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https://www.readbyqxmd.com/read/28345611/copy-number-variation-profile-in-the-placental-and-parental-genomes-of-recurrent-pregnancy-loss-families
#1
Laura Kasak, Kristiina Rull, Siim Sõber, Maris Laan
We have previously shown an extensive load of somatic copy number variations (CNVs) in the human placental genome with the highest fraction detected in normal term pregnancies. Hereby, we hypothesized that insufficient promotion of CNVs may impair placental development and lead to recurrent pregnancy loss (RPL). RPL affects ~3% of couples aiming at childbirth and idiopathic RPL represents ~50% of cases. We analysed placental and parental CNV profiles of idiopathic RPL trios (mother-father-placenta) and duos (mother-placenta)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341679/industrial-relevance-of-chromosomal-copy-number-variation-in-saccharomyces-yeasts
#2
Arthur R Gorter de Vries, Jack T Pronk, Jean-Marc G Daran
Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact and evolutionary significance of CCNV. Fundamental studies on this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but is also a key contributor to the diversity of industrially relevant traits...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28341418/a-novel-y-chromosome-microdeletion-potentially-associated-with-defective-spermatogenesis-identified-by-custom-array-comparative-genome-hybridization
#3
Tianwen He, Xiangzhong Zhang, Hua Deng, Weiping Zhou, Xin Zhao, Hui Zhao, Jian Lu, Yichun Zheng, Changbin Zhang, Liang Zhang, Aihua Yin
Male infertility is a major health problem worldwide. Oligospermia and azoospermia are the most common symptoms of this disorder. Despite recent advances, the aetiopathogenesis of defective spermatogenesis remains largely uncertain. The aim of this study is to discover unknown or novel chromosome aberrations associated with male reproductive failure. We developed a high-resolution custom array comparative genomic hybridization for initial screening of copy number variations in 10 patients with idiopathic oligozoospermia and azoospermia and eight normal fertile men...
January 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/28340313/linkage-between-mitochondrial-genome-alterations-telomere-length-and-aging-population
#4
Egija Zole, Krista Zadinane, Liana Pliss, Renate Ranka
We studied telomere length (TL) and mitochondrial DNA (mtDNA) copy number variations in individuals from Latvian Caucasian population in different age groups. We showed a positive correlation between TL and mtDNA copy number in individuals of up to 90 years of age; however, this correlation was not observed in the 90-100 years age group. While TL shortened with age and mtDNA content decreased with increasing age, in this study it was observed that mtDNA copy number in nonagenarians was slightly higher than in the 60-89 years age group...
March 24, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28339599/a-single-nucleotide-polymorphism-in-coq9-affects-mitochondrial-and-ovarian-function-and-fertility-in-holstein-cows%C3%A2
#5
M Sofia Ortega, Stephanie Wohlgemuth, Paula Tribulo, Luiz G B Siqueira, Daniel J Null, John B Cole, Marcus V Da Silva, Peter J Hansen
A single missense mutation at position 159 of coenzyme Q9 (COQ9) (G→A; rs109301586) has been associated with genetic variation in fertility in Holstein cattle, with the A allele associated with higher fertility. COQ9 is involved in the synthesis of coenzyme COQ10, a component of the electron transport system of the mitochondria. Here we tested whether reproductive phenotype is associated with the mutation and evaluated functional consequences for cellular oxygen metabolism, body weight changes, and ovarian function...
February 3, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28338218/evaluation-of-targeted-exome-sequencing-for-28-protein-based-blood-group-systems-including-the-homologous-gene-systems-for-blood-group-genotyping
#6
Elizna M Schoeman, Genghis H Lopez, Eunike C McGowan, Glenda M Millard, Helen O'Brien, Eileen V Roulis, Yew-Wah Liew, Jacqueline R Martin, Kelli A McGrath, Tanya Powley, Robert L Flower, Catherine A Hyland
BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform...
March 24, 2017: Transfusion
https://www.readbyqxmd.com/read/28337907/a-single-cell-based-platform-for-copy-number-variation-profiling-through-digital-counting-of-amplified-genomic-dna-fragments
#7
Chunmei Li, Zhilong Yu, Yusi Fu, Yuhong Pang, Yanyi Huang
We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multi-fraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infers CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of reaction mix before amplification...
