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Sandra Bouma, Mark Peterson, Erin Gatza, Sung Won Choi
Survivorship after pediatric HCT has increased over the past decade. Focus on long-term care and well-being remains critical due to risk of poor dietary habits and exaggerated sedentary behavior, which can lead to muscle weakness, increased risk for obesity, and cardiometabolic disorders. Nutrition and physical activity are key factors in survivorship; however, data are limited. Comprehensive nutritional assessments, including nutrition-focused physical examination, grip strength, and food/activity surveys, were completed in 36 pediatric HCT survivors (aged 2-25 years)...
October 21, 2016: Pediatric Transplantation
Alfred Amambua-Ngwa, Bakary Danso, Archibald Worwui, Sukai Ceesay, Nwakanma Davies, David Jeffries, Umberto D'Alessandro, David Conway
BACKGROUND: Previous genome-wide analyses of single nucleotide variation in Plasmodium falciparum identified evidence of an extended haplotype region on chromosome 6 in West Africa, suggesting recent positive selection. Such a pattern is not seen in samples from East Africa or South East Asia, so it could be marking a selective process specific to West Africa. Analyses of the haplotype structure in samples taken at different times could give clues to possible causes of selection. METHODS: This study investigates chromosome 6 extended haplotypes in The Gambia by analysing alleles at multiple microsatellite loci using genome sequence data previously obtained from clinical isolates collected in 2008, followed by genotyping of 13 loci in 439 isolates from 1984, 1991, 2008 and 2014...
October 21, 2016: Malaria Journal
Sergi Sayols, Denise Scherzinger, Holger Klein
BACKGROUND: PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed genes. Especially when working with little input material or single cells assessing the fraction of duplicate reads is an important quality control step for NGS data sets...
October 21, 2016: BMC Bioinformatics
Zhangguo Chen, Katherine Gowan, Sonia M Leach, Sawanee S Viboolsittiseri, Ameet K Mishra, Tanya Kadoishi, Katrina Diener, Bifeng Gao, Kenneth Jones, Jing H Wang
BACKGROUND: Whole genome next generation sequencing (NGS) is increasingly employed to detect genomic rearrangements in cancer genomes, especially in lymphoid malignancies. We recently established a unique mouse model by specifically deleting a key non-homologous end-joining DNA repair gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in germinal center B cells. This mouse model spontaneously develops mature B cell lymphomas (termed G1XP lymphomas). RESULTS: Here, we attempt to employ whole genome NGS to identify novel structural rearrangements, in particular inter-chromosomal translocations (CTXs), in these G1XP lymphomas...
October 21, 2016: BMC Genomics
Arvind Y M Sundaram, Timothy Hughes, Shea Biondi, Nathalie Bolduc, Sarah K Bowman, Andrew Camilli, Yap C Chew, Catherine Couture, Andrew Farmer, John P Jerome, David W Lazinski, Andrew McUsic, Xu Peng, Kamran Shazand, Feng Xu, Robert Lyle, Gregor D Gilfillan
BACKGROUND: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures...
October 21, 2016: BMC Genomics
Sanja Dacic, Liza C Villaruz, Shira Abberbock, Alyssa Mahaffey, Pimpin Incharoen, Marina N Nikiforova
Break-apart ALK FISH probe is the FDA approved approach for detection of ALK rearrangements in lung carcinoma patients who may benefit from ALK kinase inhibitors. The FISH assay can be technically challenging and difficult to interpret. ALK immunohistochemistry and next generation sequencing have been proposed as alternative approaches. In this study, we compared various ALK -FISH patterns to next -generation sequencing (NGS) for gene fusion detection, ALK immunohistochemistry (IHC) and tumor responses to crizotinib...
October 17, 2016: Oncotarget
Robbert D A Weren, Arjen R Mensenkamp, Michiel Simons, Astrid Eijkelenboom, Aisha S Sie, Hicham Ouchene, Monique van Asseldonk, Encarna B Gomez-Garcia, Marinus J Blok, Joanne A de Hullu, Marcel R Nelen, Alexander Hoischen, Johan Bulten, Bastiaan B J Tops, Nicoline Hoogerbrugge, En Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase (PARP) inhibitors, a promising novel therapy has become available for ovarian carcinoma patients with inactivating BRCA1 or BRCA2 mutations in their tumour. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumour is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue, we have developed a single molecule molecular inversion probe (smMIP)-based targeted next generation sequencing (NGS) approach...
