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cnvs are the presence of segments of dna longer than 1  kb with > 90% sequence identity which differ in the number of copies between the genomes of different individuals .
they affect more nucleotides per genome than snp variation   and contribute significantly to variation among normal individuals , both in levels of gene expression and in phenotypes of medical relevance [ 3 , 4 ] .
around 19 such loci have been identified in genome - wide surveys ; they are found to harbor both deletion and duplication alleles .
one of these is the uridine diphospho - glucuronosyltransferase 2b ( ugt 2b ) , which is a family of genes , involved in metabolizing steroid hormones and several other xenobiotics .
ugt 2b family of genes has high sequence identity and similar enzymatic functions with ugt2b4 , ugt2b7 , ugt2b10 , ugt2b11 , ugt2b15 , ugt2b17 , and ugt2b28 . in chinese population ,
heterozygous deletion polymorphism of ugt2b17 was higher ( 86% ) than homozygous deletion ( 73% ) [ 2 , 7 ] .
these polymorphisms have also been reported in samples covering american , european , and african populations [ 812 ] .
however , such polymorphisms have not been reported from south asia , particularly from india .
in addition , there are controversial reports regarding the association of ugt2b17 polymorphism with lung cancer , osteoporosis , and prostate cancer [ 8 , 12 , 13 ] .
it was therefore of interest to investigate the polymorphic condition of ugt 2b genes in the indian families as family studies are more robust to population stratification . here , we report the presence of ugt 2b gene deletion and duplication polymorphisms and also the network analysis of the ugt 2b genes , which predicts the involvement of other possible genes in the uridine diphospho - glucuronosyltransferase activity .
for this study , 31 normal members from randomly selected eight families residing in mysore ( 3 ) , mandya ( 1 ) , davangere ( 3 ) , and bangalore ( 1 ) certified by all india institute of speech and hearing ( aiish ) , mysore , and national institute of mental health and neuro sciences ( nimhans ) , bangalore , were selected .
these families were subjected to power analysis using standard parameters   by specifying an effect size range of 15501750 . performing the 1-sample ,
1-sided test using the type i error rate at 5% resulted in the power being equal to 1 .
5  ml edta blood was collected from each member of the family and genomic dna was extracted using promega wizard genomic dna purification kit .
the institutional ethics review board approved this research and informed consent was obtained from all sample donors .
genome - wide genotyping was performed using an affymetrix genome - wide human snp array 6.0 chip , which has 1.8 million combined snp and cnv markers with the median intermarker distance of 680 bases .
briefly , all snps that were called using birdseed v2 algorithm   had a quality control ( qc ) call rate of > 97% across members in families .
7.2   and affymetrix genotyping console software as prescribed in their manuals [ 1820 ] .
bonferroni correction was employed for multiple testing and the corrected data were then used for cnv testing .
we used weighted protein network analysis in a first attempt to identify steroid metabolic process associated modules and their key constituents .
weighted protein network analysis starts from the level of thousands of genes , identifies modules of physically interacting proteins , colocalized proteins , coexpressed proteins , and proteins falling under the common pathway , and relates these modules to clinical variables and gene ontology information .
we made use of tools such as genemania , biogrid , and cytoscape developed for network pathway studies to assess the functional consequences of the network topology .
genemania protein network association database , a fdr corrected hypergeometric test , was used for enrichment in the ugt 2b network .
different age group members ranging within 1373 years were subjected to whole genome scan from eight families .
nine of them were aged 1316 years and were studying at high school level ; 5 of them were aged 1625 years and had completed graduation ; 5 of them were aged 4555 years and were employees ; 3 of them were aged 4555 years and were businessmen ; 7 of them were aged 3545 years and were housewives ; and 2 of them were aged 7073 years and are grandparents .
none of these members had history of any diseases ( table 1 and figure 1 ) .
cnv analysis of eight families revealed in the first family 1a - iii-3 subject showing a 114  kb duplication polymorphism and 1a - iii-4 subject with a 114  kb deletion polymorphism .
1a - i-2 subject of the same family showed only a deletion polymorphism of 109  kb in ugt2b17 .
segregation of 111  kb heterozygous deletion genotype of ugt2b17 was seen in four subjects of the second family ( table 1 ) ( figure 1(a ) ) .
subject df1a in the third family had a duplication of 168  kb in ugt2b17 and ugt2b15 and deletion in ugt2b28 of 168  kb size which belongs to the same gene family of ugts .
however , subjects df1f and df1u of the same family show a 108  kb and a 105  kb deletion of ugt2b28 only .
subject 2df4f in the fourth family had a deletion of 216  kb in ugt2b17 and ugt2b15 .
however , subjects 2df4a and 2df4 m of the same family showed 104  kb and 100  kb deletion , respectively , of ugt2b28 . in the fifth family , subjects 2df5a and 2df5u showed a duplication of 141  kb and deletion of 146  kb in the ugt2b17 , respectively .
subject 2df2f from the sixth family had a duplication of 200  kb in ugt2b17 and ugt2b15 , while subject 2df3a from the seventh family showed a deletion of 114  kb involving ugt2b17 . in ugt2b15 , duplications in two subjects and deletion in one subject were observed , whereas in ugt2b28 duplication in one individual and deletions in five individuals were seen ( table 1 ) .
these cnvs were also validated using svs golden helix version 7.2 and the duplication breakpoints were found to be novel when checked against the online cnv database . by taking cognizance of all the 8 families , both duplication and deletion polymorphisms of ugt 2b genes
were observed in these families ( table 1 ) and the copy number state varied from 1 to 3 copies ( figure 2 ) .
