Last month, the researchers at Google DeepMind announced the release of AlphaMissense, a new missense prediction algorithm that leverages the protein structure prediction model AlphaFold to distinguish between benign and pathogenic missense variants (Cheng et al., 2023).  AlphaFold is a model for the prediction of protein structures from amino acid sequences. During the development of AlphaMissense, the AlphaFold model was fine-tuned to identify variants commonly seen in human and primate populations. Variants predicted to be common are classified as benign, while variants predicted to be novel are classified as pathogenic. The authors report that AlphaMissense achieves 90% precision when used to classify a large subset of the ClinVar database.

While these results are impressive, we wanted to see for ourselves how this new algorithm stacks up against the other in-silico predictions that are currently available in VarSeq’s vast annotation library. We compared the predictions provided by AlphaMissese to 17 other missense prediction algorithms, using a subset of the ClinVar database as a benchmark dataset. In our experiments, AlphaMissense achieves an impressive balanced accuracy of 91.5% but is outperformed by BayesDel across all metrics.

Experimental Design

We compared AlphaMissense to the following in-silico prediction algorithms currently available in VarSeq:

1. BayesDel (Feng, 2017)
2. REVEL (Ioannidis et al., 2016)
3. MetaSVM (Dong et al., 2015)
4. MetaLR (Dong et al., 2015)
5. MetaRNN (Li et al., 2022)
6. DEOGEN2 (Raimondi et al., 2017)
7. PROVEAN (Choi et al., 2012)
8. FATHMM (Shihab et al., 2013)
9. FATHMM-XF (Rogers et al., 2018)
10. FATHMM-MKL (Shihab et al., 2015)
11. PolyPhen-2 HVAR (Adzhubei et al., 2013)
12. LRT (Chun et al., 2009)
13. SIFT (Ng et al., 2003)
14. LIST S2 (Malhis et al., 2020)
15. PrimateAI (Sundaram et al., 2018)
16. MutationTaster (Schwarz et al., 2010)
17. CADD (Kircher et al., 2014)

For AlphaMissense, we classified variants as pathogenic if the score exceeded 0.564, and classified variants as benign if the score was below 0.34, as recommended by the authors. For CADD, variants were classified based on the raw scores using a threshold of 5 for a pathogenic classification and a threshold of 2 for a benign classification. For REVEL, we used a threshold of 0.5, which was the threshold that produced the best performance, according to Ioannidis et al. (2016). For all other prediction algorithms, we used the thresholds specified in the dbNSFP Function Predictions annotation source (Liu et al., 2020).

The performance of each algorithm was evaluated using the ClinVar repository for variant interpretations (Landrum et al., 2016). Variant classifications in ClinVar are contributed by both clinical and research laboratories, as well as expert panels comprised of medical professionals with a long-standing scope of work. Variants in ClinVar are classified using a five-tier system, and each variant is assigned a review status indicating the depth of evidence behind its interpretation, denoted by values ranging from 1 to 4 stars:

1. The submission comes from a single submitter or multiple submitters with conflicting interpretations.
2. Concurring interpretations are provided by at least two submitters with accompanying evidence.
3. The interpretations have been reviewed by an expert panel.
4. The ClinGen Steering Committee has evaluated and confirmed the evidence and assertion criteria, establishing its alignment with practice guidelines.

We restricted our analysis to high-quality ClinVar missense variants with a review status of at least 2 which had been classified as either Pathogenic (P), Likely Pathogenic (LP), Benign (B), or Likely Benign (LB). The truth set for ClinVar was defined as follows:

• Positives: Variants that are classified as Pathogenic (P) or Likely Pathogenic (LP)
• Negatives: Variants that are classified as Benign (B) or Likely Benign (LB)

Each classification provided by the prediction algorithms was categorized as either a True Positive, False Positive, True Negative, or False Negative as follows:

• True Positive (TP): Classified as P/LP in ClinVar and classified as P by the algorithm.
• False Positive (FP): Classified as B/LB in ClinVar but classified as P by the algorithm.
• True Negative (TN): Classified as B/LB in ClinVar and classified as B by the algorithm.
• False Negative (FN): Classified as P/LP in ClinVar but classified as B by the algorithm.

The number of variants falling into these categories was then used to compute the sensitivity, specificity, and balanced accuracy for each algorithm as follows:

Results

Specific details about the ClinVar benchmark dataset are shown in the table below, including the total number of variants with each classification. This dataset was constructed using the ClinVar 2023-10-05 annotation track and contains a total of 35,468 variants.

