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https://www.readbyqxmd.com/read/28102595/-they-can-t-find-anything-wrong-with-him-yet-mothers-experiences-of-parenting-an-infant-with-a-prenatally-diagnosed-copy-number-variant-cnv
#1
Allison Werner-Lin, Sarah Walser, Frances K Barg, Barbara A Bernhardt
Chromosome microarray (CMA) testing is used widely in prenatal settings. Some copy number variants (CNVs) detected using CMA are associated with variable or uncertain phenotype and/or possible neurocognitive involvement. Little is known about parenting an infant following such findings. Researchers conducted interviews with 23 mothers of infants diagnosed prenatally with a potentially pathogenic CNV to elicit perspectives on the child's development and disclosure of results to others. Interviews were audiotaped and analyzed for common themes...
February 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28100915/whole-exome-sequencing-study-reveals-common-copy-number-variants-in-protocadherin-genes-associated-with-childhood-obesity-in-koreans
#2
S Moon, M Y Hwang, H B Jang, S Han, Y J Kim, J-Y Hwang, H-J Lee, S I Park, J Song, B-J Kim
Recently, the prevalence of childhood obesity has significantly increased in industrialized countries, including Korea, and now controlling obesity is becoming an economic burden. However, knowledge of the risk factors associated with obesity is still limited. In this study, we aimed to discover additional obesity-associated loci in children. To achieve this, we conducted an exome-wide association analysis of copy number variation (CNV) using whole-exome sequencing (WES) data from a total of 102 cases and 86 controls...
January 19, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28096781/a-replication-study-of-schizophrenia-related-rare-copy-number-variations-in-a-han-southern-chinese-population
#3
Jianmin Yuan, Jianlin Hu, Zhiqiang Li, Fuquan Zhang, Dexiang Zhou, Chunhui Jin
BACKGROUND: Schizophrenia (SCZ) is a common, complex and severe psychiatric disorder associated with many different genetic and environmental risk factors. Evidence from genetic studies has revealed the role of genome structural variations, specifically copy number variants (CNVs), in the etiology of SCZ. Nevertheless, the occurrence of CNVs and their relation to SCZ has remained relatively unstudied in the diverse Han Chinese population. RESULTS: We used a case/control paradigm, including 476 cases and 1023 controls...
2017: Hereditas
https://www.readbyqxmd.com/read/28093192/spectrum-of-mutations-in-leiomyosarcomas-identified-by-clinical-targeted-next-generation-sequencing
#4
Paul J Lee, Naomi S Yoo, Ian S Hagemann, John D Pfeifer, Catherine E Cottrell, Haley J Abel, Eric J Duncavage
Recurrent genomic mutations in uterine and non-uterine leiomyosarcomas have not been well established. Using a next generation sequencing (NGS) panel of common cancer-associated genes, 25 leiomyosarcomas arising from multiple sites were examined to explore genetic alterations, including single nucleotide variants (SNV), small insertions/deletions (indels), and copy number alterations (CNA). Sequencing showed 86 non-synonymous, coding region somatic variants within 151 gene targets in 21 cases, with a mean of 4...
January 13, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28087349/combination-of-multiple-ligation-dependent-probe-amplification-and-illumina-miseq-amplicon-sequencing-for-tsc1-tsc2-gene-analyses-in-patients-with-tuberous-sclerosis-complex
#5
Nur Farrah Dila Ismail, Abdul Qawee Rani, Nik Mohd Ariff Nik Abdul Malik, Chia Boon Hock, Siti Nabilahuda Mohd Azlan, Salmi Abdul Razak, Wee Teik Keng, Lock Hock Ngu, Abdul Rashid Silawati, Nor AzniYahya, Narazah Mohd Yusoff, Teguh Haryo Sasongko, Zabidi Azhar Mohd Hussin
Tuberous sclerosis complex (TSC) is an autosomal dominant neurocutaneous disorder characterized by tumor growth in multiple organs and caused by mutations in either TSC1 or TSC2 genes. Because of their relatively large genomic sizes, absence of hotspots, and common type of mutations, mutation detection in TSC1 and TSC2 genes has been challenging. We devised a combination of multiple ligation-dependent probe amplification (MLPA) and amplicon sequencing (AS) to simplify the detection strategy, yet we come up with reasonably high detection rate...
