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dc.contributor.authorAlfares, Ahmed
dc.contributor.authorAlsubaie, Lamia
dc.contributor.authorAloraini, Taghrid
dc.contributor.authorAlaskar, Aljoharah
dc.contributor.authorAlthagafi, Azza Th.
dc.contributor.authorAlahmad, Ahmed
dc.contributor.authorRashid, Mamoon
dc.contributor.authorAlswaid, Abdulrahman
dc.contributor.authorAlothaim, Ali
dc.contributor.authorEyaid, Wafaa
dc.contributor.authorAbabneh, Faroug
dc.contributor.authorAlbalwi, Mohammed
dc.contributor.authorAlotaibi, Raniah
dc.contributor.authorAlmutairi, Mashael
dc.contributor.authorAltharawi, Nouf
dc.contributor.authorAlsamer, Alhanouf
dc.contributor.authorAbdelhakim, Marwa
dc.contributor.authorKafkas, Senay
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorCheung, Nicole
dc.contributor.authorAbdallah, Abdallah
dc.contributor.authorBüchmann-Møller, Stine
dc.contributor.authorFukasawa, Yoshinori
dc.contributor.authorZhao, Xiang
dc.contributor.authorRajan, Issaac
dc.contributor.authorHoehndorf, Robert
dc.contributor.authorAl Mutairi, Fuad
dc.contributor.authorGojobori, Takashi
dc.contributor.authorAlfadhel, Majid
dc.date.accessioned2020-07-21T11:52:32Z
dc.date.available2020-07-21T11:52:32Z
dc.date.issued2020-07-17
dc.date.submitted2019-05-08
dc.identifier.citationAlfares, A., Alsubaie, L., Aloraini, T., Alaskar, A., Althagafi, A., Alahmad, A., … Alfadhel, M. (2020). What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC Medical Genomics, 13(1). doi:10.1186/s12920-020-00743-8
dc.identifier.issn1755-8794
dc.identifier.pmid32680510
dc.identifier.doi10.1186/s12920-020-00743-8
dc.identifier.urihttp://hdl.handle.net/10754/664333
dc.description.abstractBACKGROUND:Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. METHODS:Three cohorts were used for this analysis: one cohort to assess the hit rate between solo, trio and trio plus testing, another cohort to examine the impact of the testing strategy of sibship genome vs trio-based analysis, and a third cohort to test the impact of an extended family analysis of up to eight family members to lower the number of candidate variants. RESULTS:The hit rates in solo, trio and trio plus testing were 39, 40, and 41%, respectively. The total number of candidate variants in the sibship testing strategy was 117 variants compared to 59 variants in the trio-based analysis. We noticed that the average number of coding candidate variants in trio-based analysis was 1192 variants and 26,454 noncoding variants, and this number was lowered by 50-75% after adding additional family members, with up to two coding and 66 noncoding homozygous variants only, in families with eight family members. CONCLUSION:There was no difference in the hit rate between solo and extended family members. Trio-based analysis was a better approach than sibship testing, even in a consanguineous population. Finally, each additional family member helped to narrow down the number of variants by 50-75%. Our findings could help clinicians, researchers and testing laboratories select the most cost-effective and appropriate sequencing approach for their patients. Furthermore, using extended family analysis is a very useful tool for complex cases with novel genes.
dc.description.sponsorshipThis research used resources from the Core Labs of King Abdullah University of Science and Technology (KAUST).
dc.publisherSpringer Nature
dc.relation.urlhttps://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-020-00743-8
dc.relation.urlhttps://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-020-00743-8
dc.rightsThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleWhat is the right sequencing approach? Solo VS extended family analysis in consanguineous populations.
dc.typeArticle
dc.contributor.departmentBio-Ontology Research Group (BORG)
dc.contributor.departmentBioinformatics
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Core Lab
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentNGS, qPCR and Single Cell Genomics
dc.contributor.departmentSanger and Third Generation Sequencing
dc.identifier.journalBMC medical genomics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.
dc.contributor.institutionDepartment of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia.
dc.contributor.institutionQassim University, Department of Pediatrics, Almulyda, Saudi Arabia.
dc.contributor.institutionDivision of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.
dc.contributor.institutionKing Abdullah International Medical Research Center, Riyadh, Saudi Arabia.
dc.contributor.institutionKing Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia.
dc.contributor.institutionDepartment of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
dc.identifier.volume13
dc.identifier.issue1
kaust.personAlthagafi, Azza
kaust.personAbdelhakim, Marwa
kaust.personKafkas, Senay
kaust.personMineta, Katsuhiko
kaust.personCheung, Nicole
kaust.personAbdallah, Abdallah
kaust.personBüchmann-Møller, Stine
kaust.personFukasawa, Yoshinori
kaust.personZhao, Xiang
kaust.personRajan, Issaac
kaust.personHoehndorf, Robert
kaust.personGojobori, Takashi
dc.date.accepted2020-06-19
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.5066525
refterms.dateFOA2020-07-21T11:53:06Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Dataset]</i> <br/> Alfares, A., Alsubaie, L., Aloraini, T., Aljoharah Alaskar, Azza Althagafi, Alahmad, A., Mamoon Rashid, Abdulrahman Alswaid, Alothaim, A., Eyaid, W., Faroug Ababneh, Albalwi, M., Raniah Alotaibi, Mashael Almutairi, Nouf Altharawi, Alhanouf Alsamer, Abdelhakim, M., Senay Kafkas, Mineta, K., … Alfadhel, M. (2020). <i>What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations</i>. figshare. https://doi.org/10.6084/M9.FIGSHARE.C.5066525. DOI: <a href="https://doi.org/10.6084/m9.figshare.c.5066525" >10.6084/m9.figshare.c.5066525</a> Handle: <a href="http://hdl.handle.net/10754/664972" >10754/664972</a></a></li></ul>
kaust.acknowledged.supportUnitCore Labs
dc.date.published-online2020-07-17
dc.date.published-print2020-12


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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.