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Read clouds uncover variation in complex regions of the human genome

Alex Bishara, Yuling Liu, Ziming Weng, Dorna Kashef-Haghighi, Daniel E. Newburger, Robert West, Arend Sidow, Serafim Batzoglou
2015 Genome Research  
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]

Alex Bishara, Yuling Liu, Dorna Kashef-Haghighi, Ziming Weng, Daniel E. Newburger, Robert West, Arend Sidow, Serafim Batzoglou
2015 Lecture Notes in Computer Science  
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

Zemin Ning, Stephen B Montgomery
2010 Genome Biology  
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

Kathryn B. Garber
2015 American Journal of Human Genetics  
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

Wenming Xiao, Leihong Wu, Gokhan Yavas, Vahan Simonyan, Baitang Ning, Huixiao Hong
2016 Pharmaceutics  
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

Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna
2013 Computer applications in the biosciences : CABIOS  
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

Noah Spies, Ziming Weng, Alex Bishara, Jennifer McDaniel, David Catoe, Justin M Zook, Marc Salit, Robert B West, Serafim Batzoglou, Arend Sidow
2017 Nature Methods  
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

Karen He, Dongliang Ge, Max He
2017 International Journal of Molecular Sciences  
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]

Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, Harianto Tjong, Francesca Menghi, Chew Yee Ngan, Edison T. Liu, Chia-Lin Wei
2017 bioRxiv   pre-print
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

Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P. Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Frank Speleman, Tim De Meyer, Björn Menten, Frederique Lisacek
2014 PLoS ONE  
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]

Noah Spies, Ziming Weng, Alex Bishara, Jennifer McDaniel, David Catoe, Justin M Zook, Marc Salit, Robert B West, Serafim Batzoglou, Arend Sidow
2016 bioRxiv   pre-print
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

Hyunhwa Lee, Jessica Gill, Taura Barr, Sijung Yun, Hyungsuk Kim
2017 Biological Research for Nursing  
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

Katherine Bourzac
2015 Nature  
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

Shilpa Nadimpalli Kobren, Undiagnosed Diseases Network, Dustin Baldridge, Matt Velinder, Joel B. Krier, Kimberly LeBlanc, Cecilia Esteves, Barbara N. Pusey, Stephan Züchner, Elizabeth Blue, Hane Lee, Alden Huang (+11 others)
2021 Genetics in Medicine  
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

Gaye Lightbody, Fiona Browne, Huiru Zheng, Valeriia Haberland, Jaine Blayney
2016 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
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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