the cnvs of ugt 2b genes were found to be in heterozygous deletion and duplication ( figure 3 ) .
the prevalence of ugt2b17 cnvs was found to be 76.4% and that of ugt2b15 was 17.6% , whereas ugt2b28 showed a prevalence of 35.2% in this study .
no zero allelic state was observed in these families and a minimum of one allele to a maximum of three alleles of ugt 2b were observed in the genotypes of the families .
the deletions and duplications observed here encompassed the complete gene structure and its flanking regions ( table 1 ) . a heat map showing the difference in heat emission for normal , deletion polymorphisms , and duplication polymorphisms of the 4q13.2 region with inferred functional copy number for all the members under study can be seen in figure 2 .
the network analysis of ugt 2b genes establishes interconnecting pathways of genes involved in steroid hormones processing and xenobiotics metabolizing such as ugt2b7 , ugt2b15 , ugt2b4 , and cyp3a4 ( figure 4 ) .
these genes function independently in their own pathways involving coexpression and colocalization of ugt2b4 , ugt2b28 , and ut2b15 with ugt2b17 proteins in the protein association network indicating the role of other ugt 2b enzymes in this pathway .
the loss or presence of ugt2b17 did not have a significant functional impact in the disease pathways .
since the gene modules in the network correspond to biological pathways , focusing the analysis on modules and their highly connected intramodular hub genes identifies the significant role played by each gene functionally . in this way
, the impact of ugt2b17 in its loss or gain status on the biological pathway can be downplayed in the earlier reported diseases .
this network also provides predictive genes involved in the steroid metabolizing pathway and xenobiotic metabolizing pathway ( table 1 ) .
perusal of the literature revealed that ugt2b17 in the 4q13.2 region is highly polymorphic and the frequency of polymorphism in this gene was found to be more in african populations , intermediate in europe and parts of west asia , and low in east asia [ 811 ] .
polymorphisms have been previously described for 1a ugts , as well as several members of family 2b ugts , including ugt2b4 , ugt2b7 , ugt2b15 , and ugt2b17 [ 7 , 2224 ] .
cnvs in the ugt 2b genes are common in the general population as suggested by xue et al .   and chew et al . .
however , the role of polymorphism in ugt2b17 remains controversial since the deletion polymorphism of ugt2b17 was found to be associated with lung cancer , osteoporosis , prostate cancer , and endometrial cancer [ 9 , 11 , 25 , 26 ] while there are also studies to relate the duplication polymorphism with lower bmd , thinner ct , higher br , and osteoporosis . on the contrary , gallagher et al .  
reported nonassociation of ugt2b17 polymorphism with the risk of lung cancer . similarly , olsson et al .   also opined
the nonassociation of ugt2b17 polymorphism with prostate cancer risk and , recently , chew et al .  
either the deletion or duplication polymorphisms in ugt2b15 are occurring along with the polymorphism of ugt2b17 , which could be due to its close proximity .
however , cnvs in ugt2b28 for the first time have also been identified from this study .
the encoded enzyme catalyzes the transfer of glucuronic acid from uridine diphosphoglucuronic acid to a diverse array of substrates including steroid hormones and lipid - soluble drugs ( table 1 ) .
cnvs are widely distributed in the genome ; these cnvs might be the consequence of recurrent events via homologous recombination .
examining the sequences of ugt 2b family genes revealed ~95% sequence identity and also found a major concentration of repeat sequences which are thought to mediate homologous recombination .
therefore , we strongly believe the role of transposition activity to be the cause of deletion and duplication polymorphism . a typical example can be seen in the twins from the first family ( figure 1 ) .
weighted protein network analysis started with ugt2b17 , identified modules of physically interacting proteins , colocalized proteins , coexpressed proteins , and proteins falling under the common pathway , and related these modules to clinical variables and gene ontology information .
in addition , identification and establishment of network pathways could help us to further understand the molecular mechanism in more refined manner than the existing one .
the present study identified de novo cnv events in the ugt 2b region . since cnvs in ugt 2b region
were identified in normal subjects and since this gene is specifically expressed to metabolize the steroids , identifying the changes at protein level as well as small sample size was a possible limitation of this study .
background and objectives . 
 uridine diphospho - glucuronosyltransferase 2b ( ugt2b ) is a family of genes involved in metabolizing steroid hormones and several other xenobiotics . 
 these ugt2b genes are highly polymorphic in nature and have distinct polymorphisms associated with specific regions around the globe . 
 copy number variations ( cnvs ) status of ugt2b17 in indian population is not known and their disease associations have been inconclusive . 
 it was therefore of interest to investigate the cnv profile of ugt2b genes . 
 methods . 
 we investigated the presence of cnvs in ugt2b genes in 31 members from eight indian families using affymetrix genome - wide human snp array 6.0 chip . 
 results . 
 our data revealed > 50% of the study members carried cnvs in ugt2b genes , of which 76% showed deletion polymorphism . 
 cnvs were observed more in ugt2b17 ( 76.4% ) than in ugt2b15 ( 17.6% ) . molecular network and 
 pathway analysis found enrichment related to steroid metabolic process , carboxylesterase activity , and sequence specific dna binding . 
 interpretation and conclusion . 
 we report the presence of ugt2b gene deletion and duplication polymorphisms in indian families . 
 network analysis indicates the substitutive role of other possible genes in the ugt activity . 
 the cnvs of ugt2b genes are very common in individuals indicating that the effect is neutral in causing any suspected diseases .