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genomics, WGS, WES, Whole Genome Sequencing, Whole Exome Sequencing, Clinical Utility

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https://www.readbyqxmd.com/read/30002876/meta-analysis-of-the-diagnostic-and-clinical-utility-of-genome-and-exome-sequencing-and-chromosomal-microarray-in-children-with-suspected-genetic-diseases
#1
Michelle M Clark, Zornitza Stark, Lauge Farnaes, Tiong Y Tan, Susan M White, David Dimmock, Stephen F Kingsmore
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011-August 2017) and meta-analysis, following MOOSE/PRISMA guidelines...
2018: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/29891567/clonal-dynamics-of-donor-derived-myelodysplastic-syndrome-after-unrelated-hematopoietic-cell-transplantation-for-high-risk-pediatric-b-lymphoblastic-leukemia
#2
Jason R Schwartz, Michael P Walsh, Jing Ma, Tamara Lamprecht, Shuoguo Wang, Gang Wu, Susana Raimondi, Brandon M Triplett, Jeffery M Klco
Donor-derived hematologic malignancies are rare complications of hematopoietic cell transplantation (HCT). Although these are commonly either a myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), in general, they are a heterogeneous group of diseases, and a unified mechanism for their development has remained elusive. Here we report next-generation sequencing, including whole-exome sequencing (WES), whole-genome sequencing (WGS), and targeted sequencing, of a case of donor-derived MDS (dMDS) following HCT for high-risk B-lymphoblastic leukemia (B-ALL) in an adolescent...
October 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29721916/integration-of-genomics-and-metabolomics-for-prioritization-of-rare-disease-variants-a-2018-literature-review
#3
Emma Graham, Jessica Lee, Magda Price, Maja Tarailo-Graovac, Allison Matthews, Udo Engelke, Jeffrey Tang, Leo A J Kluijtmans, Ron A Wevers, Wyeth W Wasserman, Clara D M van Karnebeek, Sara Mostafavi
Many inborn errors of metabolism (IEMs) are amenable to treatment; therefore, early diagnosis and treatment is imperative. Despite recent advances, the genetic basis of many metabolic phenotypes remains unknown. For discovery purposes, whole exome sequencing (WES) variant prioritization coupled with clinical and bioinformatics expertise is the primary method used to identify novel disease-causing variants; however, causation is often difficult to establish due to the number of plausible variants. Integrated analysis of untargeted metabolomics (UM) and WES or whole genome sequencing (WGS) data is a promising systematic approach for identifying disease-causing variants...
May 2, 2018: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29565419/whole-genome-sequencing-offers-additional-but-limited-clinical-utility-compared-with-reanalysis-of-whole-exome-sequencing
#4
Ahmed Alfares, Taghrid Aloraini, Lamia Al Subaie, Abdulelah Alissa, Ahmed Al Qudsi, Ahmed Alahmad, Fuad Al Mutairi, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Mohammed Albalwi, Saeed Alturki, Majid Alfadhel
PurposeWhole-exome sequencing (WES) and whole-genome sequencing (WGS) are used to diagnose genetic and inherited disorders. However, few studies comparing the detection rates of WES and WGS in clinical settings have been performed.MethodsVariant call format files were generated and raw data analysis was performed in cases in which the final molecular results showed discrepancies. We classified the possible explanations for the discrepancies into three categories: the time interval between the two tests, the technical limitations of WES, and the impact of the sequencing system type...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29254223/development-and-validation-of-a-targeted-next-generation-dna-sequencing-panel-outperforming-whole-exome-sequencing-for-the-identification-of-clinically-relevant-genetic-variants
#5
Eirwen M Miller, Nicole E Patterson, Jenna Marcus Zechmeister, Michal Bejerano-Sagie, Maria Delio, Kunjan Patel, Nivedita Ravi, Wilber Quispe-Tintaya, Alexander Maslov, Nichelle Simmons, Maria Castaldi, Jan Vijg, Rouzan G Karabakhtsian, John M Greally, Dennis Y S Kuo, Cristina Montagna
Next generation sequencing (NGS) technologies have revolutionized our approach to genomic research. The use of whole genome sequencing (WGS), whole exome sequencing (WES), transcriptome profiling, and targeted DNA sequencing has exponentially improved our understanding of the human genome and the genetic complexities underlying malignancy. Yet, WGS and WES clinical applications remain limited due to high costs and the large volume of data generated. When utilized to address biological questions in basic science studies, targeted sequencing panels have proven extremely valuable due to reduced costs and higher sequencing depth...
