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Read clouds uncover variation in complex regions of the human genome
2015
Genome Research
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Most population and genome-wide association studies have therefore been unable to consider variation in these regions. ...
We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that ...
., for contributing the two additional lanes of TruSeq read-cloud sequencing for NA12878. ...
doi:10.1101/gr.191189.115
pmid:26286554
pmcid:PMC4579342
fatcat:cqrkyhgw5benvf5ljwkylojrfa
Read Clouds Uncover Variation in Complex Regions of the Human Genome
[chapter]
2015
Lecture Notes in Computer Science
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Most population and genome-wide association studies have therefore been unable to consider variation in these regions. ...
We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that ...
., for contributing the two additional lanes of TruSeq read-cloud sequencing for NA12878. ...
doi:10.1007/978-3-319-16706-0_5
fatcat:nhcfut2gdzb5nczapaxr24who4
Out of the sequencer and into the wiki as we face new challenges in genome informatics
2010
Genome Biology
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Recent advances in NGS technologies have greatly increased the scale and scope with which we can interrogate novel genomes and uncover genetic variation. ...
of discordantly genotyped positions, he revealed that a majority occurred in regions with poorly aligned reads. ...
doi:10.1186/gb-2010-11-10-308
pmid:21067526
pmcid:PMC3218654
fatcat:qc7xatmbgfdmjikp6lxq3ftdiq
This Month in Genetics
2015
American Journal of Human Genetics
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Surprisingly, in 69% of sibling pairs in whom a putative causal variant was identified, the variant was not shared between the siblings. ...
The authors completed the largest whole-genome analysis of autism to date, and their sample included 85 quartet families: those with two affected siblings. ...
They confirmed over 1,000 multiallellic CNVs in the human genome. ...
doi:10.1016/j.ajhg.2015.02.004
pmcid:PMC4375432
fatcat:7gg3mj5ckja53pdrqo7buskmwm
Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine
2016
Pharmaceutics
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Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics ...
Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. ...
Acknowledgments: Leihong Wu is grateful to the National Center for Toxicological Research (NCTR) of the ...
doi:10.3390/pharmaceutics8020015
pmid:27110816
pmcid:PMC4932478
fatcat:xkrhpx36s5ffxjejq2unw67ccm
Using Genome Query Language to uncover genetic variation
2013
Computer applications in the biosciences : CABIOS
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Results: We provide a number of cases to showcase the use of GQL for complex evidence collection, such as the evidence for large structural variations. ...
Motivation:With high throughput DNA sequencing costs dropping below $1, 000 for human genomes, data storage, retrieval, and analysis are the major bottlenecks in biological studies. ...
ACKNOWLEDGEMENT The authors thank Alin Deutsch, Lucila Ohno-Machado, Nitin Udpa, Anand Patel, Sangwoo Kim for useful discussions and support. ...
doi:10.1093/bioinformatics/btt250
pmid:23751181
pmcid:PMC3866549
fatcat:ebwzm4mgbjaaxo2cpoqhgzjmbe
Genome-wide reconstruction of complex structural variants using read clouds
2017
Nature Methods
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Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing ...
We developed software, GROC-SVs, that takes advantage of read clouds for structural variant detection and assembly. ...
This work was supported by the Stanford Center for Computational, Evolutionary and Human Genomics (NS), R01CA183904 (NHI/NCI; RBW, SB, AS), and the BRCA Foundation (AS). ...
doi:10.1038/nmeth.4366
pmid:28714986
pmcid:PMC5578891
fatcat:kpfj7k6sjnadtiyuv3xhi4diz4
Big Data Analytics for Genomic Medicine
2017
International Journal of Molecular Sciences
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In this paper, we review the challenges of manipulating large-scale next-generation sequencing (NGS) data and diverse clinical data derived from the EHRs for genomic medicine. ...
We introduce possible solutions for different challenges in manipulating, managing, and analyzing genomic and clinical data to implement genomic medicine. ...
