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Whole genome

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By Faye Kehler Family Physician and GP Anesthetist since 1987 interested in all aspects of Medicine
Yuechi Xu, Zhongjie Sun
The discovery of the Klotho (KL) gene, which was originally identified as a putative aging-suppressor gene, has generated tremendous interest and has advanced understanding of the aging process. In mice, the overexpression of the KL gene extends the life span, whereas mutations to the KL gene shorten the life span. The human KL gene encodes the α-Klotho protein, which is a multifunctional protein that regulates the metabolism of phosphate, calcium, and vitamin D. α-Klotho also may function as a hormone, although the α-Klotho receptor(s) has not been found...
April 2015: Endocrine Reviews
(no author information available yet)
BACKGROUND: Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear. METHODS: We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis. RESULTS: AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes...
May 30, 2013: New England Journal of Medicine
David W Eyre, Farah Babakhani, David Griffiths, Jaime Seddon, Carlos Del Ojo Elias, Sherwood L Gorbach, Tim E A Peto, Derrick W Crook, A Sarah Walker
Whole-genome sequencing was used to determine whether the reductions in recurrence of Clostridium difficile infection observed with fidaxomicin in pivotal phase 3 trials occurred by preventing relapse of the same infection, by preventing reinfection with a new strain, or by preventing both outcomes. Paired isolates of C. difficile were available from 93 of 199 participants with recurrences (28 were treated with fidaxomicin, and 65 were treated with vancomycin). Given C. difficile evolutionary rates, paired samples ≤2 single-nucleotide variants (SNVs) apart were considered relapses, paired samples >10 SNVs apart were considered reinfection, and those 3-10 SNVs apart (or without whole-genome sequences) were considered indeterminate in a competing risks survival analysis...
May 1, 2014: Journal of Infectious Diseases
Meredith L Carpenter, Jason D Buenrostro, Cristina Valdiosera, Hannes Schroeder, Morten E Allentoft, Martin Sikora, Morten Rasmussen, Simon Gravel, Sonia Guillén, Georgi Nekhrizov, Krasimir Leshtakov, Diana Dimitrova, Nikola Theodossiev, Davide Pettener, Donata Luiselli, Karla Sandoval, Andrés Moreno-Estrada, Yingrui Li, Jun Wang, M Thomas P Gilbert, Eske Willerslev, William J Greenleaf, Carlos D Bustamante
Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome...
November 7, 2013: American Journal of Human Genetics
Anna A E Vinkhuyzen, Naomi R Wray, Jian Yang, Michael E Goddard, Peter M Visscher
Understanding genetic variation of complex traits in human populations has moved from the quantification of the resemblance between close relatives to the dissection of genetic variation into the contributions of individual genomic loci. However, major questions remain unanswered: How much phenotypic variation is genetic; how much of the genetic variation is additive and can be explained by fitting all genetic variants simultaneously in one model, and what is the joint distribution of effect size and allele frequency at causal variants? We review and compare three whole-genome analysis methods that use mixed linear models (MLMs) to estimate genetic variation...
2013: Annual Review of Genetics
Michael E Talkowski, Zehra Ordulu, Vamsee Pillalamarri, Carol B Benson, Ian Blumenthal, Susan Connolly, Carrie Hanscom, Naveed Hussain, Shahrin Pereira, Jonathan Picker, Jill A Rosenfeld, Lisa G Shaffer, Louise E Wilkins-Haug, James F Gusella, Cynthia C Morton
Conventional cytogenetic testing offers low-resolution detection of balanced karyotypic abnormalities but cannot provide the precise, gene-level knowledge required to predict outcomes. The use of high-resolution whole-genome deep sequencing is currently impractical for the purpose of routine clinical care. We show here that whole-genome "jumping libraries" can offer an immediately applicable, nucleotide-level complement to conventional genetic diagnostics within a time frame that allows for clinical action...
December 6, 2012: New England Journal of Medicine
Simon R Harris, Edward J P Cartwright, M Estée Török, Matthew T G Holden, Nicholas M Brown, Amanda L Ogilvy-Stuart, Matthew J Ellington, Michael A Quail, Stephen D Bentley, Julian Parkhill, Sharon J Peacock
BACKGROUND: The emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted lineages of MRSA means that it is necessary to understand transmission dynamics in terms of hospitals and the community as one entity. We assessed the use of whole-genome sequencing to enhance detection of MRSA transmission between these settings. METHODS: We studied a putative MRSA outbreak on a special care baby unit (SCBU) at a National Health Service Foundation Trust in Cambridge, UK...
February 2013: Lancet Infectious Diseases
Vincenza Colonna, Qasim Ayub, Yuan Chen, Luca Pagani, Pierre Luisi, Marc Pybus, Erik Garrison, Yali Xue, Chris Tyler-Smith, Goncalo R Abecasis, Adam Auton, Lisa D Brooks, Mark A DePristo, Richard M Durbin, Robert E Handsaker, Hyun Min Kang, Gabor T Marth, Gil A McVean
BACKGROUND: Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes...
2014: Genome Biology
Simon Gravel, Fouad Zakharia, Andres Moreno-Estrada, Jake K Byrnes, Marina Muzzio, Juan L Rodriguez-Flores, Eimear E Kenny, Christopher R Gignoux, Brian K Maples, Wilfried Guiblet, Julie Dutil, Marc Via, Karla Sandoval, Gabriel Bedoya, Taras K Oleksyk, Andres Ruiz-Linares, Esteban G Burchard, Juan Carlos Martinez-Cruzado, Carlos D Bustamante
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations...
2013: PLoS Genetics
Yaping Yang, Donna M Muzny, Fan Xia, Zhiyv Niu, Richard Person, Yan Ding, Patricia Ward, Alicia Braxton, Min Wang, Christian Buhay, Narayanan Veeraraghavan, Alicia Hawes, Theodore Chiang, Magalie Leduc, Joke Beuten, Jing Zhang, Weimin He, Jennifer Scull, Alecia Willis, Megan Landsverk, William J Craigen, Mir Reza Bekheirnia, Asbjorg Stray-Pedersen, Pengfei Liu, Shu Wen, Wendy Alcaraz, Hong Cui, Magdalena Walkiewicz, Jeffrey Reid, Matthew Bainbridge, Ankita Patel, Eric Boerwinkle, Arthur L Beaudet, James R Lupski, Sharon E Plon, Richard A Gibbs, Christine M Eng
IMPORTANCE: Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. OBJECTIVE: To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome. DESIGN, SETTING, AND PATIENTS: Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014...
November 12, 2014: JAMA: the Journal of the American Medical Association
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