January 10, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28076437/mutations-in-splicing-factor-genes-are-a-major-cause-of-autosomal-dominant-retinitis-pigmentosa-in-belgian-families
#6
Caroline Van Cauwenbergh, Frauke Coppieters, Dimitri Roels, Sarah De Jaegere, Helena Flipts, Julie De Zaeytijd, Sophie Walraedt, Charlotte Claes, Erik Fransen, Guy Van Camp, Fanny Depasse, Ingele Casteels, Thomy de Ravel, Bart P Leroy, Elfride De Baere
PURPOSE: Autosomal dominant retinitis pigmentosa (adRP) is characterized by an extensive genetic heterogeneity, implicating 27 genes, which account for 50 to 70% of cases. Here 86 Belgian probands with possible adRP underwent genetic testing to unravel the molecular basis and to assess the contribution of the genes underlying their condition. METHODS: Mutation detection methods evolved over the past ten years, including mutation specific methods (APEX chip analysis), linkage analysis, gene panel analysis (Sanger sequencing, targeted next-generation sequencing or whole exome sequencing), high-resolution copy number screening (customized microarray-based comparative genomic hybridization)...
2017: PloS One
https://www.readbyqxmd.com/read/28076398/identification-of-a-novel-mutation-in-brd4-that-causes-autosomal-dominant-syndromic-congenital-cataracts-associated-with-other-neuro-skeletal-anomalies
#7
Hyun-Seok Jin, Jeonhyun Kim, Woori Kwak, Hyeonsoo Jeong, Gyu-Bin Lim, Cha Gon Lee
Congenital cataracts can occur as a non-syndromic isolated ocular disease or as a part of genetic syndromes accompanied by a multi-systemic disease. Approximately 50% of all congenital cataract cases have a heterogeneous genetic basis. Here, we describe three generations of a family with an autosomal dominant inheritance pattern and common complex phenotypes, including bilateral congenital cataracts, short stature, macrocephaly, and minor skeletal anomalies. We did not find any chromosomal aberrations or gene copy number abnormalities using conventional genetic tests; accordingly, we conducted whole-exome sequencing (WES) to identify disease-causing genetic alterations in this family...
2017: PloS One
https://www.readbyqxmd.com/read/28074849/genetic-variants-identified-from-epilepsy-of-unknown-etiology-in-chinese-children-by-targeted-exome-sequencing
#8
Yimin Wang, Xiaonan Du, Rao Bin, Shanshan Yu, Zhezhi Xia, Guo Zheng, Jianmin Zhong, Yunjian Zhang, Yong-Hui Jiang, Yi Wang
Genetic factors play a major role in the etiology of epilepsy disorders. Recent genomics studies using next generation sequencing (NGS) technique have identified a large number of genetic variants including copy number (CNV) and single nucleotide variant (SNV) in a small set of genes from individuals with epilepsy. These discoveries have contributed significantly to evaluate the etiology of epilepsy in clinic and lay the foundation to develop molecular specific treatment. However, the molecular basis for a majority of epilepsy patients remains elusive, and furthermore, most of these studies have been conducted in Caucasian children...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068316/scalable-whole-genome-single-cell-library-preparation-without-preamplification
#9
Hans Zahn, Adi Steif, Emma Laks, Peter Eirew, Michael VanInsberghe, Sohrab P Shah, Samuel Aparicio, Carl L Hansen
Single-cell genomics is critical for understanding cellular heterogeneity in cancer, but existing library preparation methods are expensive, require sample preamplification and introduce coverage bias. Here we describe direct library preparation (DLP), a robust, scalable, and high-fidelity method that uses nanoliter-volume transposition reactions for single-cell whole-genome library preparation without preamplification. We examined 782 cells from cell lines and triple-negative breast xenograft tumors. Low-depth sequencing, compared with existing methods, revealed greater coverage uniformity and more reliable detection of copy-number alterations...
