Genomic answers for children: Dynamic analyses of &gt;1000 pediatric rare disease genomes

Cohen, Ana S A; Farrow, Emily; Abdelmoity, Ahmed; Alaimo, Joseph T.; Amudhavalli, Shivarajan; Anderson, John T.; Bansal, Lalit; Bartik, Lauren; Baybayan, Primo; Belden, Bradley; Berrios, Courtney; Biswell, Rebecca; Buczkowicz, Pawel; Buske, Orion J.; Chakraborty, Shreyasee; Cheung, Warren A.; Coffman, Keith A.; Cooper, Ashley M.; Cross, Laura; Curran, Tom; Dang, Thuy Tien T.; Elfrink, Mary; Engleman, Kendra; Fecske, Erin; Fieser, Cynthia; Fitzgerald, Keely; Fleming, Emily; Gadea, Randi; Gannon, Jennifer; Gelineau‐Morel, Rose; Gibson, Margaret; Goldstein, Jeffrey A.; Grundberg, Elin; Halpin, Kelsee; Harvey, Brian S.; Heese, Bryce A.; Hein, Wendy; Herd, Suzanne; Hughes, Susan S.; Ilyas, Mohammed; Jacobson, Jill D.; Jenkins, Janda L; Shao, Jiang; Johnston, Jeff; Keeler, Kathryn; Korlach, Jonas; Kussmann, Jennifer; Lambert, Christine; Lawson, Caitlin; Pichon, Jean-Baptiste Le; Leeder, J. Steven; Little, Vicki C.; Louiselle, Daniel; Lypka, Michael; McDonald, Brittany; Miller, Neil; Modrcin, Ann; Nair, Annapoorna; Neal, Shelby H.; Oermann, Christopher M.; Pacicca, Donna M.; Pawar, Kailash; Posey, Nyshele; Price, Nigel; Puckett, Laura; Quezada, Julio; Raje, Nikita; Rowell, William J; Rush, Eric T.; Sampath, Venkatesh; Saunders, Carol J.; Schwager, Caitlin; Schwend, Richard M.; Shaffer, Elizabeth; Smail, Craig; Soden, Sarah E; Strenk, Meghan E.; Sullivan, Bonnie; Sweeney, Brooke; Tam-Williams, Jade; Walter, Adam; Welsh, Holly; Wenger, Aaron M.; Willig, Laurel K.; Yan, Yun; Younger, Scott T.; Zhou, Dihong; Zion, Tricia; Thiffault, Isabelle; Pastinen, Tomi

doi:10.1016/j.gim.2022.02.007

Cited by 49 publications

(52 citation statements)

References 38 publications

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“…Although the vast majority of clinical sequencing currently employs short‐read sequencing platforms, long‐read sequencing platforms continue to improve in performance and throughput, which has translated to higher variant calling accuracy in historically challenging genomic contexts (Olson et al, 2022; Wenger et al, 2019). As such, clinical long‐read sequencing is emerging as an important alternative to short‐read sequencing (Cohen et al, 2022; Logsdon et al, 2020), which is evidenced by improved interrogation of clinically significant regions, including structural variants, repeat expansions, and homologous gene families, as well as the inherent benefit of variant phasing (Ameur et al, 2019; Ardui et al, 2018; Reiner et al, 2018). Cataloguing phased haplotypes among pharmacogenomic genes has been an ongoing effort of the PharmVar Consortium (Gaedigk et al, 2019), as previous technologies have had to rely on statistical phasing and/or haplotype inference.…”

Section: Discussionmentioning

confidence: 99%

Long‐read HiFi sequencing of NUDT15 : Phased full‐gene haplotyping and pharmacogenomic allele discovery

et al. 2022

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To determine the phase of NUDT15 sequence variants for more comprehensive star (*) allele diplotyping, we developed a novel long-read single-molecule real-time HiFi amplicon sequencing method. A 10.5 kb NUDT15 amplicon assay was validated using reference material positive controls and additional samples for specimen type and blinded accuracy assessment. Triplicate NUDT15 HiFi sequencing of two reference material samples had nonreference genotype concordances of >99.9%, indicating that the assay is robust. Notably, short-read genome sequencing of a subset of samples was unable to determine the phase of star (*) allele-defining NUDT15 variants, resulting in ambiguous diplotype results. In contrast, long-read HiFi sequencing phased all variants across the NUDT15 amplicons, including a *2/*9 diplotype that previously was characterized as *1/*2 in the 1000 Genomes Project v3 data set. Assay throughput was also tested using 8.5 kb amplicons from 100 Ashkenazi Jewish individuals, which identified a novel NUDT15 *1 suballele (c.−121G>A) and a rare likely deleterious coding variant (p.Pro129Arg). Both novel alleles were Sanger confirmed and assigned as *1.007 and *20, respectively, by the PharmVar Consortium. Taken together, NUDT15 HiFi amplicon sequencing is an innovative method for phased full-gene characterization and novel allele discovery, which could improve NUDT15 pharmacogenomic testing and subsequent phenotype prediction.