November 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/27630156/is-the-1000-genome-as-near-as-we-think-a-cost-analysis-of-next-generation-sequencing
#6
Kirsten J M van Nimwegen, Ronald A van Soest, Joris A Veltman, Marcel R Nelen, Gert Jan van der Wilt, Lisenka E L M Vissers, Janneke P C Grutters
BACKGROUND: The substantial technological advancements in next-generation sequencing (NGS), combined with dropping costs, have allowed for a swift diffusion of NGS applications in clinical settings. Although several commercial parties report to have broken the $1000 barrier for sequencing an entire human genome, a valid cost overview for NGS is currently lacking. This study provides a complete, transparent and up-to-date overview of the total costs of different NGS applications. METHODS: Cost calculations for targeted gene panels (TGP), whole exome sequencing (WES) and whole genome sequencing (WGS) were based on the Illumina NextSeq500, HiSeq4000, and HiSeqX5 platforms, respectively...
November 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/25169955/exome-sequence-read-depth-methods-for-identifying-copy-number-changes
#7
REVIEW
Latha Kadalayil, Sajjad Rafiq, Matthew J J Rose-Zerilli, Reuben J Pengelly, Helen Parker, David Oscier, Jonathan C Strefford, William J Tapper, Jane Gibson, Sarah Ennis, Andrew Collins
Copy number variants (CNVs) play important roles in a number of human diseases and in pharmacogenetics. Powerful methods exist for CNV detection in whole genome sequencing (WGS) data, but such data are costly to obtain. Many disease causal CNVs span or are found in genome coding regions (exons), which makes CNV detection using whole exome sequencing (WES) data attractive. If reliably validated against WGS-based CNVs, exome-derived CNVs have potential applications in a clinical setting. Several algorithms have been developed to exploit exome data for CNV detection and comparisons made to find the most suitable methods for particular data samples...
May 2015: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/24671342/genetic-counselors-views-and-experiences-with-the-clinical-integration-of-genome-sequencing
#8
Kalotina Machini, Jessica Douglas, Alicia Braxton, Judith Tsipis, Kate Kramer
In recent years, new sequencing technologies known as next generation sequencing (NGS) have provided scientists the ability to rapidly sequence all known coding as well as non-coding sequences in the human genome. As the two emerging approaches, whole exome (WES) and whole genome (WGS) sequencing, have started to be integrated in the clinical arena, we sought to survey health care professionals who are likely to be involved in the implementation process now and/or in the future (e.g., genetic counselors, geneticists and nurse practitioners)...
August 2014: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/23846343/stakeholders-opinions-on-the-implementation-of-pediatric-whole-exome-sequencing-implications-for-informed-consent
#9
Brooke L Levenseller, Danielle J Soucier, Victoria A Miller, Diana Harris, Laura Conway, Barbara A Bernhardt
Advances in whole genome and whole exome sequencing (WGS/WES) technologies have led to increased availability in clinical settings. Currently, there are few guidelines relating to the process and content of informed consent for WGS/WES, nor to which results should be returned to families. To address this gap, we conducted focus groups to assess the views of professionals, parents, and adolescents for the future implementation of WES. The discussions assessed understanding of the risks and benefits of WES, preferences for the informed consent discussion, process for return of results, and the decision-making role of the pediatric patient...
August 2014: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/23575420/genomic-sequencing-for-psychiatric-disorders-promise-and-challenge
#10
Barbara Bowles Biesecker, Holly Landrum Peay
Whole genome/exome sequencing (WGS/WES) integration into medicine will yield a new disease paradigm moving from clinical to molecular diagnosis. This paradigm will present significant challenges in the interpretation of sequence data and clinicians will face dilemmas about if, when and how to offer information to patients. Sequencing will ultimately reshape psychiatry in predicting disease risk and lead to greater understanding of aetiology, prognosis and/or treatment response. This commentary on the ethics of returning WGS/WES results describes the nature of the data as a dynamic health resource, the importance of understanding participant motivations, determinations of personal utility and potential effects of WGS/WES on self-concept and well-being...
August 2013: International Journal of Neuropsychopharmacology
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