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copy number variations

Chia Lin Chang, Chia Yu Chang, Da Xian Lee, Po Jen Cheng
Pre-eclampsia is a pregnancy-specific hypertensive disorder that affects 2-8 % of pregnancies. This disorder can lead to seizure, multi-organ failure and maternal death. The best approach to prevent pre-eclampsia-associated adverse outcomes is to be able to prevent pre-eclampsia as early as possible. Unfortunately, current diagnostic methods are ineffective at predicting the risk of pre-eclampsia during early pregnancy. In humans, low levels of a group of placenta-derived Pregnancy Specific Glycoproteins (PSGs) have been associated with intrauterine growth retardation and pre-eclampsia and there is a significant enrichment of cases with deletions in the PSG gene locus in pre-eclampsia patients...
2016: Advances in Experimental Medicine and Biology
Simon Schimmack, Ben Lawrence, Barton Kenney, Hubertus Schmitz-Winnenthal, Irvin M Modlin, Mark Kidd
BACKGROUND: Small intestinal neuroendocrine neoplasm (SI-NEN) proliferation is quantified by Ki67 measurements which capture G1-G2M phases of the cell cycle. G0 and early G1 phases, typical of slow-growing cells, can be detected by minichromosome maintenance protein (MCM) expression. We hypothesized that these replication licensing markers may provide clinically relevant information to augment Ki67 in low-grade neuroendocrine neoplasia. METHODS: Immunohistochemical staining (IHC), Western blot analysis, quantitative polymerase chain reaction, and copy number variations of MCM2, MCM3, and Ki67 were undertaken in SI-NENs (n = 22)...
October 2016: Translational Oncology
Beryl Royer-Bertrand, Matteo Torsello, Donata Rimoldi, Ikram El Zaoui, Katarina Cisarova, Rosanna Pescini-Gobert, Franck Raynaud, Leonidas Zografos, Ann Schalenbourg, Daniel Speiser, Michael Nicolas, Laureen Vallat, Robert Klein, Serge Leyvraz, Giovanni Ciriello, Nicolò Riggi, Alexandre P Moulin, Carlo Rivolta
Uveal melanoma (UM) is a rare intraocular tumor that, similar to cutaneous melanoma, originates from melanocytes. To gain insights into its genetics, we performed whole-genome sequencing at very deep coverage of tumor-control pairs in 33 samples (24 primary and 9 metastases). Genome-wide, the number of coding mutations was rather low (only 17 variants per tumor on average; range 7-28), thus radically different from cutaneous melanoma, where hundreds of exonic DNA insults are usually detected. Furthermore, no UV light-induced mutational signature was identified...
October 6, 2016: American Journal of Human Genetics
Ottó Dócs, Katalin Hegyi, Attila Mokánszky, Anikó Mónusné, Lívia Beke, Csilla András, Judit Bedekovics, Gábor Méhes
Mutation rates determined by allele-specific PCR can be highly different in KRAS exon 2 mutant colorectal carcinoma (CRC) samples suggesting intratumoural heterogeneity. To address the effect of KRAS gene copy number on the relative mutant allele frequency the KRAS locus was individually quantified following FISH analysis in 36 cases. We observed, that mutant KRAS status was associated with an elevated KRAS locus number (2.36 ± 0.42 vs 2.63 ± 0.75; p = 0.037) reflecting an increased aneuploidy status but no true amplification of the locus...
October 15, 2016: Pathology Oncology Research: POR
Nicholas J Bradshaw, Mirian A F Hayashi
NDE1 (Nuclear Distribution Element 1, also known as NudE) and NDEL1 (NDE-Like 1, also known as NudEL) are the mammalian homologues of the fungus nudE gene, with important and at least partially overlapping roles for brain development. While a large number of studies describe the various properties and functions of these proteins, many do not directly compare the similarities and differences between NDE1 and NDEL1. Although sharing a high degree structural similarity and multiple common cellular roles, each protein presents several distinct features that justify their parallel but also unique functions...
October 14, 2016: Cellular and Molecular Life Sciences: CMLS
Sereina Rutschmann, Harald Detering, Sabrina Simon, David H Funk, Jean-Luc Gattolliat, Samantha J Hughes, Pedro M Raposeiro, Rob DeSalle, Michel Sartori, Michael T Monaghan
The study of processes driving diversification requires a fully sampled and well resolved phylogeny. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L...
