Developing Cost-Effective Strategies for Molecular Diagnostics of Hereditary Disorders

This study substantiates the economic and clinical efficacy of a cascade (stratified) testing approach in molecular genetic diagnostics of hereditary disorders compared to using whole-genome sequencing (WGS) as the first-line diagnostic method. By analyzing the cost, turnaround time, and diagnostic yield of 1,140 strategies across 9 disease groups (cystic fibrosis (CF), phenylketonuria (PKU), Duchenne/ Becker muscular dystrophy (DMD/BMD), spinal muscular atrophy (SMA), hearing loss, hemophilia, hereditary spastic paraplegias (HSP), Noonan/Leopard syndromes, and ultra-rare/heterogeneous disorders), we demonstrate that the optimal strategy strictly depends on the causative variant spectrum of the pathology. For diseases with known frequent pathogenic variants (PKU, hearing loss) or a predominance of large copy-number variations (CNVs) starting with «traditional» methods is economically and clinically justified. For highly heterogeneous conditions an earlier transition to NGS panel sequencing or clinical/whole exome sequencing (CES/WES) is warranted. Cascade testing achieves diagnostic yield comparable to WGS while reducing costs up to 92% and shortening time up to 53 days per 100 samples. No universal optimal method exists; algorithm selection should be based on disease-specific characteristics and resource constraints.

1. Shatokhina O., Galeeva N., Stepanova A., et al. Spectrum of Genes for Non-GJB2-Related Non-Syndromic Hearing Loss in the Russian Population Revealed by a Targeted Deafness Gene Panel. International Journal of Molecular Sciences. 2022;23(24):15748.

2. Kuznetcova, I., Gundorova, P., Ryzhkova, O. et al. The study of the full spectrum of variants leading to hyperphenylalaninemia have revealed 10 new variants in the PAH gene. Metab Brain Dis. 2019; 34: 1547–1555.

3. Ryadninskaya N.V., Kuznetsova I.A., Ryzhkova O.P., Polyakov A.V. Rezul’taty poiska redkikh mutatsiy pri analize vsey posledovatel’nosti gena PAH [Results of the search for rare mutations in the analysis of the entire sequence of the PAH gene]. Meditsinskaya genetika [Medical Genetics]. 2022;21(10):43-45. (In Russ.)

4. Bulakh M.V., Ryzhkova O.P., Polyakov, A.V. Sarcoglycanopathies: Clinical, Molecular and Genetic Characteristics, Epidemiology, Diagnostics and Treatment Options. Russ J Genet. 2018; 54: 129– 144.

5. Zinina E.V., Bulakh M.V., Ryzhkova O.P., Shchagina O.A., Polyakov A.V. Izmeneniye spektra vyyavlennykh mutatsiy v gene DMD v zavisimosti ot metodicheskikh vozmozhnostey laboratorii [Change in the spectrum of detected mutations in the DMD gene depending on the methodological capabilities of the laboratory]. Nervno-myshechnyye bolezni [Neuromuscular Diseases]. 2023;13(1):33-43. (In Russ.)

6. Zinina E, Bulakh M, Chukhrova A, et al. Specificities of the DMD Gene Mutation Spectrum in Russian Patients. Int J Mol Sci. 2022;23(21):12710.

7. Zinina E., Bulakh M., Chukhrova A., et al. Specificities of the DMD Point Variant Spectrum in Russian Patients with Duchenne/Becker Muscular Dystrophy. Clin Genet. April 2025; 108(3):292-301. DOI:10.1111/cge.14747

8. Mikhalchuk K, Zabnenkova V, Braslavskaya S, et al. Rare Cause 5q SMA: Molecular Genetic and Clinical Analyses of Intragenic Subtle Variants in the SMN Locus. Clin Genet. 2025;108(1):58-68. doi: 10.1111/cge.14714.

9. Beskorovainaya T.S., Milovidova T.B., Schagina O.A. et al. Complex Molecular Diagnostics of Hemophilia A in Russian Patients. Russ J Genet. 2019;55: 1015–1024.

10. Kadnikova V.A., Rudenskaya G.E., Stepanova A.A., et al. Mutational Spectrum of Spast (Spg4) and Atl1 (Spg3a) Genes in Russian Patients with Hereditary Spastic Paraplegia. Sci Rep. 2019;9(1):14412.

11. Rudenskaya G.E., Kadnikova V.A., Ryzhkova O.P., et al. Spektr nasledstvennykh spasticheskikh paraplegiy u rossiyskikh bol’nykh [Spectrum of hereditary spastic paraplegias in Russian patients]. Meditsinskaya genetika [Medical Genetics]. 2020;19(4):49-50. (In Russ.)

12. Rudenskaya G.E., Kadnikova V.A., Ryzhkova O.P. Nasledstvennyye spasticheskiye paraplegii v epokhu sekvenirovaniya novogo pokoleniya: geneticheskoye raznoobraziye, epidemiologiya, problemy klassifikatsii [Hereditary spastic paraplegias in the era of next generation sequencing: genetic diversity, epidemiology, classification]. Medical Genetics [Medical Genetics]. 2018;17(8): 3-12. (In Russ.)

