquitinase that acts as a tumor and metastasis suppressor associated with disease progression in human cancer. We have used the "Calling Card System" of transposase-directed transposon insertion mapping to identify the genomic targets of BAP1 in uveal melanoma (UM). This system was developed to identify the genomic loci visited by transcription factors that bind directly to DNA; our study is the first use of the system with a chromatin-remodeling factor that binds to histones but does not interact directly with DNA...
November 6, 2018: BMC Medical Genomics
Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen, Shuang Wang
BACKGROUND: Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and transcriptomic alterations across many cancer types. Here we aim to improve our understanding of the connections between CDG mutations and altered cancer cell epigenomes and transcriptomes on pan-cancer level and how these connections contribute to the known association between epigenome and transcriptome...
November 6, 2018: BMC Medical Genomics
Pengfei Xu, Jian Yang, Junhui Liu, Xue Yang, Jianming Liao, Fanen Yuan, Yang Xu, Baohui Liu, Qianxue Chen
BACKGROUND: Glioblastoma multiforme, the most prevalent and aggressive brain tumour, has a poor prognosis. The molecular mechanisms underlying gliomagenesis remain poorly understood. Therefore, molecular research, including various markers, is necessary to understand the occurrence and development of glioma. METHOD: Weighted gene co-expression network analysis (WGCNA) was performed to construct a gene co-expression network in TCGA glioblastoma samples. Gene ontology (GO) and pathway-enrichment analysis were used to identify significance of gene modules...
November 1, 2018: BMC Medical Genomics
Omar M Ibrahim, Homood M As Sobeai, Stephen G Grant, Jean J Latimer
BACKGROUND: Nucleotide Excision Repair (NER) is a major pathway of mammalian DNA repair that is associated with drug resistance and has not been well characterized in acute lymphoblastic leukemia (ALL). The objective of this study was to explore the role of NER in relapsed ALL patients. We hypothesized that increased expression of NER genes was associated with drug resistance and relapse in ALL. METHODS: We performed secondary data analysis on two sets of pediatric ALL patients that all ultimately relapsed, and who had matched diagnosis-relapse gene expression microarray data (GSE28460 and GSE18497)...
October 30, 2018: BMC Medical Genomics
Huey Yi Chong, Pascale A Allotey, Nathorn Chaiyakunapruk
BACKGROUND: The emergence of personalized medicine (PM) has raised some tensions in healthcare systems. PM is expensive and health budgets are constrained - efficient healthcare delivery is therefore critical. Notwithstanding the cost, many countries have started to adopt this novel technology, including resource-limited Southeast Asia (SEA) countries. This study aimed to describe the status of PM adoption in SEA, highlight the challenges and to propose strategies for future development...
October 26, 2018: BMC Medical Genomics
Gordon K C Leung, Christopher C Y Mak, Jasmine L F Fung, Wilfred H S Wong, Mandy H Y Tsang, Mullin H C Yu, Steven L C Pei, K S Yeung, Gary T K Mok, C P Lee, Amelia P W Hui, Mary H Y Tang, Kelvin Y K Chan, Anthony P Y Liu, Wanling Yang, P C Sham, Anita S Y Kan, Brian H Y Chung
BACKGROUND: Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal genetic diagnosis in fetuses with structural congenital anomalies (SCAs) detected on prenatal ultrasound. METHOD: Thirty-three families with fetal SCAs on prenatal ultrasonography and normal chromosomal microarray results were recruited. Genomic DNA was extracted from various fetal samples including amniotic fluid, chorionic villi, and placental tissue...
October 25, 2018: BMC Medical Genomics
Qiong Xu, Chun-Yang Li, Yi Wang, Hui-Ping Li, Bing-Bing Wu, Yong-Hui Jiang, Xiu Xu
BACKGROUND: Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical features significantly overlapping with Verheij. CASE PRESENTATION: Here we present the first Chinese Han patient with a de novo nonsense variant (c.1357C > T, p.Gln453*) in PUF60 by clinical whole exome sequencing. The 5-year-old boy presents with dysmorphic facial features, intellectual disability, and growth retardation but without apparent cardiac, renal, ocular, and spinal anomalies...
October 23, 2018: BMC Medical Genomics
Velina Kozareva, Clayton Stroff, Maxwell Silver, Jonathan F Freidin, Nigel F Delaney
BACKGROUND: Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation sequencing (NGS) for wider discovery of small variants, they often do not include CNV analysis. Moreover, most computational techniques developed to detect CNVs from exome sequencing data are not suitable for carrier screening, as they require matched normals, very large cohorts, or extensive gene panels...
October 20, 2018: BMC Medical Genomics
Kristjan Eerik Kaseniit, Gregory J Hogan, Kevin M D'Auria, Carrie Haverty, Dale Muzzey
BACKGROUND: Noninvasive prenatal screening (NIPS) of common aneuploidies using cell-free DNA from maternal plasma is part of routine prenatal care and is widely used in both high-risk and low-risk patient populations. High specificity is needed for clinically acceptable positive predictive values. Maternal copy-number variants (mCNVs) have been reported as a source of false-positive aneuploidy results that compromises specificity. METHODS: We surveyed the mCNV landscape in 87,255 patients undergoing NIPS...
October 19, 2018: BMC Medical Genomics
Ye Zhu, Xiang Gu, Chao Xu
BACKGROUND: Nuclear genes or family-based mitochondrial screening have been the focus of genetic studies into essential hypertension. Studies into the role of mitochondria in sporadic Chinese hypertensives are lacking. The objective of the study was to explore the relationship between mitochondrial DNA (mtDNA) variations and the development of maternally inherited essential hypertension (MIEH) in China. METHODS: Yangzhou residents who were outpatients or in-patients at the Department of Cardiology in Northern Jiangsu People's Hospital (Jiangsu, China) from June 2009 to June 2015 were recruited in a 1:1 case control study of 600 gender-matched Chinese MIEH subjects and controls...