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Section: Discussionmentioning

confidence: 99%

Long‐read HiFi sequencing of NUDT15 : Phased full‐gene haplotyping and pharmacogenomic allele discovery

et al. 2022

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“…Single nucleotide variants were called using DRAGEN 3.6.3 on GRCh38 for probands and parents enrolled in the Genomic Answers for Kids initiative at Children’s Mercy Hospital 24 . The following criteria were used to select candidate variants from probands: (a) gnomAD minor allele frequency < 0.001 (internal allelic frequencies were used when gnomAD data was not available), (b) variant detection using at least two sequencing technologies (whole genome sequencing, whole genome bisulfite sequencing, 10 × linked-read sequencing, or PacBio long-read sequencing), and (c) variants occurring within 100 kb of an annotated transcription start site based on NCBI RefSeq annotations.…”

Section: Methodsmentioning

confidence: 99%

Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients

McQuerry

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Hartin

et al. 2022

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Clinical whole genome sequencing has enabled the discovery of potentially pathogenic noncoding variants in the genomes of rare disease patients with a prior history of negative genetic testing. However, interpreting the functional consequences of noncoding variants and distinguishing those that contribute to disease etiology remains a challenge. Here we address this challenge by experimentally profiling the functional consequences of rare noncoding variants detected in a cohort of undiagnosed rare disease patients at scale using a massively parallel reporter assay. We demonstrate that this approach successfully identifies rare noncoding variants that alter the regulatory capacity of genomic sequences. In addition, we describe an integrative analysis that utilizes genomic features alongside patient clinical data to further prioritize candidate variants with an increased likelihood of pathogenicity. This work represents an important step towards establishing a framework for the functional interpretation of clinically detected noncoding variants.

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“…Several publications followed suit to demonstrate the ability of LRS to assay repeat elements in clinically relevant genes such as ATXN10 (MIM# 611150) (McFarland et al, 2015;Schule et al, 2017), TAF1 (MIM# 313650) (Aneichyk et al, 2018), C9orf72 (MIM# 614260) (Ebbert et al, 2018), DMPK (MIM# 605377) (Cummings et al, 2017), SAMD12 (MIM# 618073) (Cen et al, 2019), and HTT (MIM# 613004) (Hoijer et al, 2018). More recently, Cohen et al used PacBio sequencing in a large cohort of undiagnosed patients to uncover molecular diagnoses including a pathogenic pentamer expansion in the gene STARD7 (MIM# 616712) in a patient with global developmental delay and dystonia (Cohen et al, 2022). Stevanovski et al used the adaptive sequencing protocol in the Oxford Nanopore platform to target 37 loci and showed the ability to detect repeat expansions accurately in 25 patients with neurological disorders.…”

Section: Long-read Sequencing (Lrs)mentioning

confidence: 99%

Long‐read sequencing for molecular diagnostics in constitutional genetic disorders

et al. 2022

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Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS Chromosomal microarrays (SNP arrays and array CompetitiveGenomic Hybridization [aCGH]) have been considered the gold standard to detect submicroscopic deletions and duplications greater than 50 kb in length for over a decade. Currently, CMA is a first-tier diagnostic test for many congenital disorders, including developmental delay, autism, and multiple congenital anomalies (D. T. Miller et al., 2010). Targeted arrays, often focusing on exonic regions, are also companions for panel-based or targeted gene testing. While

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Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

Cited by 49 publications

References 38 publications

Long‐read HiFi sequencing of NUDT15 : Phased full‐gene haplotyping and pharmacogenomic allele discovery

Long‐read HiFi sequencing of NUDT15 : Phased full‐gene haplotyping and pharmacogenomic allele discovery

Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients

Long‐read sequencing for molecular diagnostics in constitutional genetic disorders

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