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Challenges of sequencing human genomes

D. C. Koboldt, L. Ding, E. R. Mardis, R. K. Wilson
2010 Briefings in Bioinformatics  
Sequencing human genomes on these platforms, however, presents numerous production and bioinformatics challenges.  ...  Massively parallel sequencing technologies continue to alter the study of human genetics.  ...  Wendl for critical reading of the manuscript. We also thank Robert S.  ... 
doi:10.1093/bib/bbq016 pmid:20519329 pmcid:PMC2980933 fatcat:hmqle6a3dzgb5fy4bwfcl2ihdu

Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges

Joan Martí-Carreras, Piet Maes
2019 Virus genes  
The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago.  ...  Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced  ...  The authors would like to acknowledge the three anonymous reviewers for their help in improving the quality of this review.  ... 
doi:10.1007/s11262-018-1627-3 fatcat:gfbeznlfkfbqbnoy6ysz45ilkq

Genomics really gets personal: How exome and whole genome sequencing challenge the ethical framework of human genetics research

Holly K. Tabor, Benjamin E. Berkman, Sara Chandros Hull, Michael J. Bamshad
2011 American Journal of Medical Genetics. Part A  
Exome sequencing (ES) and whole genome sequencing (WGS) putatively identify all adverse functional alleles of protein-coding genes.  ...  We explain how use of ES/WGS challenges: (i) models under which informed consent is typically obtained; (ii) how harms associated with data sharing are considered; and (iii) the nature of obligations surrounding  ...  This research was also supported in part by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (SCH and BEB).  ... 
doi:10.1002/ajmg.a.34357 pmid:22038764 pmcid:PMC4819320 fatcat:v2pddpm3fjbdrb6rwhhjzidv3q

Delivering genome sequencing for rapid genetic diagnosis in critically ill children: parent and professional views, experiences and challenges

Melissa Hill, Jennifer Hammond, Celine Lewis, Rhiannon Mellis, Emma Clement, Lyn S. Chitty
2020 European Journal of Human Genetics  
Rapid genomic sequencing (RGS) is increasingly being used in the care of critically ill children.  ...  Here we describe a qualitative study exploring parent and professional perspectives around the usefulness of this test, the potential for unintended harms and the challenges for delivering a wider clinical  ...  We also gratefully acknowledge the contribution of Professor Maria Bitner-Glindzicz in the design and set-up of this study.  ... 
doi:10.1038/s41431-020-0667-z pmid:32561901 fatcat:dxhjozvdbvfkffin6gg2vhpjwi

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence

Stefan Taudien, Petra Galgoczy, Klaus Huse, Kathrin Reichwald, Markus Schilhabel, Karol Szafranski, Atsushi Shimizu, Shuichi Asakawa, Adam Frankish, Ivan F Loncarevic, Nobuyoshi Shimizu, Roman Siddiqui (+1 others)
2004 BMC Genomics  
Complexity and variability seem to be essential genomic features of the human DEF locus at 8p23.1 and provides an ongoing challenge for the best possible representation in the human reference sequence.  ...  This DEF locus, however, represents one of the regions in the euchromatic part of the final human genome sequence which contains segmental duplications, and recalcitrant gaps indicating high structural  ...  We would like to thank Jennifer Ashhurst, Tim Hubbard and James Gilbert (Sanger Institute, Hinxton, UK) for their support in installing and maintaining a local client of the HAVANA pipeline.  ... 
doi:10.1186/1471-2164-5-92 pmid:15588320 pmcid:PMC544879 fatcat:tdjx3b5ui5ecjfvtndt3c23pzq

From Genes to Health – Challenges and Opportunities

Muhammad Ramzan Manwar Hussain, Asifullah Khan, Hussein Sheikh Ali Mohamoud
2014 Frontiers in Pediatrics  
Dalal Al-Shaer of PACER-HD, Department of Genetic Medicine, King Abdulaziz University, SA.  ...  especially at the repetitive loci of human genome (28) .  ...  The human reference genome still carries gaps and there is an incomplete picture of the full set of genome variations in human population groups (26) .  ... 
doi:10.3389/fped.2014.00012 pmid:24624370 pmcid:PMC3939617 fatcat:dhj6fhao5rcerplt2dqbhwxk2y

Next-generation sequencing technologies: opportunities and obligations in plant genomics

