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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...-telangiectasia with double missense and in frame splice mutations. Am J Med Genet A 126A: 272–277. doi:10.1002/ajmg.a.20601 ↵Douglas JA, Boehnke M, Gillanders E, Trent JM, Gruber SB. 2001. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet 28: 361–364. doi:10...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...(Garrison et al. 2018), or restricting the alignment to either one (Mokveld et al. 2020; Sirén et al. 2020, 2021) or two haplotype paths (Avila Cartes et al. 2024). A more effective way to address this problem could be to utilize linkage disequilibrium, that is, the correlations between two or more genetic...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...(IGHV1-2*05 and IGHV4-4*01), known to be in linkage disequilibrium and typically found on the same haplotype (Ohlin 2021), were also present in our haplotype 2 and were found in 9 and 0 cells, respectively (Fig. 6C). Altogether, these data support the veracity of our analytic pipeline...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...samples with a mean per site depth of 14.75× and mean frequency of missingness of 0.11 (Supplemental Table S2). For analyses dependent on allele frequencies, such as principal component analysis (PCA)-based analyses, we pruned SNPs based on linkage disequilibrium (LD), resulting in a data set of 19...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...many of these human disease associations have been attributed to specific MHC-I and MHC-II alleles, linkage disequilibrium in this gene-dense region makes the identification of specific causative variants for disease phenotypes extremely challenging. Non–immune system loci that make up the majority...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...together from reference haplotypes.Several studies of genetic privacy have considered kth-order correlations between SNPs (k = 2 corresponds to pairwise linkage disequilibrium [LD]) to maximize the probability of reidentifying individuals (Wang et al. 2009; Samani et al. 2015; Von Thenen et al. 2019...
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Method: An efficient method to identify, date, and describe admixture events using haplotype information
- Pongsakorn Wangkumhang,
- Matthew Greenfield,
- and Garrett Hellenthal
Genome Res. August 2022 32: 1553-1564; Published in Advance July 6, 2022, doi:10.1101/gr.275994.121
...homogeneous populations.In recent years, numerous techniques have emerged that exploit expected patterns of linkage disequilibrium (LD) among single-nucleotide-polymorphisms (SNPs) in admixed populations that descend from the intermixing of multiple ancestral sources in order to identify, describe, and date...
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Method: Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model
- Ahsan Sanaullah,
- Degui Zhi,
- and Shaojie Zhang
Genome Res. July 2023 33: 1007-1014; Published in Advance June 14, 2023, doi:10.1101/gr.277673.123
..., Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213–2233. doi:10.1093/genetics/165.4.2213 ↵Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y, K Finucane H, Schoenherr S, Forer L, McCarthy S, Abecasis...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...is that they assume all single-nucleotide polymorphisms (SNPs) to be independent, and they do therefore not benefit from the information of correlated sites or they may be biased thereof in their global estimates (Tang et al. 2005; Patterson et al. 2006). A notable exception is ChromoPainter (Lawson et al. 2012...
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Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits Olivia Corradin 1 , Alina Saiakhova 1 , Batool Akhtar-Zaidi 1 , Lois Myeroff 2 , Joseph...

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