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Diagnostic Utility

Relevant publications demonstrating the diagnostic potential of clinical WGS in selected patient populations
Effect of Whole-Genome Sequencing on the Clinical Management of Acutely Ill Infants With Suspected Genetic Disease: A Randomized Clinical Trial.
Krantz ID, Medne L, Weatherly JM, et al. JAMA Pediatr. 2021;175(12):1218-1226. doi:10.1001/jamapediatrics.2021.3496

In this randomized control trial, 354 critically ill infants received WGS and were randomized to receive results at 15 days (Early) or 60 days (Delayed) after enrollment. The most common indication for testing was the presence of multiple congenital anomalies (57%). A change in management was twice as likely (21% vs. 10%; p=0.009) with WGS vs. usual care testing. The most common being: subspecialty referrals, alternations in medication, surgery or other procedures.  A two-fold increase in diagnostic yield was found with WGS compared to usual care testing. The authors conclude that for acutely ill infants in the intensive care unit, first-line WGS is associated with a significant increase in clinical management compared to usual care. These data support WGS adoption and implementation in this setting.

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care – Preliminary Report.
Smedly D, Smith KR, Martin A, et al (100,000 Genomes Project Pilot Investigators) N Engl J Med. 2021 Nov 11;385(20):1868-1880.doi: 10.1056/NEJMoa2035790.

In 4660 participants of all ages who underwent WGS, a new diagnosis was reported in 25% who had no previous diagnosis from standard of care testing. Diagnostic yield was highly variable based on indication. Of those who received a diagnosis, 14% were found in regions of the genome that would have been missed by other testing modalities. Immediate implications were reported in 25% of those who received a diagnosis. Genome sequencing in a national health care system uncovered a new diagnosis across a broad range of rare diseases.

Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: A prospective study.
Sun Y, Peng J, Liang D, et al. Hum Mutat. 2022 May;43(5):568-581.doi: 10.1002/humu.24347. Epub 2022 Mar 1.
Genome sequencing as a first-line diagnostic test for hospitalized infants.
Bowling KM, Thompson ML, Finnila CR, et al. Genet Med. 2022; 24(4): 851-861.
Diagnostic yield and treatment impact of whole-genome sequencing in paediatric neurological disorders.
Lee HF, Chi CS, Tsai CR. Dev Med Child Neurol. 2020: https://doi.org/10.1111/dmcn.14722
Successful application of genome sequencing in a diagnostic setting: 1007 index cases from a clinically heterogeneous cohort.
Bertoli-Avella AM, Beetz C, Ameziane N, Rocha ME, Guatibonza P, Pereira C, Calvo M, Herrera-Ordonez N, Segura-Castel M, Diego-Alvarez D, Zawada M, Kandaswamy KK, Werber M, Paknia O, Zielske S, Ugrinovski D, Warnack G, Kampe K, Iurașcu MI, Cozma C, Vogel F, Alhashem A, Hertecant J, Al-Shamsi AM, Alswaid AF, Eyaid W, Al Mutairi F, Alfares A, Albalwi MA, Alfadhel M, Al-Sannaa NA, Reardon W, Alanay Y, Rolfs A, Bauer P. Eur J Hum Genet. 2021 Jan;29(1):141-153. doi: 10.1038/s41431-020-00713-9. Epub 2020 Aug 28. PMID: 32860008; PMCID: PMC7852664.

This study analyzed genome sequencing (GS) data from  1007 consecutive cases with a broad spectrum of clinical presentations with onset of symptoms ranging from prenatal to 59 years of age.  The overall diagnostic yield was 21.1%. When excluding patients with  prior exome sequencing (i.e. GS was performed as a first-tier test) , the diagnostic yield was 24.7%. In 358 cases with a prior inconclusive or negative ES, an incremental diagnostic yield of 14.5% (n=52) was reported; 11 out of 52 were due to the technical superiority of GS over ES. An additional 15.1% (n=54) of cases with a prior inconclusive ES received a VUS that may or may not explain the phenotype. The authors conclude that GS should be either a standard second-line, or even first-line stand-alone test.

Genome sequencing as a diagnostic test in children with unexplained medical complexity.
Costain G, Walker S, Marano M, Veenma D, Snell M, Curtis M, Luca S, Buera J, Arje D, Reuter MS, Thiruvahindrapuram B, Trost B, Sung WWL, Yuen RKC, Chitayat D, Mendoza-Londono R, Stavropoulos J, Scherer SW, Marshall CR, Cohn RD, Cohen E, Orkin J, Meyn MS, Hayeems RZ. JAMA Netw Open. 2020;3(9):e2018109.

This prospective study  evaluated the analytical and clinical validity of whole genome sequencing (WGS) as a first-tier test compared to conventional genetic testing in a cohort of 49 children with medical complexity. The median number of conventional genetic tests was four per proband (1-13) including chromosomal microarray (n=48) and WES (n=33). For analytical validity evaluation, WGS at 36X detected 100%   of  variants (124). The overall diagnostic yield was 30.6% (15/49) and three new genetic conditions were discovered.  Clinical implications were noted in 12 patients, including an immediate medical management change in 7. The authors conclude that WGS has a role as a first-tier test in children with medical complexity.

Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. 
Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Genome Med. 2021; 13(40): https://doi.org/10.1186/s13073-021-00855-5.

Whole genome sequencing (WGS) was performed in 3219 patients over a four-year period. Initial analysis was completed using disease-specific panels or an OMIM morbid gene panel based on phenotype. In the absence of a molecular finding, additional analysis including a research WGS, was offered. The overall diagnostic yield was 40% and variants were identified in 754 different genes. Variant analysis evolved over the course of the study to include all variant types currently available via WGS. The authors state that clinical WGS has turned out to be a true game changer in the rare disease space.

A randomized controlled trial of the analytic and diagnostic performance of singleton and trio, rapid genome and exome sequencing in ill infants.
Kingsmore SF, Cakici JA, Clark MM, Gaughran M, Feddock M, Batalov S, Bainbridge MN, Carroll J, Caylor SA, Clarke C, Ding Y, ellsworth K, Farnaes L, Hildreth A, Hobbs C, James K, King CI, Lenberg J, NahasS, Prince L, Reyes I, Salz L, Sanford E, Schols P, Sweeney N, Tokita M, Veeraraghavan N, Watkins K, Wigby K, Wong T, Chowdhury S, Wright MS, Dimmock D, RCIGM Investigators.  A J Hum Gen, 2019;105:1-15.

NSIGHT2 is a prospective, randomized-controlled trial comparing rapid whole genome sequencing (WGS) and rapid whole exome sequencing (WES) to infants <4 months of age within 96 hours of NICU/PICU admission or onset of features. Singleton analysis was performed for all samples with secondary trio reanalysis performed as reflex to negative results. Gravely ill infants underwent trio, ultra-rapid WGS. The combined diagnostic yield in this study was 23%. Yield was not significantly different between rapid WGS (20%) and rapid WES (19%); however, it was higher (24%) in ultra-rapid WGS. Median time to diagnosis was similar between rWGS and rWES (11.0 d vs. 11.2 d). urWGS and rWGS combined identified two times more pathogenic and likely pathogenic variants than WES. The authors conclude that the analytical performance of rWGS is superior to rWES supporting the use of rWGS as a first-tier test in the NICU/PICU setting.

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test
Lionel AC, Costain G, Monfared N, Walker S, Reuter MS, Hosseini M, Thiruvahindrapuram B, Merico D, Jobling R, Nalpathamkalam T, Pellecchia G, Sung WWL, Wang Z, Bikangaga P, Boelman C, Carter MT, Cordeiro D, Cytrynbaum C, Dell SD, Dhir P, Dowling JJ, Heon E, Hewson S, Hiraki L, Inbar-Feigenberg M, Klatt R, Kronick J, Laxer RM, Licht C, MacDonald H, Mercimek-Andrews S, Mendoza-Londono R, Piscione T, Schneider R, Schulze A, Silverman E, Siriwardena K, Snead OC, Sondheimer N, Sutherland J, Vincent A, Wasserman JD, Weksberg R, Shuman C, Carew C, Szego MJ, Hayeems RZ, Basran R, Stavropoulos DJ, Ray PN, Bowdin S, Meyn MS, Cohn RD, Scherer SW, Marshall CR. Genet Med. 2017; Aug 3. doi: 10.1038/gim.2017.119.

In this prospective comparison of WGS to standard clinical testing (including NGS panels) in 103 pediatric patients with diverse phenotypes, the authors concluded that WGS is superior given its higher diagnostic yield. WGS confirmed significantly more diagnoses than conventional testing (41% vs 24%; P =0.01). All copy number variants reported by chromosomal microarray were detected by WGS and WGS offered more complete coverage of disease associated genes compared to WES.

The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants.
Petrikin JE, Cakici JA, Clark MM, Willig LK, Sweeney NM, Farrow EG, Saunders CJ, Thiffault I, Miller NA, Zellmer L, Herd SM, Holmes AM, Batalov S, Veeraraghavan N, Smith LD, Dimmock DP, Leeder JS, Kingsmore SF. NPJ Genom Med. 2018 Feb 9;3:6. doi: 10.1038/s41525-018-0045-8.

Rapid WGS plus standard clinical testing yielded higher genetic diagnosis rate and shorter time to diagnosis compared to standard clinical testing alone. In this partially blinded, randomized controlled trial, 65 infants (<4 months of age) with highly variable phenotypes had rapid WGS to determine diagnosis at 28 days post enrollment. Median time to diagnosis with WGS was 13 days vs. 107 days with standard clinical testing and median day of life at diagnosis was 25 days with WGS vs. 130 days with standard genetic testing. This study was terminated early due to equipoise and the growing inclusion of NGS in standard clinical testing strategies.

Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico.
Scocchia A, Wigby KM, Masser-Frye D, Del Campo M, Galarreta CI, Thorpe E, McEachern J, Robinson K, Gross A, ICSL Interpretation and Reporting Team, Ajay SS, Rajan V, Perry DL, Belmont JW, Bentley DR, Jones MC, Taft R. NPJ Genom Med. 2019;4:5.

