TY  - JOUR
A1  - Wang, Zihua
A1  - Andrews, Peter
A1  - Kendall, Jude
A1  - Ma, Beicong
A1  - Hakker, Inessa
A1  - Rodgers, Linda
A1  - Ronemus, Michael
A1  - Wigler, Michael
A1  - Levy, Dan
T1  - SMASH, a fragmentation and sequencing method for genomic copy number analysis
Y1  - 2016/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 844 
EP  - 851 
DO  - 10.1101/gr.201491.115 
VL  - 26 
IS  - 6 
UR  - http://genome.cshlp.org/content/26/6/844.abstract 
N2  - Copy number variants (CNVs) underlie a significant amount of genetic diversity and disease. CNVs can be detected by a number of means, including chromosomal microarray analysis (CMA) and whole-genome sequencing (WGS), but these approaches suffer from either limited resolution (CMA) or are highly expensive for routine screening (both CMA and WGS). As an alternative, we have developed a next-generation sequencing-based method for CNV analysis termed SMASH, for short multiply aggregated sequence homologies. SMASH utilizes random fragmentation of input genomic DNA to create chimeric sequence reads, from which multiple mappable tags can be parsed using maximal almost-unique matches (MAMs). The SMASH tags are then binned and segmented, generating a profile of genomic copy number at the desired resolution. Because fewer reads are necessary relative to WGS to give accurate CNV data, SMASH libraries can be highly multiplexed, allowing large numbers of individuals to be analyzed at low cost. Increased genomic resolution can be achieved by sequencing to higher depth. 
ER  -