He is greatly appreciative of the support from the leaderships in the Center for ...
doi:10.3390/ijms18020412
pmid:28212287
pmcid:PMC5343946
fatcat:mf2grkovdneahbkcaxn7fali5y
Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome
[article]
2017
bioRxiv
pre-print
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Acquired genomic structural variants (SVs) are major hallmarks of the cancer genome. Their complexity has been challenging to reconstruct from short-read sequencing data. ...
From modest sequencing coverage, we identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses and uncovered repetitive DNA as the major source of variation ...
Acknowledgments The authors thank P. Shreckengast for collecting the HCC1187 cells; and C. Robinett and A. Lau ...
doi:10.1101/209718
fatcat:teaa55uaovgl7ml6yyh6y6u4ve
ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
2014
PLoS ONE
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Structural genomic variations play an important role in human disease and phenotypic diversity. ...
With the rise of high-throughput sequencing tools, mate-pair/ paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. ...
Genomic microarrays uncovered copy number variation (CNV) as an important source for genomic variation in addition to single nucleotide variants (SNVs) and genomic microarrays accelerated the discovery ...
doi:10.1371/journal.pone.0113800
pmid:25503062
pmcid:PMC4264741
fatcat:uxfh3bzqwvbwlkhvulq6h6ty3i
Genome-wide reconstruction of complex structural variants using read clouds
[article]
2016
bioRxiv
pre-print
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Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing ...
We developed software, GROC-SVs, that takes advantage of read clouds for structural variant detection and assembly. ...
This work was supported by the Stanford Center for Computational, Evolutionary and Human Genomics (NS), R01CA183904 (NHI/NCI; RBW, SB, AS), and the BRCA Foundation (AS). ...
doi:10.1101/074518
fatcat:pd6sm63kwvd2finn7uhrwg4mhq
Primer in Genetics and Genomics, Article 2—Advancing Nursing Research With Genomic Approaches
2017
Biological Research for Nursing
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Conclusions: Using genomic approaches in nursing research can advance the understanding of the complex pathophysiology of disease susceptibility and different patient responses to interventions. ...
Nurses should be incorporating genomics into education, clinical practice, and research as the influence of genomics in health-care research and practice continues to grow. ...
To conduct a CGA study, researchers select a small number of candidate genes or regions in the human genome to test a hypothesis. ...
doi:10.1177/1099800416689822
pmid:28135824
fatcat:3ps2udpmo5e7tkv6be5n6xmhpm
Collaborations: Mining the motherlodes
2015
Nature
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Finding rare variations in the genome -and being sure they are not missing something -means sifting through the three billion base pairs in the genomes of tens of thousands of volunteers. ...
In 2012, 442 researchers in 32 labs jointly released ENCODE papers that connected more than 80% of the human genome to specific biological functions and identified more than 4 million regions where proteins ...
doi:10.1038/527s8a
pmid:26536225
fatcat:c7oi2s37qjhsdjh2d26cmsd4ue
Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases
2021
Genetics in Medicine
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Purpose Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. ...
Methods We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network ...
Genomic regions containing only homozygous variants in an affected individual with Knowledge of variation within human populations with and without disease can be effectively used to assess the likelihood ...
doi:10.1038/s41436-020-01084-8
pmid:33580225
pmcid:PMC8187147
fatcat:s4mbmmxe7jhx5bn7fp5mv77iyu
The role of high performance, grid and cloud computing in high-throughput sequencing
2016
2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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We have reached the era of full genome sequencing using high throughput sequencing technologies pouring out gigabases of reads in a day. ...
This paper provides an overview of the evolution of high-throughput sequencing and the tools, infrastructure and data management developing in this space to support a key area in personalized medicine. ...
large numbers of human tumors to uncover the molecular basis of cancer. ...
doi:10.1109/bibm.2016.7822643
dblp:conf/bibm/LightbodyBZHB16
fatcat:emjxedmvrnfshdtrynakwurl4q
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