Table 1 Summary of statistical methods reviewed in this paper

denovolyzeR

-

Poisson exact test

-

1,078 autism spectrum disorder (ASD) trios

https://denovolyzer.org/

[8]

DeNovoWEST

-

Simulation-based test

-

31,058 developmental disorder (DD) trios

https://github.com/HurlesGroupSanger/DeNovoWEST

[32]

TADA

Empirical Bayes method

Bayesian false discovery rate (FDR) and p-value from permutation test

Inherited variants

932 ASD trios

http://www.compgen.pitt.edu/TADA/TADA_homepage.htm

[17]

extTADA

Fully Bayesian framework

Bayesian FDR

Inherited variants

1,077 schizophrenia (SCZ) trios;

4,293 DD trios;

1,022 intellectual disability (ID) trios;

4,122 ASD trios;

356 epilepsy trios

https://github.com/hoangtn/extTADA

[40]

TADA-R

Empirical Bayes method

p-value from permutation test

Inherited variants

2,645 congenital heart disease (CHD) trios;

1,789 unaffected control trios

https://github.com/limo936/TADA-R

[41]

fitDNM

-

Score test

Functional annotations

264 epileptic encephalopathy (EE) trios;

151 severe ID trios;

354 SCZ trios;

948 ASD trios

https://github.com/TNTurnerLab/fitDNM

[42]

VARPRISM

Maximum Likelihood Estimation (MLE)-based method

Likelihood ratio test

Functional annotations

2,508 ASD trios

https://hufflab.org/software/VARPRISM/

[44]

TADA-A

MLE-based method

Bayesian FDR

Functional annotations

314 ASD trios

https://github.com/TADA-A/TADA-A

[46]

HeartENN

Deep learning-based method

Binomial test

Noncoding annotations

749 CHD trios

https://github.com/FunctionLab/HeartENN-models

[49]

mTADA

Fully Bayesian framework

Bayesian FDR

De novo variants (DNVs) from another trait

356 EE trios;

5,122 ASD trios;

4,293 DD trios;

1,012 ID trios;

1,077 SCZ trios;

1,213 CHD trios

https://github.com/hoangtn/mTADA

[50]

M-DATA

Expectation-Maximization algorithm

Joint local false discovery rate (Jlfdr)

DNVs from another trait and functional annotations

2,645 CHD trios;

5,623 ASD trios

https://github.com/JustinaXie/MDATA

[51]

DAWN

Empirical Bayes method

Bayesian FDR

Interaction network

932 ASD trios

http://www.compgen.pitt.edu/DAWN/DAWN_homepage.htm

[53, 54]

N-DATA

Empirical Bayes method

Bayesian FDR

Interaction network

2,645 CHD trios

https://github.com/JustinaXie/NDATA

[55]

VBASS

Variational inference

Bayesian FDR

Gene expression

2,645 CHD trios;

16,616 ASD trios

https://github.com/ShenLab/VBASS

[56]

EncoreDNM

Monte Carlo MLE

Likelihood ratio test

DNVs from another trait

31,058 DD trios;

6,430 ASD trios;

2,722 SCZ trios;

2,645 CHD trios;

820 ID trios;

484 Tourette disorder trios;

264 EE trios;

232 congenital hydrocephalus trios;

1,789 unaffected control trios

https://github.com/ghm17/EncoreDNM

[52]