October 11, 2016: Molecular Phylogenetics and Evolution
Mayuko Furuta, Masaki Ueno, Akihiro Fujimoto, Shinya Hayami, Satoru Yasukawa, Fumiyoshi Kojima, Koji Arihiro, Yoshiiku Kawakami, Christopher P Wardell, Yuichi Shiraishi, Hiroko Tanaka, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Naoki Tokunaga, Keith A Boroevich, Tetsuo Abe, Hiroshi Aikata, Hideki Ohdan, Kunihito Goto, Michiaki Kubo, Tatsuhiko Tsunoda, Satoru Miyano, Kazuaki Chayama, Hiroki Yamaue, Hidewaki Nakagawa
BACKGROUND & AIMS: Liver cancer has a high risk of multi-centric (MC) occurrence due to a strong carcinogenic background in the liver, in addition to a high risk of intrahepatic metastasis (IM). There are large characteristic differences between IM and MC with regards to their development and clinical outcome, but discriminating between IM and MC is usually non-trivial with respect to clinical or pathological aspects. METHODS: In this study, we performed whole-genome and RNA sequencing analyses of 49 liver nodules and two extra-hepatic metastatic tumors from 23 patients to investigate for any potential to discriminate between IM and MC at the molecular level...
October 11, 2016: Journal of Hepatology
Christopher C Angelakos, Adam J Watson, W Timothy O'Brien, Kyle S Krainock, Thomas Nickl-Jockschat, Ted Abel
Sleep disturbances and hyperactivity are prevalent in several neurodevelopmental disorders, including autism spectrum disorders (ASDs) and attention deficit-hyperactivity disorder (ADHD). Evidence from genome-wide association studies indicates that chromosomal copy number variations (CNVs) are associated with increased prevalence of these neurodevelopmental disorders. In particular, CNVs in chromosomal region 16p11.2 profoundly increase the risk for ASD and ADHD, disorders that are more common in males than females...
October 14, 2016: Autism Research: Official Journal of the International Society for Autism Research
X Zhang, H Han, T Zhang, T Sun, Y Xi, N Chen, Y Huang, R Dang, X Lan, H Chen, C Lei
Recent transcriptomic analysis of the bovine Y chromosome revealed abundant presence of multi-copy protein coding gene families on the male-specific region of the Y chromosome (MSY). Copy number variations (CNVs) of several MSY genes are closely related to semen quality and male reproduction in cattle. However, the CNVs of MSY genes in water buffalo are largely unknown. Therefore, this study aimed to investigate the CNVs of HSFY and ZNF280BY of 298 buffaloes from 17 populations distributed in China, Vietnam and Laos using quantitative PCR...
October 14, 2016: Animal Genetics
Yamilee Hurtado-Roca, Marta Ledesma, Monica Gonzalez-Lazaro, Raquel Moreno-Loshuertos, Patricio Fernandez-Silva, Jose Antonio Enriquez, Martin Laclaustra
Alterations of mitochondrial DNA copy number (mtDNAcn) in the blood (mitochondrial to nuclear DNA ratio) appear associated with several systemic diseases, including primary mitochondrial disorders, carcinogenesis, and hematologic diseases. Measuring mtDNAcn in DNA extracted from whole blood (WB) instead of from peripheral blood mononuclear cells or buffy coat may yield different results due to mitochondrial DNA present in platelets. The aim of this work is to quantify the contribution of platelets to mtDNAcn in whole blood [mtDNAcn(WB)] and to propose a correction formula to estimate leukocytes' mtDNAcn [mtDNAcn(L)] from mtDNAcn(WB)...
2016: PloS One
D Lee Taylor, William A Walters, Niall J Lennon, James Bochicchio, Andrew Krohn, J Gregory Caporaso, Taina Pennanen
: While high-throughput-sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive. We sought to design ITS primers and an Illumina protocol that would maximize coverage of the kingdom Fungi while minimizing non-target eukaryotes. We inspected alignments of the 5.8S and LSU ribosomal genes and evaluated potential primers using PrimerProspector. We tested the resulting primers using tiered-abundance mock communities and five previously characterized soil samples...
October 7, 2016: Applied and Environmental Microbiology
Kinga M Bujakowska, Rosario Fernandez-Godino, Emily Place, Mark Consugar, Daniel Navarro-Gomez, Joseph White, Emma C Bedoukian, Xiaosong Zhu, Hongbo M Xie, Xiaowu Gai, Bart P Leroy, Eric A Pierce
PURPOSE: Despite substantial progress in sequencing, current strategies can genetically solve only approximately 55-60% of inherited retinal degeneration (IRD) cases. This can be partially attributed to elusive mutations in the known IRD genes, which are not easily identified by the targeted next-generation sequencing (NGS) or Sanger sequencing approaches. We hypothesized that copy-number variations (CNVs) are a major contributor to the elusive genetic causality of IRDs. METHODS: Twenty-eight cases previously unsolved with a targeted NGS were investigated with whole-genome single-nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) arrays...
October 13, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Xingyun Su, Weibin Wang, Guodong Ruan, Min Liang, Jing Zheng, Ye Chen, Huiling Wu, Thomas J Fahey, Minxin Guan, Lisong Teng
Nuclear genetic alterations have been widely investigated in papillary thyroid cancer (PTC), however, the characteristics of the mitochondrial genome remain uncertain. We sequenced the entire mitochondrial genome of 66 PTCs, 16 normal thyroid tissues and 376 blood samples of healthy individuals. There were 2508 variations (543 sites) detected in PTCs, among which 33 variations were novel. Nearly half of the PTCs (31/66) had heteroplasmic variations. Among the 31 PTCs, 28 specimens harbored a total of 52 somatic mutations distributed in 44 sites...