R. K. Varshney, G. D. May
2012 Briefings in Functional Genomics  
The year 2003 marked the completion of the Human Genome Project. In the $9 years since then, genomics has become a vital tool for biomedical research and a driver for improved human health.  ...  An often ignored component of human health is plant-derived human nutrition.  ... 
doi:10.1093/bfgp/els001 pmid:22345600 fatcat:wpya2bij7nhxdbo2u4i2dnlhi4

The Human Genome at 10: Successes and Challenges

J. C. Venter
2011 Science  
of thousands of accurate human genome sequences.  ...  reports of the sequencing of the human genome were published.  ...  The Human Genome at 10: Successes and Challenges  ... 
doi:10.1126/science.1202812 pmid:21292962 fatcat:kq5253zf2ncltcepo2xtr4bgua

The Revolution of Genomics Technologies and their Applications in Basic and Clinical Science

Michael Halim
2022 Zenodo  
The Human Genome Project focuses on identifying and mapping human genome genes and the base pair of DNA.  ...  Genomic concepts can be used to solve a wide range of challenges, especially concerning thirdgeneration sequencing. In the current era, genomics is not only beneficial.  ...  The human genomics experiments result in genomics and the publishing of the first mouse genome and human sequence, which were major milestones [3] .  ... 
doi:10.5281/zenodo.6433757 fatcat:lxbwqjpwuncptegyl5wcoyddfq

Big Data Challenges in Genome Informatics [article]

Ka-Chun Wong
2018 arXiv   pre-print
We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in GigaBytes (GBs).  ...  It is undeniable that those genome data impose unprecedented data challenges for us. In this article, we briefly discuss the big data challenges associated with genomics in recent years.  ...  thousands of eukaryotic genomes available; for instance, the 1000 human genomes from the 1000 Genomes Project [8] .  ... 
arXiv:1803.09632v1 fatcat:2i2lucppojfi7csf27r47liccu

Two's twice as useful

Jonathan B Weitzman
2001 Genome Biology  
The availability of two sequences (each of which was generated from DNA representing pooled samples from several individuals) enables a comprehensive analysis of the human genome and highlights the challenges  ...  Comparison of the two drafts of the human genome sequence has revealed reassuring similarity but also some differences.  ...  Conclusions The authors highlight the limitations of the first drafts of the human genome.  ... 
doi:10.1186/gb-2001-2-5-reports0013 fatcat:34yc6sstjza7rdocszts46dfsu

A "Quality-First" Credo for the Human Genome Project

Maynard Olson, Phil Green
1998 Genome Research  
Of course, it is these very uncertainties that make the sequencing of the human genome a scientific and managerial challenge worthy of the committed attention of many hard-working and talented people.  ...  The Human Genome Project is lurching toward large-scale genomic sequencing.  ... 
doi:10.1101/gr.8.5.414 pmid:9582184 fatcat:kwhm2povrndyjledbfi4523ahm

Challenges in Launching Genomic Medicine Programs

Alejandra Guerchicoff
2015 Journal of Investigative Genomics  
The completion of the human genome project, an international effort to map and sequence all the human genes and marked the beginning of the "Genomic Era".  ...  The completion of a high-quality, comprehensive sequence of the human genome in 2001 was a landmark event in genetic and genomic medicine.  ... 
doi:10.15406/jig.2015.02.00022 fatcat:rewfggyahfafdikdztusi3dcre

Sequencing ancient genomes

Janet Kelso
2013 EMBnet journal  
I will outline some of the challenges in the generation and analysis of ancient genome sequence data, and discuss the evolutionary insights that have resulted from the sequencing of these genomes.  ...  The availability of these high coverage genomes provides multiple insights into the population history of both archaic and modern humans.  ... 
doi:10.14806/ej.19.a.683 fatcat:okgrueryjncf5ardnbwbz7gon4

Bioinformatics challenges of next generation sequencing

Ivo Grosse, Katrin Hoffmann
2016 it - Information Technology  
Hence, the US Department of Energy together with several other funding agencies throughout the world launched the Human Genome Project in 1990, a large-scale project of sequencing and elucidating the human  ...  Sequencing the first human genome took more than a decade and cost three billion US dollars, but sequencing got cheaper and more efficient by new sequencing technologies.  ...  the Institute of Human Genetics at Martin Luther University Halle-Wittenberg in 2011.  ... 
doi:10.1515/itit-2016-0029 fatcat:r7nn64b4q5hfdklegzaeq3jzgq
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