1. IGenomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes
- Author
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Jill Jacobson, Keith A Coffman, Susan S Hughes, Caitlin Lawson, Erin D Fecske, Ahmed T Abdelmoity, Thuy Tien T Dang, Annapoorna Nair, Janda L Jenkins, Kendra L Engleman, Daniel A Louiselle, Orion Buske, Nigel Price, Dihong Zhou, Michael Lypka, Courtney D Berrios, Laura Mb Puckett, Kelsee Halpin, Ana Sa Cohen, Nikita Raje, Aaron M Wenger, Emily G Farrow, Keely Fitzgerald, Mohammed Ilyas, Kailash Pawar, Joseph T Alaimo, Jennifer L Gannon, Laurel K Willig, Jean-Baptiste Le Pichon, Shivarajan M Amudhavalli, Christopher M Oermann, Rebecca L Biswell, Shelby H Neal, Lalit Bansal, Elizabeth Shaffer, Brittany D McDonald, Bonnie R Sullivan, Isabelle Thiffault, Christine Lambert, Ashley M Cooper, Suzanne M Herd, Holly Welsh, Julio F Quezada, Carol J Saunders, Caitlin Schwager, Brian S Harvey, Adam M Walter, Donna M Pacicca, Jennifer Kussmann, Rose N Gelineau-Morel, Margaret Gibson, Elin Grundberg, Shao Jiang, Scott T Younger, Steve Leeder, Richard M Schwend, John T Anderson, Venkatesh Sampath, Jonas Korlach, Bryce A Heese, Meghan E Strenk, Neil Miller, Vicki C Little, Ann Modrcin, Brooke R Sweeney, Randi N Gadea, Nyshele L Posey, Emily A Fleming, Wendy Hein, Cynthia Fieser, Eric T Rush, Laura A Cross, Craig Smail, William J Rowell, Kathryn Keeler, Jeffrey Goldstein, Tricia N Zion, Warren A. Cheung, Sarah Soden, Lauren Bartik, Bradley Belden, Thomas Curran, Pawel Buczkowicz, Shreyasee Chakraborty, Yun Yan, Tomi Pastinen, Primo Baybayan, Mary M Elfrink, Jeffrey J Johnston, and Jade B Tam-Williams
- Subjects
Unknown Significance ,Pedigree chart ,Computational biology ,Allele ,Biology ,Gene ,Genome ,Exome ,DNA sequencing ,Rare disease - Abstract
PURPOSETo provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids (GA4K) program.METHODSExtensive analyses of 960 families with suspected genetic disorders including short-read exome (ES) and genome sequencing (srGS); PacBio HiFi long-read GS (HiFi-GS); variant calling for small-nucleotide (SNV), structural (SV) and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants and pedigrees are stored in PhenoTips database, with data sharing through controlled access (dbGAP).RESULTSDiagnostic rates ranged from 11% for cases with prior negative genetic tests to 34.5% in naïve patients. Incorporating SVs from GS added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs than srGS. Variants and genes of unknown significance (VUS/GUS) remain the most common finding (58% of non-diagnostic cases).CONCLUSIONComputational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated by HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation, and by providing HiFi variant (SNV/SV) resources from >1,000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.
- Published
- 2021