March 24, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28336923/integrative-analysis-of-multi-omics-data-reveals-distinct-impacts-of-ddb1-cul4-associated-factors-in-human-lung-adenocarcinomas
#8
Hong Yan, Lei Bi, Yunshan Wang, Xia Zhang, Zhibo Hou, Qian Wang, Antoine M Snijders, Jian-Hua Mao
Many DDB1-CUL4 associated factors (DCAFs) have been identified and serve as substrate receptors. Although the oncogenic role of CUL4A has been well established, specific DCAFs involved in cancer development remain largely unknown. Here we infer the potential impact of 19 well-defined DCAFs in human lung adenocarcinomas (LuADCs) using integrative omics analyses, and discover that mRNA levels of DTL, DCAF4, 12 and 13 are consistently elevated whereas VBRBP is reduced in LuADCs compared to normal lung tissues...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336264/genomic-imbalances-in-syndromic-congenital-heart-disease
#9
Miriam C Molck, Milena Simioni, Társis P Vieira, Ilária C Sgardioli, Fabíola P Monteiro, Josiane Souza, Agnes C Fett-Conte, Têmis M Félix, Isabella L Monlléo, Vera Lúcia Gil-da-Silva-Lopes
OBJECTIVE: To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). METHODS: 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). RESULTS: Clinically significant copy number variations (CNVs ≥300kb) were identified in 10% (8/78) of cases...
March 20, 2017: Jornal de Pediatria
https://www.readbyqxmd.com/read/28335811/three-patients-presenting-with-severe-macrosomia-and-congenital-hypertrophic-cardiomyopathy-a-case-series
#10
Marie Vincent, Nadir Benbrik, Bénédicte Romefort, Agnès Colombel, Stéphane Bézieau, Bertrand Isidor
BACKGROUND: Macrosomia and hypertrophic cardiomyopathy are two features often associated in neonates of diabetic mothers. We report the cases of three patients with severe macrosomia and critical hypertrophic cardiomyopathy without severely unbalanced maternal diabetes. Only three patients with those two features and no uncontrolled maternal diabetes have been previously reported. CASE PRESENTATION: The first patient was a 39-week-old girl, the second patient was a 39-week-old girl, and the third patient was a 41-week-old boy...
March 24, 2017: Journal of Medical Case Reports
https://www.readbyqxmd.com/read/28332632/loss-of-chromosome-y-leads-to-down-regulation-of-kdm5d-and-kdm6c-epigenetic-modifiers-in-clear-cell-renal-cell-carcinoma
#11
Madeleine Arseneault, Jean Monlong, Naveen S Vasudev, Ruhina S Laskar, Maryam Safisamghabadi, Patricia Harnden, Lars Egevad, Nazanin Nourbehesht, Pudchalaluck Panichnantakul, Ivana Holcatova, Antonin Brisuda, Vladimir Janout, Helena Kollarova, Lenka Foretova, Marie Navratilova, Dana Mates, Viorel Jinga, David Zaridze, Anush Mukeria, Pouria Jandaghi, Paul Brennan, Alvis Brazma, Jorg Tost, Ghislaine Scelo, Rosamonde E Banks, Mark Lathrop, Guillaume Bourque, Yasser Riazalhosseini
Recent genomic studies of sporadic clear cell renal cell carcinoma (ccRCC) have uncovered novel driver genes and pathways. Given the unequal incidence rates among men and women (male:female incidence ratio approaches 2:1), we compared the genome-wide distribution of the chromosomal abnormalities in both sexes. We observed a higher frequency for the somatic recurrent chromosomal copy number variations (CNVs) of autosomes in male subjects, whereas somatic loss of chromosome X was detected exclusively in female patients (17...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28328126/quantitative-phenotypic-and-network-analysis-of-1q44-microdeletion-for-microcephaly
#12
Nicholas Raun, Janette Mailo, Egidio Spinelli, Xu He, Sarah McAvena, Logan Brand, Julia O'Sullivan, John Andersen, Lawrence Richer, Richard Tang-Wai, Francois V Bolduc
As genome wide techniques become more common, an increasing proportion of patients with intellectual disability (ID) are found to have genetic defects allowing genotype-phenotype correlations. Previously, AKT3 deletion was suggested to be responsible for microcephaly in patients with 1q43-q44 deletion syndrome, but this does not correspond to all cases. We report a case of a de novo 1q44 deletion in an 8-year-old boy with microcephaly in whom AKT3 is not deleted. We used a systematic review of the literature, our patient, and network analysis to gain a better understanding of the genetic basis of microcephaly in 1q deletion patients...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#13
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327142/exome-sequencing-identified-rare-variants-in-genes-hspg2-and-atp2b4-in-a-family-segregating-developmental-dysplasia-of-the-hip
#14
Sulman Basit, Alia M Albalawi, Essa Alharby, Khalid I Khoshhal
BACKGROUND: Developmental dysplasia of the hip (DDH) is a common pathological condition of the musculoskeletal system in infants which results in a congenital and developmental malformation of the hip joint. DDH is a spectrum of pathologies affecting the infant hip ranging from asymptomatic subtle radiographic signs through mild instability to frank dislocations with acetabular dysplasia. A Saudi family with three affected individuals with DDH was identified and genetic analysis was performed to detect the possible genetic defect(s) underlying DDH in the affected members of the family...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28326452/methyleugenol-dna-adducts-in-human-liver-are-associated-with-sult1a1-copy-number-variations-and-expression-levels
#15
Roman Tremmel, Kristin Herrmann, Wolfram Engst, Walter Meinl, Kathrin Klein, Hansruedi Glatt, Ulrich M Zanger
Methyleugenol is a rodent hepatocarcinogen occurring in many herbs and spices as well as essential oils used for flavoring. Following metabolic activation by cytochromes P450 (CYPs) and sulfotransferases (SULTs), methyleugenol can form DNA adducts. Previously, we showed that DNA adduct formation by methyleugenol in mouse liver is dependent on SULT1A1 expression and that methyleugenol DNA adducts are abundant in human liver specimens. In humans, SULT1A1 activity is affected by genetic polymorphisms, including single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs)...