October 10, 2016: International Journal of Molecular Sciences
Erin M Eggleston, Ian Hewson
This study characterizes viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10 N-40 S. Overall viral abundance decreased with depth, on average there were 1.64 ± 0.71 × 10(7) virus like particles (VLPs) in surface waters, decreasing to an average of 6.50 ± 2.26 × 10(5) VLPs in Antarctic Bottom Water. This decrease was highly correlated to bacterial abundance. There are six major water masses in the Southern Tropical Atlantic Ocean, and inclusion of water mass, temperature and salinity variables explained a majority of the variation in total viral abundance...
2016: Frontiers in Microbiology
Peilin Jia, Guangchun Han, Junfei Zhao, Pinyi Lu, Zhongming Zhao
SZGR 2.0 is a comprehensive resource of candidate variants and genes for schizophrenia, covering genetic, epigenetic, transcriptomic, translational and many other types of evidence. By systematic review and curation of multiple lines of evidence, we included almost all variants and genes that have ever been reported to be associated with schizophrenia. In particular, we collected ∼4200 common variants reported in genome-wide association studies, ∼1000 de novo mutations discovered by large-scale sequencing of family samples, 215 genes spanning rare and replication copy number variations, 99 genes overlapping with linkage regions, 240 differentially expressed genes, 4651 differentially methylated genes and 49 genes as antipsychotic drug targets...
October 12, 2016: Nucleic Acids Research
Ni Ai, Haoyang Cai, Caius Solovan, Michael Baudis
BACKGROUND: DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing methods. Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA quality is sometimes observed in genome screening experiments and may lead to unreliable copy number profiles. Depending on the extent of these artefacts and the resulting misidentification of copy number alterations/variations (CNA/CNV), it may be desirable to exclude such samples from analyses or to adapt the downstream data analysis strategy accordingly...
October 12, 2016: BMC Genomics
Jing Zhang, Xiaohong Song, Marella J Ma, Li Xiao, Tsuyoshi Kenri, Hongmei Sun, Travis Ptacek, Shaoli Li, Ken B Waites, T Prescott Atkinson, Keigo Shibayama, Kevin Dybvig, Yanmei Feng
AIM: To characterize inter- and intra-strain variability of variable-number tandem repeats (VNTRs) in Mycoplasma pneumoniae to determine the optimal multilocus VNTR analysis scheme for improved strain typing. METHODS: Whole genome assemblies and next-generation sequencing data from diverse M. pneumoniae isolates were used to characterize VNTRs and their variability, and to compare the strain discriminability of new VNTR and existing markers. RESULTS: We identified 13 VNTRs including five reported previously...
October 12, 2016: Future Microbiology
Hong Chang, Lingyi Li, Tao Peng, Ming Li, Lei Gao, Xiao Xiao
Recent studies suggest that copy number variations (CNVs) are also involved in the genetic risk of schizophrenia. Using a Cochran-Mantel-Haenszel (CMH) adjusted meta-analysis in 18,497 schizophrenia patients and 25,522 healthy controls from 14 independent samples, we conducted replication analyses of four chromosomal deletions at 1q21.1, 15q11.2, 15q13.3, and 22q11.2 Loci for their associations with schizophrenia. Only CNVs larger than 100 kb that had >50% reciprocal overlap with the canonical deletion chromosomal regions were considered...
October 11, 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Samantha L P Schilit, Masato Ohtsuka, Rolen M Quadros, Channabasavaiah B Gurumurthy
Microinjection of DNA expression cassettes into fertilized zygotes has been a standard method for generating transgenic animal models. While efficient, the injected DNA integrates randomly into the genome, leading to potential disruption of endogenous genes or regulatory elements, variation in copy number, or integration into heterochromatic regions that inhibit transgene expression. A recently developed method addresses such pitfalls of traditional transgenesis by targeting the transgene to predetermined sites in the genome that can safely harbor exogenous DNA...
October 11, 2016: Current Protocols in Human Genetics
Rajeev K Mehlotra, Noemi B Hall, Barne Willie, Catherine M Stein, Aaron Weinberg, Peter A Zimmerman, Lance T Vernon
Polymorphisms in toll-like receptor (TLR) and β-defensin (DEFB) genes have been recognized as potential genetic factors that can influence susceptibility to and severity of periodontal diseases (PD). However, data regarding associations between these polymorphisms and PD are still scarce in North American populations, and are not available in HIV+ North American populations. In this exploratory study, we analyzed samples from HIV+ adults (n = 115), who received primary HIV care at 3 local outpatient HIV clinics and were monitored for PD status...
2016: PloS One
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