13. Orlova A., Guseva D., Demina N., et al. Spectrum of Mutations in PTPN11 in Russian Cohort. Genes. 2024;15(3):345.

14. Registr patsiyentov s mukovistsidozom v Rossiyskoy Federatsii. 2023 god. Pod redaktsiyey Ye.L. Amelinoy, N.YU. Kashirskoy, Ye.I. Kondrat’yevoy, S.A. Krasovskogo, M.A. Starinovoy, A.YU. Voronkovoy, Ye.K. Gintera [Registry of patients with cystic fibrosis in the Russian Federation. 2023. Edited by E.L. Amelina, N.Yu. Kashirskaya, E.I. Kondratieva, S.A. Krasovsky, M.A. Starinova, A.Yu. Voronkova, E.K. Ginter]. Moscow: MEDPRAKTIKA-M, 2025. 70 p. (In Russ.)

15. Ryzhkova O., Mironovich O., Gundorova P., et al. Exome sequencing of 1293 patients in Russia: new knowledge about the structure of inherited diseases in Russia European Journal of Human Genetics 2022 Journal article WOSUID: WOS:000779367702383

16. Ryzhkova O.P., Chukhrova A.L., Mironovich O.L., Polyakov A.V. Razrabotka resheniya dlya analiza klinicheskogo ekzoma. Aktual’nyye voprosy fundamental’noy i klinicheskoy meditsiny: sbornik materialov kongressa molodykh uchenykh, 24–25 maya 2018 g. [Elektronnyy resurs]. Рod red. Ye.L. Choynzonova, E.V. Galazhinskogo, S.V. Popova, N.A. Bokhana, V.A. Stepanova, V.V. Zhdanova [Development of a solution for clinical exome analysis. Current issues in fundamental and clinical medicine: collection of materials from the congress of young scientists, May 24–25, 2018 [Electronic resource]. Edited by E.L. Choynzonov, E.V. Galazhinsky, S.V. Popov, N.A. Bokhan, V.A. Stepanov, V.V. Zhdanov]. Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk State University. Tomsk: Tomsk State University Publishing House, 2018:123–124. URL: http://tnimc.ru/upload/publications/proceedings/2018_young.pdf (In Russ.).

17. Doronina Y., Skatkov A. Cascade-hierarchical modeling in analyzing the dynamics of complex system resource characteristics. Information and Control Systems. 2020;3: 48-58. (In Russ.)

18. Royce W.W. Managing the Development of Large Software Systems. Proceedings of IEEE WESCON. 1970; 26: 328-388.

19. Lim R., Silver A., Silver M. et al. Targeted mutation screening panels expose systematic population bias in detection of cystic fibrosis risk. Genet Med. 2016;18: 174–179. https://doi.org/10.1038/gim.2015.52

20. WHO Human Genetics Programme. (‎2004)‎. The molecular genetic epidemiology of cystic fibrosis: report of a joint meeting of WHO/ IECFTN/ICF(‎M)‎A/ECFS, Genoa, Italy, 19 June 2002. World Health Organization

21. Mathur P., Kaur A., Agarwal K.K., et al. Unlocking the genetic blueprint of duchenne muscular dystrophy: A personalized approach with MLPA and WES. Glob Med Genet. 2025;12(2):100038. doi: 10.1016/j.gmg.2025.100038.

22. Ilic N., Krasic S., Maric N., et al. Noonan Syndrome: Relation of Genotype to Cardiovascular Phenotype-A Multi-Center Retrospective Study. Genes (Basel). 2024;15(11):1463. doi: 10.3390/genes15111463.

23. Kadnikova V.A. Molekulyarno-geneticheskoye i fenotipicheskoye raznoobraziye nasledstvennykh spasticheskikh paraplegiy. Dissertatsiya na soiskaniye uchenoy stepeni kandidata biologicheskikh nauk [Molecular genetic and phenotypic diversity of hereditary spastic paraplegias. Dissertation for the degree of Candidate of Biological Sciences]. Federal State Budgetary Scientific Institution «Research Centre for Medical Genetics.» 2022 (In Russ.)

24. Weisburd B., Sharma R., Pata V., et al. Diagnosing missed cases of spinal muscular atrophy in genome, exome, and panel sequencing data sets. Genet Med. 2025;27(4):101336. doi: 10.1016/j.gim.2024.101336

25. Lopez-Lopez D., Loucera C., Carmona R., et al. SMN1 copynumber and sequence variant analysis from next-generation sequencing data. Hum Mutat. 2020;41(12):2073-2077. doi: 10.1002/humu.24120.

26. Zhao S., Wang Y., Xin X. et al. Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene. Sci Rep. 2022; 12: 223. https://doi.org/10.1038/s41598-021-04325-1