4.3 Article

Identity-by-descent-based estimation of the X chromosome effective population size with application to sex-specific demographic history

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Genetics & Heredity

Statistical phasing of 150,119 sequenced genomes in the UK Biobank

Brian L. Browning et al.

Summary: The first release of UK Biobank's whole-genome sequence data includes 150,119 genomes. An open-source pipeline for filtering, phasing, and indexing these genomes on the UK Biobank Research Analysis Platform is presented. The pipeline allows haplotype-based methods to be applied to the UK Biobank whole-genome sequence data. Marker filtering is done using BCFtools, genotype phasing is done using Beagle, and VCF indexing is done using Tabix. The pipeline successfully phased 406 million single-nucleotide variants on chromosomes 1-22 and X with a processing time maxing at 2.6 days. The phase accuracy was assessed and improvements were made by excluding trio parents and markers with nonmajor allele frequency < 0.1%.

AMERICAN JOURNAL OF HUMAN GENETICS (2023)

Article Multidisciplinary Sciences

The sequences of 150,119 genomes in the UK Biobank

Bjarni Halldorsson et al.

Summary: A comprehensive understanding of how diversity in the human genome sequence affects phenotypic diversity relies on a reliable characterization of both sequences and phenotypic variation. In this study, whole-genome sequencing of 150,119 individuals from the UK Biobank was performed, leading to insights into the relationship between sequence variation and phenotypic traits. The analysis revealed rare variants with large effects, which were not previously identified through whole-exome sequencing and/or imputation studies.

NATURE (2022)

Article Genetics & Heredity

Fast two-stage phasing of large-scale sequence data

Brian L. Browning et al.

Summary: Haplotype phasing method presented in this study efficiently estimates haplotypes from genotype data using marker windowing and composite reference haplotypes. It employs a progressive phasing algorithm and two-stage phasing algorithm for high-frequency and low-frequency markers respectively. Performance comparison shows that Beagle 5.2 is over 20 times faster than SHAPEIT for TOPMed sequence data, while achieving similar accuracy and scalability for larger sample sizes.

AMERICAN JOURNAL OF HUMAN GENETICS (2021)

Article Genetics & Heredity

A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data

Ying Zhou et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2020)

Article Multidisciplinary Sciences

Characterizing mutagenic effects of recombination through a sequence-level genetic map

Bjarni V. Halldorsson et al.

SCIENCE (2019)

Article Genetics & Heredity

The inference of sex-biased human demography from whole-genome data

Sheila Musharoff et al.

PLOS GENETICS (2019)

Article Biochemistry & Molecular Biology

SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model

Benjamin C. Haller et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Biochemistry & Molecular Biology

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

Benjamin C. Haller et al.

MOLECULAR ECOLOGY RESOURCES (2019)

Article Genetics & Heredity

Inferring sex-specific demographic history from SNP data

Florian Clemente et al.

PLOS GENETICS (2018)

Article Genetics & Heredity

Ancestry-specific recent effective population size in the Americas

Sharon R. Browning et al.

PLOS GENETICS (2018)

Article Multidisciplinary Sciences

The UK Biobank resource with deep phenotyping and genomic data

Clare Bycroft et al.

NATURE (2018)

Article Public, Environmental & Occupational Health

Comparison of Sociodemographic and Health-Related Characteristics of UK Biobank Participants With Those of the General Population

Anna Fry et al.

AMERICAN JOURNAL OF EPIDEMIOLOGY (2017)

Article Biochemical Research Methods

XIBD: software for inferring pairwise identity by descent on the X chromosome

Lyndal Henden et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

Efficient analysis of large datasets and sex bias with ADMIXTURE

Suyash S. Shringarpure et al.

BMC BIOINFORMATICS (2016)

Editorial Material Genetics & Heredity

Admixture Models and the Breeding Systems of H. S. Jennings: A GENETICS Connection

Noah A. Rosenberg

GENETICS (2016)

Article Genetics & Heredity

A Genealogical Look at Shared Ancestry on the X Chromosome

Vince Buffalo et al.

GENETICS (2016)

Article Biochemical Research Methods

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

Jerome Kelleher et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Genetics & Heredity

A Genealogical Look at Shared Ancestry on the X Chromosome

Vince Buffalo et al.

GENETICS (2016)

Article Genetics & Heredity

Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent

Sharon R. Browning et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2015)

Article Genetics & Heredity

Detecting Identity by Descent and Estimating Genotype Error Rates in Sequence Data

Brian L. Browning et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2013)

Article Genetics & Heredity

Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History

Pier Francesco Palamara et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2012)

Review Biochemistry & Molecular Biology

Sex-specific demographic behaviours that shape human genomic variation

E. Heyer et al.

MOLECULAR ECOLOGY (2012)

Article Genetics & Heredity

Estimators of the Human Effective Sex Ratio Detect Sex Biases on Different Timescales

Leslie S. Emery et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Multidisciplinary Sciences

Genome-wide patterns of population structure and admixture in West Africans and African Americans

Katarzyna Bryc et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Genetics & Heredity

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

Alon Keinan et al.

NATURE GENETICS (2009)

Editorial Material Genetics & Heredity

Evaluating signatures of sex-specific processes in the human genome

Carlos D. Bustamante et al.

NATURE GENETICS (2009)

Review Genetics & Heredity

Effective population size and patterns of molecular evolution and variation

Brian Charlesworth

NATURE REVIEWS GENETICS (2009)

Article Genetics & Heredity

Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity

Michael F. Hammer et al.

PLOS GENETICS (2008)

Article Multidisciplinary Sciences

A second generation human haplotype map of over 3.1 million SNPs

Kelly A. Frazer et al.

NATURE (2007)

Review Genetics & Heredity

The X chromosome in population genetics

SF Schaffner

NATURE REVIEWS GENETICS (2004)