October 16, 2018: BMC Medical Genomics
Charlotte Bonte, Frederik Vercauteren
BACKGROUND: Logistic regression is a popular technique used in machine learning to construct classification models. Since the construction of such models is based on computing with large datasets, it is an appealing idea to outsource this computation to a cloud service. The privacy-sensitive nature of the input data requires appropriate privacy preserving measures before outsourcing it. Homomorphic encryption enables one to compute on encrypted data directly, without decryption and can be used to mitigate the privacy concerns raised by using a cloud service...
October 11, 2018: BMC Medical Genomics
Sergiu Carpov, Thibaud Tortech
BACKGROUND: One of the 3 tracks of iDASH Privacy & Security Workshop 2017 competition was to execute a whole genome variants search on private genomic data. Particularly, the search application was to find the top most significant SNPs (Single-Nucleotide Polymorphisms) in a database of genome records labeled with control or case. In this paper we discuss the solution submitted by our team to this competition. METHODS: Privacy and confidentiality of genome data had to be ensured using Intel SGX enclaves...
October 11, 2018: BMC Medical Genomics
Peeter Laud, Alisa Pankova
BACKGROUND: Practical applications for data analysis may require combining multiple databases belonging to different owners, such as health centers. The analysis should be performed without violating privacy of neither the centers themselves, nor the patients whose records these centers store. To avoid biased analysis results, it may be important to remove duplicate records among the centers, so that each patient's data would be taken into account only once. This task is very closely related to privacy-preserving record linkage...
October 11, 2018: BMC Medical Genomics
Hao Chen, Ran Gilad-Bachrach, Kyoohyung Han, Zhicong Huang, Amir Jalali, Kim Laine, Kristin Lauter
BACKGROUND: One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was for the data holder to encrypt the records using homomorphic encryption, and send them to an untrusted cloud for storage. The cloud could then homomorphically apply a training algorithm on the encrypted data to obtain an encrypted logistic regression model, which can be sent to the data holder for decryption...
October 11, 2018: BMC Medical Genomics
Andrey Kim, Yongsoo Song, Miran Kim, Keewoo Lee, Jung Hee Cheon
BACKGROUND: Security concerns have been raised since big data became a prominent tool in data analysis. For instance, many machine learning algorithms aim to generate prediction models using training data which contain sensitive information about individuals. Cryptography community is considering secure computation as a solution for privacy protection. In particular, practical requirements have triggered research on the efficiency of cryptographic primitives. METHODS: This paper presents a method to train a logistic regression model without information leakage...
October 11, 2018: BMC Medical Genomics
XiaoFeng Wang, Haixu Tang, Shuang Wang, Xiaoqian Jiang, Wenhao Wang, Diyue Bu, Lei Wang, Yicheng Jiang, Chenghong Wang
No abstract text is available yet for this article.
October 11, 2018: BMC Medical Genomics
Adnan Ahmad Ansari, Inkeun Park, Inki Kim, Sojung Park, Sung-Min Ahn, Jae-Lyun Lee
BACKGROUND: Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in bladder cancer. RESULTS: We created the Genomics of Drug Sensitivity in Bladder Cancer (GDBC) database, an integrated database (DB) to facilitate the genomic understanding of bladder cancer in relation to drug sensitivity, in order to promote potential therapeutic applications of targeted agents in bladder cancer treatment...
October 3, 2018: BMC Medical Genomics
Anna Pichiecchio, Giovanni Vitale, Camilla Caporali, Cecilia Parazzini, Donatella Milani, Maria Paola Recalcati, Laura D'Amico, Sabrina Signorini, Umberto Balottin, Stefano Bastianello
BACKGROUND: Mutations occurring in the orthodenticle homeobox 2 gene (OTX2) are responsible for a rare genetic syndrome, characterized mainly by microphthalmia/anophthalmia associated with extra-ocular defects such as brain malformations, pituitary abnormalities, short stature and intellectual disability. To date, the spectrum of radiological features observed in patients with OTX2 mutations has never been summarized. CASE PRESENTATION: In this report, we describe a case of large microdeletion encompassing OTX2 but not BMP4 presenting with a syndromic anophthalmia with corpus callosum hypoplasia, pituitary gland hypoplasia and vermian hypoplasia...
September 29, 2018: BMC Medical Genomics
Silke Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm, Hans J Neubauer
BACKGROUND: The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) is an important step during breast carcinogenesis. Understanding its molecular changes may help to identify high-risk DCIS that progress to IBC. Here, we describe a transcriptomic profiling analysis of matched formalin-fixed and paraffin-embedded (FFPE) DCIS and IBC components of individual breast tumours, containing both tumour compartments. The study was performed to validate progression-associated transcripts detected in an earlier gene profiling project using fresh frozen breast cancer tissue...
September 20, 2018: BMC Medical Genomics
Ann G Cirincione, Kaylyn L Clark, Maricel G Kann
BACKGROUND: Understanding the effect of human genetic variations on disease can provide insight into phenotype-genotype relationships, and has great potential for improving the effectiveness of personalized medicine. While some genetic markers linked to disease susceptibility have been identified, a large number are still unknown. In this paper, we propose a pathway-based approach to extend disease-variant associations and find new molecular connections between genetic mutations and diseases...
September 14, 2018: BMC Medical Genomics
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