What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations.

BMC Medical Genomics
Ahmed AlfaresMajid Alfadhel

Abstract

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. 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. 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. There was no difference in the hit...Continue Reading

References

Jun 17, 2011·Science Translational Medicine·Matthew N BainbridgeRichard A Gibbs
Jan 18, 2012·Annual Review of Medicine·Claudia Gonzaga-JaureguiRichard A Gibbs
Jun 12, 2012·American Journal of Human Genetics·Yun Zhu, Momiao Xiong
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Mar 6, 2015·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Sue RichardsUNKNOWN ACMG Laboratory Quality Assurance Committee
Mar 23, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Ahmed AlfaresMajid Alfadhel
Sep 22, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Sateesh MaddirevulaFowzan S Alkuraya

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Citations

Feb 13, 2021·Genes·Anna LetkoAlexander Grahofer

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Software Mentioned

Integrative Genomics Viewer
Alamut® Visual
BaseSpace Variant Interpreter

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