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Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, Cheung WA, Coffman KA, Cooper AM, Cross LA, Curran T, Dang TTT, Elfrink MM, Engleman KL, Fecske ED, Fieser C, Fitzgerald K, Fleming EA, Gadea RN, Gannon JL, Gelineau-Morel RN, Gibson M, Goldstein J, Grundberg E, Halpin K, Harvey BS, Heese BA, Hein W, Herd SM, Hughes SS, Ilyas M, Jacobson J, Jenkins JL, Jiang S, Johnston JJ, Keeler K, Korlach J, Kussmann J, Lambert C, Lawson C, Le Pichon JB, Leeder JS, Little VC, Louiselle DA, Lypka M, McDonald BD, Miller N, Modrcin A, Nair A, Neal SH, Oermann CM, Pacicca DM, Pawar K, Posey NL, Price N, Puckett LMB, Quezada JF, Raje N, Rowell WJ, Rush ET, Sampath V, Saunders CJ, Schwager C, Schwend RM, Shaffer E, Smail C, Soden S, Strenk ME, Sullivan BR, Sweeney BR, Tam-Williams JB, Walter AM, Welsh H, Wenger AM, Willig LK, Yan Y, Younger ST, Zhou D, Zion TN, Thiffault I, Pastinen T. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet Med 2022; 24:1336-1348. [PMID: 35305867 DOI: 10.1016/j.gim.2022.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using 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 >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Shivarajan M Amudhavalli
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - John T Anderson
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Lalit Bansal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rebecca L Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Keith A Coffman
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Ashley M Cooper
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Laura A Cross
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO
| | - Thuy Tien T Dang
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Mary M Elfrink
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Erin D Fecske
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Cynthia Fieser
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Keely Fitzgerald
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rose N Gelineau-Morel
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey Goldstein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Kelsee Halpin
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Brian S Harvey
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Wendy Hein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Suzanne M Herd
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Mohammed Ilyas
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jill Jacobson
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Kathryn Keeler
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Jonas Korlach
- Pacific Biosciences of California, Inc, Menlo Park, CA
| | | | | | - Caitlin Lawson
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Vicki C Little
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Neil Miller
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Allergy Immunology Pulmonary and Sleep Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Annapoorna Nair
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Donna M Pacicca
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Kailash Pawar
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nyshele L Posey
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Nigel Price
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Julio F Quezada
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nikita Raje
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO
| | | | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, MO
| | - Venkatesh Sampath
- Division of Neonatology, Children's Mercy Hospital Kansas City, Kansas City, MO
| | - Carol J Saunders
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Richard M Schwend
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Elizabeth Shaffer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Sarah Soden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Brooke R Sweeney
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Adam M Walter
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Laurel K Willig
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Yun Yan
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Scott T Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Children's Mercy Research Institute, Kansas City, MO.
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