Total Variants in ClinVar 2023-08-03	2,254,932
Variants with Classification of P/LP/B/LB	1,070,385
2+ Star Variants with Required Classification	191,149
Missense Variants with Required Classification/Status	35,468
Pathogenic	4,315 (12.2%)
Likely Pathogenic	9,309 (26.2%)
Likely Benign	14,017 (39.5%)
Benign	7,827 (22.1%)

The sensitivity, specificity, and balanced accuracy statistics for each algorithm are shown in Table 2, with all algorithms sorted by balanced accuracy.

	TP	FN	TN	FP	Sensitivity	Specificity	Balanced Accuracy
BayesDel	12,803	763	20,951	735	94.4%	96.6%	95.5%
AlphaMissense	10,893	1,407	18,897	1,116	88.6%	94.4%	91.5%
REVEL	12,632	1,047	19,573	2,162	92.3%	90.1%	91.2%
MetaSVM	11,861	1,630	18,990	2,604	87.9%	87.9%	87.9%
MetaLR	11,774	1,717	18,337	3,257	87.3%	84.9%	86.1%
PROVEAN	12,051	1,672	17,092	4,719	87.8%	78.4%	83.1%
DEOGEN2	11,344	2,968	18,221	2,755	79.3%	86.9%	83.1%
FATHMM-XF	11,660	749	14,270	5,994	94.0%	70.4%	82.2%
PolyPhen	11,156	1,471	14,684	5,558	88.4%	72.5%	80.4%
MetaRNN	13,053	502	14,017	7,827	96.3%	64.2%	80.2%
LRT	11,253	1,152	12,521	6,009	90.7%	67.6%	79.1%
CADD	348	260	11,732	13	57.2%	99.9%	78.6%
SIFT	12,305	1,316	14,817	7,572	90.3%	66.2%	78.3%
MutationTaster	13,253	371	12,433	9,411	97.3%	56.9%	77.1%
LIST S2	11,899	1,728	14,475	7,201	87.3%	66.8%	77.0%
FATHMM	10,718	2,863	15,245	6,432	78.9%	70.3%	74.6%
FATHMM-MKL	13,208	320	9489	12,188	97.6%	43.8%	70.7%
PrimateAI	5,481	7,933	20,394	968	40.9%	95.5%	68.2%

Using ClinVar as a benchmark, BayesDel achieves the highest balanced accuracy (95.5%), while performing extremely well in terms of both sensitivity and specificity, with all metrics exceeding 94%. AlphaMissense has the second-highest balanced accuracy at 91.5%, while also maintaining high sensitivity and specificity metrics of 88.6% and 94.4%, respectively. REVEL also performed well, achieving the third-highest balanced accuracy, with all metrics exceeding 90%. While AlphaMissense achieves slightly higher specificity and balanced accuracy than REVEL, the overall performance between these two algorithms is comparable.

Conclusion

In this blog post, we compared AlphaMissense to 17 other in-silico prediction algorithms, using ClinVar as a benchmark dataset. Of these algorithms, BayesDel, AlphaMissense, and REVEL demonstrated the highest overall performance, with all three algorithms achieving high balanced accuracy without sacrificing either sensitivity or specificity. These results are consistent with the findings of Tian et al., who also compared REVEL and BayesDel to a number of other prediction algorithms and found that these two algorithms outperformed competing methods in terms of both positive and negative predictive value (Tian et al., 2019).

While AlphaMissense demonstrated excellent performance, it was outperformed by BayesDel across all metrics. The superior performance of BayesDel is likely attributable to the algorithm’s incorporation of population frequency into its model, which allows it to more easily identify benign variants. The performance of AlphaMissense relative to BayesDel is impressive, given that it does not directly incorporate any population frequency information.

Golden Helix recently released a new annotation track containing the complete set of AlphaMissense predictions for all single nucleotide missense variants from 19,000 protein-coding genes for both GRCh37 and GRCh38 coordinates. These missense predictions make an excellent addition to VarSeq’s already extensive collection of functional prediction scores. I hope this blog post helped to give you an idea of how the AlphaMissense predictions compare to other in-silico prediction algorithms. If you have any questions about functional predictions in VarSeq, please don’t hesitate to reach out to us at support@goldenhelix.com.

References

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