LOHAS (Loss-of-heterozygosity analysis suite)

 

·          Introduction:

Loss-Of-Heterozygosity Analysis Suite (LOHAS) written in R and R GUI was developed for studies of homozygosity disequilibrium (HD). HD describes a phenomenon in which a non-random pattern is observed for a sizable run of homozygosity (ROH) in the human genome. HD can result from autozygosity, natural selection, and chromosomal aberrations. LOHAS can be used to identify ROHs associated with complex disorders, detect loss of heterozygosity (LOH) in cancer research, and characterize long contiguous stretches of homozygosity (LCSH) in population genetics studies using SNP genotype data. LOHAS can estimate homozygous intensity, identify samples with unusual genomes, cluster samples with close HD structures, and map the genomic segments bearing HD by analyzing genome-wide SNP data and whole-genome sequencing data.

 

·          Software downloading:

Version

System

Download Files

File Type

File Size

Update Time

LOHAS 2.2

Windows

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

RAR

109 Mb

2016/Oct/16

LOHAS 2.1

Windows

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

RAR

105 Mb

2014/Nov/10

LOHAS 2.0

Windows

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

RAR

108 Mb

2013/Feb/20

LOHAS 1.1

Windows

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

RAR

10.5 Mb

2011/Nov/30

LOHAS 1.0

Windows

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

RAR

10.5 Mb

2010/Jan/26

 Download files: R language and ActiveTcl

 

·          User guide downloading:

Version

System

Download Files

File Type

File Size

Update Time

LOHAS 2.1

Windows

PDF

1.67 Mb

2014/Nov/16

 

·          Output files of five illustrative examples provided in LOHAS software (Illustration of the five examples):

Examples

Example 1

 Example 2

 Example 3

Example 4

Example 5

Update Time

Output file

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

描述: 描述: 描述: 描述: 描述: Z:\genetics\pooledDNA\rar_icon.jpg

2014/Nov/10

File size

11.9 Mb

42.1 Mb

88.5 Mb

19.7 Mb

19.3 Mb

 

·          Citations:

Yang, H.-C.*, Chang, L.-C., Huggins, R. M., Chen, C.-H. and Mullighan, C. G. (2011/05). LOHAS: Loss-of-heterozygosity analysis   suite. Genetic Epidemiology 35, 247-260. (http://onlinelibrary.wiley.com/doi/10.1002/gepi.20573/abstract)

Yang, H.-C.* and Li, H.-W. (2014/06). Analysis of homozygosity disequilibrium using whole-genome sequencing data. BMC Proceedings 8, S15. (http://www.biomedcentral.com/1753-6561/8/S1/S15)

 Yang, H.-C.* and Lin, Y.-T. (2016/11). Homozygosity disequilibrium and its gene regulation. BMC Proceedings10, 27. (http://rdcu.be/mHtp)

 

·          Other references:

Yang, H.-C.*, Chang, L.-C., Liang, Y.-J., Lin, C.-H. and Wang, P.-L. (2012/04). A genome-wide homozygosity association study identifies runs of homozygosity associated with rheumatoid arthritis in the human Major Histocompatibility Complex. PLoS One 7, e34840. (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034840)

 

·          Correspondence:

Hsin-Chou Yang, Institute of Statistical Science, Academia Sinica, 128, Academia Road, Section 2 Nankang, Taipei 115, Taiwan.  (Fax) 886-2-27831523; (Tel) 886-2-27889311 ext. 113; (E-mail) hsinchou@stat.sinica.edu.tw