Aggregate variant calling using short reads enables population and disease studies for paralogous genes.

Timofey Prodanov, Sang Yoon Byun, Vikas Bansal

Abstract read

In one paragraph

Article in HGG advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Timofey ProdanovInstitute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.

Sang Yoon ByunComputer Science and Engineering, University of California, San Diego, San Diego, CA, USA.

Vikas BansalComputer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Department of Pediatrics, School of Medicine, University of California, San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, USA. Electronic address: vibansal@ucsd.edu.

Funding

Refining Mendelian disease analysis via detection of clinically relevant repeat variantsR01HG010149 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna, Vikas Bansal · 2018 to 2026

$4.5M

NHGRI NIH HHS R01 HG010149

6 · The paper itself

Abstract

Variant calling in paralogous genes using short-read sequencing is problematic due to mapping ambiguity between highly similar sequences. Aggregate variant calling, which treats paralogous loci as a single locus by realigning reads to a masked reference genome, can enable variant detection in paralogous genes. We used our informatics tool Parascopy to assess the accuracy of aggregate variant calling in paralogous genes using short-read data. Parascopy achieved significantly higher recall compared to standard variant calling without sacrificing precision. We identified 158 paralogous genes with over 25 percentage points improvement in recall using simulated data and 118 genes with at least 10 percentage points improvement in recall across Genome in a Bottle (GIAB) reference samples. Across 1000 Genomes samples, aggregate genotypes in paralogous genes were highly concordant between whole-genome and whole-exome data (r

Indexed as

Genetics, PopulationGenetic VariationHaplotypesHigh-Throughput Nucleotide SequencingHumansSequence Analysis, DNASoftwaredisease association analysishaplotype phasinghigh-throughput DNA sequencingparalogous genespopulation genomicssegmental duplicationsvariant calling using short reads

Identifiers

PMID42478050

DOI10.1016/j.xhgg.2026.100653

PMCPMC13475201

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.