Inside Genebench-Pro

What happened

Note: File previews show excerpts from the full datasets.

Estimate whether a nested structural subhaplotype inside an anonymous inversion-like locus has a calibrated clinical association and credible expression support.

A nested copy-dosage signal can be confounded by the broader inversion orientation, so dosage calibration, expression support, and clinical modeling have to remain distinct.

Clinical and covariate data for the full cohort.

Quantify a focal case-control Hi-C loop-strength difference after removing low-mappability and structural-variant artifacts from the expected-contact background.

The target loop is defined at 20 kb resolution, but the expected-contact model is distorted unless low-mappability contacts and a case-only SV stripe are masked first.

Target-resolution bin annotations.

Map a chromosome-1 quantitative-trait locus in an eight-founder recombinant population by reconstructing founder ancestry before testing the phenotype association.

The visible marker data are biallelic, but the biological signal is founder ancestry. A defensible analysis therefore has to reconstruct founder state, check marker orientation, and separate the QTL from a batch-aligned nuisance peak.

Marker identifiers, chromosomes, and genetic-map positions.

Infer parent-specific ancestry proportions and recent admixture timing from phased local-ancestry tracts after repairing reciprocal artifacts and a chromosome-specific label inversion.

Ancestry fractions and pulse times both change if reciprocal tract artifacts, chromosome-local label inversion, or map denominators are handled incorrectly.

Phased local-ancestry tracts with coordinates, ancestry labels, posterior values, and QC annotations.

Infer which of two haploid loci is under stronger positive selection from ancient allele-frequency time series while accounting for allele orientation, directional error, drift, and changing population size.

Why it matters

Estimate whether a synthetic TXR1-directed inhibitor has positive clinical utility in tumors whose target activation is driven by a structural variant. TXR1, TXR1i, DLR1, and star-allele labels are synthetic benchmark labels.

The target subgroup has to be recovered from long-read, expression, tumor-quality, and pharmacogenomic evidence before benefit and toxicity can be interpreted as a treatment decision.

Registry covariates, therapy, week-16 assessment, benefit, and early toxicity.

Decide whether an apparent lncRNA dependency is transcript-specific or driven by nearby-locus and neighbor-gene effects.

Transcript-directed evidence has to survive controls for local DNA-locus perturbation, neighbor-gene repression, guide swaps, GC toxicity, and plate effects.

Guide coordinates, targets, distances, and GC features.

Estimate direct disease effects for two nearby proteins using cis multivariable Mendelian randomization (cis-MVMR) while handling assay scale, allele orientation, winner's curse, LD, and residual local pleiotropy.

The two proteins share a correlated locus. The analysis has to move from marginal associations to conditional, LD-aware disease effects on a common protein scale.

Screening-stage protein association summaries for PROTA.

Estimate ancestry-specific carrier frequencies, residual risk after a negative screen, partner carrier frequency, and affected-conceptus risk from carrier-screening assay data.

The residual-risk estimate depends on pseudogene-aware carrier calls, founder-haplotype collapse, ancestry-specific assay calibration, and standardization from tested partners back to the full partner roster.

Screening-roster adults with ancestry and screening context.

Estimate a genotype effect on activated-monocyte expression after removing ambient RNA and technical contamination from single-cell RNA-seq data.

Ambient RNA affects both target expression and the marker panel used to call activation state, so correction has to occur before the eQTL model.

Per-cell UMI counts for marker genes, contamination markers, and the target gene.

What to watch

Noisy ancient trajectories are not directly comparable until both loci are placed on the same derived-allele scale and the provided sample-level sequencing-error values are modeled directly.

Read-count time series for locus A.