March 22, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28325848/hierarchically-aligning-10-legume-genomes-establishes-a-family-level-genomics-platform
#16
Jinpeng Wang, Pengchuan Sun, Yuxian Li, Yinzhe Liu, Jigao Yu, Xuelian Ma, Sangrong Sun, Nanshan Yang, Ruiyan Xia, Tianyu Lei, Xiaojian Liu, Beibei Jiao, Yue Xing, Weina Ge, Li Wang, Zhenyi Wang, Xiaoming Song, Min Yuan, Di Guo, Lan Zhang, Jiaqi Zhang, Dianchuan Jin, Wei Chen, Yuxin Pan, Tao Liu, Ling Jin, Jinshuai Sun, Jiaxiang Yu, Rui Cheng, Xueqian Duan, Shaoqi Shen, Jun Qin, Mengchen Zhang, Andrew H Paterson, Xiyin Wang
Mainly due to their economic importance, genomes of 10 legumes, including soybean, wild peanuts, barrel medic, etc, have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by wide-spread gene losses after the polyploidizations...
March 21, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28325361/warthin-like-papillary-renal-cell-carcinoma-clinicopathologic-morphologic-immunohistochemical-and-molecular-genetic-analysis-of-11-cases
#17
Faruk Skenderi, Monika Ulamec, Tomas Vanecek, Petr Martinek, Reza Alaghehbandan, Maria Pane Foix, Iva Babankova, Delia Perez Montiel, Isabel Alvarado-Cabrero, Marian Svajdler, Pavol Dubinský, Dana Cempirkova, Michal Pavlovsky, Semir Vranic, Ondrej Daum, Ondrej Ondic, Kristyna Pivovarcikova, Kvetoslava Michalova, Milan Hora, Pavla Rotterova, Adela Stehlikova, Martin Dusek, Michal Michal, Ondrej Hes
Oncocytic papillary renal cell carcinoma (PRCC) is a distinct subtype of PRCC, listed as a possible new variant of PRCC in the 2016 WHO classification. It is composed of papillae aligned by large single-layered eosinophilic cells showing linearly arranged oncocytoma-like nuclei. We analyzed clinicopathologic, morphologic, immunohistochemical and molecular-genetic characteristics of 11 oncocytic PRCCs with prominent tumor lymphocytic infiltrate, morphologically resembling Warthin's tumor. The patients were predominantly males (8/11, 73%), with an average age of 59years (range 14-76), and a mean tumor size of 7cm (range 1-22cm)...
April 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28325066/comprehensive-analysis-to-explain-reduced-or-increased-sod1-enzymatic-activity-in-als-patients-and-their-relatives
#18
Isil Keskin, Anna Birve, Mariusz Berdynski, Karin Hjertkvist, Reza Rofougaran, Torbjörn K Nilsson, Jonathan D Glass, Stefan L Marklund, Peter M Andersen
OBJECTIVE: To characterise stabilities in erythrocytes of mutant SOD1 proteins, compare SOD1 enzymatic activities between patients with different genetic causes of ALS and search for underlying causes of deviant SOD1 activities in individuals lacking SOD1 mutations. METHODS: Blood samples from 4072 individuals, ALS patients with or without a SOD1 mutation, family members and controls were studied. Erythrocyte SOD1 enzymatic activities normalised to haemoglobin content were determined, and effects of haemoglobin disorders on dismutation assessed...
March 21, 2017: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
https://www.readbyqxmd.com/read/28324009/whole-exome-sequencing-for-diagnosis-of-turner-syndrome-towards-next-generation-sequencing-and-newborn-screening
#19
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context, Objectives: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in females and is not currently part of newborn screening. Diagnosis is often delayed resulting in missed crucial diagnostic and therapeutic opportunities. This study sought to determine if whole-exome sequencing (WES) as part of a potential newborn screening program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on women with TS (n=27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
January 24, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#20
Sílvia Vilarinho, Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
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