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 genotype data. LOHAS can estimate homozygosity 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 next-generation sequencing data.

 

·            Applications:

LOHAS has been successfully applied to analyze the data from the following large-scale genomic studies:

(1) a study of general populations – the HapMap Project (Yang et al., Genetic Epidemiology, 2011) and 1000 Genomes Project;

(2) a study of cancer research – the acute lymphoblastic leukemia study (Yang et al., Genetic Epidemiology, 2011);

(3) a study of complex diseases – the Welcome Trust Case-Control Consortium and North American Rheumatoid Arthritis Consortium (Yang et al., PLoS One, 2012);

(4) a next-generation sequencing and gene regulation study – the T2D-GENES Project (Yang and Li, BMC Proceedings, 2014; Yang and Lin, BMC Proceedings 2016);

(5) a pharmacogenomics and pharmacoepigenomics study – the GOLDN Project (Yang and Chen, BMC Proceedings, 2018).

 

·            Software downloading:

Version System Download Files File Type File Size Update Time LOHAS 2.3 Windows RAR 111 Mb 2019/Mar/07 LOHAS 2.2 Windows RAR 109 Mb 2016/Oct/16 LOHAS 2.1 Windows RAR 105 Mb 2014/Nov/10 LOHAS 2.0 Windows RAR 108 Mb 2013/Feb/20 LOHAS 1.1 Windows RAR 10.5 Mb 2011/Nov/30 LOHAS 1.0 Windows 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 2.3 Windows PDF 1.94 Mb 2019/Mar/07

 

·            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 2019/Mar/07 File size 35 Mb 119 Mb 34.1 Mb 76.1 Mb 79.7 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 Proceedings 10, 27. (http://rdcu.be/mHtp)

Yang, H.-C.* and Chen, C.-W. (2018/09). Homozygosity disequilibrium associated with treatment response and its methylation regulation. BMC Proceedings 12, 45. (https://rdcu.be/6Z4m)

 

·            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) 886-2-27886833; (Tel) 886-2-27875686; (E-mail) hsinchou@stat.sinica.edu.tw