October 21, 2016: Human Mutation
Yang Liu, Saad M Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V Maldonado Dos Santos, Babu Valliyodan, Prasad P Calyam, Nirav Merchant, Henry T Nguyen, Dong Xu, Trupti Joshi
BACKGROUND: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS)...
October 6, 2016: BMC Bioinformatics
Anthony Gonçalves, François Bertucci, Arnaud Guille, Severine Garnier, José Adelaide, Nadine Carbuccia, Oliver Cabaud, Pascal Finetti, Serge Brunelle, Gilles Piana, Jeanne Tomassin-Piana, Maria Paciencia, Eric Lambaudie, Cornel Popovici, Renaud Sabatier, Carole Tarpin, Magali Provansal, Jean-Marc Extra, François Eisinger, Hagay Sobol, Patrice Viens, Marc Lopez, Christophe Ginestier, Emmanuelle Charafe-Jauffret, Max Chaffanet, Daniel Birnbaum
BACKGROUND: Routine feasibility and clinical impact of genomics-based tumor profiling in advanced breast cancer (aBC) remains to be determined. We conducted a pilot study to evaluate whether precision medicine could be prospectively implemented for aBC patients in a single center and to examine whether patient-derived tumor xenografts (PDX) could be obtained in this population. RESULTS: Thirty-four aBC patients were included. Actionable targets were found in 28 patients (82%)...
October 18, 2016: Oncotarget
D Kabzińska, H Mierzewska, J Senderek, A Kochański
The Warburg micro syndrome (WARBM) is a genetically heterogeneous syndrome linked to at least 4 loci. At the clinical level, WARBM is characterized by microcephaly, microphthalmia, microcornea, congenital cataracts, corpus callosum hypoplasia, severe mental retardation, and hypogonadism. In some families additional clinical features have been reported. The presence of uncommon clinical features (peripheral neuropathy, cardiomyopathy) may result in misdirected molecular diagnostics. Using the next generation sequencing approach (NGS), we were able to diagnose WARBM1 syndrome by detection of a new mutation within the RAB3GAP1 gene...
2016: Folia Neuropathologica
Elizabeth J Bhoj, Zhenming Yu, Qiaoning Guan, Rebecca Ahrens-Nicklas, Kajia Cao, Minjie Luo, Tanya Tischler, Matthew A Deardorff, Elaine Zackai, Avni B Santani
INTRODUCTION: RASopathies include disorders generally characterized by developmental delay, specific heart defects, short stature, cardiac hypertrophy, and facial dysmorphisms. Next-generation sequencing (NGS)-based panels have widespread acceptance as a diagnostic tool for RASopathies. MATERIALS AND METHODS: The first 126 patients evaluated by clinical examination and the NGS RASopathy panel at the Children's Hospital of Philadelphia were enrolled. We calculated diagnosis rate, correlated reported clinical findings with positive or negative test results, and identified final molecular diagnoses in 28/96 patients who tested negative for RASopathies...
October 20, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Tai-Heng Chen, Xia Tian, Pao-Lin Kuo, Hui-Ping Pan, Lee-Jun C Wong, Yuh-Jyh Jong
BACKGROUND: Fetal akinesia deformation sequence (FADS) refers to a broad spectrum of disorder with the absent fetal movement as the unifying feature. The etiology of FADS is heterogeneous and the majority remains unknown. Prenatal diagnosis of FADS due to neuromuscular origin has relied on clinical features and fetal muscle pathology, which can be unrevealing. The recent advance of next generation sequencing (NGS) can provide definitive molecular diagnosis effectively. METHODS AND RESULTS: An 18-week old fetus presented with akinesia and multiple contractures of joints...
