bioRxivBioinformaticsPreprint
A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA
Chen-Shan ChiniD, Sairam BeheraiD, Ginger MetcalfiD, Richard A. GibbsiD, Eric BoerwinkleiD, Fritz Joachim SedlazeckiD
- Citations
- 13
Abstract
Lp(a) is an important factor in Coronary Heart disease risk, and its expression is correlated with the length of the LPA gene. The KIV-2 region of LPA consists of variable tandem repeats whose number is highly variable across individuals. Little is known about the inner diversity of the KIV-2 repeats themselves. Here we utilize a pan-genome graph approach across 47 haplotype resolved assemblies to identify unexpected variation across KIV-2.
- organism: human
- assay: whole-genome sequencing
- research focus: variant calling
- approach: statistical model
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing
Raphael O. Betschart, Georgios Koliopanos, … Andreas Ziegler·BioMedPeer-reviewed·Jun 4, 2024
- Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk
Sairam Behera, Jonathan R. Belyeu, … Fritz Joachim Sedlazeck·BMC Medical GenomicsPeer-reviewed·Oct 24, 2024
- KILDA: identifying KIV-2 repeats from kmers
Corentin Molitor, Timothy Labidi, … Claire Bardel·bioRxiv·Jan 17, 2025
- Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries
Seyedeh Maryam Zekavat, Sanni Ruotsalainen, … Brian Custer·Nature CommunicationsPeer-reviewed·Jun 28, 2018
- Investigation of an LPA KIV-2 nonsense mutation in 11,000 individuals: the importance of linkage disequilibrium structure in LPA genetics.
Silvia Di Maio, Rebecca Grüneis, … Stefan Coassin·Genome MedicinePeer-reviewed·Aug 21, 2020
- A novel method for predicting Lp(a) levels from routine outpatient genomic testing identifies those at risk of cardiovascular disease across a diverse cohort
Natalie Telis, Hang Dai, … Kelly M. Schiabor Barrett·medRxiv·Nov 1, 2024