Whole-genome sequencing and variant discovery in C. elegans

2008 ◽  
Vol 5 (2) ◽  
pp. 183-188 ◽  
Author(s):  
LaDeana W Hillier ◽  
Gabor T Marth ◽  
Aaron R Quinlan ◽  
David Dooling ◽  
Ginger Fewell ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
C Elegans ◽  
Variant Discovery

scholarly journals Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. elegans

PLoS ONE ◽  
2010 ◽  
Vol 5 (11) ◽  
pp. e13922 ◽  
Author(s):  
Katherine P. Weber ◽  
Subhajyoti De ◽  
Iwanka Kozarewa ◽  
Daniel J. Turner ◽  
M. Madan Babu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Genetic Changes ◽  
C Elegans

scholarly journals Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing

PLoS ONE ◽  
2008 ◽  
Vol 3 (12) ◽  
pp. e4012 ◽  
Author(s):  
Yufeng Shen ◽  
Sumeet Sarin ◽  
Ye Liu ◽  
Oliver Hobert ◽  
Itsik Pe'er
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Throughput ◽  
Whole Genome ◽  
C Elegans ◽  
Mutant Identification

scholarly journals Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Masao Nagasaki ◽  
◽  
Jun Yasuda ◽  
Fumiki Katsuoka ◽  
Naoki Nariai ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Variant ◽  
Whole Genome ◽  
Variant Discovery

scholarly journals Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis

2016 ◽  
Vol 25 (17) ◽  
pp. 3754-3767 ◽  
Author(s):  
Xingyi Guo ◽  
Maria Delio ◽  
Nousin Haque ◽  
Raquel Castellanos ◽  
Matthew S. Hestand ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Breakpoint Region ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
22Q11.2 Deletion ◽  
Bac Clone ◽  
Variant Discovery

scholarly journals Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Teruaki Tozaki ◽  
Aoi Ohnuma ◽  
Mio Kikuchi ◽  
Taichiro Ishige ◽  
Hironaga Kakoi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Variants ◽  
Industrial Applications ◽  
Whole Genome ◽  
X Chromosomes ◽  
Variant Discovery ◽  
Functional Variants ◽  
Thoroughbred Racehorses ◽  
Using Data

AbstractThe Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.

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