The human genetic epidemiology of COVID-19

MEK Niemi, MJ Daly, A Ganna - Nature Reviews Genetics, 2022 - nature.com
Human genetics can inform the biology and epidemiology of coronavirus disease 2019
(COVID-19) by pinpointing causal mechanisms that explain why some individuals become …

HIV-1 and human genetic variation

PJ McLaren, J Fellay - Nature Reviews Genetics, 2021 - nature.com
Over the past four decades, research on the natural history of HIV infection has described
how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research …

Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection

AJ Mentzer, D O'connor, S Bibi, I Chelysheva… - Nature medicine, 2023 - nature.com
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine immunogenicity
varies between individuals, and immune responses correlate with vaccine efficacy. Using …

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

M Kanai, R Elzur, W Zhou, KHH Wu, H Rasheed… - Cell genomics, 2022 - cell.com
Meta-analysis is pervasively used to combine multiple genome-wide association studies
(GWASs). Fine-mapping of meta-analysis studies is typically performed as in a single-cohort …

Pan-UK Biobank GWAS improves discovery, analysis of genetic architecture, and resolution into ancestry-enriched effects

KJ Karczewski, R Gupta, M Kanai, W Lu, K Tsuo… - MedRxiv, 2024 - medrxiv.org
Large biobanks, such as the UK Biobank (UKB), enable massive phenome by genome-wide
association studies that elucidate genetic etiology of complex traits. However, individuals …

Africa-specific human genetic variation near CHD1L associates with HIV-1 load

PJ McLaren, I Porreca, G Iaconis, HP Mok… - Nature, 2023 - nature.com
HIV-1 remains a global health crisis, highlighting the need to identify new targets for
therapies. Here, given the disproportionate HIV-1 burden and marked human genome …

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

J Howard-McCombe, A Jamieson, A Carmagnini… - Current Biology, 2023 - cell.com
The European wildcat population in Scotland is considered critically endangered as a result
of hybridization with introduced domestic cats, 1, 2 though the time frame over which this …

A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes

T Naito, K Suzuki, J Hirata, Y Kamatani… - Nature …, 2021 - nature.com
Conventional human leukocyte antigen (HLA) imputation methods drop their performance
for infrequent alleles, which is one of the factors that reduce the reliability of trans-ethnic …

HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases

T Naito, Y Okada - Seminars in immunopathology, 2022 - Springer
Variations of human leukocyte antigen (HLA) genes in the major histocompatibility complex
region (MHC) significantly affect the risk of various diseases, especially autoimmune …

Rapid genotype imputation from sequence with reference panels

RW Davies, M Kucka, D Su, S Shi, M Flanagan… - Nature …, 2021 - nature.com
Inexpensive genotyping methods are essential to modern genomics. Here we present
QUILT, which performs diploid genotype imputation using low-coverage whole-genome …