Document Detail


Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing.
MedLine Citation:
PMID:  19953122     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Characterisation of breakpoints in disease-associated balanced chromosome rearrangements (DBCRs), which disrupt or inactivate specific genes, has facilitated the molecular elucidation of a wide variety of genetic disorders. However, conventional methods for mapping chromosome breakpoints, such as in situ hybridisation with fluorescent dye-labelled bacterial artificial chromosome clones (BAC-FISH), are laborious, time consuming and often with insufficient resolution to unequivocally identify the disrupted gene. By combining DNA array hybridisation with chromosome sorting, the efficiency of breakpoint mapping has dramatically improved. However, this can only be applied when the physical properties of the derivative chromosomes allow them to be flow sorted. To characterise the breakpoints in all types of balanced chromosome rearrangements more efficiently and more accurately, we performed massively parallel sequencing using Illumina 1G analyser and ABI SOLiD systems to generate short sequencing reads from both ends of DNA fragments. We applied this method to four different DBCRs, including two reciprocal translocations and two inversions. By identifying read pairs spanning the breakpoints, we were able to map the breakpoints to a region of a few hundred base pairs that could be confirmed by subsequent PCR amplification and Sanger sequencing of the junction fragments. Our results show the feasibility of paired-end sequencing of systematic breakpoint mapping and gene finding in patients with disease-associated chromosome rearrangements.
Authors:
Wei Chen; Reinhard Ullmann; Claudia Langnick; Corinna Menzel; Zofia Wotschofsky; Hao Hu; Andreas Döring; Yuhui Hu; Hui Kang; Andreas Tzschach; Maria Hoeltzenbein; Heidemarie Neitzel; Susanne Markus; Eberhard Wiedersberg; Gerd Kistner; Conny M A van Ravenswaaij-Arts; Tjitske Kleefstra; Vera M Kalscheuer; Hans-Hilger Ropers
Publication Detail:
Type:  Case Reports; Journal Article     Date:  2009-12-02
Journal Detail:
Title:  European journal of human genetics : EJHG     Volume:  18     ISSN:  1476-5438     ISO Abbreviation:  Eur. J. Hum. Genet.     Publication Date:  2010 May 
Date Detail:
Created Date:  2010-04-22     Completed Date:  2010-07-15     Revised Date:  2013-05-31    
Medline Journal Info:
Nlm Unique ID:  9302235     Medline TA:  Eur J Hum Genet     Country:  England    
Other Details:
Languages:  eng     Pagination:  539-43     Citation Subset:  IM    
Affiliation:
Max Planck Institute for Molecular Genetics, Berlin, Germany. wei.chen@mdc-berlin.de
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MeSH Terms
Descriptor/Qualifier:
Base Sequence
Child, Preschool
Chromosome Aberrations*
Chromosome Breakage*
Female
Gene Rearrangement / genetics*
Humans
Infant
Infant, Newborn
Male
Molecular Sequence Data
Pregnancy
Sequence Analysis, DNA / methods*
Comments/Corrections

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