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From Prado-Martinez et al. Nature 2013 July 2013 \Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms." From the BBC News July 2013 From the Genome Technology Aug 2013 From the Cell Aug 2013 Cotney et al. 2013 Cell 154:185 use ChIP-seq analysis to do comparative regulatory evolution in mammals. From Genome Technology Aug 2013 From Nature Aug 2013 \Meissner and colleagues analyze whole-genome bisulphite sequencing data sets" from 2013 Nature 500:477 From PNAS Aug 2013 A.Achilli et al. (2013, PNAS 110:14308) use complete mitochondria genomes to track human migration to the Americas. From the PNAS Sept 2013 Segmenting the human genome based on states of neutral genetic divergence. Kuruppumullage Don et al. 2013 PNAS 110:14699 Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from humanorangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to di▯erent divergence states ... Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants - including those associated with cancer and other diseases - and to improve computational predictions of noncoding functional elements. From PNAS Aug 2013 Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators Marvig et al. PLoSGenetics Sept 9 2013 \a genomic analysis of bacteria from a Pseudomonas aeruginosa lineage capable of being passed from one individual infected with cystic ▯brosis to another. The team sequenced 55 P. aeruginosa isolates found in 21 Danish cystic ▯brosis patients over nearly four decades, from 1972 to 2008. The group also tracked down genes that appear to have bolstered pathogenicity and patient adaptation." Pathoadaptive genes From Genome Technology Sept 2013 With 4K Tumor Genomes Analyzed, N of One Discusses Challenges, Lessons Learned, and Future Plans | September 04, 2013 By Monica Heger Last month, genetic analysis and interpretation ▯rm N of One said that it had interpreted sequence data from over 4,000 tumors, including from whole genomes, exomes, and targeted panels. Founded in 2008, the company has 30 employees and its customers include diagnostic companies, cancer centers, and other healthcare providers. It also has a small direct patient business, where individual oncologists refer patients directly to N of One, CEO Chris Cournoyer told Clinical Sequencing News. Its clients do the sequencing and variant calling, while N of One takes that data, interprets it and gene rates a clinical report that can be returned to the physician. The company uses a proprietary analysis framework, which it calls PrecisionWorks, for curation. It also has its own database, MarkerMine. From PLoS Biology Sept 2013 From Nature Aug 2013 Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. by G.Lang et al. 2013 Nature Aug 29 2013 \Here we use whole-genome whole-population sequencing to examine the dynamics of genome sequence evolution at high temporal resolution in 40 replicate Saccharomyces cerevisiae populations growing in rich medium for 1000 generations". { \for a total of 480 sequenced" genomes. From Genome Alberta Sept 2013 The tiger genome and comparative analysis with lion and snow leopard genomes. Yun Sung Cho et al. Nature Communications Sept 17 2013 \Four US studies are set to explore how genomic data can best help healthy and ill newborns. They must also settle some questions of ethics." \Hundreds of babies in the United States will have their genomes sequences as part of a US $25million programme unveiled on 4 September ... [they will] test whether sequencing can provide more information than conventional tests that screen newborns for genetic and other disorders." ‘‘The day when all children will be sequenced at birth { if not before { draws ever nearer" From Nature 12 Sept 2013 \The New York Genome Center o▯cially launched at its new facility in downtown Manhattan . . . it is currently working to hire the bioinformatics, genome sequencing, and lab specialists who will ▯ll the seven- oor, 170,000-square-foot facility The sequencing space houses 16 Illumina HiSeq machines and a BioNano Genomics Irys DNA mapping instrument already in place, and the center has room apportioned for as many as 80 sequencers total. The center currently has around 16 bioinformaticians, but it is recruiting more and expects to eventually have around 100." (From Genome Technology Sept 20). From Genome Technology Sept 20 Genomic Analysis of MERS Coronaviruses Reveals Complex Transmission Patterns By a GenomeWeb sta▯ reporter Deep sequencing of the coronavirus behind a Middle East respiratory syndrome has indicated that virus has been introduced into the human population a number of times, according to a new study appearing in the Lancet yesterday. For the Lancet study, researchers at Saudi Arabia’s Ministry of Health, the Well come Trust Sanger Center in the UK, and elsewhere analyzed genomic data from 21 viral isolates and found that there was likely a complex transmission chain. From Genome Technology Sept 17 From Genome Technology Sept 18 From Genome Technology Sept 18 HudsonAlpha Sequencing 500 Trio Exomes to Elucidate Rare Genetic Disorders under CSER Grant By Julia Karow The HudsonAlpha Institute for Biotechnology has embarked on a research project to analyze the genomes of 500 children with unexplained genetic disorders and their parents in order to provide at least some families with a molecular diagnosis. The project, funding with up to $7.6 million over four years, is of four that received a total of up to $27 million this summer under the National Human Genome Research Institute’s Clinical Sequencing Exploratory Research, or CSER, program. In late 2011, NHGRI awarded the ▯rst