In a resource limited setting, clinical WGS was provided at no-cost to 60 children with a mean age of 7.6 years who met testing criteria. Indications included 77% with suspected pattern of malformation and 23% with primary neurological presentation. The overall diagnostic yield was 68%. 41/60 had a genomic finding consistent with the phenotype. This included 76% of those referred for suspected malformations and 43% referred for primary neurological presentation. (p=0.0455). Post-test counseling was modified for both patient with and without a molecular diagnosis. The absence of diagnosis helpful in 6 of 19 cases without molecular diagnosis.

Whole genome sequencing expands diagnostic utility and improves clinical management in pediatric medicine
Stavropoulos DJ, Merico D, Jobling R, Bowdin S, Monfared N, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Yuen RKC, Szego MJ, Hayeems RZ, Shaul RZ, Brudno M, Girdea M, Frey B, Alipanahi B, Ahmed S, Babul-Hirji R, Badilla Porras R, Carter MT, Chad L, Chaudhry A, Chitayat D, Jougheh Doust S, Cytrynbaum C, Dupuis L, Ejaz R, Fishman L, Guerin A, Hashemi B, Helal M, Hewson S, Inbar-Feigenberg M, Kannu P, Karp N, Kim RH, Kronick J, Liston E, MacDonald H, Mercimek-Mahmutoglu S, Mendoza-Londono R, Nasr E, Nimmo G, Parkinson N, Quercia N, Raiman J, Roifman M, Schulze A, Shugar A, Shuman C, Sinajon P, Siriwardena K, Weksberg R, Yoon G, Carew C, Erickson R, Leach RA, Klein R, Ray PN, Meyn MS, Scherer SW, Cohn RD, Marshall CR. NPJ Genomic Medicine, 2016; 1.

A prospective study evaluated the diagnostic yield of WGS compared to standard clinical testing on 100 consecutive children referred for chromosomal microarray. The authors concluded that as a first-tier test, WGS reduces the number of genetic investigations and potentially the time to diagnosis, ultimately acting as a more cost-effective approach. WGS diagnosis rate was 34% compared to 13% for the total from standard clinical testing (CMA plus targeted gene sequencing (P value = 0.0009). CNV resolution is greater for WGS than CMA, typically detecting >1,500 unbalanced changes that cannot be found using CMA. Split read mapping can further reveal complex overlapping CNVs missed by CMA.

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability
Anna Lindstrand, Jesper Eisfeldt, Maria Pettersson, Claudia M. B. Carvalho, Malin Kvarnung, Giedre Grigelioniene, Britt-Marie Anderlid, Olof Bjerin, Peter Gustavsson, Anna Hammarsjö, Patrik Georgii-Hemming, Erik Iwarsson, Maria Johansson-Soller, Kristina Lagerstedt-Robinson, Agne Lieden, Måns Magnusson, Marcel Martin, Helena Malmgren, Magnus Nordenskjöld, Ameli Norling, Ellika Sahlin, Henrik Stranneheim, Emma Tham, Josephine Wincent, Sofia Ygberg, Anna Wedell, Valtteri Wirta, Ann Nordgren, Johanna Lundin and Daniel Nilsson. Genome Med. 2019; 11: 68. Published online 2019 Nov 7. doi: 10.1186/s13073-019-0675-1

Using short-read whole genome sequencing (WGS), the authors evaluated three cohorts to determine in which WGS would be an ideal first-tier diagnostic test.  The cohorts included: a cohort with validated copy number variants (CNVs) (cohort 1, n=68), individuals referred for monogenic multi-gene panels (cohort 2, n=156), and 100 prospective, consecutive cases referred to chromosomal microarray (CMA). CMA was performed using a custom oligonucleotide microarray with a median probe spacing of approximately 18kb and WGS performed using PCR-free, paired-end sequencing at 30X. Overall 27% of individuals harbored clinically relevant genetic variants by WGS compared to 12% by CMA. The authors concluded that study showed the power of WGS as a first-tier diagnostic test to detect a variety of CNVs and SNVs as well as single tandem repeats, regions of heterozygosity and chromosomal rearrangements.

Periodic reanalysis of whole-genome sequencing data enhances the diagnostic advantage over standard clinical genetic testing
Costain G, Jobling R, Walker S, Reuter MS, Snell M, Bowdin S, Cohn RD, Dupuis L, Hewson S, Mercimek-Andrews S, Shuman C, Sondheimer N, Weksberg R, Yoon G, Meyn MS, Stavropoulos DJ, Scherer SW, Mendoza-Londono R, Marshall CR. Eur J Hum Genet. 2018;26(5):740–744. doi:10.1038/s41431-018-0114-6.
Interpretation of genomic sequencing results in healthy and ill newborns: Results from the BabySeq Project
Ceyhan-Birsoy O, Murry JB, Machini K, Lebo MS, Yu TW, Fayer S, Genetti CA, Schwartz TS, Agrawal PB, Parad RB, Holm IA, McGuire AL, Green RB, Rehm HL, Beggs AH, The BabySeq Project Team.. Am J Hum Genet. 2019; 104(1): 76–93. doi: 10.1016/j.ajhg.2018.11.016

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