Practical implications of imputations with large reference panels

Recently, the Haplotype Reference Consortium (HRC) released a large imputation panel that allows more accurate imputation of genetic variants.

Haplotype reference consortium panel: Practical implications of ...

We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low- ...

We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low-frequency variants.

Practical implications of imputations with large reference panels.

Home Research Research Publication Haplotype reference consortium panel: Practical implications of imputations with large reference panels. Iglesias AI, van ...

(PDF) Haplotype reference consortium panel: Practical implications ...

We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low- ...

GeneImp: Fast Imputation to Large Reference Panels Using ... - NCBI

Our algorithm is motivated by a second pivotal advancement in genotype imputation, i.e., the availability of large reference haplotype panels. Most imputation ...

Genotype Imputation from Large Reference Panels

However, rare variants, which are more often associated with dramatic functional consequences, tend to have low levels of pairwise linkage ...

A population-specific reference panel for improved genotype ...

A crucial component of GWAS is genotype imputation, which requires a large reference panel of sequenced individuals with similar ancestry to the ...

The size and composition of haplotype reference panels impact the ...

Low-coverage whole-genome sequencing (lcWGS) followed by genotype imputation has emerged as an alternative with comparable costs to genotyping ...

The effects of reference panel perturbations on the accuracy of ...

Even though it is intuitive that the quality of a reference panel should play a role in the accuracy of imputation, it is nonetheless unclear to ...

Assessment of Imputation Quality: Comparison of Phasing ... - Frontiers

Figure 3. Imputation quality measures usable without knowledge of true genotypes. Phasing tools marked with an asterix indicate the use of a reference panel for ...

Reconstruction of private genomes through reference-based ...

Our results show that genomes in imputation server reference panels can be vulnerable to reconstruction, implying that additional safeguards may ...

Genotype imputation accuracy and the quality metrics of the minor ...

Finally, despite the impact of the θ value, distant ancestries in the reference panel contributed only a few additional variants passing a ...

Opening the Black Box of Imputation Software to Study the Impact of ...

However, this work does help elucidate the performance of our reference panel and could provide avenues for improvements to existing imputation ...

How local reference panels improve imputation in French populations

Public reference panels widely used for imputation include the 1000 Genomes Project (1000G), the HRC panel and the TOPMED panel. The size and ...

A One-Penny Imputed Genome from Next-Generation Reference ...

In general, one should perform genotype imputation using the largest reference panel that is available because the number of accurately imputed variants ...

Systematic assessment of imputation performance using the 1000 ...

... imputation practice. First, in a study of imputation accuracy, we ... To speed up whole-genome imputation from a large reference panel ...

Meta-imputation: An efficient method to combine genotype data after ...

In the scenarios we examined, the method consistently outperforms imputation using a single reference panel and achieves accuracy comparable to imputation using ...

Genotype imputation and reference panel: a systematic evaluation ...

Here, 622 imputations were conducted with 394 customized reference panels for Han Chinese and European populations. Besides validating the fact that ...

Practical Issues in Imputation-Based Association Mapping - PLOS

We find that imputation-based methods can be robust to imputation accuracy and can improve power to detect associations, even when average imputation accuracy ...