| Literature DB >> 33200402 |
Arthur Stefanski1,2, Yamile Calle-López2,3, Costin Leu1,4,5, Eduardo Pérez-Palma1,2, Elia Pestana-Knight2, Dennis Lal1,2,4,6.
Abstract
OBJECTIVE: Clinical genetic sequencing is frequently utilized to diagnose individuals with neurodevelopmental disorders (NDDs). Here we perform a meta-analysis and systematic review of the success rate (diagnostic yield) of clinical sequencing through next-generation sequencing (NGS) across NDDs. We compare the genetic testing yield across NDD subtypes and sequencing technology.Entities:
Keywords: autism; epilepsy; genetics; neurodevelopmental disorders; sequencing
Mesh:
Year: 2020 PMID: 33200402 PMCID: PMC7839709 DOI: 10.1111/epi.16755
Source DB: PubMed Journal: Epilepsia ISSN: 0013-9580 Impact factor: 5.864
Figure 1Process of data search, identification, and filtering
Figure 2Separation of 103 unique studies included. We collected 103 studies which included heterogeneous types of NDDs. We were able to separate these into 107 distinct disorder cohorts, 81 cohorts by seizure type, 41 DEE cohorts, 21 cohorts by age at onset, and 109 sequencing technology cohorts. Abbreviations: ASD, autism spectrum disorder; DD, developmental delay; DEE, developmental epileptic encephalopathy; ES, exome sequencing; FE, focal epilepsy; GE & FE, combined generalized and focal epilepsy; GE, generalized epilepsy; ID, intellectual disability; panel, targeted gene panel sequencing; WS, West syndrome
Figure 3Forest plot of meta‐analysis of the overall diagnostic yield from 103 studies. Abbreviations: CI, confidence interval; I2, estimated proportion of the variance in study estimates that is due to heterogeneity; Proportion, fraction of individuals with a positive genetic test (ie, pathogenic or likely pathogenic variant)
Diagnostic yield across different categories
| Grouping | Subgroup |
No. of incl. cohorts |
No. of incl. individuals |
Diagnostic yield (95% CI) |
|---|---|---|---|---|
| Overall | 103 | 32 310 | 23.7% (22%–26%) | |
| By disorder | ASD | 14 | 1530 | 17.1% (11%–25%) |
| Epilepsy | 72 | 27 923 | 24.0% (22%–27%) | |
| ID | 21 | 2863 | 28.2% (22%–35%) | |
| By seizure type | FE | 15 | 1944 | 15.8% (10%–24%) |
| GE | 7 | 1258 | 24.3% (18%–32%) | |
| GE & FE | 59 | 26 888 | 24.8% (22%–28%) | |
| By disorder subtype | Epilepsy without ID | 8 | 1224 | 9.3% (4%–23%) |
| ASD with ID or DD | 7 | 591 | 24.6% (18%–32%) | |
| Epilepsy with ID | 15 | 1290 | 27.9% (24%–33%) | |
| By other DEEs | WS | 16 | 768 | 19.3% (14%–26%) |
| Other DEEs | 8 | 232 | 38.8% (23%–57%) | |
| By age of onset | Any Age | 5 | 1080 | 6.6% (2%–22%) |
| Childhood | 3 | 171 | 14.7% (4–42%) | |
| Neonatal/Infantile | 13 | 986 | 29.3% (23%–36%) | |
| By sequencing technology | Panel | 73 | 28 665 | 22.6% (20%–25%) |
| ES | 36 | 3720 | 27.3% (24%–31%) |
For details of the grouping and subgrouping see Section 2.
Abbreviations: ASD, autism spectrum disorder; CI, confidence interval; DD, developmental delay; DEE, developmental epileptic encephalopathy; ES, exome sequencing; FE, focal epilepsy; GE & FE, combined generalized and focal epilepsy; GE, generalized epilepsy; ID, intellectual disability; panel, targeted gene panel sequencing; WS, West syndrome.
Figure 4Diagnostic yield by sequencing technology. The mean yield in ES is higher compared to panel testing, even though the difference is not statistically significant‐ 27.2% vs 22.6% (P = .071). Abbreviations: ES, exome sequencing; panel, targeted gene panel sequencing
Figure 5Inequality‐adjusted Human Development Index (IHDI) by country group. Countries with sequencing studies have a significantly higher median Inequality‐adjusted Human Development Index (IHDI), compared to countries without sequencing studies 0.84 vs 0.56 (P = 5.8 × 10‐11)