scholarly journals Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

2009 ◽  
Vol 19 (9) ◽  
pp. 1527-1541 ◽  
Author(s):  
K. J. McKernan ◽  
H. E. Peckham ◽  
G. L. Costa ◽  
S. F. McLaughlin ◽  
Y. Fu ◽  
...  
Keyword(s):  
Human Genome ◽  
Structural Variation ◽  
Massively Parallel ◽  
Short Read

scholarly journals REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data

2020 ◽  
Author(s):  
Russell Lewis McLaughlin
Keyword(s):  
Structural Variation ◽  
Sequence Data ◽  
Neurological Diseases ◽  
Repeat Expansion ◽  
Sequencing Data ◽  
Short Read ◽  
Short Read Sequencing ◽  
Repeat Expansions ◽  
Paired End Sequencing

Abstract Motivation Repeat expansions are an important class of genetic variation in neurological diseases. However, the identification of novel repeat expansions using conventional sequencing methods is a challenge due to their typical lengths relative to short sequence reads and difficulty in producing accurate and unique alignments for repetitive sequence. However, this latter property can be harnessed in paired-end sequencing data to infer the possible locations of repeat expansions and other structural variation. Results This article presents REscan, a command-line utility that infers repeat expansion loci from paired-end short read sequencing data by reporting the proportion of reads orientated towards a locus that do not have an adequately mapped mate. A high REscan statistic relative to a population of data suggests a repeat expansion locus for experimental follow-up. This approach is validated using genome sequence data for 259 cases of amyotrophic lateral sclerosis, of which 24 are positive for a large repeat expansion in C9orf72, showing that REscan statistics readily discriminate repeat expansion carriers from non-carriers. Availabilityand implementation C source code at https://github.com/rlmcl/rescan (GNU General Public Licence v3).

scholarly journals Mechanisms for Structural Variation in the Human Genome

2013 ◽  
Vol 1 (2) ◽  
pp. 81-90 ◽  
Author(s):  
Benjamin B. Currall ◽  
Colby Chiangmai ◽  
Michael E. Talkowski ◽  
Cynthia C. Morton
Keyword(s):  
Human Genome ◽  
Structural Variation

scholarly journals Erratum to: Mechanisms for Structural Variation in the Human Genome

2013 ◽  
Vol 1 (3) ◽  
pp. 201-201
Author(s):  
Benjamin B. Currall ◽  
Colby Chiang ◽  
Michael E. Talkowski ◽  
Cynthia C. Morton
Keyword(s):  
Human Genome ◽  
Structural Variation

scholarly journals Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

GigaScience ◽  
2014 ◽  
Vol 3 (1) ◽  
Author(s):  
Hongzhi Cao ◽  
Alex R Hastie ◽  
Dandan Cao ◽  
Ernest T Lam ◽  
Yuhui Sun ◽  
...  
Keyword(s):  
Human Genome ◽  
Rapid Detection ◽  
Structural Variation ◽  
Genome Mapping ◽  
Mapping Technology

scholarly journals Mobile elements create structural variation: Analysis of a complete human genome

2009 ◽  
Vol 19 (9) ◽  
pp. 1516-1526 ◽  
Author(s):  
J. Xing ◽  
Y. Zhang ◽  
K. Han ◽  
A. H. Salem ◽  
S. K. Sen ◽  
...  
Keyword(s):  
Human Genome ◽  
Structural Variation ◽  
Mobile Elements ◽  
Variation Analysis
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