Features and applications of haplotypes in crop breeding

JA Bhat, D Yu, A Bohra, SA Ganie… - Communications …, 2021‏ - nature.com
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens
resource-constrained agricultural production systems worldwide. Genomics-assisted …

Genotype imputation for genome-wide association studies

J Marchini, B Howie - Nature Reviews Genetics, 2010‏ - nature.com
In the past few years genome-wide association (GWA) studies have uncovered a large
number of convincingly replicated associations for many complex human diseases …

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 …

Reference-based phasing using the Haplotype Reference Consortium panel

PR Loh, P Danecek, PF Palamara, C Fuchsberger… - Nature …, 2016‏ - nature.com
Haplotype phasing is a fundamental problem in medical and population genetics. Phasing is
generally performed via statistical phasing in a genotyped cohort, an approach that can yield …

NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity

T Moriyama, R Nishii, V Perez-Andreu, W Yang… - Nature …, 2016‏ - nature.com
Widely used as anticancer and immunosuppressive agents, thiopurines have narrow
therapeutic indices owing to frequent toxicities, partly explained by TPMT genetic …

A linear complexity phasing method for thousands of genomes

O Delaneau, J Marchini, JF Zagury - Nature methods, 2012‏ - nature.com
Human-disease etiology can be better understood with phase information about diploid
sequences. We present a method for estimating haplotypes, using genotype data from …

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

KE Lotterhos, MC Whitlock - Molecular ecology, 2015‏ - Wiley Online Library
Although genome scans have become a popular approach towards understanding the
genetic basis of local adaptation, the field still does not have a firm grasp on how sampling …

A general approach for haplotype phasing across the full spectrum of relatedness

J O'Connell, D Gurdasani, O Delaneau, N Pirastu… - PLoS …, 2014‏ - journals.plos.org
Many existing cohorts contain a range of relatedness between genotyped individuals, either
by design or by chance. Haplotype estimation in such cohorts is a central step in many …

Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis

ID Iliev, VA Funari, KD Taylor, Q Nguyen, CN Reyes… - Science, 2012‏ - science.org
The intestinal microflora, typically equated with bacteria, influences diseases such as
obesity and inflammatory bowel disease. Here, we show that the mammalian gut contains a …

The genome of the domesticated apple (Malus × domestica Borkh.)

R Velasco, A Zharkikh, J Affourtit, A Dhingra… - Nature …, 2010‏ - nature.com
We report a high-quality draft genome sequence of the domesticated apple (Malus×
domestica). We show that a relatively recent (> 50 million years ago) genome-wide …