six CSER grants. From Genome Technology Oct 28 China-led Study Unearths Sequences Under Selection in Tibetan Boar, Domestic Pigs By a GenomeWeb sta▯ reporter NEW YORK (GenomeWeb News) A study appearing online yesterday in Nature Genetics highlights the genomic changes, adaptation, and selective sweeps that have shaped wild boar and pig populations in Asia and beyond. An international team led by investigators in China began by sequencing the genome of a Tibetan wild boar, before doing low-coverage resequencing on dozens more wild boars and pigs. Comparisons of the sequences and variants therein o▯ered a peek at existing genetic diversity and relationships between pig populations, along with past events in pig evolution and domestication. From Genome Technology Sept 18 San Antonio 1K Cancer Genomes Project Aims to Couple Clinical Outcomes with Genomic Alterations By Monica Heger South Texas Accelerated Research Therapeutics, or START, and BGI Tech kicked o▯ a project last week that aims to sequence at least 1,000 and potentially up to 10,000 cancer genomes from patients at primary diagnosis and correlate the genomic alterations with extensive clinical outcome data about the patients’ drug regimen and disease progression. The goal of the project is to aid cancer drug development by identifying both new targets as well as gaining a better understanding of response and resistance to existing drugs. START Will collect the patient specimens and clinical data, while BGI Tech, the commercial services subsidiary of BGI, will perform the sequencing. From PLoS Genetics Sept 23 From BBC News Sept 22 From New England J Medicine Sept 26 \From September 2007 through March 2011, we performed whole-genome sequencing on isolates obtained from all symptomatic patients with C. di▯cile infection ..." \Of 1250 C. di▯cile cases that were evaluated, 1223 (98%) were successfully sequenced." \Over a 3-year period, 45% of C. di▯cile cases in Oxfordshire were genetically distinct from all previous cases. Genetically diverse sources, in addition to symptomatic patients, play a major part in C. di▯cile transmission." From Nature Sept 25 Single-cell Hi-C reveals cell-to-cell variability in chromosome structure Nagano et al. Here we introduce single-cell Hi-C, combined with genome- wide statistical analysis and structural modelling of single-copy X chromosomes, to show that individual chromosomes maintain domain organization at the megabase scale, but show variable cell-to-cell chromosome structures at larger scales. Despite this structural stochasticity, localization of active gene domains to boundaries of chromosome territories is a hallmark of chromosomal conformation. From Nature Genetics Sept 26 Emerging landscape of oncogenic signatures across human cancers Ciriello et al. Projects such as The Cancer Genome Atlas (TCGA) provide molecular tumor maps in unprecedented detail. The interpretation of these maps remains a major challenge. Here we distilled thousands of genetic and epigenetic features altered in cancers to 500 selected functional events From Genome Technology Sept 25 UCSF Studying Exome Sequencing for Metabolic and Immune Disorders, Predicting PGx Risk in Children By Molika Ashford The University of California San Francisco plans to begin a three-part project next year investigating the risks and bene▯ts of using exome sequencing to help diagnose metabolic and immune disorders and discover important pharmacogenomic variants in infants. . . . The project, led by the university’s Robert Nussbaum, will be split into three linked studies which the group expects to conduct simultaneously. The ▯rst will be a retrospective analysis of dried blood spots from children with metabolic disorders collected by the California Department of Public Health through a routine banking program. The second project will o▯er exome analysis to patients recruited through the lab of UCSF’s Jennifer Puck for a disorder called Severe Combined Immunode▯ciency. And in the third arm of the study, researchers will o▯er sequencing to parents of newborns at the UCSF Benio▯ Childrens Hospital to identify pharmacogenomic variants associated with drug metabolism and adverse reactions to medications. From Clinical Sequencing News Sept 25 Children’s Mercy Hospital Explores Rapid WGS for Newborn Screening, Disease Diagnosis By Julia Karow This is the third in a series of pro▯les of centers awarded grants this year by the NIH under the Genomic Sequencing and Newborn Screening Disorders research program. Researchers at Children’s Mercy Hospital in Kansas City are embarking on a study of the value of rapid whole-genome sequencing in newborns, both for diagnosing sick babies and for routine newborn screening. Earlier this month, the team, led by Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children’s Mercy, received more than $5 million in grant funding over ▯ve years from the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Human Genome Research Institute for the project, one of four that received a total of $25 million. From The Daily Scan Oct 1 A University of Texas Health Science Center and Baylor College of Medicine team consider the clinical applicability of sequencing for another PNAS study. By doing exome sequencing, collecting medical histories and family information for 81 volunteers, and applying a bioinformatics analysis, the researchers detected alterations that appear to explain 24 individuals’ medical conditions. Together with family history pro▯les, the study also turned up variants linked to half a dozen inherited conditions. "Our report demonstrates
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