Bioinformatics & AI

Week of 3 November 2026

8 articles

Geno'X Veille — genox-veille.fr

Key takeaways this week

►MitImpact 4 — all 49,704 possible mitochondrial DNA SNVs annotated, tRNA and rRNA included, with posterior probabilities of pathogenicity usable within ACMG/AMP.
►PredictSNPprot — on a circularity-controlled benchmark, 21 missense predictors range from 0.63 to 0.76 AUC; the consensus model reaches 0.82 (preprint).
►UK Biobank panel — 490,319 genomes: better phasing than TOPMed r3 in almost all populations, largest gains in East and South Asia.
►Pheno+ — EHR-integrated HPO phenotyping: workflow time cut by 66% over 8 cases, causative gene ranked first by Exomiser in 17 of 17 cases (preprint).
►Inversions — multi-platform benchmark: complex and heterozygous inversions remain difficult; Sniffles2 and Severus lead on recall.

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Pathogenicity prediction

MitImpact 4: a genome-wide resource for the interpretation of coding and non-coding mitochondrial DNA variants

Mitochondrial DNA variants

Pathogenicity predictionPathogenicity prediction

Nucleic Acids Res 2026· OctRead

Pathogenicity prediction

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

Missense variants

Pathogenicity predictionBenchmarkPathogenicity prediction

bioRxiv 2026· NovRead

Algorithm benchmark

A haplotype reference panel constructed from 490,319 UK Biobank genomes improves genotype imputation for global populations

Genotype imputation

Algorithm benchmarkBenchmark

Nat Genet 2026· OctRead

Clinical pipeline

Pheno+: An Electronic Health Record-Integrated, Clinician-in-the-Loop Application for Efficient Phenotyping in Clinical Genomics

Monogenic disorders (HPO phenotyping)

Clinical pipelineClinical pipeline

medRxiv 2026· NovRead

Clinical pipeline

vardictcpp: a C++ reimplementation of VarDict variant caller

Variant calling

Clinical pipelineNew tool

GigaByte 2026· OctRead

Multi-genome benchmark for simple and complex genome inversion detection

Inversions (structural variants)

Long-readBenchmarkSV caller

Genome Biol 2026· AugRead

HGVD: Human Genetic Variation Database update 2026 with sequencing of 4344 genetically diverse Japanese individuals

Allele frequencies in the Japanese population

Nucleic Acids Res 2026· OctRead

Language model / AI

Cross-task benchmarking reveals variable transferability of deep learning models across molecular quantitative trait loci

Non-coding regulatory variants

Language model / AIBenchmark

Brief Bioinform 2026· SepRead

References and sources

Mitochondrial DNA variants. Nucleic Acids Res 2026. PMID 42952409. Score 6/10. https://pubmed.ncbi.nlm.nih.gov/42952409/
Missense variants. bioRxiv 2026. doi:10.64898/2026.10.30.763022. Score 6/10. https://www.biorxiv.org/content/10.64898/2026.10.30.763022v1
Genotype imputation. Nat Genet 2026. PMID 42963394. Score 6/10. https://pubmed.ncbi.nlm.nih.gov/42963394/
Monogenic disorders (HPO phenotyping). medRxiv 2026. doi:10.64898/2026.11.02.26366992. Score 5/10. https://www.medrxiv.org/content/10.64898/2026.11.02.26366992v1
Variant calling. GigaByte 2026. PMID 42964349. Score 5/10. https://pubmed.ncbi.nlm.nih.gov/42964349/
Inversions (structural variants). Genome Biol 2026. PMID 42958560. Score 5/10. https://pubmed.ncbi.nlm.nih.gov/42958560/
Allele frequencies in the Japanese population. Nucleic Acids Res 2026. PMID 42935248. Score 5/10. https://pubmed.ncbi.nlm.nih.gov/42935248/
Non-coding regulatory variants. Brief Bioinform 2026. PMID 42960994. Score 5/10. https://pubmed.ncbi.nlm.nih.gov/42960994/

27 October 2026