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Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
- Degui Zhi,
- Xiaoqian Jiang,
- and Arif Harmanci
Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
...AD [Karczewski et al. 2020] and dbSNP [Sherry et al. 2001]), and for building genotype imputation outsourcing services (Das et al. 2016; Sun et al. 2022). For example, NIH's TOPMed (Kowalski et al. 2019; Taliun et al. 2021) and the Haplotype Reference Consortium (HRC) (McCarthy et al. 2016) serve as reference...
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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
...of 400 haplotypesHere we use PLIGHT_Exact, using the full Li-Stephens model. Two individuals were selected, and the first half of the SNP genotypes were taken from one individual and the other half from the second. The mutation rate was set to 0, whereas the fixed per-base recombination rate cl was set...
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Method: HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
- Peter Edge,
- Vineet Bafna,
- and Vikas Bansal
Genome Res. May 2017 27: 801-812; Published in Advance December 9, 2016, doi:10.1101/gr.213462.116
...partitioning optimization O(RVd′) Yes No Discrete (R) Number of reads (all algorithms process reads for each haplotype block separately); (N) total number of variants; (V) maximum number of variants in a read; (d) maximum read depth per site; (d′) maximum number of reads crossing a site (equivalent to d except...
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Method: Genotype imputation via matrix completion
- Eric C. Chi,
- Hua Zhou,
- Gary K. Chen,
- Diego Ortega Del Vecchyo,
- and Kenneth Lange
Genome Res. March 2013 23: 509-518; Published in Advance December 10, 2012, doi:10.1101/gr.145821.112
..., a typical window spans 3w total SNPs. Algorithm 1 is applied to the entire window, but only the middle block of w SNPs is imputed. The window is then shifted over by w SNPs, and the process repeated. The sliding window strategy permits information to propagate from the left and right thirds into the middle...
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Methods: Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies
- Bjarni V. Halldórsson,
- Vineet Bafna,
- Ross Lippert,
- Russell Schwartz,
- Francisco M. De La Vega,
- Andrew G. Clark,
- and Sorin Istrail
Genome Res. August 2004 14: 1633-1640; doi:10.1101/gr.2570004
...power for identifying phenotype–genotype associations would be minimally compromised. In this paper, we give an algorithmic framework for selecting a minimum informative set of SNPs avoiding any reference to haplotype blocks. We argue that the selection of tagging SNPs can be partitioned into the three...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes. Footnotes...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
..., TX-Phase applies PBWT to compressed reference panel blocks, enabling an efficient search for the S “nearest neighbors” of the current estimate of the phased haplotypes based on the longest common suffix (LCS) at each randomly selected genomic position across the phasing window. The aggregate...
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Methods: Intra- and interpopulation genotype reconstruction from tagging SNPs
- Peristera Paschou,
- Michael W. Mahoney,
- Asif Javed,
- Judith R. Kidd,
- Andrew J. Pakstis,
- Sheng Gu,
- Kenneth K. Kidd,
- and Petros Drineas
Genome Res. January 2007 17: 96-107; Published in Advance December 6, 2006, doi:10.1101/gr.5741407
...targeting 90%–99% of the training set spectral variance and reconstruction error in the test set. Discussion Most existing tSNP selection methods are either based on the arbitrary definition of haplotype block boundaries, or in the currently most common block-free approaches; tSNPs are picked based...
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Methods: An MCMC algorithm for haplotype assembly from whole-genome sequence data
- Vikas Bansal,
- Aaron L. Halpern,
- Nelson Axelrod,
- and Vineet Bafna
Genome Res. August 2008 18: 1336-1346; doi:10.1101/gr.077065.108
...genotyping methods determine the two alleles at an individual SNP and are unable to provide information about haplotypes, the combination of alleles present at multiple SNPs along a single chromosome. Haplotypes observed in human populations are a result of shuffling of ancestral haplotypes through...
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Methods: Haplotype and Missing Data Inference in Nuclear Families
- Shin Lin,
- Aravinda Chakravarti,
- and David J. Cutler
Genome Res. August 2004 14: 1624-1632; Published in Advance July 15, 2004, doi:10.1101/gr.2204604
...arbitrarily absorbed into adjacent blocks. With nuclear family data, our program reconstructs the haplotypes of parents with children's genotypes used to constrain the former's haplotype space. The iterative stochastic sampling process underlying both SSD and our previous program is retained. In all...

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