January 9, 2017: Nature Methods
https://www.readbyqxmd.com/read/28062980/assessment-of-an-apobec3b-truncating-mutation-c-783delg-in-patients-with-breast-cancer
#10
Hoda Radmanesh, Tessa Spethmann, Julia Enßen, Peter Schürmann, Sabin Bhuju, Robert Geffers, Natalia Antonenkova, Elza Khusnutdinova, Ariane Sadr-Nabavi, Fatemeh Homaei Shandiz, Tjoung-Won Park-Simon, Peter Hillemanns, Hans Christiansen, Natalia Bogdanova, Thilo Dörk
PURPOSE: APOBEC3B belongs to the family of DNA-editing enzymes. A copy number variant targeting the genomic APOBEC3A-APOBEC3B locus has a significant impact on breast cancer risk, but the relative contribution of APOBEC3B is uncertain. In this study, we investigate a loss-of-function mutation that selectively targets APOBEC3B, for its association with breast cancer risk. METHODS: We performed exome sequencing on genomic DNA samples of 6 Byelorussian patients with familial breast cancer...
January 6, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28061750/genomecat-a-versatile-tool-for-the-analysis-and-integrative-visualization-of-dna-copy-number-variants
#11
Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann
BACKGROUND: The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. RESULTS: We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs...
January 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28059126/an-exploratory-study-of-predisposing-genetic-factors-for-digeorge-velocardiofacial-syndrome
#12
Laia Vergés, Francesca Vidal, Esther Geán, Alexandra Alemany-Schmidt, Maria Oliver-Bonet, Joan Blanco
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28056497/taxonomic-distribution-repeats-and-functions-of-the-s1-domain-containing-proteins-as-members-of-the-ob-fold-family
#13
Evgeniia I Deryusheva, Andrey V Machulin, Olga M Selivanova, Oxana V Galzitskaya
Proteins of the nucleic acid-binding proteins superfamily perform such functions as of processing, transport, storage, stretching, translation and degradation of RNA. It is one of the 16 superfamilies containing the OB-fold in protein structures. Here, we have analyzed the superfamily of nucleic acid-binding proteins (the number of sequences exceeds 200000) and obtained that this superfamily prevalently consists of proteins containing the cold shock DNA-binding domain (about 131000 protein sequences). Proteins containing the S1 domain compose 57% from the cold shock DNA-binding domain family...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28056283/-copy-number-variants-analysis-in-whole-genome-of-patients-with-lipoma-tethered-cord-syndrome
#14
B Z Tao, X G Yu, C Cheng, R Zong, Z Y Zhao, L K Wang, A J Shang
Objective: To explore the abnormality of chromosomes of patients with lipoma tethered cord syndrome and the probable association between Copy Number Variations (CNV) and lipoma tethered cord syndrome. Methods: By using the Agilent SurePrint G3 Human CGH 8×60K Microarray Kit, we performed genome-wide screening for CNV on 11 patients with lipoma tethered cord syndrome adopted by the Neurosurgery Department of Chinese PLA General Hospital and their healthy parents from March 2015 to May 2015. We analyze CNVs got by the kit against the gene databases...
