README.md

metadata

license: apache-2.0
tags:
  - biology
  - genomics
  - dna
  - variant-effect-prediction
  - complex-traits
  - gwas
  - fine-mapping
size_categories:
  - 10K<n<100K

evals_complex_traits

Variant-effect-prediction benchmark of UKBB fine-mapped complex-trait SNVs vs low-PIP SNVs, 1:9 matched within consequence categories on (chrom, consequence_final) plus subset-targeted distance bins, with MAF entering as a continuous matching feature.

Description

Positives	UKBB SuSiE+FINEMAP fine-mapped variants with max(PIP) > 0.9 across 119 traits
Negatives	max(PIP) < 0.01 across 119 traits, 1:9 matched per positive
Genome build	GRCh38 (lifted from hg19)
Variant type	SNVs only
Coordinates	1-based (pos is 1-based; ref/alt are single bases)
Matching ratio	1:9

Splits

Split	Variants (pos + 9·neg)	Positives	Chromosomes
train	11,630	1,163	odd: 1, 3, …, X
test	10,000	1,000	even: 2, 4, …, Y
total	21,630	2,163

Columns

Column	Type	Description
chrom, pos, ref, alt	str / int / str / str	Variant coordinates (1-based, GRCh38)
label	bool	True for high-PIP positive, False for low-PIP matched negative
subset	str	Consequence-group label for stratified eval
match_group	int	Integer ID grouping each positive with its 9 matched negatives
rsid	str	dbSNP rsID (when available)
pip	float	Maximum PIP across the 119 traits
traits	str	Comma-separated list of traits with PIP > 0.9 (positives only)
MAF	float	UKBB EUR minor allele frequency
ld_score	float	UKBB EUR LD score (passthrough, not a matching feature)
consequence, consequence_cre, consequence_final, consequence_group	str	Ensembl VEP consequence + grouping
distance_tss_pc, distance_tss_nc, distance_tss	int	Distances to nearest protein-coding / non-protein-coding TSS (and min, used for consequence_group recategorization)
tss_closest_pc_gene_id, tss_closest_nc_gene_id, tss_closest_gene_id	str	Ensembl gene IDs (passthrough — gene-id was not used in matching)
distance_exon_pc, distance_exon_nc, distance_exon	int	Same shape, for nearest exon
exon_closest_pc_gene_id, exon_closest_nc_gene_id, exon_closest_gene_id	str	Same shape
distance_tss_pc_bin, distance_exon_pc_bin	str	Subset-prefixed bin labels used as exact-match keys; BIN_NA outside the binned subsets

Per-subset retention

Subset	n_pos in dataset_all	matched (kept)	retention
distal	1,193	1,193	100.0%
missense_variant	454	454	100.0%
tss_proximal	244	244	100.0%
3_prime_UTR_variant	78	78	100.0%
non_coding_transcript_exon_variant	75	75	100.0%
5_prime_UTR_variant	56	56	100.0%
synonymous_variant	33	33	100.0%
splicing	30	30	100.0%
mature_miRNA_variant	2	0	0.0%
total	2,165	2,163	99.9%

Matching design

Matching is exact on every categorical key, then Euclidean-nearest on the (RobustScaler-scaled) continuous features as a within-group tie-breaker. Without replacement, k=9.

• Continuous features: distance_tss_pc, distance_tss_nc, distance_exon_pc, distance_exon_nc, MAF.
• Categorical features:
  • chrom, consequence_final
  • distance_tss_pc_bin — tss_proximal: edges [0, 100, 1000, ∞]; BIN_NA elsewhere
  • distance_exon_pc_bin —
    • tss_proximal: edges [0, 100, 1000, ∞]
    • splicing: edges [0, 5, 30, ∞]
    • BIN_NA elsewhere

Gene-ID columns are kept as passthrough metadata but not used as match keys.

Matched-feature AUPRC diagnostic

Each continuous matching feature f is scored as a single-feature predictor within each subset: {f}_auprc = max(AP(label, +f), AP(label, −f)). Baseline = 0.1 for 1:9 matching.

Per-(subset, feature) AUPRC table

subset	n	distance_tss_pc	distance_tss_nc	distance_exon_pc	distance_exon_nc	MAF
distal	1,193	0.101	0.102	0.109	0.105	0.101
missense_variant	454	0.108	0.106	0.102	0.104	0.108
tss_proximal	244	0.114	0.114	0.110	0.108	0.101
3_prime_UTR_variant	78	0.119	0.116	0.108	0.108	0.114
non_coding_transcript_exon_variant	75	0.110	0.112	0.124	0.100	0.106
5_prime_UTR_variant	56	0.123	0.109	0.102	0.110	0.109
synonymous_variant	33	0.120	0.106	0.107	0.111	0.107
splicing	30	0.124	0.131	0.108	0.131	0.122

Provenance

Built by the bolinas-dna eval pipeline at commit main.

• Curation pipeline: snakemake/evals
• Matching algorithm: src/bolinas/pipelines/evals/matching.py
• Diagnostic helper: src/bolinas/pipelines/evals/matching_qc.py

The curation is a from-scratch reimplementation of the TraitGym complex-traits pipeline.

License

Released under the same terms as its sources. UKBB summary-level data and the Finucane lab fine-mapping release are intended for non-commercial research; check upstream license if you plan to use commercially.

Citation

• TraitGym — Benegas et al. 2025, bioRxiv 2025.02.11.637758
• UKBB fine-mapping — Wang et al. (Nat Commun 2021) and the Finucane lab release
• LD scores — Bulik-Sullivan et al. (Nat Genet 2015)