October 20, 2016: Prenatal Diagnosis
Steen Kølvraa, Ripudaman Singh, Elizabeth A Normand, Sadeem Qdaisat, Ignatia B Van denVeyver, Laird Jackson, Lotte Hatt, Palle Schelde, Niels Uldbjerg, Else Marie Vestergaard, Li Zhao, Rui Chen, Chad A Shaw, Amy M Breman, Arthur L Beaudet
OBJECTIVE: Non-invasive prenatal testing (NIPT) based on fetal cells in maternal blood has the advantage over NIPT based on circulating cell-free fetal DNA in that there is no contamination with maternal DNA. This will most likely result in better detection of chromosomal aberrations including subchromosomal defects. The objective of this study was to test whether fetal cells enriched from maternal blood can be used for cell-based NIPT. METHODS: We present a method for enriching fetal cells from maternal blood, subsequent amplification of the fetal genome and detection of chromosomal and subchromosomal variations in the genome...
October 19, 2016: Prenatal Diagnosis
Kai Song, Li Li, Guofan Zhang
Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies...
October 20, 2016: Scientific Reports
N Aleksandrova, E Shubina, A Ekimov, T Kodyleva, I Mukosey, N Makarova, E Kulakova, L Levkov, D Trofimov, G Sukhikh
Chromosomal aneuploidies are known for being the main cause of abnormal development of embryos with normal morphology, their implantation failure and early reproductive losses in IVF treatments. Preimplantation genetic screening (PGS) allows selecting embryos with normal chromosomal content and increases IVF treatment efficiency due to higher implantation rates and less frequent early pregnancy losses. New technologies used for PGS allow making genome-wide analysis of the presence of all chromosomes in embryos...
October 2016: Gynecological Endocrinology
Juliana Blin, Emiliano P Ricci
Next Generation Sequencing (NGS) techniques have revolutionized most biomedical research fields over the past decade by allowing a broader vision on biological processes that occur at the molecular level. Among these, ribosome profiling or footprinting is a powerful tool to study mRNA translation in a transcriptome-wide manner. Ribosome profiling has been used to study the impact of translational control of gene expression under many different cellular conditions including viral infections. Indeed, translation is a critical step during the viral replication cycle in which the infected cell is embezzled to produce viral proteins...
October 2016: Médecine Sciences: M/S
Julie Yamaguchi, Catherine A Brennan, Elodie Alessandri, Jean-Christophe Plantier, Gavin Cloherty, Michael G Berg
HIV-2 exhibits a natural history of infection distinct from HIV-1. Primarily found in West Africa and in only 10-20% of HIV infections in this region, patients with HIV-2 typically exhibit a slower progression to AIDS, lower viral loads, and decreased rates of transmission. Here we used next-generation sequencing (NGS) to determine the sequence and phylogenetic classification of 9 HIV-2 genomes. We identified a patient with a series of mutations in an invariant cytotoxic lymphocyte (CTL)-restricted gag epitope required for retroviral structure and replication, and implicated in long-term non-progression to AIDS...
October 19, 2016: AIDS Research and Human Retroviruses
Lei Wei, Antonios Papanicolau-Sengos, Song Liu, Jianmin Wang, Jeffrey M Conroy, Sean T Glenn, Elizabeth Brese, Qiang Hu, Kiersten Marie Miles, Blake Burgher, Maochun Qin, Karen Head, Angela R Omilian, Wiam Bshara, John Krolewski, Donald L Trump, Candace S Johnson, Carl D Morrison
BACKGROUND: The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent to the excised neoplasm is often used for this purpose as it is simultaneously collected and generally contains the same tissue type as the neoplasm. Following NGS analysis, we and others have frequently observed low-level somatic mutations in these non-neoplastic tissues, which may impose additional challenges to somatic mutation detection as it complicates germline variant filtering...
October 19, 2016: BMC Medical Genomics
Jonathan Sandoval-Castillo, Catherine R M Attard, Shashikanth Marri, Chris J Brauer, Luciana M Möller, Luciano B Beheregaray
Captive breeding programs are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programs have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding...
October 18, 2016: Molecular Ecology Resources
Anna Dominiczak
Human primary or essential hypertension is a complex, polygenic trait with some 50% contribution from genes and environment. Richard Lifton and colleagues provided elegant dissection of several rare Mendelian forms of hypertension, exemplified by the glucocorticoid remediable aldosteronism and Liddle's syndrome. These discoveries illustrate that a single gene mutation can explain the entire pathogenesis of severe, early onset hypertension as well as dictating the best treatment.The dissection of the much more common polygenic hypertension has proven much more difficult...
September 2016: Journal of Hypertension
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