Structural variation in the sequencing era

SS Ho, AE Urban, RE Mills - Nature Reviews Genetics, 2020 - nature.com
Identifying structural variation (SV) is essential for genome interpretation but has been
historically difficult due to limitations inherent to available genome technologies. Detection …

Structural variation in the 3D genome

M Spielmann, DG Lupiáñez, S Mundlos - Nature Reviews Genetics, 2018 - nature.com
Structural and quantitative chromosomal rearrangements, collectively referred to as
structural variation (SV), contribute to a large extent to the genetic diversity of the human …

A structural variation reference for medical and population genetics

RL Collins, H Brand, KJ Karczewski, X Zhao, J Alföldi… - Nature, 2020 - nature.com
Structural variants (SVs) rearrange large segments of DNA and can have profound
consequences in evolution and human disease,. As national biobanks, disease-association …

Pan-genomics in the human genome era

RM Sherman, SL Salzberg - Nature Reviews Genetics, 2020 - nature.com
Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …

Mapping and characterization of structural variation in 17,795 human genomes

HJ Abel, DE Larson, AA Regier, C Chiang, I Das… - Nature, 2020 - nature.com
A key goal of whole-genome sequencing for studies of human genetics is to interrogate all
forms of variation, including single-nucleotide variants, small insertion or deletion (indel) …

Pangenome graphs

JM Eizenga, AM Novak, JA Sibbesen… - Annual review of …, 2020 - annualreviews.org
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

RM Sherman, J Forman, V Antonescu, D Puiu… - Nature …, 2019 - nature.com
We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct
a set of DNA sequences that is present in these individuals but missing from the reference …

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

M Cretu Stancu, MJ Van Roosmalen, I Renkens… - Nature …, 2017 - nature.com
Despite improvements in genomics technology, the detection of structural variants (SVs)
from short-read sequencing still poses challenges, particularly for complex variation. Here …

The need for a human pangenome reference sequence

KH Miga, T Wang - Annual Review of Genomics and Human …, 2021 - annualreviews.org
The reference human genome sequence is inarguably the most important and widely used
resource in the fields of human genetics and genomics. It has transformed the conduct of …

Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary …

Y Zhou, L Yang, X Han, J Han, Y Hu, F Li… - Genome …, 2022 - genome.cshlp.org
A cattle pangenome representation was created based on the genome sequences of 898
cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in …