January 3, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28046094/analysis-of-genetic-variation-in-cyp450-genes-for-clinical-implementation
#15
Liuh Ling Goh, Chia Wei Lim, Wey Cheng Sim, Li Xian Toh, Khai Pang Leong
BACKGROUND: Genetic determinants of drug response remain stable throughout life and offer great promise to patient-tailored drug therapy. The adoption of pharmacogenetic (PGx) testing in patient care requires accurate, cost effective and rapid genotyping with clear guidance on the use of the results. Hence, we evaluated a 32 SNPs panel for implementing PGx testing in clinical laboratories. METHODS: We designed a 32-SNP panel for PGx testing in clinical laboratories...
2017: PloS One
https://www.readbyqxmd.com/read/28046031/confirmation-of-the-ovol2-promoter-mutation-c-307t-c-in-posterior-polymorphous-corneal-dystrophy-1
#16
Doug D Chung, Ricardo F Frausto, Aleck E Cervantes, Katherine M Gee, Marina Zakharevich, Evelyn M Hanser, Edwin M Stone, Elise Heon, Anthony J Aldave
PURPOSE: To identify the genetic basis of posterior polymorphous corneal dystrophy (PPCD) in families mapped to the PPCD1 locus and in affected individuals without ZEB1 coding region mutations. METHODS: The promoter, 5' UTR, and coding regions of OVOL2 was screened in the PPCD family in which linkage analysis established the PPCD1 locus and in 26 PPCD probands who did not harbor a ZEB1 mutation. Copy number variation (CNV) analysis in the PPCD1 and PPCD3 intervals was performed on DNA samples from eight probands using aCGH...
2017: PloS One
https://www.readbyqxmd.com/read/28046008/cell-free-dna-provides-a-good-representation-of-the-tumor-genome-despite-its-biased-fragmentation-patterns
#17
Xiangyuan Ma, Liangjun Zhu, Xue Wu, Hua Bao, Xiaonan Wang, Zhili Chang, Yang W Shao, Zhenxin Wang
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28044414/flexible-and-scalable-full-length-cyp2d6-long-amplicon-pacbio-sequencing
#18
Henk P J Buermans, Rolf H A M Vossen, Seyed Yahya Anvar, William G Allard, Henk-Jan Guchelaar, Stefan J White, Johan T den Dunnen, Jesse J Swen, Tahar van der Straaten
Cytochrome P450 2D6 (CYP2D6) is among the most important genes involved in drug metabolism. Specific variants are associated with changes in the enzyme's amount and activity. Multiple technologies exist to determine these variants, like the AmpliChip CYP450 test, Taqman qPCR, or Second-Generation Sequencing, however, sequence homology between cytochrome P450 genes and pseudogene CYP2D7 impairs reliable CYP2D6 genotyping, and variant phasing cannot accurately be determined using these assays. To circumvent this, we sequenced CYP2D6 using the Pacific Biosciences RSII and obtained high-quality, full-length, phased CYP2D6 sequences, enabling accurate variant calling and haplotyping of the entire gene-locus including exonic, intronic, and upstream and downstream regions...
January 3, 2017: Human Mutation
https://www.readbyqxmd.com/read/28042670/the-genetic-basis-of-cerebral-palsy
#19
REVIEW
Michael C Fahey, Alastair H Maclennan, Doris Kretzschmar, Jozef Gecz, Michael C Kruer
Although prematurity and hypoxic-ischaemic injury are well-recognized contributors to the pathogenesis of cerebral palsy (CP), as many as one-third of children with CP may lack traditional risk factors. For many of these children, a genetic basis to their condition is suspected. Recent findings have implicated copy number variants and mutations in single genes in children with CP. Current studies are limited by relatively small patient numbers, the underlying genetic heterogeneity identified, and the paucity of validation studies that have been performed...
January 1, 2017: Developmental Medicine and Child Neurology
https://www.readbyqxmd.com/read/28042135/developing-a-risk-scoring-model-for-ankylosing-spondylitis-based-on-a-combination-of-hla-b27-single-nucleotide-polymorphism-and-copy-number-variant-markers
#20
(no author information available yet)
No abstract text is available yet for this article.
January 2017: Journal of Rheumatology
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